Params: ./cmzasha --no-stderr --filter 350 37 Rfam/cm/RF00012.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00012_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin Build: release Host: xmen.cs.washington.edu pid: 1510 ----cmFile: Rfam/cm/RF00012.cm (global) ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #68730,sp|U43703.1|SC43703 Saccharomyces cerevisiae chromosome XVI cosmid 9545. ----isReversed: 1 ----hitSequence: AACACAUUCAACAGUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACUCUUCAAAAGAGCCACUGAAUCCAACUUGGUUGAUGAGCCCCAUAACCUUUGUACCCCAGAGUGAGGAAAUGAAAUCGAAUUUAAAUUAGCUUGGUCCGCAAUCCUUAGCGGUUCGGCCAUCUAUAAUUUUGAAUAAAAUUUUGCUUUGCCGUUGCAAUUGUGAUAACUUCCUUUGGAAUUUGUUGCGAUAUUUAAUGGCGCGAUGAUCUUGACCCAUCCUAUGUGCUUCCAUUUUGGAAGGAUAGGGAUUCAUGGGUGGGUACAAAUGGCAGUCUGACAAG hit 0 : 7964 7634 (rev) 68.50 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA +C +UC:::+:+++GAUC+U::CUAU:GGA CGUC:CUCU::G+CU+U++:+:::A 28521 AACACAUUCAACAGUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACUCUUCAAAAGA 28580 >>-------------((((------------.--..((((((((((((,.,,,,,,,,,, 61 gucAaaCAacccAAAccagGAUGAUGAgacg.cA..gccuucgcuccca.GAGCGUGAau 116 G+CA AA CC AAC::GG+UGAUGAG C CA :C+UU:G::CCC+ GAG G G+A+ 28581 GCCACUGAAUCC-AACUUGGUUGAUGAGCC-cCAuaACCUUUGUACCCCaGAGUGAGGAA 28638 ,,<......................................................... 117 cCg......................................................... 119 G 28639 AUGaaaucgaauuuaaauuagcuugguccgcaauccuuagcgguucggccaucuauaauu 28698 .....................----<<---<<<<<-<<<<<_______>>>>>->>>>>- 120 .....................CGGCgcgcaucugguguugguUuuuuUccuacUucacuU 158 CG++:: + :++:U::::: UUU+ ::::: :++: 28699 uugaauaaaauuuugcuuugcCGUUGCAAUUGUGAUAACUUCCUUUGGAAUUUGUUGCGA 28758 ->>>,,,......,,,,,,,,,......<<<--<<<<<<__________>>>>>>-->>> 159 GgcuuuU......GAUGAUCGU......uccUaucucccUcuuUUUuGuggggaaUagga 206 +::UU + GAUGAUC U :CCUAU+U ::UC++UUUUG+:: G AUAGG: 28759 UAUUUAAuggcgcGAUGAUCUUgacccaUCCUAUGUGCUUCCAUUUUGGAAGG-AUAGGG 28817 .........,))))))))))))-.------)))) 207 .........Ugggagcgaaggca.GUCUGAcugg 230 UGGG::C:AA+G:+ GUCUGAC::G 28818 auucaugggUGGGUACAAAUGGCaGUCUGACAAG 28851 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #69605,sp|Y00887.1|SCDFR1 Yeast DFR1 gene for dihydrofolate reductase (EC 1.5.1.3) ----isReversed: 0 ----hitSequence: AACACAUUCUACAGUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACUCUUCAAAAGAGCCACUGAAUCCAACUUGGUUGAUGAGUCCCAUAACCUUUGUACCCCAGAGUGAGAAACCGAAAUUGAAUCUAAAUUAGCUUGGUCCGCAAUCCUUAGCGGUUCGGCCAUCUAUAAUUUUGAAUAAAAAUUUUGCUUUGCCGUUGCAUUUGUAGUUUUUUCCUUUGGAAGUAAUUACAAUAUUUUAUGGCGCGAUGAUCUUGACCCAUCCUAUGUACUUCUUUUUUGAAGGGAUAGGGCUCUAUGGGUGGGUACAAAUGGCAGUCUGACAAG hit 1 : 158 489 (fwd) 86.39 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA +C +UC ::+:+++GAUC+U::CUAU:GGA CGUC:CUCU::G+CU+U++:+:: A 158 AACACAUUCUACAGUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACUCUUCAAAAGA 217 >>-------------((((------------.--..((((((((((((,.,,,,,,,,,, 61 gucAaaCAacccAAAccagGAUGAUGAgacg.cA..gccuucgcuccca.GAGCGUGAau 116 G+CA AA CC AAC::GG+UGAUGAG C CA :C+UU:G::CCC+ GAG G GAA+ 218 GCCACUGAAUCC-AACUUGGUUGAUGAGUC-cCAuaACCUUUGUACCCCaGAGUGAGAAA 275 ,,<......................................................... 117 cCg......................................................... 119 CCG 276 CCGaaauugaaucuaaauuagcuugguccgcaauccuuagcgguucggccaucuauaauu 335 ......................----<<---<<<<<-<<<<<_______>>>>>->>>>> 120 ......................CGGCgcgcaucugguguugguUuuuuUccuacUucacu 157 CG++:: ++:U:GU::+:: UUU+ ::+:: U:A:+ 336 uugaauaaaaauuuugcuuugcCGUUGCAUUUGUAGUUUUUUCCUUUGGAAGUAAUUACA 395 -->>>,,,......,,,,,,,,,......<<<--<<<<<<__________>>>>>>-->> 158 UGgcuuuU......GAUGAUCGU......uccUaucucccUcuuUUUuGuggggaaUagg 205 +::UUU+ GAUGAUC U :CCUAU+U:C:UCUUUUUUG :G:G AUAGG 396 AUAUUUUAuggcgcGAUGAUCUUgacccaUCCUAUGUACUUCUUUUUUGAAGGG-AUAGG 454 >.........,))))))))))))-.------)))) 206 a.........Ugggagcgaaggca.GUCUGAcugg 230 : UGGG::C:AA+G:+ GUCUGAC::G 455 GcucuaugggUGGGUACAAAUGGCaGUCUGACAAG 489 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #69606,sp|M26668.1|SCDFR1A Saccharomyces cerevisiae dihydrofolate reductase (DFR1) gene, complete cds. ----isReversed: 0 ----hitSequence: AACACAUUCUACAGUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACUCUUCAAAAGAGCCACUGAAUCCAACUUGGUUGAUGAGUCCCAUAACCUUUGUACCCCAGAGUGAGAAACCGAAAUUGAAUCUAAAUUAGCUUGGUCCGCAAUCCUUAGCGGUUCGGCCAUCUAUAAUUUUGAAUAAAAAUUUUGCUUUGCCGUUGCAUUUGUAGUUUUUUCCUUUGGAAGUAAUUACAAUAUUUUAUGGCGCGAUGAUCUUGACCCAUCCUAUGUACUUCUUUUUUGAAGGGAUAGGGCUCUAUGGGUGGGUACAAAUGGCAGUCUGACAAG hit 2 : 157 488 (fwd) 86.39 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA +C +UC ::+:+++GAUC+U::CUAU:GGA CGUC:CUCU::G+CU+U++:+:: A 157 AACACAUUCUACAGUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACUCUUCAAAAGA 216 >>-------------((((------------.--..((((((((((((,.,,,,,,,,,, 61 gucAaaCAacccAAAccagGAUGAUGAgacg.cA..gccuucgcuccca.GAGCGUGAau 116 G+CA AA CC AAC::GG+UGAUGAG C CA :C+UU:G::CCC+ GAG G GAA+ 217 GCCACUGAAUCC-AACUUGGUUGAUGAGUC-cCAuaACCUUUGUACCCCaGAGUGAGAAA 274 ,,<......................................................... 117 cCg......................................................... 119 CCG 275 CCGaaauugaaucuaaauuagcuugguccgcaauccuuagcgguucggccaucuauaauu 334 ......................----<<---<<<<<-<<<<<_______>>>>>->>>>> 120 ......................CGGCgcgcaucugguguugguUuuuuUccuacUucacu 157 CG++:: ++:U:GU::+:: UUU+ ::+:: U:A:+ 335 uugaauaaaaauuuugcuuugcCGUUGCAUUUGUAGUUUUUUCCUUUGGAAGUAAUUACA 394 -->>>,,,......,,,,,,,,,......<<<--<<<<<<__________>>>>>>-->> 158 UGgcuuuU......GAUGAUCGU......uccUaucucccUcuuUUUuGuggggaaUagg 205 +::UUU+ GAUGAUC U :CCUAU+U:C:UCUUUUUUG :G:G AUAGG 395 AUAUUUUAuggcgcGAUGAUCUUgacccaUCCUAUGUACUUCUUUUUUGAAGGG-AUAGG 453 >.........,))))))))))))-.------)))) 206 a.........Ugggagcgaaggca.GUCUGAcugg 230 : UGGG::C:AA+G:+ GUCUGAC::G 454 GcucuaugggUGGGUACAAAUGGCaGUCUGACAAG 488 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #69607,sp|X16541.1|SCDFR1G Saccharomyces cerevisiae DNA for dihydrofolate reductase (EC 1.5.1.3) ----isReversed: 1 ----hitSequence: AACACAUUCUACAGUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACUCUUCAAAAGAGCCACUGAAUCCAACUUGGUUGAUGAGUCCCAUAACCUUUGUACCCCAGAGUGAGAAACCGAAAUUGAAUCUAAAUUAGCUUGGUCCGCAAUCCUUAGCGUUCGGCCAUCUAUAAUUUUGAAUAAAAAUUUUGCUUUGCCGUUGCAUUUGUAGUUUUUUCCUUUGGAAGUAAUUACAAUAUUUUAUGGCGCGAUGAUCUUGACCCAUCCUAUGUACUUCUUUUUUGAAGGGAUAGGGCUCUAUGGGUGGGUACAAAUGGCAGUCUGACAAG hit 3 : 1167 837 (rev) 86.44 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA +C +UC ::+:+++GAUC+U::CUAU:GGA CGUC:CUCU::G+CU+U++:+:: A 1435 AACACAUUCUACAGUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACUCUUCAAAAGA 1494 >>-------------((((------------.--..((((((((((((,.,,,,,,,,,, 61 gucAaaCAacccAAAccagGAUGAUGAgacg.cA..gccuucgcuccca.GAGCGUGAau 116 G+CA AA CC AAC::GG+UGAUGAG C CA :C+UU:G::CCC+ GAG G GAA+ 1495 GCCACUGAAUCC-AACUUGGUUGAUGAGUC-cCAuaACCUUUGUACCCCaGAGUGAGAAA 1552 ,,<......................................................... 117 cCg......................................................... 119 CCG 1553 CCGaaauugaaucuaaauuagcuugguccgcaauccuuagcguucggccaucuauaauuu 1612 .....................----<<---<<<<<-<<<<<_______>>>>>->>>>>- 120 .....................CGGCgcgcaucugguguugguUuuuuUccuacUucacuU 158 CG++:: ++:U:GU::+:: UUU+ ::+:: U:A:+ 1613 ugaauaaaaauuuugcuuugcCGUUGCAUUUGUAGUUUUUUCCUUUGGAAGUAAUUACAA 1672 ->>>,,,......,,,,,,,,,......<<<--<<<<<<__________>>>>>>-->>> 159 GgcuuuU......GAUGAUCGU......uccUaucucccUcuuUUUuGuggggaaUagga 206 +::UUU+ GAUGAUC U :CCUAU+U:C:UCUUUUUUG :G:G AUAGG: 1673 UAUUUUAuggcgcGAUGAUCUUgacccaUCCUAUGUACUUCUUUUUUGAAGGG-AUAGGG 1731 .........,))))))))))))-.------)))) 207 .........Ugggagcgaaggca.GUCUGAcugg 230 UGGG::C:AA+G:+ GUCUGAC::G 1732 cucuaugggUGGGUACAAAUGGCaGUCUGACAAG 1765 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #69613,sp|M18578.1|SCDIHRG S.cerevisiae dihydrofolate reductase gene, complete cds, and U3 small nuclear RNA (snR17A) gene. ----isReversed: 0 ----hitSequence: AACACAUUCUACAGUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACUCUUCAAAAGAGCCACUGAAUCCAACUUGGUUGAUGAGUCCCAUAACCUUUGUACCCCAGAGUGAGAAACCGAAAUGAAUCUAAAUUAGCUUGGUCCGCAAUCCUUAGCGGUUCGGCCAUCUAUAAUUUUGAAUAAAAAUUUUGCUUUGCCGUUGCAUUUGUAGUUUUUUCCUUUGGAAGUAAUUACAAUAUUUUAUGGCGCGAUGAUCUUGACCCAUCCUAUGUACUUCUUUUUUGAAGGGAUAGGGCUCUAUGGGUGGGUACAAAUGGCAGUCUGACAAG hit 4 : 158 488 (fwd) 86.44 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA +C +UC ::+:+++GAUC+U::CUAU:GGA CGUC:CUCU::G+CU+U++:+:: A 158 AACACAUUCUACAGUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACUCUUCAAAAGA 217 >>-------------((((------------.--..((((((((((((,.,,,,,,,,,, 61 gucAaaCAacccAAAccagGAUGAUGAgacg.cA..gccuucgcuccca.GAGCGUGAau 116 G+CA AA CC AAC::GG+UGAUGAG C CA :C+UU:G::CCC+ GAG G GAA+ 218 GCCACUGAAUCC-AACUUGGUUGAUGAGUC-cCAuaACCUUUGUACCCCaGAGUGAGAAA 275 ,,<......................................................... 117 cCg......................................................... 119 CCG 276 CCGaaaugaaucuaaauuagcuugguccgcaauccuuagcgguucggccaucuauaauuu 335 .....................----<<---<<<<<-<<<<<_______>>>>>->>>>>- 120 .....................CGGCgcgcaucugguguugguUuuuuUccuacUucacuU 158 CG++:: ++:U:GU::+:: UUU+ ::+:: U:A:+ 336 ugaauaaaaauuuugcuuugcCGUUGCAUUUGUAGUUUUUUCCUUUGGAAGUAAUUACAA 395 ->>>,,,......,,,,,,,,,......<<<--<<<<<<__________>>>>>>-->>> 159 GgcuuuU......GAUGAUCGU......uccUaucucccUcuuUUUuGuggggaaUagga 206 +::UUU+ GAUGAUC U :CCUAU+U:C:UCUUUUUUG :G:G AUAGG: 396 UAUUUUAuggcgcGAUGAUCUUgacccaUCCUAUGUACUUCUUUUUUGAAGGG-AUAGGG 454 .........,))))))))))))-.------)))) 207 .........Ugggagcgaaggca.GUCUGAcugg 230 UGGG::C:AA+G:+ GUCUGAC::G 455 cucuaugggUGGGUACAAAUGGCaGUCUGACAAG 488 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #70424,sp|X96770.1|SCLACHXVI S.cerevisiae chromosome XVI, left arm DNA ----isReversed: 1 ----hitSequence: AACACAUUCAACAGUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACUCUUCAAAAGAGCCACUGAAUCCAACUUGGUUGAUGAGCCCCAUAACCUUUGUACCCCAGAGUGAGGAAAUGAAAUCGAAUUUAAAUUAGCUUGGUCCGCAAUCCUUAGCGGUUCGGCCAUCUAUAAUUUUGAAUAAAAUUUUGCUUUGCCGUUGCAAUUGUGAUAACUUCCUUUGGAAUUUGUUGCGAUAUUUAAUGGCGCGAUGAUCUUGACCCAUCCUAUGUGCUUCCAUUUUGGAAGGAUAGGGAUUCAUGGGUGGGUACAAAUGGCAGUCUGACAAG hit 5 : 54558 54228 (rev) 68.50 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA +C +UC:::+:+++GAUC+U::CUAU:GGA CGUC:CUCU::G+CU+U++:+:::A 1229 AACACAUUCAACAGUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACUCUUCAAAAGA 1288 >>-------------((((------------.--..((((((((((((,.,,,,,,,,,, 61 gucAaaCAacccAAAccagGAUGAUGAgacg.cA..gccuucgcuccca.GAGCGUGAau 116 G+CA AA CC AAC::GG+UGAUGAG C CA :C+UU:G::CCC+ GAG G G+A+ 1289 GCCACUGAAUCC-AACUUGGUUGAUGAGCC-cCAuaACCUUUGUACCCCaGAGUGAGGAA 1346 ,,<......................................................... 117 cCg......................................................... 119 G 1347 AUGaaaucgaauuuaaauuagcuugguccgcaauccuuagcgguucggccaucuauaauu 1406 .....................----<<---<<<<<-<<<<<_______>>>>>->>>>>- 120 .....................CGGCgcgcaucugguguugguUuuuuUccuacUucacuU 158 CG++:: + :++:U::::: UUU+ ::::: :++: 1407 uugaauaaaauuuugcuuugcCGUUGCAAUUGUGAUAACUUCCUUUGGAAUUUGUUGCGA 1466 ->>>,,,......,,,,,,,,,......<<<--<<<<<<__________>>>>>>-->>> 159 GgcuuuU......GAUGAUCGU......uccUaucucccUcuuUUUuGuggggaaUagga 206 +::UU + GAUGAUC U :CCUAU+U ::UC++UUUUG+:: G AUAGG: 1467 UAUUUAAuggcgcGAUGAUCUUgacccaUCCUAUGUGCUUCCAUUUUGGAAGG-AUAGGG 1525 .........,))))))))))))-.------)))) 207 .........Ugggagcgaaggca.GUCUGAcugg 230 UGGG::C:AA+G:+ GUCUGAC::G 1526 auucaugggUGGGUACAAAUGGCaGUCUGACAAG 1559 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #71634,sp|X05499.1|SCSNR17A Yeast SNR17A gene for U3 small nuclear RNA ----isReversed: 0 ----hitSequence: AACACAUUCUACAGUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACUCUUCAAAAGAGCCACUGAAUCCAACUUGGUUGAUGAGUCCCAUAACCUUUGUACCCCAGAGUGAGAAACCGAAAUUGAAUCUAAAUUAGCUUGGUCCGCAAUCCUUAGCGGUUCGGCCAUCUAUAAUUUUGAAUAAAAAUUUUCUUUGCCGUUGCAUUUGUAGUUUUUUCCUUUGGAAGUAAUUACAAUAUUUUAUGGCGCGAUGAUCUUGACCCAUCCUAUGUACUUCUUUUUUGAAGGGAUAGGGCUCUAUGGGUGGGUACAAAUGGCAGUCUGACAAG hit 6 : 124 454 (fwd) 86.44 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA +C +UC ::+:+++GAUC+U::CUAU:GGA CGUC:CUCU::G+CU+U++:+:: A 124 AACACAUUCUACAGUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACUCUUCAAAAGA 183 >>-------------((((------------.--..((((((((((((,.,,,,,,,,,, 61 gucAaaCAacccAAAccagGAUGAUGAgacg.cA..gccuucgcuccca.GAGCGUGAau 116 G+CA AA CC AAC::GG+UGAUGAG C CA :C+UU:G::CCC+ GAG G GAA+ 184 GCCACUGAAUCC-AACUUGGUUGAUGAGUC-cCAuaACCUUUGUACCCCaGAGUGAGAAA 241 ,,<......................................................... 117 cCg......................................................... 119 CCG 242 CCGaaauugaaucuaaauuagcuugguccgcaauccuuagcgguucggccaucuauaauu 301 .....................----<<---<<<<<-<<<<<_______>>>>>->>>>>- 120 .....................CGGCgcgcaucugguguugguUuuuuUccuacUucacuU 158 CG++:: ++:U:GU::+:: UUU+ ::+:: U:A:+ 302 uugaauaaaaauuuucuuugcCGUUGCAUUUGUAGUUUUUUCCUUUGGAAGUAAUUACAA 361 ->>>,,,......,,,,,,,,,......<<<--<<<<<<__________>>>>>>-->>> 159 GgcuuuU......GAUGAUCGU......uccUaucucccUcuuUUUuGuggggaaUagga 206 +::UUU+ GAUGAUC U :CCUAU+U:C:UCUUUUUUG :G:G AUAGG: 362 UAUUUUAuggcgcGAUGAUCUUgacccaUCCUAUGUACUUCUUUUUUGAAGGG-AUAGGG 420 .........,))))))))))))-.------)))) 207 .........Ugggagcgaaggca.GUCUGAcugg 230 UGGG::C:AA+G:+ GUCUGAC::G 421 cucuaugggUGGGUACAAAUGGCaGUCUGACAAG 454 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #71635,sp|X05498.1|SCSNR17B Yeast SNR17B gene for U3 small nuclear RNA ----isReversed: 0 ----hitSequence: AACACAUUCAACAGUAGGAUCAUUUCUAUAUUAAUCGUCACUCUUUGACUCUUCAAAAGAGCCACUGAAUCCAACUUGGUUGAUGAGCCCCAUAACCUUUGUACCCCAGAGUGAGGAAAUGAAAUCGAAUUUAAAUUAGCUUGGUCCGCAAUCCUUAGCGGUUCGGCCAUCUAUAAUUUUGAAUAAAAUUUUGCUUUGCCGUUGCAAUUGUGAUAACUUCCUUUGGAAUUUGUUGCGAUAUUUAAUGGCGCGAUGAUCUUGACCCAUCCUAUGUGCUUCCAUUUUGGAAGGAUAGGGAUUCAUGGGUGGGUACAAAUGGCAGUCUGACAAG hit 7 : 324 654 (fwd) 64.81 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA +C +UC:::+:+++GAUC+U::CUAU::+A CG+::CUCU::G+CU+U++:+:::A 324 AACACAUUCAACAGUAGGAUCAUUUCUAUAUUAAUCGUCACUCUUUGACUCUUCAAAAGA 383 >>-------------((((------------.--..((((((((((((,.,,,,,,,,,, 61 gucAaaCAacccAAAccagGAUGAUGAgacg.cA..gccuucgcuccca.GAGCGUGAau 116 G+CA AA CC AAC::GG+UGAUGAG C CA :C+UU:G::CCC+ GAG G G+A+ 384 GCCACUGAAUCC-AACUUGGUUGAUGAGCC-cCAuaACCUUUGUACCCCaGAGUGAGGAA 441 ,,<......................................................... 117 cCg......................................................... 119 G 442 AUGaaaucgaauuuaaauuagcuugguccgcaauccuuagcgguucggccaucuauaauu 501 .....................----<<---<<<<<-<<<<<_______>>>>>->>>>>- 120 .....................CGGCgcgcaucugguguugguUuuuuUccuacUucacuU 158 CG++:: + :++:U::::: UUU+ ::::: :++: 502 uugaauaaaauuuugcuuugcCGUUGCAAUUGUGAUAACUUCCUUUGGAAUUUGUUGCGA 561 ->>>,,,......,,,,,,,,,......<<<--<<<<<<__________>>>>>>-->>> 159 GgcuuuU......GAUGAUCGU......uccUaucucccUcuuUUUuGuggggaaUagga 206 +::UU + GAUGAUC U :CCUAU+U ::UC++UUUUG+:: G AUAGG: 562 UAUUUAAuggcgcGAUGAUCUUgacccaUCCUAUGUGCUUCCAUUUUGGAAGG-AUAGGG 620 .........,))))))))))))-.------)))) 207 .........Ugggagcgaaggca.GUCUGAcugg 230 UGGG::C:AA+G:+ GUCUGAC::G 621 auucaugggUGGGUACAAAUGGCaGUCUGACAAG 654 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #72255,sp|M26648.1|SCUG17C Yeast (S.cerevisiae) U3 small nuclear RNA (SNR17A) gene, complete sequence. ----isReversed: 0 ----hitSequence: AACACAUUCUACAGUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACUCUUCAAAAGAGCCACUGAAUCCAACUUGGUUGAUGAGUCCCAUAACCUUUGUACCCCAGAGUGAGAAACCGAAAUUGAAUCUAAAUUAGCUUGGUCCGCAAUCCUUAGCGGUUCGGCCAUCUAUAAUUUUGAAUAAAAAUUUUGCUUUGGCGUUGCAUUUGUAGUUUUUUCCUUUGGAAGUAAUUACAAUAUUUUAUGGCGCGAUGAUCUUGACCCAUCCUAUGUACUUCUUUUUUGAAGGGAUAGGGCUCUAUGGGUGGGUACAAAUGGCAGUCUGACAAG hit 8 : 339 670 (fwd) 86.39 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA +C +UC ::+:+++GAUC+U::CUAU:GGA CGUC:CUCU::G+CU+U++:+:: A 339 AACACAUUCUACAGUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACUCUUCAAAAGA 398 >>-------------((((------------.--..((((((((((((,.,,,,,,,,,, 61 gucAaaCAacccAAAccagGAUGAUGAgacg.cA..gccuucgcuccca.GAGCGUGAau 116 G+CA AA CC AAC::GG+UGAUGAG C CA :C+UU:G::CCC+ GAG G GAA+ 399 GCCACUGAAUCC-AACUUGGUUGAUGAGUC-cCAuaACCUUUGUACCCCaGAGUGAGAAA 456 ,,<......................................................... 117 cCg......................................................... 119 CCG 457 CCGaaauugaaucuaaauuagcuugguccgcaauccuuagcgguucggccaucuauaauu 516 ......................----<<---<<<<<-<<<<<_______>>>>>->>>>> 120 ......................CGGCgcgcaucugguguugguUuuuuUccuacUucacu 157 CG++:: ++:U:GU::+:: UUU+ ::+:: U:A:+ 517 uugaauaaaaauuuugcuuuggCGUUGCAUUUGUAGUUUUUUCCUUUGGAAGUAAUUACA 576 -->>>,,,......,,,,,,,,,......<<<--<<<<<<__________>>>>>>-->> 158 UGgcuuuU......GAUGAUCGU......uccUaucucccUcuuUUUuGuggggaaUagg 205 +::UUU+ GAUGAUC U :CCUAU+U:C:UCUUUUUUG :G:G AUAGG 577 AUAUUUUAuggcgcGAUGAUCUUgacccaUCCUAUGUACUUCUUUUUUGAAGGG-AUAGG 635 >.........,))))))))))))-.------)))) 206 a.........Ugggagcgaaggca.GUCUGAcugg 230 : UGGG::C:AA+G:+ GUCUGAC::G 636 GcucuaugggUGGGUACAAAUGGCaGUCUGACAAG 670 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #72276,sp|M26649.1|SCUR17D Yeast (S.cerevisiae) U3 small nuclear RNA. ----isReversed: 0 ----hitSequence: GUCGACGUACUUCAUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACUCUUCAAAAGAGCCACUGAAUCCAACUUGGUUGAUGAGUCCCAUAACCUUUGUACCCCAGAGUGAGAAACCGAAAUUGAAUCUAAAUUAGCUUGGUCCGCAAUCCUUAGCGGUUCGGCCAUCUAUAAUUUUGAAUAAAAAUUUUGCUUUGGCGUUGCAUUUGUAGUUUUUUCCUUUGGAAGUAAUUACAAUAUUUUAUGGCGCGAUGAUCUUGACCCAUCCUAUGUACUUCUUUUUUGAAGGGAUAGGGCUCUAUGGGUGGGUACAAAUGGCAGUCUGACAAG hit 9 : 1 332 (fwd) 83.68 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 + :U:CUUC:+++GAUC+U::CUAU:GGA CGUC:CUCU::G+CU+U++:AAAG: 1 GUCGACGUACUUCAUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACUCUUCAAAAGA 60 >>-------------((((------------.--..((((((((((((,.,,,,,,,,,, 61 gucAaaCAacccAAAccagGAUGAUGAgacg.cA..gccuucgcuccca.GAGCGUGAau 116 G:CA AA CC AAC::GG+UGAUGAG C CA :C+UU:G::CCC+ GAG G GAA+ 61 GCCACUGAAUCC-AACUUGGUUGAUGAGUC-cCAuaACCUUUGUACCCCaGAGUGAGAAA 118 ,,<......................................................... 117 cCg......................................................... 119 CCG 119 CCGaaauugaaucuaaauuagcuugguccgcaauccuuagcgguucggccaucuauaauu 178 ......................----<<---<<<<<-<<<<<_______>>>>>->>>>> 120 ......................CGGCgcgcaucugguguugguUuuuuUccuacUucacu 157 CG++:: ++:U:GU::+:: UUU+ ::+:: U:A:+ 179 uugaauaaaaauuuugcuuuggCGUUGCAUUUGUAGUUUUUUCCUUUGGAAGUAAUUACA 238 -->>>,,,......,,,,,,,,,......<<<--<<<<<<__________>>>>>>-->> 158 UGgcuuuU......GAUGAUCGU......uccUaucucccUcuuUUUuGuggggaaUagg 205 +::UUU+ GAUGAUC U :CCUAU+U:C:UCUUUUUUG :G:G AUAGG 239 AUAUUUUAuggcgcGAUGAUCUUgacccaUCCUAUGUACUUCUUUUUUGAAGGG-AUAGG 297 >.........,))))))))))))-.------)))) 206 a.........Ugggagcgaaggca.GUCUGAcugg 230 : UGGG::C:AA+G:+ GUCUGAC::G 298 GcucuaugggUGGGUACAAAUGGCaGUCUGACAAG 332 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #75244,sp|Z75143.1|SCYOR235W S.cerevisiae chromosome XV reading frame ORF YOR235w ----isReversed: 0 ----hitSequence: AACACAUUCUACAGUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACUCUUCAAAAGAGCCACUGAAUCCAACUUGGUUGAUGAGUCCCAUAACCUUUGUACCCCAGAGUGAGAAACCGAAAUUGAAUCUAAAUUAGCUUGGUCCGCAAUCCUUAGCGGUUCGGCCAUCUAUAAUUUUGAAUAAAAAUUUUGCUUUGCCGUUGCAUUUGUAGUUUUUUCCUUUGGAAGUAAUUACAAUAUUUUAUGGCGCGAUGAUCUUGACCCAUCCUAUGUACUUCUUUUUUGAAGGGAUAGGGCUCUAUGGGUGGGUACAAAUGGCAGUCUGACAAG hit 10 : 859 1190 (fwd) 86.39 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA +C +UC ::+:+++GAUC+U::CUAU:GGA CGUC:CUCU::G+CU+U++:+:: A 859 AACACAUUCUACAGUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACUCUUCAAAAGA 918 >>-------------((((------------.--..((((((((((((,.,,,,,,,,,, 61 gucAaaCAacccAAAccagGAUGAUGAgacg.cA..gccuucgcuccca.GAGCGUGAau 116 G+CA AA CC AAC::GG+UGAUGAG C CA :C+UU:G::CCC+ GAG G GAA+ 919 GCCACUGAAUCC-AACUUGGUUGAUGAGUC-cCAuaACCUUUGUACCCCaGAGUGAGAAA 976 ,,<......................................................... 117 cCg......................................................... 119 CCG 977 CCGaaauugaaucuaaauuagcuugguccgcaauccuuagcgguucggccaucuauaauu 1036 ......................----<<---<<<<<-<<<<<_______>>>>>->>>>> 120 ......................CGGCgcgcaucugguguugguUuuuuUccuacUucacu 157 CG++:: ++:U:GU::+:: UUU+ ::+:: U:A:+ 1037 uugaauaaaaauuuugcuuugcCGUUGCAUUUGUAGUUUUUUCCUUUGGAAGUAAUUACA 1096 -->>>,,,......,,,,,,,,,......<<<--<<<<<<__________>>>>>>-->> 158 UGgcuuuU......GAUGAUCGU......uccUaucucccUcuuUUUuGuggggaaUagg 205 +::UUU+ GAUGAUC U :CCUAU+U:C:UCUUUUUUG :G:G AUAGG 1097 AUAUUUUAuggcgcGAUGAUCUUgacccaUCCUAUGUACUUCUUUUUUGAAGGG-AUAGG 1155 >.........,))))))))))))-.------)))) 206 a.........Ugggagcgaaggca.GUCUGAcugg 230 : UGGG::C:AA+G:+ GUCUGAC::G 1156 GcucuaugggUGGGUACAAAUGGCaGUCUGACAAG 1190 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #75245,sp|Z75144.1|SCYOR236W S.cerevisiae chromosome XV reading frame ORF YOR236w ----isReversed: 0 ----hitSequence: AACACAUUCUACAGUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACUCUUCAAAAGAGCCACUGAAUCCAACUUGGUUGAUGAGUCCCAUAACCUUUGUACCCCAGAGUGAGAAACCGAAAUUGAAUCUAAAUUAGCUUGGUCCGCAAUCCUUAGCGGUUCGGCCAUCUAUAAUUUUGAAUAAAAAUUUUGCUUUGCCGUUGCAUUUGUAGUUUUUUCCUUUGGAAGUAAUUACAAUAUUUUAUGGCGCGAUGAUCUUGACCCAUCCUAUGUACUUCUUUUUUGAAGGGAUAGGGCUCUAUGGGUGGGUACAAAUGGCAGUCUGACAAG hit 11 : 158 489 (fwd) 86.39 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA +C +UC ::+:+++GAUC+U::CUAU:GGA CGUC:CUCU::G+CU+U++:+:: A 158 AACACAUUCUACAGUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACUCUUCAAAAGA 217 >>-------------((((------------.--..((((((((((((,.,,,,,,,,,, 61 gucAaaCAacccAAAccagGAUGAUGAgacg.cA..gccuucgcuccca.GAGCGUGAau 116 G+CA AA CC AAC::GG+UGAUGAG C CA :C+UU:G::CCC+ GAG G GAA+ 218 GCCACUGAAUCC-AACUUGGUUGAUGAGUC-cCAuaACCUUUGUACCCCaGAGUGAGAAA 275 ,,<......................................................... 117 cCg......................................................... 119 CCG 276 CCGaaauugaaucuaaauuagcuugguccgcaauccuuagcgguucggccaucuauaauu 335 ......................----<<---<<<<<-<<<<<_______>>>>>->>>>> 120 ......................CGGCgcgcaucugguguugguUuuuuUccuacUucacu 157 CG++:: ++:U:GU::+:: UUU+ ::+:: U:A:+ 336 uugaauaaaaauuuugcuuugcCGUUGCAUUUGUAGUUUUUUCCUUUGGAAGUAAUUACA 395 -->>>,,,......,,,,,,,,,......<<<--<<<<<<__________>>>>>>-->> 158 UGgcuuuU......GAUGAUCGU......uccUaucucccUcuuUUUuGuggggaaUagg 205 +::UUU+ GAUGAUC U :CCUAU+U:C:UCUUUUUUG :G:G AUAGG 396 AUAUUUUAuggcgcGAUGAUCUUgacccaUCCUAUGUACUUCUUUUUUGAAGGG-AUAGG 454 >.........,))))))))))))-.------)))) 206 a.........Ugggagcgaaggca.GUCUGAcugg 230 : UGGG::C:AA+G:+ GUCUGAC::G 455 GcucuaugggUGGGUACAAAUGGCaGUCUGACAAG 489 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #75392,sp|Z73499.1|SCYPL143W S.cerevisiae chromosome XVI reading frame ORF YPL143w ----isReversed: 1 ----hitSequence: AACACAUUCAACAGUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACUCUUCAAAAGAGCCACUGAAUCCAACUUGGUUGAUGAGCCCCAUAACCUUUGUACCCCAGAGUGAGGAAAUGAAAUCGAAUUUAAAUUAGCUUGGUCCGCAAUCCUUAGCGGUUCGGCCAUCUAUAAUUUUGAAUAAAAUUUUGCUUUGCCGUUGCAAUUGUGAUAACUUCCUUUGGAAUUUGUUGCGAUAUUUAAUGGCGCGAUGAUCUUGACCCAUCCUAUGUGCUUCCAUUUUGGAAGGAUAGGGAUUCAUGGGUGGGUACAAAUGGCAGUCUGACAAG hit 12 : 461 131 (rev) 68.50 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA +C +UC:::+:+++GAUC+U::CUAU:GGA CGUC:CUCU::G+CU+U++:+:::A 2077 AACACAUUCAACAGUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACUCUUCAAAAGA 2136 >>-------------((((------------.--..((((((((((((,.,,,,,,,,,, 61 gucAaaCAacccAAAccagGAUGAUGAgacg.cA..gccuucgcuccca.GAGCGUGAau 116 G+CA AA CC AAC::GG+UGAUGAG C CA :C+UU:G::CCC+ GAG G G+A+ 2137 GCCACUGAAUCC-AACUUGGUUGAUGAGCC-cCAuaACCUUUGUACCCCaGAGUGAGGAA 2194 ,,<......................................................... 117 cCg......................................................... 119 G 2195 AUGaaaucgaauuuaaauuagcuugguccgcaauccuuagcgguucggccaucuauaauu 2254 .....................----<<---<<<<<-<<<<<_______>>>>>->>>>>- 120 .....................CGGCgcgcaucugguguugguUuuuuUccuacUucacuU 158 CG++:: + :++:U::::: UUU+ ::::: :++: 2255 uugaauaaaauuuugcuuugcCGUUGCAAUUGUGAUAACUUCCUUUGGAAUUUGUUGCGA 2314 ->>>,,,......,,,,,,,,,......<<<--<<<<<<__________>>>>>>-->>> 159 GgcuuuU......GAUGAUCGU......uccUaucucccUcuuUUUuGuggggaaUagga 206 +::UU + GAUGAUC U :CCUAU+U ::UC++UUUUG+:: G AUAGG: 2315 UAUUUAAuggcgcGAUGAUCUUgacccaUCCUAUGUGCUUCCAUUUUGGAAGG-AUAGGG 2373 .........,))))))))))))-.------)))) 207 .........Ugggagcgaaggca.GUCUGAcugg 230 UGGG::C:AA+G:+ GUCUGAC::G 2374 auucaugggUGGGUACAAAUGGCaGUCUGACAAG 2407 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #75393,sp|Z73500.1|SCYPL144W S.cerevisiae chromosome XVI reading frame ORF YPL144w ----isReversed: 1 ----hitSequence: AACACAUUCAACAGUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACUCUUCAAAAGAGCCACUGAAUCCAACUUGGUUGAUGAGCCCCAUAACCUUUGUACCCCAGAGUGAGGAAAUGAAAUCGAAUUUAAAUUAGCUUGGUCCGCAAUCCUUAGCGGUUCGGCCAUCUAUAAUUUUGAAUAAAAUUUUGCUUUGCCGUUGCAAUUGUGAUAACUUCCUUUGGAAUUUGUUGCGAUAUUUAAUGGCGCGAUGAUCUUGACCCAUCCUAUGUGCUUCCAUUUUGGAAGGAUAGGGAUUCAUGGGUGGGUACAAAUGGCAGUCUGACAAG hit 13 : 1688 1358 (rev) 68.50 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA +C +UC:::+:+++GAUC+U::CUAU:GGA CGUC:CUCU::G+CU+U++:+:::A 735 AACACAUUCAACAGUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACUCUUCAAAAGA 794 >>-------------((((------------.--..((((((((((((,.,,,,,,,,,, 61 gucAaaCAacccAAAccagGAUGAUGAgacg.cA..gccuucgcuccca.GAGCGUGAau 116 G+CA AA CC AAC::GG+UGAUGAG C CA :C+UU:G::CCC+ GAG G G+A+ 795 GCCACUGAAUCC-AACUUGGUUGAUGAGCC-cCAuaACCUUUGUACCCCaGAGUGAGGAA 852 ,,<......................................................... 117 cCg......................................................... 119 G 853 AUGaaaucgaauuuaaauuagcuugguccgcaauccuuagcgguucggccaucuauaauu 912 .....................----<<---<<<<<-<<<<<_______>>>>>->>>>>- 120 .....................CGGCgcgcaucugguguugguUuuuuUccuacUucacuU 158 CG++:: + :++:U::::: UUU+ ::::: :++: 913 uugaauaaaauuuugcuuugcCGUUGCAAUUGUGAUAACUUCCUUUGGAAUUUGUUGCGA 972 ->>>,,,......,,,,,,,,,......<<<--<<<<<<__________>>>>>>-->>> 159 GgcuuuU......GAUGAUCGU......uccUaucucccUcuuUUUuGuggggaaUagga 206 +::UU + GAUGAUC U :CCUAU+U ::UC++UUUUG+:: G AUAGG: 973 UAUUUAAuggcgcGAUGAUCUUgacccaUCCUAUGUGCUUCCAUUUUGGAAGG-AUAGGG 1031 .........,))))))))))))-.------)))) 207 .........Ugggagcgaaggca.GUCUGAcugg 230 UGGG::C:AA+G:+ GUCUGAC::G 1032 auucaugggUGGGUACAAAUGGCaGUCUGACAAG 1065 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #76503,sp|AL121770.1|SPAC821 S.pombe chromosome I cosmid c821. ----isReversed: 1 ----hitSequence: UCGACGAUACUCCAUAGGAUCAUUUCUAUAGUAUACGUCCGGCUUGGGUUUCCUAACCUAGCCACAGAACUCAACACGGAUGAUGAUAGGAGGCACCGUUGCCCUCAGAGUGAGGACUUUUAAUUCUUUGAAGGCAUGCUUUUCGAUUAGGUUUUUUACCUAAUUGUUUUGCUGUCUUUCUAUGCGAUGAUCUCUUACAUGAUAUGUUUCCUUUUGGUCGUAUUAUGUAGGGCAGCUGGUGUUUUCUGACGUG hit 14 : 10682 10430 (rev) 77.78 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 ++C :U::::C:+++:AU++U+:CUA+AG+AU+CG+CC++CU:+G++UU:++:A:::: 24771 UCGACGAUACUCCAUAGGAUCAUUUCUAUAGUAUACGUCCGGCUUGGGUUUCCUAACCUA 24830 >>-------------((((--------------.((((((((((((,.,,,,,,,,,,,, 61 gucAaaCAacccAAAccagGAUGAUGAgacgcA.gccuucgcuccca.GAGCGUGAaucC 118 G:CA A AAC+C AAC::GGAUGAUGA A+G C::CG:U:CC+ AG GUGA + C 24831 GCCACAGAACUC-AACACGGAUGAUGAUAGGAGg--CACCGUUGCCCuCAGAGUGAGGAC 24887 <.............----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,, 119 g.............CGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuU 165 : GGC::GC+U:::G :U:GGUUUUUU CC:A:UU:::UUG:::U+U 24888 UuuuaauucuuugaAGGCAUGCUUUUCGAUUAGGUUUUUUACCUAAUUGUUUUGCUGUCU 24947 ........,,,,,,,,,...<<<--<<<<<<__________>>>>>>-->>>..,))))) 166 ........GAUGAUCGU...uccUaucucccUcuuUUUuGuggggaaUagga..Ugggag 212 GAUGAUC ::: AU:U+++UC+UUUU+GU +G:AU+::: GG:A: 24948 uucuaugcGAUGAUCUCuuaCAUGAUAUGUUUCCUUUUGGU--CGUAUUAUGuaGGGCAG 25005 ).))))))-------)))) 213 c.gaaggcaGUCUGAcugg 230 C G::G++ UCUGAC::G 25006 CuGGUGUU-UUCUGACGUG 25023 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #76684,sp|AL031743.1|SPBC26H8 S.pombe chromosome II cosmid c26H8. ----isReversed: 1 ----hitSequence: UCGACGAUACUCCAUAGGAUCAUUUCUAUAGUAUACGUCCGGCUUGGGUUUCCUAACCUAGCCACAGAACUCAACACGGAUGAUGAUAGAAGGCACCGUUGCCCGCAGAGUGAGAAUUUUUACUUCUUUGAGGAUGUGCUGAUCGAUUUGGCUUUUUGCUUAAUUGUUGUGCUAUCUUUAUUUGCGAUGAUCUCUUACAUGAUAUGUUCCUUUUGGUCGUGUCAUGUAGGGCAGCUGGUGUUUUCUGACGUG hit 15 : 18723 18472 (rev) 55.10 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 ++C :U::::C:+++:AU++U+:CUA+AG+AU+CG+CC++CU:+G++UU:++:A:::: 20798 UCGACGAUACUCCAUAGGAUCAUUUCUAUAGUAUACGUCCGGCUUGGGUUUCCUAACCUA 20857 >>-------------((((--------------.((((((((((((,.,,,,,,,,,,,, 61 gucAaaCAacccAAAccagGAUGAUGAgacgcA.gccuucgcuccca.GAGCGUGAaucC 118 G:CA A AAC+C AAC::GGAUGAUGA A++ C::CG:U:CC+ AG GUGA + 20858 GCCACAGAACUC-AACACGGAUGAUGAUAGAAGg--CACCGUUGCCCgCAGAGUGAGAAU 20914 <.............----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,, 119 g.............CGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuU 165 G +::GC+::::G :UU+G UUUUU C+UA:UU::::UG:: U+U 20915 UuuuacuucuuugaGGAUGUGCUGAUCGAUUUGGCUUUUUGCUUAAUUGUUGUGCUAUCU 20974 ........,,,,,,,,,...<<<--<<<<<<__________>>>>>>-->>>..,))))) 166 ........GAUGAUCGU...uccUaucucccUcuuUUUuGuggggaaUagga..Ugggag 212 GAUGAUC ::: A::U+ +UC+UUUU+GU +G::U ::: GG:A: 20975 uuauuugcGAUGAUCUCuuaCAUGAUAUG-UUCCUUUUGGU--CGUGUCAUGuaGGGCAG 21031 ).))))))-------)))) 213 c.gaaggcaGUCUGAcugg 230 C G::G++ UCUGAC::G 21032 CuGGUGUU-UUCUGACGUG 21049 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #77617,sp|X13850.1|SPSNRU3 Fission yeast U3 small nuclear RNA gene ----isReversed: 0 ----hitSequence: GUAUCGAUACUCCAUAGGAUCAUUUCUAUAGUAUACGUCCUUCUUGGGUUUCCUAACCUAGCCACAGAAGUGAACACGGAUGAUGAUAGGAGGCACCGUUGCCUCAGAGUGAGGACUUUUAAUUCUUUGAAGGCAUGCUUUUCGAUUAGGUUUUUUACCUAAUUGUUUUGCUGUCAGAGUAUGCGAUGAUCUCUUACAUGAUAUGUUUCCUUUUGGUCGUAUUAUGUAGGGCAGCUGGUGUUUUCUGACGUG hit 16 : 317 568 (fwd) 77.16 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 + A C :U::::C:+++:AU++U+:CUA+AG+AU+CG+CC+UCU:+G++UU:++:A:::: 317 GUAUCGAUACUCCAUAGGAUCAUUUCUAUAGUAUACGUCCUUCUUGGGUUUCCUAACCUA 376 >>-------------((((--------------.((((((((((((,,,,,,,,,,,,,< 61 gucAaaCAacccAAAccagGAUGAUGAgacgcA.gccuucgcucccaGAGCGUGAaucCg 119 G:CA A AA+++ AAC::GGAUGAUGA A+G C::CG:U:CC AG GUGA + C: 377 GCCACAGAAGUG-AACACGGAUGAUGAUAGGAGg--CACCGUUGCCUCAGAGUGAGGACU 433 .............----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,. 120 .............CGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuU. 165 GGC::GC+U:::G :U:GGUUUUUU CC:A:UU:::UUG:::U++ 434 uuuaauucuuugaAGGCAUGCUUUUCGAUUAGGUUUUUUACCUAAUUGUUUUGCUGUCAg 493 .......,,,,,,,,,...<<<--<<<<<<__________>>>>>>-->>>..,)))))) 166 .......GAUGAUCGU...uccUaucucccUcuuUUUuGuggggaaUagga..Ugggagc 213 GAUGAUC ::: AU:U+++UC+UUUU+GU +G:AU+::: GG:A:C 494 aguaugcGAUGAUCUCuuaCAUGAUAUGUUUCCUUUUGGU--CGUAUUAUGuaGGGCAGC 551 .))))))-------)))) 214 .gaaggcaGUCUGAcugg 230 G::G++ UCUGAC::G 552 uGGUGUU-UUCUGACGUG 568 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #77619,sp|X56982.1|SPSNU3A S. pombe snu3a gene for U3A small nuclear RNA ----isReversed: 0 ----hitSequence: UCGACGAUACUCCAUAGGAUCAUUUCUAUAGUAUACGUCCGGCUUGGGUUUCCUAACCUAGCCACAGAACUCAACACGGAUGAUGAUAGGAGGCACCGUUGCCCUCAGAGUGAGGACUUUUAAUUCUUUGAAGGCAUGCUUUUCGAUUAGGUUUUUUACCUAAUUGUUUUGCUGUCUUUCUAUGCGAUGAUCUCUUACAUGAUAUGUUUCCUUUUGGUCGUAUUAUGUAGGGCAGCUGGUGUUUUCUGACGUG hit 17 : 38 290 (fwd) 77.78 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 ++C :U::::C:+++:AU++U+:CUA+AG+AU+CG+CC++CU:+G++UU:++:A:::: 38 UCGACGAUACUCCAUAGGAUCAUUUCUAUAGUAUACGUCCGGCUUGGGUUUCCUAACCUA 97 >>-------------((((--------------.((((((((((((,.,,,,,,,,,,,, 61 gucAaaCAacccAAAccagGAUGAUGAgacgcA.gccuucgcuccca.GAGCGUGAaucC 118 G:CA A AAC+C AAC::GGAUGAUGA A+G C::CG:U:CC+ AG GUGA + C 98 GCCACAGAACUC-AACACGGAUGAUGAUAGGAGg--CACCGUUGCCCuCAGAGUGAGGAC 154 <.............----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,, 119 g.............CGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuU 165 : GGC::GC+U:::G :U:GGUUUUUU CC:A:UU:::UUG:::U+U 155 UuuuaauucuuugaAGGCAUGCUUUUCGAUUAGGUUUUUUACCUAAUUGUUUUGCUGUCU 214 ........,,,,,,,,,...<<<--<<<<<<__________>>>>>>-->>>..,))))) 166 ........GAUGAUCGU...uccUaucucccUcuuUUUuGuggggaaUagga..Ugggag 212 GAUGAUC ::: AU:U+++UC+UUUU+GU +G:AU+::: GG:A: 215 uucuaugcGAUGAUCUCuuaCAUGAUAUGUUUCCUUUUGGU--CGUAUUAUGuaGGGCAG 272 ).))))))-------)))) 213 c.gaaggcaGUCUGAcugg 230 C G::G++ UCUGAC::G 273 CuGGUGUU-UUCUGACGUG 290 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #77620,sp|X56189.1|SPSNU3B S. pombe snu3b gene for U3B small nuclear RNA ----isReversed: 0 ----hitSequence: UCGACGAUACUCCAUAGGAUCAUUUCUAUAGUAUACGUCCGGCUUGGGUUUCCUAACCUAGCCACAGAACUCAACACGGAUGAUGAUAGAAGGCACCGUUGCCCGCAGAGUGAGAAUUUUUACUUCUUUGAGGAUGUGCUGAUCGAUUUGGCUUUUUGCUUAAUUGUUGUGCUAUCUUUAUUUGCGAUGAUCUCUUACAUGAUAUGUUCCUUUUGGUCGUGUCAUGUAGGGCAGCUGGUGUUUUCUGACGUG hit 18 : 90 341 (fwd) 55.10 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 ++C :U::::C:+++:AU++U+:CUA+AG+AU+CG+CC++CU:+G++UU:++:A:::: 90 UCGACGAUACUCCAUAGGAUCAUUUCUAUAGUAUACGUCCGGCUUGGGUUUCCUAACCUA 149 >>-------------((((--------------.((((((((((((,.,,,,,,,,,,,, 61 gucAaaCAacccAAAccagGAUGAUGAgacgcA.gccuucgcuccca.GAGCGUGAaucC 118 G:CA A AAC+C AAC::GGAUGAUGA A++ C::CG:U:CC+ AG GUGA + 150 GCCACAGAACUC-AACACGGAUGAUGAUAGAAGg--CACCGUUGCCCgCAGAGUGAGAAU 206 <.............----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,, 119 g.............CGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuU 165 G +::GC+::::G :UU+G UUUUU C+UA:UU::::UG:: U+U 207 UuuuacuucuuugaGGAUGUGCUGAUCGAUUUGGCUUUUUGCUUAAUUGUUGUGCUAUCU 266 ........,,,,,,,,,...<<<--<<<<<<__________>>>>>>-->>>..,))))) 166 ........GAUGAUCGU...uccUaucucccUcuuUUUuGuggggaaUagga..Ugggag 212 GAUGAUC ::: A::U+ +UC+UUUU+GU +G::U ::: GG:A: 267 uuauuugcGAUGAUCUCuuaCAUGAUAUG-UUCCUUUUGGU--CGUGUCAUGuaGGGCAG 323 ).))))))-------)))) 213 c.gaaggcaGUCUGAcugg 230 C G::G++ UCUGAC::G 324 CuGGUGUU-UUCUGACGUG 341 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----sequence: #48890,sp|V00190.1|DDRNA1 Gene for small nuclear RNA D2 of slime mold (D. discoideum). ----isReversed: 0 ----hitSequence: AUGACCAAACUCUUAGGAUCAUUUCUAGAGUAUCGUCUAUUAAAAUUAUUCAUCAAUAAUUUUUCCUCUUUCACAGCUAGGAUGAUGAUACACACUCACUAUACGAAAGCGUGAAACCGUUAUUAUCAAAUGAUUCAUUUAUUUGUUAUUAACAUUGAUGACCGUCUAAUUCAGGGAUGAAUUGGUUGUAUGGUGGGAUUCGUACUGG hit 19 : 62 269 (fwd) 59.88 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 A ++C A::: UC:+++:AU+A+U:+UA:::+AU +:::U++:A+U+UU:++:AA+:: 62 AUGACCAAAC-UCUUAGGAUCAUUUCUAGAGUAUCGUCUAUUAAAAUUAUUCAUCAAUAA 120 >>----------..---((((--------------((((((((((((,.,,,,,,,,,,, 61 gucAaaCAaccc..AAAccagGAUGAUGAgacgcAgccuucgcuccca.GAGCGUGAauc 117 :U C++ + +A+C:AGGAUGAUGA AC+CA C::::::::C AGCGUGAA+C 121 UUUUUCCUCUUUcaCAGCUAGGAUGAUGAUACACA--CUCACUAUACGaAAGCGUGAAAC 178 ,<----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<< 118 CgCGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUucc 177 CG ++++ A+C:::U+:U:++UUU+UU+:U:+U:::C+U+ GAUGA CGU 179 CG---UUAUUAUCAAAUGAUUCAUUUAUUUGUUAUUAACAUU------GAUGACCGU--- 226 --<<<<<<__________>>>>>>-->>>.....,))))))))))))-------)))) 178 UaucucccUcuuUUUuGuggggaaUagga.....UgggagcgaaggcaGUCUGAcugg 230 C::::UC G+::::A UG::::::::G++ UC ACU:G 227 ---CUAAUUCAG----GGAUGAA------uugguUGUAUGGUGGGAU--UCGUACUGG 269 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----sequence: #49086,sp|K00789.1|DDURD2 D.discoideum D2 small nuclear RNA. ----isReversed: 0 ----hitSequence: AUGACCAAACUCUUAGGAUCAUUUCUAGAGYAYYGUCUAUUAAAAUUAUUCAUCAAUAAUUUUUCCUCUUUCAUAGYYAGGAYGAYGAUACACACUCACUAUACGAAAGYGYGAAAYYGUUAUUAUCAAAUGAUUCAUUUAUUUGUUAUUAACAUUGAYGAYYGUCUAAUUCAGGGAUGAAUUGGUUGUAUGGUGGGAUUCGUACUGG hit 20 : 2 209 (fwd) 43.20 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 A ++C A::: UC:+++:AU+A+U:+UA:::+A+ +:::U++:A+U+UU:++:AA+:: 2 AUGACCAAAC-UCUUAGGAUCAUUUCUAGAGYAYYGUCUAUUAAAAUUAUUCAUCAAUAA 60 >>----------..---((((--------------((((((((((((,.,,,,,,,,,,, 61 gucAaaCAaccc..AAAccagGAUGAUGAgacgcAgccuucgcuccca.GAGCGUGAauc 117 :U C++ + A+++AGGA GA GA AC+CA C::::::::C AG+G GAA++ 61 UUUUUCCUCUUUcaUAGYYAGGAYGAYGAUACACA--CUCACUAUACGaAAGYGYGAAAY 118 ,<----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<< 118 CgCGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUucc 177 G ++++ A+C:::U+:U:++UUU+UU+:U:+U:::C+U+ GA GA+ GU 119 YG---UUAUUAUCAAAUGAUUCAUUUAUUUGUUAUUAACAUU------GAYGAYYGU--- 166 --<<<<<<__________>>>>>>-->>>.....,))))))))))))-------)))) 178 UaucucccUcuuUUUuGuggggaaUagga.....UgggagcgaaggcaGUCUGAcugg 230 C::::UC G+::::A UG::::::::G++ UC ACU++ 167 ---CUAAUUCAG----GGAUGAA------uugguUGUAUGGUGGGAU--UCGUACUGG 209 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz ----sequence: #7138,sp|U27297.1|EG27297 Euglena gracilis U3 small nucleolar RNA. ----isReversed: 0 ----hitSequence: AGACUGUACUCCACAAGGAUCAUUUCUUGAGGAAGUAUCAGUCCGAUUCACAGAGAACACUACAAUCUUCAACAGCCACGAUGAUGACUGGCAGCUUUCCUCUCGGAGCGUGAGGCAGCGAGCGACCUCGGUCGCAUCGCAUCGAUGAUCGCAGAUGAGAGGUCAGCAAUUUGAGUGGU hit 21 : 2 180 (fwd) 37.48 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 A+AC :::+::+C+AG+AUCA+UU+U ::GGA G+ UC::UC+GA+UC ++GAG+::+: 2 AGACUGUACUCCACAAGGAUCAUUUCUUGAGGAAGUAUCAGUCCGAUUCACAGAGAACAC 61 >>-------------((((--------------.((((((((((((,,,,,,,,,,,,,< 61 gucAaaCAacccAAAccagGAUGAUGAgacgcA.gccuucgcucccaGAGCGUGAaucCg 119 ::CAA C+ C ++A+CCA+GAUGAUGA+ +GCA +++U+C+CUC+ GAGCGUGA +C G 62 UACAAUCUUCAACAGCCACGAUGAUGACUGGCAgCUUUCCUCUCG--GAGCGUGAGGCAG 119 ----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<-- 120 CGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUa 179 CG +GC :C:::+:::+++U+ +U++::: :::C: GAUGA G 120 CG---AGCGACCUCGGUCGCAUCGCAUCGAUGAUCGCA--------GAUGAGAGG----- 163 <<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 180 ucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 :C +++ UUUG G:GG U 164 ----UCAGCAAUUUGAGUGG-------U----------------------- 180 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mam.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/mam.dat.fasta.gz ----sequence: #7289,sp|AC139728.3|AC139728 Carollia perspicillata clone 29G20, complete sequence. ----isReversed: 0 ----hitSequence: AAGACUGUACUUUCGGGGAUCAUUUCUAUAGUUCGUCACUAGAGAAGUUUCUCUGAAUGUGUAGAAUACCCUAAACCAUGAGGAGGAGGUGCAGUGUUCUCUCCUGAGCAAUACCUCUUCUGGUAUUGCUUUUAGAACUGCCAAUAGCCAUUGAUGAUUGUUCUUCUCUUCCUUCAGAAGAGUAAGAGGGGGAGAACACAGUCUGAGUGG hit 22 : 90984 91193 (fwd) 48.25 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CU:U:C+U:C :+GAU+AUU::UA++G+ G+ +C++++::AGU+U+U+:G:A+G: 90984 AAGACUGUACUUUCGGGGAUCAUUUCUAUAGUUCGUCACUAGAGAAGUUUCUCUGAAUGU 91043 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 G: AA A+CC AAACCA:GA GA GAG GCAG::UUC:C CC: GAGC A++CC C 91044 GUAGAAUACCCUAAACCAUGAGGAGGAGGUGCAGUGUUCUCUCCU-GAGCA--AUACCUC 91100 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 +C+ G A+ ::+U:U G:+ U :C A:U+:: +U+ GAUGAU GUUC:U+: 91101 UUCUGGUAUUGCUUUUAGAACU----GCCAAUAGCCAUU------GAUGAUUGUUCUUCU 91150 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CU::CU U G::GA:UA:GA :GG G:GAA::CAGUCUGA:UGG 91151 CUUCCU------UCAGAAGAGUAAGA-GGGGGAGAACACAGUCUGAGUGG 91193 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mam.dat.fasta.gz ----sequence: #15032,sp|AF176810.1|AF176810 Bos taurus U3 small nuclear RNA, partial sequence. ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGAACGUGUAGAGCACCCGAAACCACGAGGAGGAGAUAAAGCGUUCUCUUCUGAGCGUGAAGUCGGCUUUGGGUGUUGCUUCUGCAGCUGCCGUUAGCCAUUGAUGAUCGUUCUUCUUUUCCUUUUAGGAGAUGAAGAGGGAGAGAACGUAAUCUGAGUGG hit 23 : 1 214 (fwd) 87.57 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C:U:C+:+GAU+AUU::UA++G+ G+ +C++++::AGU+U+U+:G:A:G: 1 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGAACGU 60 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+CC+AAACCA:GA GA GAGA + A:C:UUC:CU C: GAGCGUGAA++C: 61 GUAGAGCACCCGAAACCACGAGGAGGAGAUAAAGCGUUCUCUUCU-GAGCGUGAAGUCG- 118 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+ U :G: G++G:UU+U :C++CU:C: UU GC:+UUGAUGAUCGUUC:U 119 ---GCUU-UGGGU-GUUGCUUCU---GCAGCUGCCGUUAGCCAUUGAUGAUCGUUCUU-- 168 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CU: CUUUU +G :GA :GA :G AG:GAA:G:A UCUGA:UGG 169 CUUUUCCUUUUAGGAGAUGA---AGA-GGGAGAGAACGUAAUCUGAGUGG 214 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #4769,sp|AC074336.14|AC074336 Mus musculus Strain C57BL6/J chromosome 1 BAC, RP23-366C17, Complete Sequence, complete sequence. ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGUGUAGAGCACCUGAAACCACGAGGACGAGACGUAGCGUCCCCUCCUGAGCGUGAAGCCGGCUCUAGGUGCUGCAUGAUUGCAGCUGCCUCUUGCCAUUGAUGAUCGUUCUUCUCUCCUUCAGGAGGGUGAGAGGGAAGGAACGCAGUCUGAGUGG hit 24 : 194216 194429 (fwd) 95.05 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C+::C+:+GAU+AUU::UA++G+ G+ +C++++::AGU+U+U+:G::+G: 194216 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGU 194275 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C++AAACCA:GA GA GAGACG+AGC:U:C: UCC: GAGCGUGAA+CC: 194276 GUAGAGCACCUGAAACCACGAGGACGAGACGUAGCGUCCCCUCCU-GAGCGUGAAGCCG- 194333 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C +::G: G:+G:+U+ UU:C+:CU:C::+U+GC:+UUGAUGAUCGUUC:U+: 194334 ---GCUC-UAGGU-GCUGCAUGA-UUGCAGCUGCCUCUUGCCAUUGAUGAUCGUUCUUCU 194387 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 UCC:UC G+:GGG : :GA :GGA :G:A:GCAGUCUGA:UGG 194388 CUCCUUCA-----GGAGGGUG--AGA-GGGAAGGAACGCAGUCUGAGUGG 194429 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #5057,sp|AC098642.5|AC098642 Genomic sequence for Mus musculus, clone RP23-270O7, complete sequence. ----isReversed: 1 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGUGUAGAGCACCUGAAACCACGAGGACGAGACGUAGCAUCCCCUACUGAGCGUGAAGCCGGCUCUAGGUGCUGCUUGAUUGCAGCUGCCUCUUGCCAUUGAUGAUCAUUCUUCUCUCCUUCGGGAGGGUGAGAGGGAGGGAACGCAGUCUGAGUGG hit 25 : 48519 48306 (rev) 89.34 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C+::C+:+GAU+AUU::UA++G+ G+ +C++++::AGU+U+U+:G::+G: 140316 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGU 140375 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C++AAACCA:GA GA GAGACG+AGC:U:C:CU:C: GAGCGUGAA+CC: 140376 GUAGAGCACCUGAAACCACGAGGACGAGACGUAGCAUCCCCUACU-GAGCGUGAAGCCG- 140433 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C +::G: G:+G:UU+ UU:C+:CU:C::+U+GC:+UUGAUGAUC UUC:U+: 140434 ---GCUC-UAGGU-GCUGCUUGA-UUGCAGCUGCCUCUUGCCAUUGAUGAUCAUUCUUCU 140487 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CUC: UC G+ :GG :U :GA :G:AG:G:A:GCAGUCUGA:UGG 140488 CUCCUUC------GGGAGG-GUGAGA-GGGAGGGAACGCAGUCUGAGUGG 140529 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #5330,sp|AC109138.10|AC109138 Mus musculus, clone RP23-41B18, complete sequence. ----isReversed: 1 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGUGUAGAGCACCUGAAACCACGAGGACGAGACAUAGCGUCCCCUCCUGAGCGUGAAGCUGGCUCUAGGUGCUGCUUGAUUGCAGCUGCCUCUUGCCAUUGAUGAUCGUUCUUCUCUCCUUCGGGAGGGUGAGAGGGAGGGAACGCAGUCUGAGUGG hit 26 : 86930 86717 (rev) 95.45 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C+::C+:+GAU+AUU::UA++G+ G+ +C++++::AGU+U+U+:G::+G: 182226 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGU 182285 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C++AAACCA:GA GA GAGAC++AGC:U:C:CUCC: GAGCGUGAA+C : 182286 GUAGAGCACCUGAAACCACGAGGACGAGACAUAGCGUCCCCUCCU-GAGCGUGAAGCUG- 182343 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C +::G: G:+G:UU+ UU:C+:CU:C::+U+GC:+UUGAUGAUCGUUC:U+: 182344 ---GCUC-UAGGU-GCUGCUUGA-UUGCAGCUGCCUCUUGCCAUUGAUGAUCGUUCUUCU 182397 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CUC: UC G+ :GG :U :GA :GGAG:G:A:GCAGUCUGA:UGG 182398 CUCCUUC------GGGAGG-GUGAGA-GGGAGGGAACGCAGUCUGAGUGG 182439 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #5713,sp|AC119809.10|AC119809 Mus musculus, clone RP24-505E24, complete sequence. ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGUGUAGAGCACCUGAAACCACGAGGACGAGACGUAGCGUCCCCUCCUGAGCGUGAAGCCGGCUCUAGGUGCUGCAUGAUUGCAGCUGCCUCUUGCCAUUGAUGAUCGUUCUUCUCUCCUUCAGGAGGGUGAGAGGGAAGGAACGCAGUCUGAGUGG hit 27 : 3290 3503 (fwd) 95.05 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C+::C+:+GAU+AUU::UA++G+ G+ +C++++::AGU+U+U+:G::+G: 3290 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGU 3349 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C++AAACCA:GA GA GAGACG+AGC:U:C: UCC: GAGCGUGAA+CC: 3350 GUAGAGCACCUGAAACCACGAGGACGAGACGUAGCGUCCCCUCCU-GAGCGUGAAGCCG- 3407 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C +::G: G:+G:+U+ UU:C+:CU:C::+U+GC:+UUGAUGAUCGUUC:U+: 3408 ---GCUC-UAGGU-GCUGCAUGA-UUGCAGCUGCCUCUUGCCAUUGAUGAUCGUUCUUCU 3461 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 UCC:UC G+:GGG : :GA :GGA :G:A:GCAGUCUGA:UGG 3462 CUCCUUCA-----GGAGGGUG--AGA-GGGAAGGAACGCAGUCUGAGUGG 3503 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #24100,sp|AL603682.36|AL603682 Mouse DNA sequence from clone RP23-235J5 on chromosome 11 ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGUGUAGAGCACCUGAAACCACGAGGACGAGACGUAGCAUCCCCUACUGAGCGUGAAGCCGGCUCUAGGUGCUGCUUGAUUGCAGCUGCCUCUUGCCAUUGAUGAUCAUUCUUCUCUCCUUCGGGAGGGUGAGAGGGAGGGAACGCAGUCUGAGUGG hit 28 : 56958 57171 (fwd) 89.34 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C+::C+:+GAU+AUU::UA++G+ G+ +C++++::AGU+U+U+:G::+G: 56958 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGU 57017 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C++AAACCA:GA GA GAGACG+AGC:U:C:CU:C: GAGCGUGAA+CC: 57018 GUAGAGCACCUGAAACCACGAGGACGAGACGUAGCAUCCCCUACU-GAGCGUGAAGCCG- 57075 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C +::G: G:+G:UU+ UU:C+:CU:C::+U+GC:+UUGAUGAUC UUC:U+: 57076 ---GCUC-UAGGU-GCUGCUUGA-UUGCAGCUGCCUCUUGCCAUUGAUGAUCAUUCUUCU 57129 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CUC: UC G+ :GG :U :GA :G:AG:G:A:GCAGUCUGA:UGG 57130 CUCCUUC------GGGAGG-GUGAGA-GGGAGGGAACGCAGUCUGAGUGG 57171 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #24875,sp|AL669902.8|AL669902 Mouse DNA sequence from clone RP23-459P8 on chromosome 11 ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGUGUAGAGCACCCGAAACCACGAGGACGAGACGUAGCGUUCCCUCCUGAGCGUGAAGCCGGCUCUAGGUGCUGCUUGACUGCAGCUGCCUCCUGCCAUUGAUGAUCGUUCUUCCCUCCUUUGGGAGGGUGAGAGGGAGGGAACGCAGUCUGAGUGG hit 29 : 56811 57024 (fwd) 99.12 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C+::C+:+GAU+AUU::UA++G+ G+ +C++++::AGU+U+U+:G::+G: 56811 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGU 56870 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+CC+AAACCA:GA GA GAGACG+AGC:UUC:CUCC: GAGCGUGAA+CC: 56871 GUAGAGCACCCGAAACCACGAGGACGAGACGUAGCGUUCCCUCCU-GAGCGUGAAGCCG- 56928 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C +::G: G:+G:UU+ U:C+:CU:C::+ +GC:+UUGAUGAUCGUUC:U+ 56929 ---GCUC-UAGGU-GCUGCUUGA-CUGCAGCUGCCUCCUGCCAUUGAUGAUCGUUCUUC- 56981 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 C UC+U UU+G+ GGG U :GA :GGAG:GAA:GCAGUCUGA:UGG 56982 ---CCUCCU-UUGGGAGGG--UGAGA-GGGAGGGAACGCAGUCUGAGUGG 57024 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #24875,sp|AL669902.8|AL669902 Mouse DNA sequence from clone RP23-459P8 on chromosome 11 ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGUGUAGAGCACCCGAAACCACGAGGACGAGACGUAGCGUUCCCUCCUGAGCGUGAAGCCGGCUCUAGGUGCUGCUUGACUGCAGCUGCCUCCUGCCAUUGAUGAUCGUUCUUCCCUCCUUUGGGAGGGUGAGAGGGAGGGAACGCAGUCUGAGUGG hit 30 : 62201 62414 (fwd) 99.12 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C+::C+:+GAU+AUU::UA++G+ G+ +C++++::AGU+U+U+:G::+G: 62201 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGU 62260 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+CC+AAACCA:GA GA GAGACG+AGC:UUC:CUCC: GAGCGUGAA+CC: 62261 GUAGAGCACCCGAAACCACGAGGACGAGACGUAGCGUUCCCUCCU-GAGCGUGAAGCCG- 62318 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C +::G: G:+G:UU+ U:C+:CU:C::+ +GC:+UUGAUGAUCGUUC:U+ 62319 ---GCUC-UAGGU-GCUGCUUGA-CUGCAGCUGCCUCCUGCCAUUGAUGAUCGUUCUUC- 62371 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 C UC+U UU+G+ GGG U :GA :GGAG:GAA:GCAGUCUGA:UGG 62372 ---CCUCCU-UUGGGAGGG--UGAGA-GGGAGGGAACGCAGUCUGAGUGG 62414 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #24875,sp|AL669902.8|AL669902 Mouse DNA sequence from clone RP23-459P8 on chromosome 11 ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGUGUAGAGCACCCGAAACCACGAGGACGAGACGUAGCGUUCCCUCCUGAGCGUGAAGCCGGCUCUAGGUGCUGCUUGACUGCAGCUGCCUCCUGCCAUUGAUGAUCGUUCUUCCCUCCUUUGGGAGGGUGAGAGGGAGGGAACGCAGUCUGAGUGG hit 31 : 75860 76073 (fwd) 99.12 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C+::C+:+GAU+AUU::UA++G+ G+ +C++++::AGU+U+U+:G::+G: 75860 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGU 75919 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+CC+AAACCA:GA GA GAGACG+AGC:UUC:CUCC: GAGCGUGAA+CC: 75920 GUAGAGCACCCGAAACCACGAGGACGAGACGUAGCGUUCCCUCCU-GAGCGUGAAGCCG- 75977 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C +::G: G:+G:UU+ U:C+:CU:C::+ +GC:+UUGAUGAUCGUUC:U+ 75978 ---GCUC-UAGGU-GCUGCUUGA-CUGCAGCUGCCUCCUGCCAUUGAUGAUCGUUCUUC- 76030 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 C UC+U UU+G+ GGG U :GA :GGAG:GAA:GCAGUCUGA:UGG 76031 ---CCUCCU-UUGGGAGGG--UGAGA-GGGAGGGAACGCAGUCUGAGUGG 76073 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #24875,sp|AL669902.8|AL669902 Mouse DNA sequence from clone RP23-459P8 on chromosome 11 ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGUGUAGAGCACCCGAAACCACGAGGACGAGACGUAGCGUUCCCUCCUGAGCGUGAAGCCGGCUCUAGGUGCUGCUUGACUGCAGCUGCCUCCUGCCAUUGAUGAUCGUUCUUCCCUCCUUUGGGAGGGUGAGAGGGAGGGAACGCAGUCUGAGUGG hit 32 : 84942 85155 (fwd) 99.12 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C+::C+:+GAU+AUU::UA++G+ G+ +C++++::AGU+U+U+:G::+G: 84942 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGU 85001 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+CC+AAACCA:GA GA GAGACG+AGC:UUC:CUCC: GAGCGUGAA+CC: 85002 GUAGAGCACCCGAAACCACGAGGACGAGACGUAGCGUUCCCUCCU-GAGCGUGAAGCCG- 85059 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C +::G: G:+G:UU+ U:C+:CU:C::+ +GC:+UUGAUGAUCGUUC:U+ 85060 ---GCUC-UAGGU-GCUGCUUGA-CUGCAGCUGCCUCCUGCCAUUGAUGAUCGUUCUUC- 85112 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 C UC+U UU+G+ GGG U :GA :GGAG:GAA:GCAGUCUGA:UGG 85113 ---CCUCCU-UUGGGAGGG--UGAGA-GGGAGGGAACGCAGUCUGAGUGG 85155 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #26605,sp|AL844548.7|AL844548 Mouse DNA sequence from clone RP23-263D22 on chromosome 2 ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCACUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGGCUACGUAGAGCACCCGAAACCAGGAGGAUGAGACAUACCUCCCCUCCUGAGCGUGAAGCCGGCUCUAGGUGCUGCUUGAGUGCAGCUGCCUCUUGUCAUUGAUGGUUGUUCUUCUGUCCUUCAGGAGGGUGAGAGGGAGGGAAUGCAGUCUGAGUGG hit 33 : 113077 113289 (fwd) 74.98 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU :+: C+:+GAU+A:U::UA++G+ G+ +C++++::A:U+U+U+:G :+: 113077 AAGACUAUACUUUCAGGGAUCACUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGGCUAC 113136 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+CC+AAACCA GA GAUGAGAC + C+U:C:CUCC: GAGCGUGAA+CC: 113137 GUAGAGCACCCGAAACCAGGAGGAUGAGAC-AUACCUCCCCUCCU-GAGCGUGAAGCCG- 113193 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 :C+C +::G: G:+G:UU+ +U:C+:CU:C::+U+G::+UUGAUG U GUUC:U+U 113194 ---GCUC-UAGGU-GCUGCUUGA-GUGCAGCUGCCUCUUGUCAUUGAUGGUUGUUCUUCU 113247 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 +UCC:UC G+:GGG U :GA :GGAG:G:A+G AGUCUGA UGG 113248 GUCCUUCA-----GGAGGG--UGAGA-GGGAGGGAAUGCAGUCUGAGUGG 113289 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #69343,sp|X63743.1|MMSNRNA M.musculus DNA sequence for U3A snRNA ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUUGUUACUAGAGAAGUUUCUCUGACUGUGUAGAGCACCCGAAACCACGAGGAGGAGACAGAGUGUCCUUUCCUGAGCGUGAAGCCGGCUUUUAGUGCUGCAUUUUGCAACUGCUAUCUGCCAUUGAUGAUCGUUCUCAACUCUCUUGAGGGUUGAGAGGGAGAGGACACAGUCUGAGUGG hit 34 : 815 1026 (fwd) 90.75 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C+::C+:+GAU+AUU::UA++G+ UG+ +C++++::AGU+U+U+:G::+G: 815 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUUGUUACUAGAGAAGUUUCUCUGACUGU 874 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+CC+AAACCA:GA GA GAGAC+ AG::U:C::UCC: GAGCGUGAA+CC: 875 GUAGAGCACCCGAAACCACGAGGAGGAGACAGAGUGUCCUUUCCU-GAGCGUGAAGCCG- 932 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+ U::G: G +G:+UU UU:C+ CU:C::U +GC:+UUGAUGAUCGUUC 933 ---GCUU-UUAGU-GCUGCAUU--UUGCAACUGCUAUCUGCCAUUGAUGAUCGUUC---- 981 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 :: :CUCU UU G+G: :: GA :GGA::G:A::CAGUCUGA:UGG 982 UCAACUCUCUUGAGGGUUGA----GA-GGGAGAGGACACAGUCUGAGUGG 1026 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #69349,sp|X04258.1|MMSNU3P Mouse U3 RNA pseudogene ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGUGUAGAGCACCUGAAACCACGAGGACGAGACGUAGCGUCCCCUCCUGAGCGUGAAGCCGGCUCUAGGUGCUGCAUGAUUGCAGCUGCCUCUUGCCAUUGAUGAUCGUUCUUCUCUCCUUCAGGAGGGUGAGAGGGAAGGAACGCAGUCUGAGUGG hit 35 : 312 525 (fwd) 95.05 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C+::C+:+GAU+AUU::UA++G+ G+ +C++++::AGU+U+U+:G::+G: 312 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGU 371 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C++AAACCA:GA GA GAGACG+AGC:U:C: UCC: GAGCGUGAA+CC: 372 GUAGAGCACCUGAAACCACGAGGACGAGACGUAGCGUCCCCUCCU-GAGCGUGAAGCCG- 429 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C +::G: G:+G:+U+ UU:C+:CU:C::+U+GC:+UUGAUGAUCGUUC:U+: 430 ---GCUC-UAGGU-GCUGCAUGA-UUGCAGCUGCCUCUUGCCAUUGAUGAUCGUUCUUCU 483 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 UCC:UC G+:GGG : :GA :GGA :G:A:GCAGUCUGA:UGG 484 CUCCUUCA-----GGAGGGUG--AGA-GGGAAGGAACGCAGUCUGAGUGG 525 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #73401,sp|M23705.1|MMU3B1A Mus musculus small nuclear RNA (U3B.1) gene. ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGUGUAGAGCACCCGAAACCACGAGGACGAGACGUAGCGUUCCCUCCUGAGCGUGAAGCCGGCUCUAGGUGCUGCUUGACUGCAGCUGCCUCCUGCCAUUGAUGAUCGUUCUUCCCUCCUUUGGGAGGGUGAGAGGGAGGGAACGCAGUCUGAGUGG hit 36 : 702 915 (fwd) 99.12 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C+::C+:+GAU+AUU::UA++G+ G+ +C++++::AGU+U+U+:G::+G: 702 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGU 761 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+CC+AAACCA:GA GA GAGACG+AGC:UUC:CUCC: GAGCGUGAA+CC: 762 GUAGAGCACCCGAAACCACGAGGACGAGACGUAGCGUUCCCUCCU-GAGCGUGAAGCCG- 819 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C +::G: G:+G:UU+ U:C+:CU:C::+ +GC:+UUGAUGAUCGUUC:U+ 820 ---GCUC-UAGGU-GCUGCUUGA-CUGCAGCUGCCUCCUGCCAUUGAUGAUCGUUCUUC- 872 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 C UC+U UU+G+ GGG U :GA :GGAG:GAA:GCAGUCUGA:UGG 873 ---CCUCCU-UUGGGAGGG--UGAGA-GGGAGGGAACGCAGUCUGAGUGG 915 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #73402,sp|M23706.1|MMU3B2A Mus musculus small nuclear RNA (U3B.2) gene. ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGUGUAGAGCACCCGAAACCACGAGGACGAGACGUAGCGUUCCCUCCUGAGCGUGAAGCCGGCUCUAGGUGCUGCUUGACUGCAGCUGCCUCCUGCCAUUGAUGAUCGUUCUUCCCUCCUUUGGGAGGGUGAGAGGGAGGGAACGCAGUCUGAGUGG hit 37 : 530 743 (fwd) 99.12 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C+::C+:+GAU+AUU::UA++G+ G+ +C++++::AGU+U+U+:G::+G: 530 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGU 589 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+CC+AAACCA:GA GA GAGACG+AGC:UUC:CUCC: GAGCGUGAA+CC: 590 GUAGAGCACCCGAAACCACGAGGACGAGACGUAGCGUUCCCUCCU-GAGCGUGAAGCCG- 647 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C +::G: G:+G:UU+ U:C+:CU:C::+ +GC:+UUGAUGAUCGUUC:U+ 648 ---GCUC-UAGGU-GCUGCUUGA-CUGCAGCUGCCUCCUGCCAUUGAUGAUCGUUCUUC- 700 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 C UC+U UU+G+ GGG U :GA :GGAG:GAA:GCAGUCUGA:UGG 701 ---CCUCCU-UUGGGAGGG--UGAGA-GGGAGGGAACGCAGUCUGAGUGG 743 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #73403,sp|M23707.1|MMU3B3A Mus musculus small nuclear RNA (U3B.3) gene. ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGUGUAGAGCACCCGAAACCACGAGGACGAGACGUAGCGUUCCCUCCUGAGCGUGAAGCCGGCUCUAGGUGCUGCUUGACUGCAGCUGCCUCCUGCCAUUGAUGAUCGUUCUUCCCUCCUUUGGGAGGGUGAGAGGGAGGGAACGCAGUCUGAGUGG hit 38 : 503 716 (fwd) 99.12 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C+::C+:+GAU+AUU::UA++G+ G+ +C++++::AGU+U+U+:G::+G: 503 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGU 562 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+CC+AAACCA:GA GA GAGACG+AGC:UUC:CUCC: GAGCGUGAA+CC: 563 GUAGAGCACCCGAAACCACGAGGACGAGACGUAGCGUUCCCUCCU-GAGCGUGAAGCCG- 620 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C +::G: G:+G:UU+ U:C+:CU:C::+ +GC:+UUGAUGAUCGUUC:U+ 621 ---GCUC-UAGGU-GCUGCUUGA-CUGCAGCUGCCUCCUGCCAUUGAUGAUCGUUCUUC- 673 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 C UC+U UU+G+ GGG U :GA :GGAG:GAA:GCAGUCUGA:UGG 674 ---CCUCCU-UUGGGAGGG--UGAGA-GGGAGGGAACGCAGUCUGAGUGG 716 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #73406,sp|X14852.1|MMU3PS15 Mouse U3(psi)3B.15 DNA for U3 small nuclear RNA processed pseudogene ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCACUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGGCUACGUAGAGCACCCGAAACCAGGAGGAUGAGACAUACCUCCCCUCCUGAGCGUGAAGCCGGCUCUAGGUGCUGCUUGAGUGCAGCUGCCUCUUGUCAUUGAUGGUUGUUCUUCUGUCCUUCAGGAGGGUGAGAGGGAGGGAAUGCAGUCUGAGUGG hit 39 : 160 372 (fwd) 74.98 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU :+: C+:+GAU+A:U::UA++G+ G+ +C++++::A:U+U+U+:G :+: 160 AAGACUAUACUUUCAGGGAUCACUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGGCUAC 219 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+CC+AAACCA GA GAUGAGAC + C+U:C:CUCC: GAGCGUGAA+CC: 220 GUAGAGCACCCGAAACCAGGAGGAUGAGAC-AUACCUCCCCUCCU-GAGCGUGAAGCCG- 276 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 :C+C +::G: G:+G:UU+ +U:C+:CU:C::+U+G::+UUGAUG U GUUC:U+U 277 ---GCUC-UAGGU-GCUGCUUGA-GUGCAGCUGCCUCUUGUCAUUGAUGGUUGUUCUUCU 330 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 +UCC:UC G+:GGG U :GA :GGAG:G:A+G AGUCUGA UGG 331 GUCCUUCA-----GGAGGG--UGAGA-GGGAGGGAAUGCAGUCUGAGUGG 372 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #73407,sp|X14853.1|MMU3PS4 Mouse U3(psi)3B.4 DNA for U3 small nuclear RNA processed pseudogene ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGUGUAGAGCACCUGAAACCACGAGGACGAGACAUAGCGUCCCCUCCUGAGCGUGAAGCUGGCUCUAGGUGCUGCUUGAUUGCAGCUGCCUCUUGCCAUUGAUGAUCGUUCUUCUCUCCUUCGGGAGGGUGAGAGGGAGGGAACGCAGUCUGAGUGG hit 40 : 167 380 (fwd) 95.45 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C+::C+:+GAU+AUU::UA++G+ G+ +C++++::AGU+U+U+:G::+G: 167 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGU 226 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C++AAACCA:GA GA GAGAC++AGC:U:C:CUCC: GAGCGUGAA+C : 227 GUAGAGCACCUGAAACCACGAGGACGAGACAUAGCGUCCCCUCCU-GAGCGUGAAGCUG- 284 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C +::G: G:+G:UU+ UU:C+:CU:C::+U+GC:+UUGAUGAUCGUUC:U+: 285 ---GCUC-UAGGU-GCUGCUUGA-UUGCAGCUGCCUCUUGCCAUUGAUGAUCGUUCUUCU 338 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CUC: UC G+ :GG :U :GA :GGAG:G:A:GCAGUCUGA:UGG 339 CUCCUUC------GGGAGG-GUGAGA-GGGAGGGAACGCAGUCUGAGUGG 380 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #73408,sp|X14854.1|MMU3PS9 Mouse U3(psi)3B.9 DNA for U3 small nuclear RNA processed pseudogene ----isReversed: 0 ----hitSequence: AGGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAAAGGUUUCUCUGACUGUGUAGAGCACCCGAAACCACGAGGACGAGAUGUAGCGUCCCCUCCUAAGUGUGAAGCCGGUUCUAGGUGCUGCUUGAUUGCAGCUGCCUCUUGCCAUUGAUGAUCGUUCUUCCCUCCUUCAGGAGGGUGAGAGGGAGAGAACGCAGUCUGAGUGG hit 41 : 213 426 (fwd) 85.81 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 A+++CUAU:C+::C+:+GAU+AU+:+UA++G+ G+ +C+++++:+GU+U+U+:G::+G: 213 AGGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAAAGGUUUCUCUGACUGU 272 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+CC+AAACCA:GA GA GAGA G+AGC:U:C CUCC: AG GUGAA+CC: 273 GUAGAGCACCCGAAACCACGAGGACGAGAUGUAGCGUCCCCUCCU-AAGUGUGAAGCCG- 330 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 G +C +::G: G:+G:UU+ UU:C+:CU:C::+U+ C:+UUGAUGAUCGUUC:U+ 331 ---GUUC-UAGGU-GCUGCUUGA-UUGCAGCUGCCUCUUGCCAUUGAUGAUCGUUCUUC- 383 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 C UC+U U G+ GGG U :GA :GGAG G:A:GCAGUCUGA:UGG 384 ---CCUCCU-UCAGGAGGG--UGAGA-GGGAGAGAACGCAGUCUGAGUGG 426 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #76586,sp|M60173.1|MMUG3B4 Mouse small nuclear RNA (U3B.4) gene. ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGUGUAGAGCACCCGAAACCACGAGGACGAGACGUAGCGUUCCCUCCUGAGCGUGAAGCCGGCUCUAGGUGCUGCUUGACUGCAGCUGCCUCCUGCCAUUGAUGAUCGUUCUUCCCUCCUUUGGGAGGGUGAGAGGGAGGGAACGCAGUCUGAGUGG hit 42 : 1085 1298 (fwd) 99.12 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C+::C+:+GAU+AUU::UA++G+ G+ +C++++::AGU+U+U+:G::+G: 1085 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGU 1144 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+CC+AAACCA:GA GA GAGACG+AGC:UUC:CUCC: GAGCGUGAA+CC: 1145 GUAGAGCACCCGAAACCACGAGGACGAGACGUAGCGUUCCCUCCU-GAGCGUGAAGCCG- 1202 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C +::G: G:+G:UU+ U:C+:CU:C::+ +GC:+UUGAUGAUCGUUC:U+ 1203 ---GCUC-UAGGU-GCUGCUUGA-CUGCAGCUGCCUCCUGCCAUUGAUGAUCGUUCUUC- 1255 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 C UC+U UU+G+ GGG U :GA :GGAG:GAA:GCAGUCUGA:UGG 1256 ---CCUCCU-UUGGGAGGG--UGAGA-GGGAGGGAACGCAGUCUGAGUGG 1298 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/org.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/phg.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #583,sp|AB007644.1|AB007644 Arabidopsis thaliana genomic DNA, chromosome 5, TAC clone:K19P17. ----isReversed: 0 ----hitSequence: CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCGUACCUCUGUUUCCUUGAUUUCUCAAGAGACAGGCCCUUAACCCUGGUUGAUGAACCAUGACCGUGCGGCUAGAGCGUGAUUGACGGCUACGAUCGUCCUCGGACGCAUCCGGUGCUGUAGAGGAUCGUUACUCGGCUCGGUUUCUACCUUGCCGGGGUGGUCGCACGGCGGUCUGACAGG hit 43 : 28031 28246 (fwd) 79.20 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 +ACCU::::::++CAGGAUC:+:UCUAUA:G U CGU:CCUCUG:+:C UUGA++:::: 28031 CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCU-CGUACCUCUGUUUCCUUGAUUUCUC 28089 >>----------...---((((--------------.((((((((((((,,,,,,,,,,, 61 gucAaaCAaccc...AAAccagGAUGAUGAgacgcA.gccuucgcucccaGAGCGUGAau 116 :: A+ACA +CC AA CC:GG+UGAUGA C++ C:::GC:+C:AGAGCGUGA+U 28090 AAGAGACAGGCCcuuAACCCUGGUUGAUGAACCAUGa--CCGUGCGGCUAGAGCGUGAUU 28147 ,,<----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<< 117 cCgCGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuc 176 +CGGC:: +A+ +G+ ++:GG+ ++ +UCC:+ U ++UG:: GA GAUCGU:: 28148 -GACGGCUACGAU-CGUCCUCGGACGC-AUCCGG-U---GCUGUA----GAGGAUCGUUA 28196 <--<<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 177 cUaucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CU+ :+C::++UUU U ::G+: G::U:G+:GC:::G+ GUCUGAC:GG 28197 CUC-GGCUCGGUUUCUACCUUGCC--GGGGUGGUCGCACGGCG-GUCUGACAGG 28246 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #1097,sp|AB013387.1|AB013387 Arabidopsis thaliana genomic DNA, chromosome 5, TAC clone:K18G13. ----isReversed: 0 ----hitSequence: CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCGUACCUCUGUUUCCUUGAUUUCUCAAGAGACAGGCCUUUUACCCUGGUUGAUGAACCAUGACCGUGCGGCUAGAGCGUGAUUGACGGCCACGAUCGUCUUCGGACGCAUCCGGUGCUGUAGAGGAUCGUUACUCGGCUCGGUUCUACCUUGCCGGGGUGGUCGCACGGCGGUCUGACAGG hit 44 : 24664 24878 (fwd) 72.81 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 +ACCU::::::++CAGGAUC:+:UCUAUA:G U CGU:CCUCUG:+:C UUGA++:::: 24664 CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCU-CGUACCUCUGUUUCCUUGAUUUCUC 24722 >>----------...---((((--------------.((((((((((((,,,,,,,,,,, 61 gucAaaCAaccc...AAAccagGAUGAUGAgacgcA.gccuucgcucccaGAGCGUGAau 116 :: A+ACA +CC A CC:GG+UGAUGA C++ C:::GC:+C:AGAGCGUGA+U 24723 AAGAGACAGGCCuuuUACCCUGGUUGAUGAACCAUGa--CCGUGCGGCUAGAGCGUGAUU 24780 ,,<----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<< 117 cCgCGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuc 176 +CGGC:: +A+ +G+ +:GG+ ++ +UCC:+ U ++UG:: GA GAUCGU:: 24781 -GACGGCCACGAU-CGUCUUCGGACGC-AUCCGG-U---GCUGUA----GAGGAUCGUUA 24829 <--<<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 177 cUaucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CU+ :+C::++UU U ::G+: G::U:G+:GC:::G+ GUCUGAC:GG 24830 CUC-GGCUCGGUU-CUACCUUGCC--GGGGUGGUCGCACGGCG-GUCUGACAGG 24878 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #1519,sp|AB017066.1|AB017066 Arabidopsis thaliana genomic DNA, chromosome 5, P1 clone:MGN6. ----isReversed: 1 ----hitSequence: CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCGUACCUCUGUUUCCUUGAUUUCUCAAGAGACAGGCCCUUUACCCUGGUUGAUGAACCAUGACCGUGCGGCUAGAGCGUGAUUGACGGCUACGAUCGUCCUCGGACGCAUUCGGUGCUGUAGAGGAUCGUUACUCGGUUCGGUUCUACCUUGCUGGGGUGGUCGCACGGCGGUCUGACAGG hit 45 : 17528 17314 (rev) 67.31 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 +ACCU::::::++CAGGAUC:+:UCUAUA:G U CGU:CCUCUG:+:C UUGA++:::: 43853 CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCU-CGUACCUCUGUUUCCUUGAUUUCUC 43911 >>----------...---((((--------------.((((((((((((,,,,,,,,,,, 61 gucAaaCAaccc...AAAccagGAUGAUGAgacgcA.gccuucgcucccaGAGCGUGAau 116 :: A+ACA +CC A CC:GG+UGAUGA C++ C:::GC:+C:AGAGCGUGA+U 43912 AAGAGACAGGCCcuuUACCCUGGUUGAUGAACCAUGa--CCGUGCGGCUAGAGCGUGAUU 43969 ,,<----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<< 117 cCgCGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuc 176 +CGGC:: +A+ +G+ ++:G++ ++ +U+C:+ U ++UG:: GA GAUCGU:: 43970 -GACGGCUACGAU-CGUCCUCGGACGC-AUUCGG-U---GCUGUA----GAGGAUCGUUA 44018 <--<<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 177 cUaucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CU+ ++:::++UU U :::+ U G::U:G+:GC:::G+ GUCUGAC:GG 44019 CUC-GGUUCGGUU-CUACCUUGC--UGGGGUGGUCGCACGGCG-GUCUGACAGG 44067 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #1519,sp|AB017066.1|AB017066 Arabidopsis thaliana genomic DNA, chromosome 5, P1 clone:MGN6. ----isReversed: 1 ----hitSequence: CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCGUACCUCUGUUUCCUUGAUUUCUCAAGAGACAGGCCCUAAACCCUGGUUGAUGAACCAUGACCGUGCGGCUAGAGCGUGAUUGACGGCUACGAUUGUCCUCGGACGCAUCCGGUGCUGUAGAGGAUCGUUACUCGGCUCGGUUUACCCUAGCCGGGGUGGUCGCACGGCGGUCUGACAGG hit 46 : 15263 15049 (rev) 72.49 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 +ACCU::::::++CAGGAUC:+:UCUAUA:G U CGU:CCUCUG:+:C UUGA++:::: 46118 CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCU-CGUACCUCUGUUUCCUUGAUUUCUC 46176 >>----------...---((((--------------.((((((((((((,,,,,,,,,,, 61 gucAaaCAaccc...AAAccagGAUGAUGAgacgcA.gccuucgcucccaGAGCGUGAau 116 :: A+ACA +CC AA CC:GG+UGAUGA C++ C:::GC:+C:AGAGCGUGA+U 46177 AAGAGACAGGCCcuaAACCCUGGUUGAUGAACCAUGa--CCGUGCGGCUAGAGCGUGAUU 46234 ,,<----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<< 117 cCgCGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuc 176 +CGGC:: +A+ UG+ ++:GG+ ++ +UCC:+ U ++UG:: GA GAUCGU:: 46235 -GACGGCUACGAU-UGUCCUCGGACGC-AUCCGG-U---GCUGUA----GAGGAUCGUUA 46283 <--<<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 177 cUaucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CU+ :+C :++UU U : G+: G::U:G+:GC:::G+ GUCUGAC:GG 46284 CUC-GGCUCGGUU-UACCCUAGCC--GGGGUGGUCGCACGGCG-GUCUGACAGG 46332 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #1683,sp|AB018115.1|AB018115 Arabidopsis thaliana genomic DNA, chromosome 5, P1 clone:MJP23. ----isReversed: 1 ----hitSequence: CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCGUACCUCUGUUUCCUUGAUUUCUCAAGAGACAGGCCCUUAACCCUGGUUGAUGAACCAUGACCGUGCGGCUAGAGCGUGAUUGACGGCUACGAUCGUCCUCGGACGCAUCCGGUGCUGUAGAGGAUCGUUACUCGGCUCGGUUCUACCUUGCCGGGGUGGUCGCACGGCGGUCUGACAGG hit 47 : 11504 11290 (rev) 76.32 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 +ACCU::::::++CAGGAUC:+:UCUAUA:G U CGU:CCUCUG:+:C UUGA++:::: 20324 CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCU-CGUACCUCUGUUUCCUUGAUUUCUC 20382 >>----------...---((((--------------.((((((((((((,,,,,,,,,,, 61 gucAaaCAaccc...AAAccagGAUGAUGAgacgcA.gccuucgcucccaGAGCGUGAau 116 :: A+ACA +CC AA CC:GG+UGAUGA C++ C:::GC:+C:AGAGCGUGA+U 20383 AAGAGACAGGCCcuuAACCCUGGUUGAUGAACCAUGa--CCGUGCGGCUAGAGCGUGAUU 20440 ,,<----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<< 117 cCgCGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuc 176 +CGGC:: +A+ +G+ ++:GG+ ++ +UCC:+ U ++UG:: GA GAUCGU:: 20441 -GACGGCUACGAU-CGUCCUCGGACGC-AUCCGG-U---GCUGUA----GAGGAUCGUUA 20489 <--<<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 177 cUaucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CU+ :+C::++UU U ::G+: G::U:G+:GC:::G+ GUCUGAC:GG 20490 CUC-GGCUCGGUU-CUACCUUGCC--GGGGUGGUCGCACGGCG-GUCUGACAGG 20538 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #8834,sp|AC007067.4|AC007067 Genomic sequence for Arabidopsis thaliana BAC T10O24 from Chromosome 1, complete sequence. ----isReversed: 0 ----hitSequence: CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCGUACCUCUGUUUCCUUGAUUUCUAAGGAGACAGGCCCUAAACCCUGGUUGAUGAACCAUGACCGUGCGGUCAGAGCGUGAUUGAUGGCUACGAUCGUCUUCGGACGCAUCCGGUGCUGUAGAGGAUCGUUACUCGGCUUGGUCUUCCUUGCCGGGGUGGUCGCACGGCGGUCUGACAGG hit 48 : 50711 50924 (fwd) 68.50 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 +ACCU+:C:::++CAGGAUC:+:UCUAUA:G U CGU:CCUCUG:+:C UUGA++:::A 50711 CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCU-CGUACCUCUGUUUCCUUGAUUUCUA 50769 >>----------...---((((--------------.((((((((((((,,,,,,,,,,, 61 gucAaaCAaccc...AAAccagGAUGAUGAgacgcA.gccuucgcucccaGAGCGUGAau 116 :+ A+ACA +CC AA CC:GG+UGAUGA C++ C:::GC:+:CAGAGCGUGA+U 50770 AGGAGACAGGCCcuaAACCCUGGUUGAUGAACCAUGa--CCGUGCGGUCAGAGCGUGAUU 50827 ,,<----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<< 117 cCgCGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuc 176 + GGC:: +A+ +G+ +:GG+ ++ +UCC:+ U ++UG:: GA GAUCGU:: 50828 -GAUGGCUACGAU-CGUCUUCGGACGC-AUCCGG-U---GCUGUA----GAGGAUCGUUA 50876 <--<<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 177 cUaucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CU+ :+C:+++U UU +:G+: G::UG:+:GC:::G+ GUCUGAC:GG 50877 CUC-GGCUUGGUC--UUCCUUGCC--GGGGUGGUCGCACGGCG-GUCUGACAGG 50924 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #9532,sp|AC093490.2|AC093490 Oryza sativa (japonica cultivar-group) chromosome 5 clone OJ1127_B08, complete sequence. ----isReversed: 1 ----hitSequence: CGACCUUACUUGAACAGGAUCUGUUCUACAGGCUCGUACCGUUGCAUCCUUUACCAAUAAGGAGGCAAGCUCUCAAGUCUGGUUGAUGCCGACAUAACCUCCGGGCCAGAGCGUGAUUUUAACGGCUAGGAUGCAUGUUUGAGCCAUCCGACGGCUGCAGAGGAUCGUUCCUGCCUGGUUCACUCCGGUGCAGGGUGGCCCAGAGGUUGUCUGACAGA hit 49 : 14113 13896 (rev) 64.35 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 +ACCU+:C:U:++CA+GAUC::+UCUA A:G U CGU:C + UG+::C UU+A++:A:A 98156 CGACCUUACUUGAACAGGAUCUGUUCUACAGGCU-CGUACCGUUGCAUCCUUUACCAAUA 98214 >>----------...---((((--------.------.((((((((((((,,,,,,,,,, 61 gucAaaCAaccc...AAAccagGAUGAUGA.gacgcA.gccuucgcucccaGAGCGUGAa 115 :+ A++CAA+C AA+:C:GG+UGAUG GAC++A C:UC :::CCAGAGCGUGA+ 98215 AGGAGGCAAGCUcucAAGUCUGGUUGAUGCcGACAUAa--CCUCCGGGCCAGAGCGUGAU 98272 ,,.,<----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,, 116 uc.CgCGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGU 174 U+ +CGGC::G+A+ + UGU+ G+ ++ +UC +AC ++UG:: GA GAUCGU 98273 UUuAACGGCUAGGAU-GCAUGUUUGAGCC-AUCCGACG---GCUGCA----GAGGAUCGU 98323 <<<--<<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 175 uccUaucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 :CCU+: U UC U G : AGG:UGG::: GA:G++ GUCUGAC:G: 98324 UCCUGCCUGGUUCA-----CUCCGGUGCAGGGUGGCCCAGAGGUU-GUCUGACAGA 98373 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #9725,sp|AC123596.12|AC123596 Medicago truncatula clone mth1-17n5, complete sequence. ----isReversed: 1 ----hitSequence: CGACCUUACUUGAACAGGAUCUGUUCUAUAGGAUUGUACUACUGUGUCCUUGAUUUCUAAGGAGAUAGGAACAUAUGUCUGGUAGAUGAGUUGUGACCGUGUGAUCAGAGCGUGAUUAACGGCCAGGAUGAUGUGUGCAUCAUCUUCAGCUGUAGAUGAUCGUUCUUGGCCUAGUUCAACUAACCGGGAUGGUCACAUGGUUGUCUGACAGA hit 50 : 60479 60268 (rev) 49.96 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 +ACCU+:C:::++CAGGAUC: :UCUA+A:GAU +GU:C+ CUG: :C UUGA++:::A 59577 CGACCUUACUUGAACAGGAUCUGUUCUAUAGGAU-UGUACUACUGUGUCCUUGAUUUCUA 59635 >>----------...---((((--------------.((((((((((((,,,,,,,,,,, 61 gucAaaCAaccc...AAAccagGAUGAUGAgacgcA.gccuucgcucccaGAGCGUGAau 116 :+ A+A A + + A +:C:GG+ GAUGAG G+ C: :G::::CAGAGCGUGA+U 59636 AGGAGAUAGGAAcauAUGUCUGGUAGAUGAGUUGUGa--CCGUGUGAUCAGAGCGUGAUU 59693 ,,<----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<< 117 cCgCGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuc 176 +CGGC::G+A+ ::GUG:: +U ::CUU:: +UG:: GAUGAUCGUUC 59694 -AACGGCCAGGAUGAUGUGUGC------AU-CAUCUUCAGCUGUA----GAUGAUCGUUC 59741 <--<<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 177 cUaucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 :U + :: +UU U:: + :GAUG::::C: :G++ GUCUGAC:G: 59742 UU--GGCCUAGUU-CAACUAACCG---GGAUGGUCACAUGGUU-GUCUGACAGA 59788 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #99643,sp|AP004474.1|AP004474 Lotus corniculatus var. japonicus genomic DNA, chromosome 1, clone:LjT13B22, TM0009. ----isReversed: 0 ----hitSequence: CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCGUACAACUGUAUCCUUGAGUUCUAAGGAGACAGGAACCAAAGUCUGGUUGAUGAACACUGACCGUGUGAUCAGAGCGUGAUUAAUAGUCGUCCGAUUGACCUUCGGGUUCAUCAGAUCGACGGUGGAGGAUCGUUCUCAGCGGGUAUCACCGGCUGGGGUGGUCACACGGUUGUCUGACAGG hit 51 : 40163 40379 (fwd) 46.88 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 +ACCU+:C:::+ CAGGAUC:::UCUA+A:G U CGU:C+ CUG:::C UUGA +:::A 40163 CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCU-CGUACAACUGUAUCCUUGAGUUCUA 40221 >>----------...---((((------------.--.((((((((((((,,,,,,,,,, 61 gucAaaCAaccc...AAAccagGAUGAUGAgacg.cA.gccuucgcucccaGAGCGUGAa 115 :+ A+ACA + + AA+:C:GG+UGAUGA + C:::G::::CAGAGCGUGA+ 40222 AGGAGACAGGAAccaAAGUCUGGUUGAUGAACA-cUGa--CCGUGUGAUCAGAGCGUGAU 40278 ,,,<----.<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,, 116 ucCgCGGC.gcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGU 174 U G+C +C +A :::: :U+ G UU +UC +A: :::: UG GA GAUCGU 40279 UAAUAGUCgUCCGAUUGAC-CUUCGGGUUCAUCAGAUCGACGGUG------GAGGAUCGU 40331 <<<--<<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 175 uccUaucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 :C: A :: +U U + :: U :G:UG::::C:::G++ GUCUGAC:G: 40332 UCUCA-GCGGGUAU-----CACCGGC-UGGGGUGGUCACACGGUU-GUCUGACAGG 40379 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #100251,sp|AP006393.1|AP006393 Lotus corniculatus var. japonicus genomic DNA, chromosome 1, clone:LjT03B16, TM0276. ----isReversed: 0 ----hitSequence: CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCGUACAACUGUAUCCUUGAGUUCUAAGGAGACAGGAACCAAAGUCUGGUUGAUGAACCAUGACCGUGUGAUCAGAGAGUCGUCCGAUUAACCUUUGGGUUCAUCUGAUUGACGGUGGAGGAUUGUUCUCAGCUGGUAUCACCGGCUGGGGUGGUCACACGGUUGUCUGAUAGA hit 52 : 89759 89965 (fwd) 41.39 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 +ACCU+:C:::+ CAGGAUC:::UCUA+A:G U CGU:C+ CUG:::C UUGA +:::A 89759 CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCU-CGUACAACUGUAUCCUUGAGUUCUA 89817 >>----------...---((((--------------.((((((((((((,,,,,,,,,,, 61 gucAaaCAaccc...AAAccagGAUGAUGAgacgcA.gccuucgcucccaGAGCGUGAau 116 :+ A+ACA + + AA+:C: G+UGAUGA C++ C:::G::::CAGAG GU ++ 89818 AGGAGACAGGAAccaAAGUCUGGUUGAUGAACCAUGa--CCGUGUGAUCAGAGAGUCGUC 89875 ,,<----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<< 117 cCgCGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuc 176 C + : :: U++G UU+ +UC++A U:: : UG GA GAU GU:C 89876 CGA---------UUAACCUUUGGGUUC-AUCUGAUUGACGGUG------GAGGAUUGUUC 89919 <--<<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 177 cUaucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 : +:+C ++U+ U G+:+ :G:UG::::C:::G++ GUCUGA :G: 89920 U---CAGCUGGUA-UCACCGGCUG---GGGUGGUCACACGGUU-GUCUGAUAGA 89965 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #100251,sp|AP006393.1|AP006393 Lotus corniculatus var. japonicus genomic DNA, chromosome 1, clone:LjT03B16, TM0276. ----isReversed: 1 ----hitSequence: CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCGUACAACUGUAUCCUUGAGUUCUAAGGAGACAGGAACCAAAGUCUGGUUGAUGAACACUGACCGUGUGAUCAGAGCGUGAUUAAUAGUCGUCCGAUUGACCUUCGGGUUCAUCAGAUCGACGGUGGAGGAUCGUUCUCAGCGGGUAUCACCGGCUGGGGUGGUCACACGGUUGUCUGACAGG hit 53 : 39231 39015 (rev) 46.88 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 +ACCU+:C:::+ CAGGAUC:::UCUA+A:G U CGU:C+ CUG:::C UUGA +:::A 52424 CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCU-CGUACAACUGUAUCCUUGAGUUCUA 52482 >>----------...---((((------------.--.((((((((((((,,,,,,,,,, 61 gucAaaCAaccc...AAAccagGAUGAUGAgacg.cA.gccuucgcucccaGAGCGUGAa 115 :+ A+ACA + + AA+:C:GG+UGAUGA + C:::G::::CAGAGCGUGA+ 52483 AGGAGACAGGAAccaAAGUCUGGUUGAUGAACA-cUGa--CCGUGUGAUCAGAGCGUGAU 52539 ,,,<----.<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,, 116 ucCgCGGC.gcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGU 174 U G+C +C +A :::: :U+ G UU +UC +A: :::: UG GA GAUCGU 52540 UAAUAGUCgUCCGAUUGAC-CUUCGGGUUCAUCAGAUCGACGGUG------GAGGAUCGU 52592 <<<--<<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 175 uccUaucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 :C: A :: +U U + :: U :G:UG::::C:::G++ GUCUGAC:G: 52593 UCUCA-GCGGGUAU-----CACCGGC-UGGGGUGGUCACACGGUU-GUCUGACAGG 52640 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #119321,sp|AL137898.1|ATT20K12 Arabidopsis thaliana DNA chromosome 3, BAC clone T20K12 ----isReversed: 1 ----hitSequence: CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCGUACCUCUGUUUCCUUGAUUUCUAAGGAGACAGGCCCUUAACCCUGGUUGAUGAACCAUGGCCGUGCGAUCAGAGCGUGAUUGACGGCUACGAUCGUCUUAGGACGCAUCUGGUGCUGUAGAGGAUCGUUACUCGGCUCGGUUCUACCUUGCCGGGGUGGUUGCACGGCGGUCUGACAGG hit 54 : 44750 44536 (rev) 70.43 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 +ACCU+:C:::++CAGGAUC:+:UCUAUA:G U CGU:CCUCUG:+:C UUGA++:::A 64406 CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCU-CGUACCUCUGUUUCCUUGAUUUCUA 64464 >>----------...---((((--------------.((((((((((((,,,,,,,,,,, 61 gucAaaCAaccc...AAAccagGAUGAUGAgacgcA.gccuucgcucccaGAGCGUGAau 116 :+ A+ACA +CC AA CC:GG+UGAUGA C++ C:::GC:::CAGAGCGUGA+U 64465 AGGAGACAGGCCcuuAACCCUGGUUGAUGAACCAUGg--CCGUGCGAUCAGAGCGUGAUU 64522 ,,<----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<< 117 cCgCGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuc 176 +CGGC:: +A+ +G+ :+:G++ +++ +C:+:U ++UG:: GA GAUCGU:: 64523 -GACGGCUACGAU-CGUCUUAGGACGCA--UCUGGU---GCUGUA----GAGGAUCGUUA 64571 <--<<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 177 cUaucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CU+ :+C::++UU U ::G+: G::UG:::GC:::G+ GUCUGAC:GG 64572 CUC-GGCUCGGUU-CUACCUUGCC--GGGGUGGUUGCACGGCG-GUCUGACAGG 64620 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #119561,sp|X52629.1|ATU3BSNR A.thaliana gene for U3B small nuclear RNA (snRNA) ----isReversed: 0 ----hitSequence: CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCGUACCUCUGUUUCCUUGAUUUCUCAAGAGACAGGCCCUUAACCCUGGUUGAUGAACCAUGACCGUGCGGCUAGAGCGUGAUUGACGGCUACGAUCGUCCUCGGACGCAUCCAGUGCUGUAGAGGAUCGUUACUCGGCUCGGUUUCUACCUUGCCGGGGUGGUCGCACGGCGGUCUGACAGG hit 55 : 326 541 (fwd) 81.17 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 +ACCU::::::++CAGGAUC:+:UCUAUA:G U CGU:CCUCUG:+:C UUGA++:::: 326 CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCU-CGUACCUCUGUUUCCUUGAUUUCUC 384 >>----------...---((((--------------.((((((((((((,,,,,,,,,,, 61 gucAaaCAaccc...AAAccagGAUGAUGAgacgcA.gccuucgcucccaGAGCGUGAau 116 :: A+ACA +CC AA CC:GG+UGAUGA C++ C:::GC:+C:AGAGCGUGA+U 385 AAGAGACAGGCCcuuAACCCUGGUUGAUGAACCAUGa--CCGUGCGGCUAGAGCGUGAUU 442 ,,<----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<< 117 cCgCGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuc 176 +CGGC:: +A+ +G+ ++:GG+ ++ +UCC:+ U ++UG:: GA GAUCGU:: 443 -GACGGCUACGAU-CGUCCUCGGACGC-AUCCAG-U---GCUGUA----GAGGAUCGUUA 491 <--<<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 177 cUaucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CU+ :+C::++UUU U ::G+: G::U:G+:GC:::G+ GUCUGAC:GG 492 CUC-GGCUCGGUUUCUACCUUGCC--GGGGUGGUCGCACGGCG-GUCUGACAGG 541 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #119562,sp|X52630.1|ATU3CSNR A.thaliana U3C snRNA gene ----isReversed: 0 ----hitSequence: CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCGUACCUCUGUUUCCUUGAUUUCUCAAGAGACAGGCCUUAAACCCUGGUUGAUGAACCAUGACCGUGCGGCUAGAGCGUGAUUGACGGCUACGAUCGUCCUUGGAUGCAUCCGGUGCUGUAGAGGAUCGUUACUCGGCUCGGUUCUACCUUGUCGGGGUGGUCGCACGGCGGUCUGACAGG hit 56 : 530 744 (fwd) 79.68 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 +ACCU::::::++CAGGAUC:+:UCUAUA:G U CGU:CCUCUG:+:C UUGA++:::: 530 CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCU-CGUACCUCUGUUUCCUUGAUUUCUC 588 >>----------...---((((--------------.((((((((((((,,,,,,,,,,, 61 gucAaaCAaccc...AAAccagGAUGAUGAgacgcA.gccuucgcucccaGAGCGUGAau 116 :: A+ACA +CC AA CC:GG+UGAUGA C++ C:::GC:+C:AGAGCGUGA+U 589 AAGAGACAGGCCuuaAACCCUGGUUGAUGAACCAUGa--CCGUGCGGCUAGAGCGUGAUU 646 ,,<----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<< 117 cCgCGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuc 176 +CGGC:: +A+ +G+ +++GG+U++ +UCC++ U ++UG:: GA GAUCGU:: 647 -GACGGCUACGAU-CGUCCUUGGAUGC-AUCCGG-U---GCUGUA----GAGGAUCGUUA 695 <--<<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 177 cUaucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CU+ : C::++UU U ::G : G::U:G+:GC:::G+ GUCUGAC:GG 696 CUC-GGCUCGGUU-CUACCUUGUC--GGGGUGGUCGCACGGCG-GUCUGACAGG 744 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #119563,sp|X58068.1|ATU3D A.thaliana U3D snRNA gene ----isReversed: 0 ----hitSequence: CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCGUACCUCUGUUUCCUUGAUUUCUCAAGAGACAGGCCCUUAACCCUGGUUGAUGAACCAUGACCGUGCGGCUAGAGCGUGAUUGACGGCUACGAUCGUCCUCGGACGCAUCCGGUGCUGUAGAGGAUCGUUACUCGGCUCGGUUCUACCUUGCCGGGGUGGUCGCACGGCGGUCUGACAGG hit 57 : 103 317 (fwd) 76.32 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 +ACCU::::::++CAGGAUC:+:UCUAUA:G U CGU:CCUCUG:+:C UUGA++:::: 103 CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCU-CGUACCUCUGUUUCCUUGAUUUCUC 161 >>----------...---((((--------------.((((((((((((,,,,,,,,,,, 61 gucAaaCAaccc...AAAccagGAUGAUGAgacgcA.gccuucgcucccaGAGCGUGAau 116 :: A+ACA +CC AA CC:GG+UGAUGA C++ C:::GC:+C:AGAGCGUGA+U 162 AAGAGACAGGCCcuuAACCCUGGUUGAUGAACCAUGa--CCGUGCGGCUAGAGCGUGAUU 219 ,,<----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<< 117 cCgCGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuc 176 +CGGC:: +A+ +G+ ++:GG+ ++ +UCC:+ U ++UG:: GA GAUCGU:: 220 -GACGGCUACGAU-CGUCCUCGGACGC-AUCCGG-U---GCUGUA----GAGGAUCGUUA 268 <--<<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 177 cUaucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CU+ :+C::++UU U ::G+: G::U:G+:GC:::G+ GUCUGAC:GG 269 CUC-GGCUCGGUU-CUACCUUGCC--GGGGUGGUCGCACGGCG-GUCUGACAGG 317 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #188164,sp|AL512546.1|H0410G08 Oryza sativa genomic DNA, chromosome4, BAC clone: H0410G08, complete sequence. ----isReversed: 0 ----hitSequence: CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCGUACCGUUGCAUCCUUGACUAAUGAGGAGGCAAGCACUUAAGCUUGGUUGAUGACGCAUGACCUGUGGGCCAGAGCGUGAUUAACGGCCGGAUCACUGGCUGAUUUGAUCCCACGGCUUUAGAGGAUCGUUUCUUGCCGGGCCUCGCCUGGCCAGGAUGGCUCUCAGGUUGUCUGACAGG hit 58 : 31303 31517 (fwd) 76.18 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 +ACCU+: :U:++CAGGAUC::+UCUAUA:G U CGU:CC+ UG+::C UUGA++:A: 31303 CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCU-CGUACCGUUGCAUCCUUGACUAAUG 31361 >>----------...---((((--------------.((((((((((((,,,,,,,,,,, 61 gucAaaCAaccc...AAAccagGAUGAUGAgacgcA.gccuucgcucccaGAGCGUGAau 116 :+ A++CAA+C+ AA+C::GG+UGAUGA+ C++ C:U:::::CCAGAGCGUGA+U 31362 AGGAGGCAAGCAcuuAAGCUUGGUUGAUGACGCAUGa--CCUGUGGGCCAGAGCGUGAUU 31419 ,,<----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<< 117 cCgCGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuc 176 +CGGC: G+A+:++++G+UG:UUU +U:C C +++:+U++: GA GAUCGU 31420 -AACGGCC-GGAUCACUGGCUGAUUUG-AUCC--C-ACGGCUUUA----GAGGAUCGU-- 31467 <--<<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 177 cUaucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 :U+U:+CC++++ U + +GG+:A : UGG:::::A:G++ GUCUGAC::G 31468 UUCUUGCCGGGCC-UCGCCUGGCCAGGA--UGGCUCUCAGGUU-GUCUGACAGG 31517 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #192874,sp|X14411.1|LEU3SNRN Tomato U3 small nuclear RNA gene ----isReversed: 0 ----hitSequence: CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCGUACCAUUGUAUCCUUGAAUUCUAAGGAGACAGGAAUCCAAGUCUGGUUGAUGAAGCAUGGCCAUGUGACCAGAGCGUGAUUAACAGCUAUCCAUGGUUUCUCGAGCUGUGGUUACAGUAGAUGAUCGUUCUUAGACCCUUAAUCUCAGGCCUAAGAUGGUCUCAUGGCUGUCUGACAGA hit 59 : 489 703 (fwd) 66.93 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 +ACCU+:C:::+:CAGGAUC:::UCUAUA:G U CGU:CC UG:::C UUGA:+:::A 489 CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCU-CGUACCAUUGUAUCCUUGAAUUCUA 547 >>----------...---((((--------------((((((((((((,,,,,,,,,,,, 61 gucAaaCAaccc...AAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAauc 117 :+ A+ACA + + AA+:C:GG+UGAUGA C++ GCC:U::::CC: GAGCGUGA+U 548 AGGAGACAGGAAuccAAGUCUGGUUGAUGAAGCAUGGCCAUGUGACCA-GAGCGUGAUU- 605 ,<----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<< 118 CgCGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUucc 177 + ::GC +:: : :+:G UU+U + C:+: : ::+ G:: GAUGAUCGUUC: 606 AA----CAGC-UAUCC-AUGGUUUCUCGAGCUGUGGUUACAGUA----GAUGAUCGUUCU 655 --<<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 178 UaucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 UA :C: U U U :G: UA:GA :GG::::A:GGC+GUCUGAC:G: 656 UAGACCCUUAAU----CUCAGGCCUAAGA-UGGUCUCAUGGCUGUCUGACAGA 703 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #198574,sp|AL606444.3|OSJN00019 Oryza sativa genomic DNA, chromosome 4, BAC clone: OSJNBa0043L09. ----isReversed: 1 ----hitSequence: CGACCUUACUUGAACGGGAUCUGUUCUAUAGGCUCGUACCGUUGCAUCCUUGACUAAUAAGGAGGCAAGCACUUAAGCUUGGUUGAUGACGCAUGACCUGUGGGCCAGAGCGUGAUUAACGGCCGGAUCACUGGCUGAUUUGAUCCCACGGCUGUAGAGGAUCGUUUCUUGCCGGGCCUCGCCUGGCCAGGAUGGCUCUCAGGUUCUCUGACAGG hit 60 : 140423 140209 (rev) 72.34 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 +ACCU+:C:U:++C:GGAUC::+UCUAUA:G U CGU:CC+ UG+::C UUG:++:A:A 19080 CGACCUUACUUGAACGGGAUCUGUUCUAUAGGCU-CGUACCGUUGCAUCCUUGACUAAUA 19138 >>----------...---((((--------------.((((((((((((,,,,,,,,,,, 61 gucAaaCAaccc...AAAccagGAUGAUGAgacgcA.gccuucgcucccaGAGCGUGAau 116 :+ A++CAA+C+ AA+C::GG+UGAUGA+ C++ C:U:::::CCAGAGCGUGA+U 19139 AGGAGGCAAGCAcuuAAGCUUGGUUGAUGACGCAUGa--CCUGUGGGCCAGAGCGUGAUU 19196 ,,<----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<< 117 cCgCGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuc 176 +CGGC: G+A+:++++G+UG:UUU +U:C C +++:+UG+: GA GAUCGU 19197 -AACGGCC-GGAUCACUGGCUGAUUUG-AUCC--C-ACGGCUGUA----GAGGAUCGU-- 19244 <--<<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 177 cUaucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 :U+U:+CC++++ U + +GG+:A : UGG:::::A:G++ UCUGAC::G 19245 UUCUUGCCGGGCC-UCGCCUGGCCAGGA--UGGCUCUCAGGUU-CUCUGACAGG 19294 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #199205,sp|X79685.1|OSU3SNRN O.sativa L. (Indica cv.IR24) U3 snRNA gene promoter ----isReversed: 0 ----hitSequence: CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCGUACCGUUGCAUCCUUGACUAAUAAGGAGGCAAGCACUUAAGCUUGGUUGAUGACGCAUGACCUGUGGGCCAGAGCGUGAUUAACGGCCGGAUCACUGGCUGAUUUGAUCCCACGGCUGUAGAGGAUCGUUUCUUGCCGGGCCUCGCCUGGCCAGGAUGGCUCUCAGGUUGUCUGACAGG hit 61 : 140 354 (fwd) 79.34 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 +ACCU+:C:U:++CAGGAUC::+UCUAUA:G U CGU:CC+ UG+::C UUGA++:A:A 140 CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCU-CGUACCGUUGCAUCCUUGACUAAUA 198 >>----------...---((((--------------.((((((((((((,,,,,,,,,,, 61 gucAaaCAaccc...AAAccagGAUGAUGAgacgcA.gccuucgcucccaGAGCGUGAau 116 :+ A++CAA+C+ AA+C::GG+UGAUGA+ C++ C:U:::::CCAGAGCGUGA+U 199 AGGAGGCAAGCAcuuAAGCUUGGUUGAUGACGCAUGa--CCUGUGGGCCAGAGCGUGAUU 256 ,,<----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<< 117 cCgCGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuc 176 +CGGC: G+A+:++++G+UG:UUU +U:C C +++:+UG+: GA GAUCGU 257 -AACGGCC-GGAUCACUGGCUGAUUUG-AUCC--C-ACGGCUGUA----GAGGAUCGU-- 304 <--<<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 177 cUaucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 :U+U:+CC++++ U + +GG+:A : UGG:::::A:G++ GUCUGAC::G 305 UUCUUGCCGGGCC-UCGCCUGGCCAGGA--UGGCUCUCAGGUU-GUCUGACAGG 354 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #209225,sp|X63065.1|TAU3SNRA T.aestivum U3 snRNA gene ----isReversed: 0 ----hitSequence: CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCUCGUACCGCUGCAUCCUUUACCAAUAAGGAGGCAAGCACUUCAGUCUGGUUGAUGCAUCUGACCUCUGGGCCAGAGCGUGAUUAACGGCCAGGAUUCCCUUAUGGGGGCAAUCCACGGCUGUAGAGGAUCGUUCCUGCCUUGCUCAUGCUUGUGCAGGGUGGCCCAGAGGUUGUCUGACAGA hit 62 : 859 1073 (fwd) 84.54 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 +ACCU+:C:U:++CA+GAUC::+UCUAUA:G U CGU:CC+CUG+::C UU+A++:A:A 859 CGACCUUACUUGAACAGGAUCUGUUCUAUAGGCU-CGUACCGCUGCAUCCUUUACCAAUA 917 >>----------...---((((--------------((((((((((((,,,,,,,,,,,, 61 gucAaaCAaccc...AAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAauc 117 :+ A++CAA+C+ +A+:C:GG+UGAUG C+ A C:UC::::CCAGAGCGUGA+U 918 AGGAGGCAAGCAcuuCAGUCUGGUUGAUGCAUCUGA--CCUCUGGGCCAGAGCGUGAUU- 974 ,<----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<< 118 CgCGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUucc 177 +CGGC::G+A+:+++U::+GG ++++UCC+:: :+UG:: GA GAUCGU:CC 975 AACGGCCAGGAUUCCCUUAUGGGGGCAAUCCACG----GCUGUA----GAGGAUCGUUCC 1026 --<<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 178 UaucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 U+ :C:++CU UG +:G:+ AGG:UGG::::GA:G++ GUCUGAC:G: 1027 UG--CCUUGCUC--AUGCUUGUG-CAGGGUGGCCCAGAGGUU-GUCUGACAGA 1073 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #214076,sp|Z29641.1|ZMU3SNRNG Zea mays of USE gene encoding U3snRNA. ----isReversed: 0 ----hitSequence: CGACCUUACUUGAACAGGAUCUGUUCUAUAGGAUCGUACUGUUGCAUCUUUGAUUAAUAAGAAGGCAAGUACUUAAACCUGGUUGAUGAGAAUUUGACCUGUGGGCCAGAGCGUGAUUUAACGGCCAGGACUUUGCCUUGGUGCAUUGUCUGGAGCUGCAGAUGAUCGUUCUUGGCCAGGCUUAAUGUCUGGCUAGGGUGGCCUACAGGCUGUUUGACAGG hit 63 : 760 980 (fwd) 99.58 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 +ACCU+:C:U:++CAGGAUC::+UCUA+A:GAU CGU:C++ UG+::CUUUGA++:A:A 760 CGACCUUACUUGAACAGGAUCUGUUCUAUAGGAU-CGUACUGUUGCAUCUUUGAUUAAUA 818 >>----------...---((((--------------..((((((((((((,,,,,,,,,, 61 gucAaaCAaccc...AAAccagGAUGAUGAgacgcA..gccuucgcucccaGAGCGUGAa 115 :+ A++CAA+++ AAACC:GG+UGAUGAGA +++ C:U::+::CCAGAGCGUGA+ 819 AGAAGGCAAGUAcuuAAACCUGGUUGAUGAGAAUUUga--CCUGUGGGCCAGAGCGUGAU 876 ,,,<----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,< 116 ucCgCGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUu 175 U+ +CGGC::G+A::U:+ ::U:+ U++ +U+:U:: +:A::UG:: GAUGAUCGU: 877 UUAACGGCCAGGACUUUG-CCUUGGUGC-AUUGUCU-GGAGCUGCA----GAUGAUCGUU 929 <<--<<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 176 ccUaucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 C:U+ ::C:++CUU UGU+:G:: UA:G:UGG::+::A:G++ GU UGAC:GG 930 CUUG-GCCAGGCUU-AAUGUCUGGC-UAGGGUGGCCUACAGGCU-GUUUGACAGG 980 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro02.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro03.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro04.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro05.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/rod.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/rod.dat.fasta.gz ----sequence: #13581,sp|K00780.1|RN3B Rat U3B small nuclear RNA. ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGUGUAGAGCACCCGAAACCACGAGGACGAGACAUAGCGUCCCCUCCUGAGCGUGAAGCCGGCUCUAGGUGCUGCUUCUGUGCAGCUGCCUCUUGCCAUUGAUGAUCGUUCUUCUCUCCUUCGGGGGGGUAAGAGGGAGGGAACGCAGUCUGAGUGG hit 64 : 1 214 (fwd) 103.49 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C+::C+:+GAU+AUU::UA++G+ G+ +C++++::AGU+U+U+:G::+G: 1 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGU 60 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+CC+AAACCA:GA GA GAGAC++AGC:U:C:CUCC: GAGCGUGAA+CC: 61 GUAGAGCACCCGAAACCACGAGGACGAGACAUAGCGUCCCCUCCU-GAGCGUGAAGCCG- 118 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C +::G: G:+G:UU+U +U:C+:CU:C::+U+GC:+UUGAUGAUCGUUC:U+: 119 ---GCUC-UAGGU-GCUGCUUCU-GUGCAGCUGCCUCUUGCCAUUGAUGAUCGUUCUUCU 172 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 +UCC U + GGG+:UA:GA :GGAG:G:A:GCAGUCUGA:UGG 173 CUCCUU-------CGGGGGGGUAAGA-GGGAGGGAACGCAGUCUGAGUGG 214 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/rod.dat.fasta.gz ----sequence: #19702,sp|V01267.1|RNRNA3 Rattus norvegicus U3 snRNA ----isReversed: 0 ----hitSequence: GUGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGUGUAGAGCCCACGAAACCACGAGGACGAGACAUAGCGUCCCCUCCUGAGCGUGAAGCCGGCUCUAGGUGCUGCUUCUGCCUCUUGCCAUUGGCAGCUGAUGAUCGUCUUCUCUCCUUCGGGGGGGUAAGAGGGAGGGAACGCAGUCUGAGUGG hit 65 : 2 213 (fwd) 88.58 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 + ++CUAU:C+::C+:+GAU+AUU::UA++G+ G+ +C++++::AGU+U+U+:G::+G: 2 GUGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGU 61 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+C + C+AAACCA:GA GA GAGAC++AGC:U:C:CUCC: GAGCGUGAA+CC+ 62 GUAGAGCCCACGAAACCACGAGGACGAGACAUAGCGUCCCCUCCU-GAGCGUGAAGCCG- 119 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C U::G: :UG+UU+ U +CU: U:C::UUGGC+ +UGAUGAUCG UC:U+: 120 ---GCUC-UAGGU-GCUGCUUC--UGCCUCUUGCCAUUGGCAGCUGAUGAUCG-UCUUCU 171 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 +UCC U + GGG+:UA:GA :GGAG:G:A:GCAGUCUGA:UGG 172 CUCCUU-------CGGGGGGGUAAGA-GGGAGGGAACGCAGUCUGAGUGG 213 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/rod.dat.fasta.gz ----sequence: #20793,sp|X02717.1|RNU3B1 Rat gene for small nuclear RNA U3B (U3B.7) ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGUGUAGAGCACCCGAAACCACGAGGACGAGACAUAGCGUCCCCUCCUGAGCGUGAAGCCGGCUCUAGGUGCUGCUUCUGUGCAGCUGCCUCUUGCCAUUGAUGAUCGUUCUUCUCUCCUUCGGGAGGGUAAGAGGGAGGGAACGCAGUCUGAGUGG hit 66 : 550 763 (fwd) 100.49 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C+::C+:+GAU+AUU::UA++G+ G+ +C++++::AGU+U+U+:G::+G: 550 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGU 609 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+CC+AAACCA:GA GA GAGAC++AGC:U:C:CUCC: GAGCGUGAA+CC: 610 GUAGAGCACCCGAAACCACGAGGACGAGACAUAGCGUCCCCUCCU-GAGCGUGAAGCCG- 667 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C +::G: G:+G:UU+U +U:C+:CU:C::+U+GC:+UUGAUGAUCGUUC:U+: 668 ---GCUC-UAGGU-GCUGCUUCU-GUGCAGCUGCCUCUUGCCAUUGAUGAUCGUUCUUCU 721 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CUC: UC G+ :GG :UA:GA :GGAG:G:A:GCAGUCUGA:UGG 722 CUCCUUC------GGGAGG-GUAAGA-GGGAGGGAACGCAGUCUGAGUGG 763 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/rod.dat.fasta.gz ----sequence: #20794,sp|X02718.1|RNU3B2 Rat gene for small nuclear RNA U3B (U3B.4) ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGUGUAGAGCACCCGAAACCACGAGGACGAGACAUAGCGUCCCCUCCUGAGCGUGAAGCCGGCUCUAGGUGCUGCUUCUGUGCAGCUGCCUCUUGCCAUUGAUGAUCGUUCUUCUCUCCUUCGGGAGAGUAAGAGGGAGGGAACGCAGUCUGAGUGG hit 67 : 121 334 (fwd) 101.09 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C+::C+:+GAU+AUU::UA++G+ G+ +C++++::AGU+U+U+:G::+G: 121 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGU 180 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+CC+AAACCA:GA GA GAGAC++AGC:U:C:CUCC: GAGCGUGAA+CC: 181 GUAGAGCACCCGAAACCACGAGGACGAGACAUAGCGUCCCCUCCU-GAGCGUGAAGCCG- 238 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C +::G: G:+G:UU+U +U:C+:CU:C::+U+GC:+UUGAUGAUCGUUC:U+: 239 ---GCUC-UAGGU-GCUGCUUCU-GUGCAGCUGCCUCUUGCCAUUGAUGAUCGUUCUUCU 292 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CU C U + G GA:UA:GA :GGAG:G:A:GCAGUCUGA:UGG 293 CUCCUU-------CGGGAGAGUAAGA-GGGAGGGAACGCAGUCUGAGUGG 334 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/rod.dat.fasta.gz ----sequence: #20795,sp|X02722.1|RNU3D Rat gene for small nuclear RNA U3D ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGUGUAGAGCACCCGAAACCACGAGGAGGAGACGUAGCGUUCUCUCCUGAGCGUGAAGCCGGCUCUUAGUGUUGCUUCCUGCAACUGCUAUUGGCCAUUGAUGAUCGUUCUCGAGCCUCUCUGAGGUUCGAGAGGGAGAGAACGCAGUCUGAGUGG hit 68 : 550 762 (fwd) 97.90 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C+::C+:+GAU+AUU::UA++G+ G+ +C++++::AGU+U+U+:G::+G: 550 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGU 609 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+CC+AAACCA:GA GA GAGACG+AGC:UUC:CUCC: GAGCGUGAA+CC: 610 GUAGAGCACCCGAAACCACGAGGAGGAGACGUAGCGUUCUCUCCU-GAGCGUGAAGCCG- 667 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C U::G: GU+G:UU+ U:C+ACU:C::UUGGC:+UUGAUGAUCGUUC: + 668 ---GCUC-UUAGU-GUUGCUUC--CUGCAACUGCUAUUGGCCAUUGAUGAUCGUUCUCGA 720 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 :C CU UG G: :GA :GGAG:GAA:GCAGUCUGA:UGG 721 GCCUCU-------CUGAGGUUCGAGA-GGGAGAGAACGCAGUCUGAGUGG 762 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/rod.dat.fasta.gz ----sequence: #20796,sp|X02719.1|RNU3P1 Rat pseudogene for small nuclear RNA U3 (H3.1) ----isReversed: 0 ----hitSequence: AAGACCAUACUUUCAAGGAUCAUUUUUAUAGUUCGUUACUAGAGAAGUUGCUCUGACUGUGUGGAACACUGAAACCAUGAGGAUGAGACAUAGUGUCCCCUCCUGAGCGUGAAGCCGGCUCUAGGUGCUGCUUCUGUGCAGCUGCCUCUUGCCAUUGAUGAUCGUUCUUCUCUCCUUCCGGAGGGUGAGAGGGAGGGAACGCAGUCUGAGUGG hit 69 : 51 263 (fwd) 86.05 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++C AU:C+::C+++GAU+AUU: UA++G+ G+ +C++++ :AGU+ +U++G::+G: 51 AAGACCAUACUUUCAAGGAUCAUUUUUAUAGUUCGUUACUAGAGAAGUUGCUCUGACUGU 110 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU AACA+ + AACCA:GA GAUGAGAC++AG :U:C:CUCC: GAGCGUGAA+CC: 111 GUGGAACACUGA-AACCAUGAGGAUGAGACAUAGUGUCCCCUCCU-GAGCGUGAAGCCG- 167 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C +::G: G:+G:UU+U +U:C+:CU:C::+U+GC:+UUGAUGAUCGUUC:U+: 168 ---GCUC-UAGGU-GCUGCUUCU-GUGCAGCUGCCUCUUGCCAUUGAUGAUCGUUCUUCU 221 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 UCC:UC+ G+:GGG : :GA :GGAG:G:A: CAGUCUGA:UGG 222 CUCCUUCC-----GGAGGGUG--AGA-GGGAGGGAACGCAGUCUGAGUGG 263 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/rod.dat.fasta.gz ----sequence: #20797,sp|X02720.1|RNU3P2 Rat pseudogene for small nuclear RNA U3 (H3.3) ----isReversed: 0 ----hitSequence: AGGACUAUACUUUCAUGGAUCAUUUCUAUAGUUUGUUACUAGAGAAGUUUCUCUGACUGUGUAGAGCACCCGAAACCACAAAGACGAGACAUAGCGCCCCCUCCUGAGCGUGAAGCUGGCUCUAGGUGCUGCUUCUGUGCAGCUGCCUUUUGCCAUUGAUGAUCGUUCUCUCUUCGGGAGAGUGAGAGGGAGGGAACACAGUCUGAGUGG hit 70 : 51 260 (fwd) 75.95 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 A+++CUAU:C+::C+ +GAU+AUU::UA++G+ UG+ +C++++::AGU+U+U+ G::+G: 51 AGGACUAUACUUUCAUGGAUCAUUUCUAUAGUUUGUUACUAGAGAAGUUUCUCUGACUGU 110 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+CC+AAACCA: A GA GAGAC++AG : :C:CUCC: GAGCGUGAA+C : 111 GUAGAGCACCCGAAACCACAAAGACGAGACAUAGCGCCCCCUCCU-GAGCGUGAAGCUG- 168 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C U::G: G:+G:UU+U +U:C+:CU:C::UU+GC:+UUGAUGAUCGUUC: 169 ---GCUC-UAGGU-GCUGCUUCU-GUGCAGCUGCCUUUUGCCAUUGAUGAUCGUUCUCU- 221 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 C:UC +G+:G G U :GA :GGAG:G: : CAGUCUGA:UGG 222 ---CUUC-----GGGAGAG--UGAGA-GGGAGGGAACACAGUCUGAGUGG 260 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/rod.dat.fasta.gz ----sequence: #21444,sp|M11466.1|RNUG3PSA Rat U3 small nuclear RNA pseudogene, clone U3-1. ----isReversed: 0 ----hitSequence: AGGACUAUACUUUCAUGGAUCAUUUCUAUAGUUUGUUACUAGAGAAGUUUCUCUGACUGUGUAGAGCACCCGAAACCACAAAGACGAGACAUAGCGCCCCCUCCUGAGCGUGAAGCUGGCUCUAGGUGCUGCUUCUGUGCAGCUGCCCUUUGCCAUUGAUGAUCGUUCUCUCCUUCGGGAGAGUGAGAGGGAGGGAACACAGUCUGAGUGG hit 71 : 121 331 (fwd) 76.67 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 A+++CUAU:C+::C+ +GAU+AUU::UA++G+ UG+ +C++++::AGU+U+U+ G::+G: 121 AGGACUAUACUUUCAUGGAUCAUUUCUAUAGUUUGUUACUAGAGAAGUUUCUCUGACUGU 180 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+CC+AAACCA: A GA GAGAC++AG : :C:CUCC: GAGCGUGAA+C : 181 GUAGAGCACCCGAAACCACAAAGACGAGACAUAGCGCCCCCUCCU-GAGCGUGAAGCUG- 238 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C U::G: G:+G:UU+U +U:C+:CU:C::UU+GC:+UUGAUGAUCGUUC: 239 ---GCUC-UAGGU-GCUGCUUCU-GUGCAGCUGCCCUUUGCCAUUGAUGAUCGUUCU--- 289 <<<<<__________>>>>>>--.>>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUa.ggaUgggagcgaaggcaGUCUGAcugg 230 U C:UC +G+:G G :GA :GGAG:G: : CAGUCUGA:UGG 290 CUCCUUC-----GGGAGAGU---gAGA-GGGAGGGAACACAGUCUGAGUGG 331 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/rod.dat.fasta.gz ----sequence: #21445,sp|M11467.1|RNUG3PSB Rat U3 small nuclear RNA pseudogene, clone U3-2. ----isReversed: 0 ----hitSequence: AAGACUAUACUUUUAGGGAUCAUUUCCAUAGUUUGUUACUAGAAAAGUUUCCCUGACUGUGUAGAGCACCCGAAGCCAUGAGGACGAGAAACAGCAAACAGCAUCCCCUCCUGAGUGUGAAGCCGGCUCUAGGUGCUGCUUCUGCGUGGCUGCCUCUUGCCACUAACGAUCUCGUCCUUCACUCCUACGGGAGGGUGAGAGGGAGGGAACGCAGUCUGAGUGG hit 72 : 117 339 (fwd) 53.96 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C+:: +:+:AU+AUU:+ A++G+ UG+ +C+++++:AGU+U+:+: ::+G: 117 AAGACUAUACUUUUAGGGAUCAUUUCCAUAGUUUGUUACUAGAAAAGUUUCCCUGACUGU 176 >>-------------((((--------------.......((((((((((((,,,,,,,, 61 gucAaaCAacccAAAccagGAUGAUGAgacgcA.......gccuucgcucccaGAGCGUG 113 GU A+CA+CC+AA+CCA:GA GA GAGA +CA GC:U:C:CUCC: GAG GUG 177 GUAGAGCACCCGAAGCCAUGAGGACGAGAAACAgcaaacaGCAUCCCCUCCU-GAGUGUG 235 ,,,,,<----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,, 114 AaucCgCGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCG 173 AA+CC: GC+C +::G: G:++:UU+U + :++:CU:C::+U+GC:++U A GAUC 236 AAGCCG----GCUC-UAGGU-GCUGCUUCU-GCGUGGCUGCCUCUUGCCACUAACGAUC- 287 ,<<<--<<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 174 UuccUaucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 UC U+: UC:CUC+ U G+G:GG :U GA :GGAG:G:A:GCAGUCUGA:UGG 288 -UCGUCCUUCACUCC--UACGGGAGG-GUGAGA-GGGAGGGAACGCAGUCUGAGUGG 339 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/rod.dat.fasta.gz ----sequence: #21446,sp|M11468.1|RNUG3PSC Rat U3 small nuclear RNA pseudogene, clone U3-3. ----isReversed: 0 ----hitSequence: AAGACCAUACUUUCAAGGAUCAUUUUUAUAGUUCGUUACUAGAGAAGUUGCUCUGACUGUGUGGAACACCUGAAACCAUGAGGAUGAGACAUAGUGUCCCCUCCUGAGCGUGAAGCCGGCUCUAGGUGCUGCUUCUGUGCAGCUGCCUCUUGCCAUUGAUGAUCGUUCUUCUCUCCUUCCGGAGGGUGAGAGGGAGGGAACGCAGUCUGAGUGG hit 73 : 114 327 (fwd) 90.53 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++C AU:C+::C+++GAU+AUU: UA++G+ G+ +C++++ :AGU+ +U++G::+G: 114 AAGACCAUACUUUCAAGGAUCAUUUUUAUAGUUCGUUACUAGAGAAGUUGCUCUGACUGU 173 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU AACA+C++AAACCA:GA GAUGAGAC++AG :U:C:CUCC: GAGCGUGAA+CC: 174 GUGGAACACCUGAAACCAUGAGGAUGAGACAUAGUGUCCCCUCCU-GAGCGUGAAGCCG- 231 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C +::G: G:+G:UU+U +U:C+:CU:C::+U+GC:+UUGAUGAUCGUUC:U+: 232 ---GCUC-UAGGU-GCUGCUUCU-GUGCAGCUGCCUCUUGCCAUUGAUGAUCGUUCUUCU 285 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 UCC:UC+ G+:GGG : :GA :GGAG:G:A: CAGUCUGA:UGG 286 CUCCUUCC-----GGAGGGUG--AGA-GGGAGGGAACGCAGUCUGAGUGG 327 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/rod.dat.fasta.gz ----sequence: #21496,sp|J01884.1|RNUR3A Rat U3A small nuclear RNA. ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGUGUAGAGCACCCGAAACCACGAGGAGGAGACGUAGCGUUCUCUCCUGAGCGUGAAGCCGGCUCUUAGUGUUGCUUCCGUGCAACUGCUAUUGGCCAUUGAUGAUCGUUCUCGGUCCUCUCUGAGGGGCGAGAGGGAGAGAACGCAGUCUGAGUGG hit 74 : 1 214 (fwd) 103.05 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C+::C+:+GAU+AUU::UA++G+ G+ +C++++::AGU+U+U+:G::+G: 1 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCGUUACUAGAGAAGUUUCUCUGACUGU 60 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+CC+AAACCA:GA GA GAGACG+AGC:UUC:CUCC: GAGCGUGAA+CC: 61 GUAGAGCACCCGAAACCACGAGGAGGAGACGUAGCGUUCUCUCCU-GAGCGUGAAGCCG- 118 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C U::G: GU+G:UU++ +U:C+ACU:C::UUGGC:+UUGAUGAUCGUUC: +: 119 ---GCUC-UUAGU-GUUGCUUCC-GUGCAACUGCUAUUGGCCAUUGAUGAUCGUUCUCGG 172 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 ::C CU UG G::: :GA :GGAG:GAA:GCAGUCUGA:UGG 173 UCCUCU-------CUGAGGGGCGAGA-GGGAGAGAACGCAGUCUGAGUGG 214 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----sequence: #50068,sp|X07319.1|XBSNRNU3 Xenopus borealis U3 snRNA ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGGUUUUACCUGGUGAGAUGUGCUCUAAAGUGUCUGAACUCACAAACCACGAGGAAGAGCGUCAGUGUCUUCUCCUGAGCGUGAAGUGAGCUCUCAGUGCUGCUUCAUUGUGGCUGCUGUUUGCUAUUGAUGAACGUUCUACUUCCCCUUUAUUAUUGGGGAGAUGGA hit 75 : 1 197 (fwd) 56.44 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:CUU: +:+:AU+A++::UA++G: U + :C+++ ::++U+U :+: :AAG: 1 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGGUUUUACCUGGUGAGAUGUGCUCUAAAGU 60 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GUC +A C CAAACCA+GA GA GAG ++CAG+ U+++CUCC GAGCGUGAA++ : 61 GUCUGAACUCACAAACCACGAGGAAGAGCGUCAGUGUCUUCUCCU-GAGCGUGAAGUGA- 118 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C U::G: G:++:UU+ UU:++:CU:C::UU+GC:+UUGAUGA CGUUC: +: 119 ---GCUC-UCAGU-GCUGCUUCA-UUGUGGCUGCUGUUUGCUAUUGAUGAACGUUCUACU 172 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 ::CCCU U+ UU UGGG::: +:GA 173 UCCCCUUUA-UUAUUGGGGAGAUGGA------------------------ 197 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----sequence: #51921,sp|X07318.1|XLSNRNU3 Xenopus laevis U3 snRNA ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGGUUGUACCUGGUGAAAUGUGCUCGAAAGUGUCUGAACUCACAAACCACGAGGAAGAGCGUCAGUGUUUUCUCCUGAGCGUGAAGUGAGCUCACAGUGCUGCUUCAUUGUGGCUGCUGUUUGCUAUUGAUGAACGUUCUGCUCCCCUUUAUUAUUGGGGAGAUAGAGGGAGAGAACACAAGCUGAGUGG hit 76 : 1 219 (fwd) 84.84 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:CUU:C+:+:AU+A+U::UA++G: UG+ :C+++ ::A+U+U :+:G:AAG: 1 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGGUUGUACCUGGUGAAAUGUGCUCGAAAGU 60 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GUC +A C CAAACCA:GA GA GAG ++CAG::UU::CUCC: GAGCGUGAA++ : 61 GUCUGAACUCACAAACCACGAGGAAGAGCGUCAGUGUUUUCUCCU-GAGCGUGAAGUGA- 118 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C ::G: G:++:UU+ UU:++:CU:C:: U+GC:+UUGAUGA CGUUC: +: 119 ---GCUC-ACAGU-GCUGCUUCA-UUGUGGCUGCUGUUUGCUAUUGAUGAACGUUCUGCU 172 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 C:CC U UU U GG:A: +:GA :GGAG::AA::CA CUGA:UGG 173 CCCCUUUA--UUAUUGGGGAGAUAGA-GGGAGAGAACACAAGCUGAGUGG 219 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----sequence: #52062,sp|Z12613.1|XLU3AG X.laevis U3A gene for U3 small nuclear RNA ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGGUUGUACCUGGUGAAAUGUGCUCGAAAGUGUCUGAACUCACAAACCACGAGGAAGAGCGUCAGUGUUCUCUCCUGAGCGUGAAGUGAGCUCACAGUGCUGCUUCAUUGUGGCUGCUGUUUGCUAUUGAUGAACGUUCUGCUCCCCUUUAUUAUUGGGGAGAUGGAGGGAGAGAACACAGGCUGAGUGG hit 77 : 694 912 (fwd) 88.39 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:CUU:C+:+:AU+A+U::UA++G: UG+ :C+++ ::A+U+U :+:G:AAG: 694 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGGUUGUACCUGGUGAAAUGUGCUCGAAAGU 753 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GUC +A C CAAACCA:GA GA GAG ++CAG::UUC:CUCC: GAGCGUGAA++ : 754 GUCUGAACUCACAAACCACGAGGAAGAGCGUCAGUGUUCUCUCCU-GAGCGUGAAGUGA- 811 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C ::G: G:++:UU+ UU:++:CU:C:: U+GC:+UUGAUGA CGUUC: +: 812 ---GCUC-ACAGU-GCUGCUUCA-UUGUGGCUGCUGUUUGCUAUUGAUGAACGUUCUGCU 865 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 C:CC U UU U GG:A: +:GA :GGAG:GAA::CAG CUGA:UGG 866 CCCCUUUA--UUAUUGGGGAGAUGGA-GGGAGAGAACACAGGCUGAGUGG 912 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum01.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum01.dat.fasta.gz ----sequence: #9590,sp|AC003014.1|AC003014 Human PAC clone RP1-290B4 from Xq23, complete sequence. ----isReversed: 0 ----hitSequence: UGAAGACUAUUUUCAAGGUUCAUUUCUAUAGUUCACUACUGGAGAAGUUUCUCUGAACAUGUGGAACACCAGGAAACAUGAGGAAGAAGCACAGCAUUCUCUCCUAAAUGUGAAGCCAGCUGUUGGUGUUGCUUUGCUAUAACUGCUAUUUGCCAUUGAUGAUUAUUUUCCUCUUCUUCCCAGAGAGUAAGAGGGAGAGGAUGCAGUCUGUGUGG hit 78 : 12062 12276 (fwd) 46.16 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 +A+ :U:+:U:C+++G U+AUU::UA++G+ +C +C++++::AGU+U+U++G:A:+: 12062 UGAAGACUAUUUUCAAGGUUCAUUUCUAUAGUUCACUACUGGAGAAGUUUCUCUGAACAU 12121 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 G: AACA+C + AA:CA:GA GA GA C+CAGC:U C:CUCC: A GUGAA+CC 12122 GUGGAACACCAGGAAACAUGAGGAAGAAGCACAGCAUUCUCUCCU-AAAUGUGAAGCCA- 12179 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC++ U: G: GU++ UUU U ++ACU:C :UU+GC +UUGAUGAU UU:: +: 12180 ---GCUG-UUGGU-GUUGCUUUG-CUAUAACUGCUAUUUGCCAUUGAUGAUUAUUUUCCU 12233 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CU:C:UC+ :G:GA:UA::A :GGAG:G A:GCAGUCUG :UG: 12234 CUUCUUCCC------AGAGAGUAAGA-GGGAGAGGAUGCAGUCUGUGUGG 12276 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz ----sequence: #672,sp|AC005378.2|AC005378 Homo sapiens PAC clone RP5-1137M13 from 7q33-q35, complete sequence. ----isReversed: 1 ----hitSequence: CUAGUAACACUUCCAUGCACCAUUUCUAUAGUUUCUUACCAGAGAAGUUUCUCUGAACAUGUGGAGCACCGGAAACCACGAGGAGGCGGCUCAGCAUUCACUCCUGAGCAUGAAGCUGGCUCUUGGUGGUGCUUCUCUGCAAUUGCCUUUUGCUGCUGAUGAUCACUCUUCUCUUCCUUUGGGAGAGUGAAAGGGAAAGGAAGCCAUCUGAAGGG hit 79 : 79834 79620 (rev) 42.08 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 A A::::UCC+ + A +AUU::UA+AG+ U + +CC+++::AGU+U+ + GAA::: 49203 CUAGUAACACUUCCAUGCACCAUUUCUAUAGUUUCUUACCAGAGAAGUUUCUCUGAACAU 49262 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 :U A+CA+C +AAACC GA GA G G C+CAGC:U C UCC: GAGC UGAA+C G 49263 GUGGAGCACCGGAAACCACGAGGAGGCGGCUCAGCAUUCACUCCU-GAGCAUGAAGCUG- 49320 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C U::G: :+G:UU+U U:C+: U:C::UU+GCU +UGAUGAUC U :U+ 49321 ---GCUC-UUGGU-GGUGCUUCU-CUGCAAUUGCCUUUUGCUGCUGAUGAUCACUCUUC- 49373 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 :C:UC+U UU+G+:G:G U : A :GGA G A:GC+ UCUGA GG 49374 --UCUUCCU-UUGGGAGAG--UGAAA-GGGAAAGGAAGCCAUCUGAAGGG 49417 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz ----sequence: #1370,sp|AC006515.7|AC006515 Homo sapiens 3p22-7 PAC RPCI5-1053D16 (Roswell Park Cancer Institute Human PAC Library) complete sequence. ----isReversed: 1 ----hitSequence: AAUUGUAUACUUUCAGGGAUCAUUCCAUAGGUUGUUACUAGAGAAGUUUUUUUAGAUGUGUAGAACACUGGAAACCACGAGGAGGAGGCGCAGCAUUCUCUCUUGACCAUGAAGCCGGCUCUUGGUGUUGUUUCAUUGCAACUGUCAUUUGCCAUUGAUGAUCGUUCUCUUCCUCUGGGAGAGUAAGAGGGAGAGGACACAGUUUGAGUGG hit 80 : 57464 57254 (rev) 47.96 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA UAU:C+U +:+GAU+AUU:: A++G UG+ C++++::AGU+UUU+: A+G: 166079 AAUUGUAUACUUUCAGGGAUCAUUCC-AUAGGUUGUUACUAGAGAAGUUUUUUUAGAUGU 166137 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU AACA+ +AAACCA:GA GA GAG CGCAG :U C:CUC:: GA C UGAA+CC: 166138 GUAGAACACUGGAAACCACGAGGAGGAGGCGCAGCAUUCUCUCUU-GACCAUGAAGCCG- 166195 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C U::+: GU+G UU+ UU C+ACU:+::UU+GC:+UUGAUGAUCGUUC: 166196 ---GCUC-UUGGU-GUUGUUUCA-UUGCAACUGUCAUUUGCCAUUGAUGAUCGUUCU--- 166246 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 C:UC+U U+G+:G G UA:GA ::GAG:G A: CAGU UGA:UGG 166247 ---CUUCCU-CUGGGAGAG--UAAGA-GGGAGAGGACACAGUUUGAGUGG 166289 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz ----sequence: #1945,sp|AC007952.15|AC007952 Homo sapiens chromosome 17, clone RP11-160E2, complete sequence. ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGUGUAGAGCACCGAAAACCCCGAGGAAGAGAGGUAGCGUUUUCUCCUGAGCGUGAAGCCGGCUUUCUGGCGUUGCUUGGCUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCUCUCCGUAUUGGGGAGUGAGAGGGAGAGAACGCGGUCUGAGUGG hit 81 : 42151 42366 (fwd) 99.36 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C:U:C+:+GAU+AUU::UA++G+ UG+ +C++++::AGU+U+U+:G:A:G: 42151 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGU 42210 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C +AAACC::GA GA GAGA+G+AGC:UU::CUCC: GAGCGUGAA+CC: 42211 GUAGAGCACCGAAAACCCCGAGGAAGAGAGGUAGCGUUUUCUCCU-GAGCGUGAAGCCG- 42268 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+ +:::G: GU+G:UU+ U:C+ACU:C::: GC:+UUGAUGAUCGUUC:U+: 42269 ---GCUUUCUGGC-GUUGCUUGG-CUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCU 42323 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CUCC U UU GGGA:U :GA :GGAG::AA:GC GUCUGA::GG 42324 CUCCGUAUU------GGGGAGUGAGA-GGGAGAGAACGCGGUCUGAGUGG 42366 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz ----sequence: #1945,sp|AC007952.15|AC007952 Homo sapiens chromosome 17, clone RP11-160E2, complete sequence. ----isReversed: 1 ----hitSequence: AAGGCUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUCUUUGAACGUGUAGAGCACCGAAAACCCCGAGGAAGAGAGGUAGCGUUUUCUCCUGAGCGUGAAGCCGGCUUUCUGGCGUUGCUUGGCUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCUCUCCGUAUUGGGGAGUGAGAGGGAGAGAACGCGGUCUGAGUGG hit 82 : 92875 92660 (rev) 96.81 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA+ CUAU:C:U:C+:+GAU+AUU::UA++G+ UG+ +C++++::AGU+U+U+:G:A:G: 65229 AAGGCUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUCUUUGAACGU 65288 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C +AAACC::GA GA GAGA+G+AGC:UU::CUCC: GAGCGUGAA+CC: 65289 GUAGAGCACCGAAAACCCCGAGGAAGAGAGGUAGCGUUUUCUCCU-GAGCGUGAAGCCG- 65346 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+ +:::G: GU+G:UU+ U:C+ACU:C::: GC:+UUGAUGAUCGUUC:U+: 65347 ---GCUUUCUGGC-GUUGCUUGG-CUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCU 65401 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CUCC U UU GGGA:U :GA :GGAG::AA:GC GUCUGA::GG 65402 CUCCGUAUU------GGGGAGUGAGA-GGGAGAGAACGCGGUCUGAGUGG 65444 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz ----sequence: #1945,sp|AC007952.15|AC007952 Homo sapiens chromosome 17, clone RP11-160E2, complete sequence. ----isReversed: 1 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGUGUAGAGCACCGAAAACCCCGAGGAAGAGAGGUAGCGUUUUCUCCUGAGCGUGAAGCCGGCUUUCUGGCGUUGCUUGGCUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCUCUCCGUAUUGGGGAGUGAGAGGGAGAGAACGCGGUCUGAGUGG hit 83 : 44375 44160 (rev) 99.36 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C:U:C+:+GAU+AUU::UA++G+ UG+ +C++++::AGU+U+U+:G:A:G: 113729 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGU 113788 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C +AAACC::GA GA GAGA+G+AGC:UU::CUCC: GAGCGUGAA+CC: 113789 GUAGAGCACCGAAAACCCCGAGGAAGAGAGGUAGCGUUUUCUCCU-GAGCGUGAAGCCG- 113846 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+ +:::G: GU+G:UU+ U:C+ACU:C::: GC:+UUGAUGAUCGUUC:U+: 113847 ---GCUUUCUGGC-GUUGCUUGG-CUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCU 113901 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CUCC U UU GGGA:U :GA :GGAG::AA:GC GUCUGA::GG 113902 CUCCGUAUU------GGGGAGUGAGA-GGGAGAGAACGCGGUCUGAGUGG 113944 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz ----sequence: #2532,sp|AC008929.3|AC008929 Homo sapiens chromosome 5, complete sequence. ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGCUCAUUACUAGAGAAGUUCCCCUGAACGUGUAGAACACUGGCAACCAUGAGGAGGACAUGCAGUGUUCUGUCCUGAGUGUGAAGCUGGGUCUUGGUGUUGCUUUGCUGCAAGUACCAUUUGCCACUGAUGAUUGUUUUUGUCUCCCUCUGGGACAGUAAGGGAAAGGACACAGUCUGAGUGA hit 84 : 76720 76932 (fwd) 60.52 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C:U:C+:+:AU+AUU::UA++G ++ C++++::AGU+ +:+:G:A:G: 76720 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGCUCAUUACUAGAGAAGUUCCCCUGAACGU 76779 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU AACA+ ++AA CA:GA GA GA+A GCAG::U C: UCC: GAG GUGAA+C : 76780 GUAGAACACUGGCAACCAUGAGGAGGACAUGCAGUGUUCUGUCCU-GAGUGUGAAGCUG- 76837 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 G +C U::G+ :U+G:UUU U:C+A:U+C::UU+ C:++UGAUGAU GUU :U+U 76838 ---GGUC-UUGGU-GUUGCUUUG-CUGCAAGUACCAUUUGCCACUGAUGAUUGUUUUUGU 76891 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 :CCCU UGGG: A +: :GGA :G A::CAGUCUGA:UG 76892 CUCCCU-------CUGGGACAGUAA--GGGAAAGGACACAGUCUGAGUGA 76932 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz ----sequence: #3100,sp|AC010170.3|AC010170 Homo sapiens 3p22-21.3 BAC RPCI11-487J21 (Roswell Park Cancer Institute Human BAC Library) complete sequence. ----isReversed: 1 ----hitSequence: AAUUGUAUACUUUCAGGGAUCAUUCCAUAGGUUGUUACUAGAGAAGUUUUUUUAGAUGUGUAGAACACUGGAAACCACGAGGAGGAGGCGCAGCAUUCUCUCUUGACCAUGAAGCCGGCUCUUGGUGUUGUUUCAUUGCAACUGUCAUUUGCCAUUGAUGAUCGUUCUCUUCCUCUGGGAGAGUAAGAGGGAGAGGACACAGUUUGAGUGG hit 85 : 130706 130496 (rev) 47.96 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA UAU:C+U +:+GAU+AUU:: A++G UG+ C++++::AGU+UUU+: A+G: 43272 AAUUGUAUACUUUCAGGGAUCAUUCC-AUAGGUUGUUACUAGAGAAGUUUUUUUAGAUGU 43330 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU AACA+ +AAACCA:GA GA GAG CGCAG :U C:CUC:: GA C UGAA+CC: 43331 GUAGAACACUGGAAACCACGAGGAGGAGGCGCAGCAUUCUCUCUU-GACCAUGAAGCCG- 43388 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C U::+: GU+G UU+ UU C+ACU:+::UU+GC:+UUGAUGAUCGUUC: 43389 ---GCUC-UUGGU-GUUGUUUCA-UUGCAACUGUCAUUUGCCAUUGAUGAUCGUUCU--- 43439 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 C:UC+U U+G+:G G UA:GA ::GAG:G A: CAGU UGA:UGG 43440 ---CUUCCU-CUGGGAGAG--UAAGA-GGGAGAGGACACAGUUUGAGUGG 43482 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz ----sequence: #4297,sp|AC013402.9|AC013402 Homo sapiens BAC clone RP11-134N15 from 2, complete sequence. ----isReversed: 0 ----hitSequence: AAGACUAUUCUUCUAGGGAUCUUUUCUAUAGUUCAGUACCAGAGAUGGUUCUCUGACAGUGUGGAGCACCAGAAACCAUGAGAAGGAGGCACAGCAAUCUCUCCUGAGCAUGGAGCCUGCUCUUGGUGUUGUUUUGCUGCAGCUGCUGUUUGCCAUUGAUGAUCGUUCUCUUCUUUCAGGAGAGUAAGAAGGCGAGGAUGCAGUCUGAGUGG hit 86 : 38350 38561 (fwd) 58.07 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU CU:C +:+GAU+ U:::UA+AG+ + +CC+++:::G +U+U+: A:AG 38350 AAGACUAUUCUUCUAGGGAUCUUUUCUAUAGUUCAGUACCAGAGAUGGUUCUCUGACAGU 38409 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C +AAACCA:GA A GAG C+CAGC: C:C CC GAGC UG+A+CC 38410 GUGGAGCACCAGAAACCAUGAGAAGGAGGCACAGCAAUCUCUCCU-GAGCAUGGAGCCU- 38467 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C U: G: G++G UUU U C++CU:C :UU+GC +UUGAUGAUCGUUC: 38468 ---GCUC-UUGGU-GUUGUUUUG-CUGCAGCUGCUGUUUGCCAUUGAUGAUCGUUCU--- 38518 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 C:UCUU U G+:G G UA:GA GG G:G :GCAGUCUGA:UGG 38519 ---CUUCUU-UCAGGAGAG--UAAGA-AGGCGAGGAUGCAGUCUGAGUGG 38561 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz ----sequence: #5897,sp|AC022616.9|AC022616 Homo sapiens chromosome 8, clone RP11-726G23, complete sequence. ----isReversed: 0 ----hitSequence: AAUGCUAUACUUUCAUGGGUCAUUUCUAUAGUUUGUUAUUAGAGAAGUUUCUCUGAAUGUGUUGAGCACCAGAAACCACGAGGAGAUGCAGCAUUCUCUCCUGAACGGGAAGCCAGCUUUUGGCAUUGCUUUGAUGCAACUACCAUUUGCCAUUGAUGGCAAUGCAUCGCUUCCUCUAGGAGUGUAAGAGGGAGUGGAUGCAGUCAGAGUGG hit 87 : 186616 186827 (fwd) 44.51 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA CUAU:C+U:C+ +G U+AUU::UA++:+ UG+ +:++++::AGU+U+U+ G:A+G: 186616 AAUGCUAUACUUUCAUGGGUCAUUUCUAUAGUUUGUUAUUAGAGAAGUUUCUCUGAAUGU 186675 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C +AAACCA:GA GA GA C AGC:U C:CUCC: GA CG GAA+CC 186676 GUUGAGCACCAGAAACCACGAGGA-GAUGC--AGCAUUCUCUCCU-GAACGGGAAGCCA- 186730 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+ U::G: U+G:UUU +U:C+A U:C::UU+GC +UUGAUG U C U+: 186731 ---GCUU-UUGGC-AUUGCUUUG-AUGCAACUACCAUUUGCCAUUGAUGGCAAUGCAUCG 186784 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 U:CCUCU+ GG:G :UA G :GGAG:G A:GCAGUC GA:UGG 186785 CUUCCUCUA------GGAGUGUAAGA-GGGAGUGGAUGCAGUCAGAGUGG 186827 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz ----sequence: #6541,sp|AC025614.12|AC025614 Homo sapiens chromosome 3 clone RP11-69K20, complete sequence. ----isReversed: 1 ----hitSequence: AAGACUAUACUUUGAGGGAUCAUUUCUAUAGUUUGUUACUGGAGAAGUUUCUCUGAAUAUGUAGAGCACCACAAAUCACGAGGAAAAAGCGCAGCAUUCUCUCCUGAGCAUGAAGCCAGUUUUCAGUGUUGCUUCGAUGUAACUGCCUUCUGCCCUUGAUGAUCAUUCUUCUCUCCUCCCUGGAGAGUAAGAGGGAGAGGAGGCAGUCUGAGUGG hit 88 : 45521 45307 (rev) 70.86 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU::+U: +:+GAU+AUU::UA++G+ UG+ +C++++::AGU+U+U+: :A+:: 126563 AAGACUAUACUUUGAGGGAUCAUUUCUAUAGUUUGUUACUGGAGAAGUUUCUCUGAAUAU 126622 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C CAAA:CA:GA GA A CGCAGC:U C:CUCC: GAGC UGAA+CC+ 126623 GUAGAGCACCACAAAUCACGAGGAAAAAGCGCAGCAUUCUCUCCU-GAGCAUGAAGCCA- 126680 ---<<---<<<<<-<<<<<_______>>>>>->>.>>>-->>>,,,,,,,,,,,,<<<-- 121 GGCgcgcaucugguguugguUuuuuUccuacUuc.acuUGgcuuuUGAUGAUCGUuccUa 179 G:+ + :G: GU++:UU+ +U:++ACU:C : +UG:C UUGAUGAUC UUC:U+ 126681 ---GUUU-UCAGU-GUUGCUUCG-AUGUAACUGCcUUCUGCC-CUUGAUGAUCAUUCUUC 126733 <<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 180 ucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 :CU CCUC+ UGG GA:UA:GA :GGAG:G A:GCAGUCUGA:UG: 126734 UCU-CCUCC-----CUGGAGAGUAAGA-GGGAGAGGAGGCAGUCUGAGUGG 126777 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz ----sequence: #6976,sp|AC027237.8|AC027237 Homo sapiens chromosome 15, clone RP11-253M7, complete sequence. ----isReversed: 0 ----hitSequence: AAGAGUAUAAUUUCAGGCAUCAAUUCUGUAGUUCCUUACUAGAGAAGUUUCUCUUAACAUGUACAACACUGGAAACCAUGAGGAGGUGGCAGCACAGCAUUCUCUGCUGAGCGUGAGGUUGGCUCUUGGUGUUGCUUUGCUGCAACUGUCAUUUGCCAUUGAUGAUGGUUCUUCUCUUCCUCCGAGGGAGAGAAUGCAGUCUGAGUGG hit 89 : 41712 41919 (fwd) 43.44 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++ UAU: :U: +:+ AU+A:U::U ++G+ + +C++++::A:U+U+ +: :A: : 41712 AAGAGUAUAAUUUCAGGCAUCAAUUCUGUAGUUCCUUACUAGAGAAGUUUCUCUUAACAU 41771 >>-------------((((------------.--..((((((((((((,,,,,,,,,,,, 61 gucAaaCAacccAAAccagGAUGAUGAgacg.cA..gccuucgcucccaGAGCGUGAauc 117 GU AACA+ +AAACCA:GA GA G G C+ CA GC:UUC:CU C: GAGCGUGA ++ 41772 GUACAACACUGGAAACCAUGAGGAGGUGGCAgCAcaGCAUUCUCUGCU-GAGCGUGAGGU 41830 ,<----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<< 118 CgCGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUucc 177 : GC+C U::+: GU+G:UUU U:C+ACU:+::UU+GC:+UUGAUGAU GU 41831 UG----GCUC-UUGGU-GUUGCUUUG-CUGCAACUGUCAUUUGCCAUUGAUGAUGGU--- 41880 --<<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 178 UaucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 ::: :UCUU : ::: :G AG:GAA:GCAGUCUGA:UGG 41881 ---UCUUCUCUU----CCUCCGA-------GGGAGAGAAUGCAGUCUGAGUGG 41919 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz ----sequence: #7029,sp|AC027347.5|AC027347 Homo sapiens chromosome 5 clone CTD-2562I21, complete sequence. ----isReversed: 1 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGCUCAUUACUAGAGAAGUUCCCCUGAACGUGUAGAACACUGGCAACCAUGAGGAGGACAUGCAGUGUUCUGUCCUGAGUGUGAAGCUGGGUCUUGGUGUUGCUUUGCUGCAAGUACCAUUUGCCACUGAUGAUUGUUUUUGUCUCCCUCUGGGACAGUAAGGGAAAGGACACAGUCUGAGUGA hit 90 : 7814 7602 (rev) 60.52 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C:U:C+:+:AU+AUU::UA++G ++ C++++::AGU+ +:+:G:A:G: 140380 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGCUCAUUACUAGAGAAGUUCCCCUGAACGU 140439 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU AACA+ ++AA CA:GA GA GA+A GCAG::U C: UCC: GAG GUGAA+C : 140440 GUAGAACACUGGCAACCAUGAGGAGGACAUGCAGUGUUCUGUCCU-GAGUGUGAAGCUG- 140497 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 G +C U::G+ :U+G:UUU U:C+A:U+C::UU+ C:++UGAUGAU GUU :U+U 140498 ---GGUC-UUGGU-GUUGCUUUG-CUGCAAGUACCAUUUGCCACUGAUGAUUGUUUUUGU 140551 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 :CCCU UGGG: A +: :GGA :G A::CAGUCUGA:UG 140552 CUCCCU-------CUGGGACAGUAA--GGGAAAGGACACAGUCUGAGUGA 140592 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz ----sequence: #7195,sp|AC036222.23|AC036222 Homo sapiens chromosome 17, clone RP11-433M22, complete sequence. ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUAGUUGCUAGAGAAGUUUCUCUGGACAUGUGGAGCACCAGAAACCAUGAGAAGGAGAUGUAGUGUUCUCUCCGGAGCAUGAAGCUGGCUCUUGGUGUUGCUUCGCUGCACCUGCCAUUUGCCAUUGACAAUCAUUCUUCUCUUCCUCUGGGAGAGUAAGGAGGAGAGGACACAGUCUGAGUGG hit 91 : 129635 129849 (fwd) 64.46 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:::U C+:+GAU+AUU::UA++G G+ C++++::AGU+U+U+:G A::: 129635 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUAGUUGCUAGAGAAGUUUCUCUGGACAU 129694 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C +AAACCA:GA A GAGA G+AG::U C:CUCC GAGC UGAA+C : 129695 GUGGAGCACCAGAAACCAUGAGAAGGAGAUGUAGUGUUCUCUCCG-GAGCAUGAAGCUG- 129752 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C U::G: G +G:UU+ U:C+ CU:C::UU+GC:+UUGA AUC U:C:U+: 129753 ---GCUC-UUGGU-GUUGCUUCG-CUGCACCUGCCAUUUGCCAUUGACAAUCAUUCUUCU 129806 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CU:CCUCU GG:GA:UA:G: GGAG:G A::CAGUCUGA:UGG 129807 CUUCCUCUG------GGAGAGUAAGG-AGGAGAGGACACAGUCUGAGUGG 129849 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz ----sequence: #9153,sp|AC083849.6|AC083849 Homo sapiens BAC clone RP11-163I18 from 7, complete sequence. ----isReversed: 0 ----hitSequence: CUAGUAACACUUCCAUGCACCAUUUCUAUAGUUUCUUACCAGAGAAGUUUCUCUGAACAUGUGGAGCACCGGAAACCACGAGGAGGCGGCUCAGCAUUCACUCCUGAGCAUGAAGCUGGCUCUUGGUGGUGCUUCUCUGCAAUUGCCUUUUGCUGCUGAUGAUCACUCUUCUCUUCCUUUGGGAGAGUGAAAGGGAAAGGAAGCCAUCUGAAGGG hit 92 : 28395 28609 (fwd) 42.08 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 A A::::UCC+ + A +AUU::UA+AG+ U + +CC+++::AGU+U+ + GAA::: 28395 CUAGUAACACUUCCAUGCACCAUUUCUAUAGUUUCUUACCAGAGAAGUUUCUCUGAACAU 28454 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 :U A+CA+C +AAACC GA GA G G C+CAGC:U C UCC: GAGC UGAA+C G 28455 GUGGAGCACCGGAAACCACGAGGAGGCGGCUCAGCAUUCACUCCU-GAGCAUGAAGCUG- 28512 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C U::G: :+G:UU+U U:C+: U:C::UU+GCU +UGAUGAUC U :U+ 28513 ---GCUC-UUGGU-GGUGCUUCU-CUGCAAUUGCCUUUUGCUGCUGAUGAUCACUCUUC- 28565 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 :C:UC+U UU+G+:G:G U : A :GGA G A:GC+ UCUGA GG 28566 --UCUUCCU-UUGGGAGAG--UGAAA-GGGAAAGGAAGCCAUCUGAAGGG 28609 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz ----sequence: #9819,sp|AC090515.2|AC090515 Homo sapiens chromosome 15 clone RP11-30K9 map 15q21.3, complete sequence. ----isReversed: 1 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUGUAUAGUUCGUUACUAGAGAAUUUUCUCUGAAUGUGUAGAACACCAGAAACCACAAGGAGGAGGCGCAGCGUUCUCUCCUGAGCGUGAAGCCGGGUCCUGGUGUUGCUUCACUGCAACUGCCAUUUGCCAUUGAUGAUUGUUCUUCUCUUCCUUUGGGAGAGUAAGAGGCAAAGGAUGCAGUCUGAAUGG hit 93 : 52813 52599 (rev) 75.30 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C+U:C+:+GAU+A+U::UA++G+ G+ +C++++::A+U+U+U+:G:A+G: 128785 AAGACUAUACUUUCAGGGAUCAUUUGUAUAGUUCGUUACUAGAGAAUUUUCUCUGAAUGU 128844 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU AACA+C +AAACCA A GA GAG CGCAGC U C: U C: GAGCGUGAA+CC: 128845 GUAGAACACCAGAAACCACAAGGAGGAGGCGCAGCGUUCUCUCCU-GAGCGUGAAGCCG- 128902 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 G +C :::G: GU+G:UU+ U:C+ACU:C:::U+ C:+UUGAUGAU GUUC:U+ 128903 ---GGUC-CUGGU-GUUGCUUCA-CUGCAACUGCCAUUUGCCAUUGAUGAUUGUUCUUC- 128955 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 :C:UC+U UU+G+:G:G UA:GA :G A :G A GCAGUCUGA UGG 128956 --UCUUCCU-UUGGGAGAG--UAAGA-GGCAAAGGAUGCAGUCUGAAUGG 128999 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz ----sequence: #399,sp|AC092040.2|AC092040 Homo sapiens chromosome 3 clone RP11-129B22, complete sequence. ----isReversed: 0 ----hitSequence: AAGAUUAUACUUUCAGGAAUCAUUUCUAUAGUUUGUUACUAGAGAAAGUUCUCUGAAUGUGUAAAGCAUGAAAAACCACAAGGAGACACAGUGUCUGCUCCUGACUGAAAAGCCAGCUCUUGGUGUUGCUCUGCUGCAACUGCUAUUUGCCAUUGAUAACCAUUCUUCUCUUCCUCUGGGAUAGUAAGAGGGAGAGACUGCAGUCUGAGUGG hit 94 : 151625 151836 (fwd) 42.82 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++ UAU:C+U:C+:+ AU+++U::UA++G+ UG+ +C++++::A+++U+ +:G:A+G: 151625 AAGAUUAUACUUUCAGGAAUCAUUUCUAUAGUUUGUUACUAGAGAAAGUUCUCUGAAUGU 151684 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU AA+CA + +AAACCA: A GA GA+AC AG :: CUCC: GA G AA+CC 151685 GUAAAGCAUGAAAAACCACAAGGA-GACAC--AGUGUCUGCUCCU-GACUGAAAAGCCA- 151739 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C U: G: GU+G:U U U:C+ACU:C :UU+GC +UUGAU A C UUC:U+: 151740 ---GCUC-UUGGU-GUUGCUCUG-CUGCAACUGCUAUUUGCCAUUGAUAACCAUUCUUCU 151793 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 C :CCUCU GG: A:UA:GA :GGAG :: CAGUCUGA:UGG 151794 CUUCCUCUG------GGAUAGUAAGA-GGGAGAGACUGCAGUCUGAGUGG 151836 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz ----sequence: #865,sp|AC092805.2|AC092805 Homo sapiens chromosome 1 clone RP11-99A8, complete sequence. ----isReversed: 0 ----hitSequence: AAGACUAUAUUUUCAGGGAUCAUUUCUACAGUGCACUACUAGAGAAGUUUCUGUGAACUUGUAGAGCACCGGAAACCAUGAGCAGGAAGUGCAGCGUUCUCUCCUGAGCAUGAAGCCGGCUCUUGGUGUGGCUUCGCUGCAACUGCCAUUGGCCAUUGAUGAUCGUUCUUCUCUUCUCUGGGAGAGUAAGAGAGAGAGGACACAGUCUGAGUGG hit 95 : 19984 20197 (fwd) 74.64 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:::U:C+:GGAU+AUU::UA +G+ +C +C+ ++::AGU+U+UG:G:A::: 19984 AAGACUAUAUUUUCAGGGAUCAUUUCUACAGUGCACUACUAGAGAAGUUUCUGUGAACUU 20043 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C +AAACCA:GA A GA GCAG :U C:CUC : GAGC UGAA+CC: 20044 GUAGAGCACCGGAAACCAUGAGCAGGAAGUGCAGCGUUCUCUCCU-GAGCAUGAAGCCG- 20101 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C U::G: GU:G:UU+ U:C:ACU:C::UUGGC:+UUGAUGAUCGUUC:U+: 20102 ---GCUC-UUGGU-GUGGCUUCG-CUGCAACUGCCAUUGGCCAUUGAUGAUCGUUCUUCU 20155 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CU:C U UG+ G:GA:UA:GA : GAG:G A: CAGUCUGA:UGG 20156 CUUC------UCUGG-GAGAGUAAGA-GAGAGAGGACACAGUCUGAGUGG 20197 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz ----sequence: #5707,sp|AC124917.4|AC124917 Homo sapiens chromosome 1 clone RP5-910L7, complete sequence. ----isReversed: 0 ----hitSequence: AAGACUAUAUUUUCAGGGAUCAUUUCUACAGUGCACUACUAGAGAAGUUUCUGUGAACUUGUAGAGCACCGGAAACCAUGAGCAGGAAGUGCAGCGUUCUCUCCUGAGCAUGAAGCCGGCUCUUGGUGUGGCUUCGCUGCAACUGCCAUUGGCCAUUGAUGAUCGUUCUUCUCUUCUCUGGGAGAGUAAGAGAGAGAGGACACAGUCUGAGUGG hit 96 : 109955 110168 (fwd) 74.64 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:::U:C+:GGAU+AUU::UA +G+ +C +C+ ++::AGU+U+UG:G:A::: 109955 AAGACUAUAUUUUCAGGGAUCAUUUCUACAGUGCACUACUAGAGAAGUUUCUGUGAACUU 110014 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C +AAACCA:GA A GA GCAG :U C:CUC : GAGC UGAA+CC: 110015 GUAGAGCACCGGAAACCAUGAGCAGGAAGUGCAGCGUUCUCUCCU-GAGCAUGAAGCCG- 110072 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C U::G: GU:G:UU+ U:C:ACU:C::UUGGC:+UUGAUGAUCGUUC:U+: 110073 ---GCUC-UUGGU-GUGGCUUCG-CUGCAACUGCCAUUGGCCAUUGAUGAUCGUUCUUCU 110126 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CU:C U UG+ G:GA:UA:GA : GAG:G A: CAGUCUGA:UGG 110127 CUUC------UCUGG-GAGAGUAAGA-GAGAGAGGACACAGUCUGAGUGG 110168 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz ----sequence: #5924,sp|AC127487.5|AC127487 Homo sapiens chromosome 8, clone RP11-729C3, complete sequence. ----isReversed: 1 ----hitSequence: AAUGCUAUACUUUCAUGGGUCAUUUCUAUAGUUUGUUAUUAGAGAAGUUUCUCUGAAUGUGUUGAGCACCAGAAACCACGAGGAGAUGCAGCAUUCUCUCCUGAACGGGAAGCCAGCUUUUGGCAUUGCUUUGAUGCAACUACCAUUUGCCAUUGAUGGCAAUGCAUCGCUUCCUCUAGGAGUGUAAGAGGGAGUGGAUGCAGUCAGAGUGG hit 97 : 48044 47833 (rev) 44.51 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA CUAU:C+U:C+ +G U+AUU::UA++:+ UG+ +:++++::AGU+U+U+ G:A+G: 13412 AAUGCUAUACUUUCAUGGGUCAUUUCUAUAGUUUGUUAUUAGAGAAGUUUCUCUGAAUGU 13471 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C +AAACCA:GA GA GA C AGC:U C:CUCC: GA CG GAA+CC 13472 GUUGAGCACCAGAAACCACGAGGA-GAUGC--AGCAUUCUCUCCU-GAACGGGAAGCCA- 13526 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+ U::G: U+G:UUU +U:C+A U:C::UU+GC +UUGAUG U C U+: 13527 ---GCUU-UUGGC-AUUGCUUUG-AUGCAACUACCAUUUGCCAUUGAUGGCAAUGCAUCG 13580 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 U:CCUCU+ GG:G :UA G :GGAG:G A:GCAGUC GA:UGG 13581 CUUCCUCUA------GGAGUGUAAGA-GGGAGUGGAUGCAGUCAGAGUGG 13623 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz ----sequence: #6845,sp|AC139138.2|AC139138 Homo sapiens chromosome 17, clone XXfos-82524G9, complete sequence. ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAGUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGUGUAGAGCACCGAAAACCACGAGGAAGAGAGGUAGCGUUUUCUCCUGAGCGUGAAGCCGGCUUUUUGGCGUUGCUUCGCUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCUCUCCGUAUUGGGGAGUGAGAGGGAGAGAACGCGGUCUGAGUGG hit 98 : 40602 40817 (fwd) 100.46 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C:U:C+:+GAU+A U::UA++G+ UG+ +C++++::A U+U+U+:G:A:G: 40602 AAGACUAUACUUUCAGGGAUCAGUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGU 40661 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C +AAACCA:GA GA GAGA+G+AGC:UU::CUCC: GAGCGUGAA+CC: 40662 GUAGAGCACCGAAAACCACGAGGAAGAGAGGUAGCGUUUUCUCCU-GAGCGUGAAGCCG- 40719 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+ +U::G: GU+G:UU+ U:C+ACU:C::U GC:+UUGAUGAUCGUUC:U+: 40720 ---GCUUUUUGGC-GUUGCUUCG-CUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCU 40774 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CUCC U UU GGGA:U :GA :GGAG::AA:GC GUCUGA:UGG 40775 CUCCGUAUU------GGGGAGUGAGA-GGGAGAGAACGCGGUCUGAGUGG 40817 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz ----sequence: #6937,sp|AC140106.1|AC140106 Homo sapiens chromosome 17, clone XXfos-801239H9, complete sequence. ----isReversed: 1 ----hitSequence: AAGACUAUACUUUCAGGGAUCAGUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGUGUAGAGCACCGAAAACCACGAGGAAGAGAGGUAGCGUUUUCUCCUGAGCGUGAAGCCGGCUUUUUGGCGUUGCUUCGCUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCUCUCCGUAUUGGGGAGUGAGAGGGAGAGAACGCGGUCUGAGUGG hit 99 : 19802 19587 (rev) 100.46 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C:U:C+:+GAU+A U::UA++G+ UG+ +C++++::A U+U+U+:G:A:G: 21147 AAGACUAUACUUUCAGGGAUCAGUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGU 21206 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C +AAACCA:GA GA GAGA+G+AGC:UU::CUCC: GAGCGUGAA+CC: 21207 GUAGAGCACCGAAAACCACGAGGAAGAGAGGUAGCGUUUUCUCCU-GAGCGUGAAGCCG- 21264 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+ +U::G: GU+G:UU+ U:C+ACU:C::U GC:+UUGAUGAUCGUUC:U+: 21265 ---GCUUUUUGGC-GUUGCUUCG-CUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCU 21319 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CUCC U UU GGGA:U :GA :GGAG::AA:GC GUCUGA:UGG 21320 CUCCGUAUU------GGGGAGUGAGA-GGGAGAGAACGCGGUCUGAGUGG 21362 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz ----sequence: #8836,sp|AF020531.1|AF020531 Homo sapiens U3 small nuclear RNA (U3a) gene, promoter region and complete sequence. ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGUGUAGAGCACCGAAAACCACGAGGAAGAGAAGUAGCGUUUUCUCCUGAGCGUGAAGCCGGCUUUCUGGCGUUGCUUGGCUGUAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCUCCCCGUAUUGGGGAGUGAGAGGGAGAGAACGCGGUCUGAGUGG hit 100 : 104 319 (fwd) 97.62 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C:U:C+:+GAU+AUU::UA++G+ UG+ +C++++::AGU+U+U+:G:A:G: 104 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGU 163 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C +AAACCA:GA GA GAGA G+AGC:UU::CUCC: GAGCGUGAA+CC: 164 GUAGAGCACCGAAAACCACGAGGAAGAGAAGUAGCGUUUUCUCCU-GAGCGUGAAGCCG- 221 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+ +:::G: GU++:UU+ U:++ACU:C::: GC:+UUGAUGAUCGUUC:U+: 222 ---GCUUUCUGGC-GUUGCUUGG-CUGUAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCU 276 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 C:CC U UU GG:A:U :GA :GGAG::AA:GC GUCUGA:UGG 277 CCCCGUAUU------GGGGAGUGAGA-GGGAGAGAACGCGGUCUGAGUGG 319 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz ----sequence: #8839,sp|AF020534.1|AF020534 Homo sapiens U3 small nuclear RNA (U3b1) gene, promoter region and complete sequence. ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAGUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGUGUAGAGCACCGAAAACCACGAGGAAGAGAGGUAGCGUUUUCUCCUGAGCGUGAAGCCGGCUUUUUGGCGUUGCUUCGCUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCUCUCCGUAUUGGGGAGUGAGAGGGAGAGAACGCGGUCUGAGUGG hit 101 : 361 576 (fwd) 100.46 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C:U:C+:+GAU+A U::UA++G+ UG+ +C++++::A U+U+U+:G:A:G: 361 AAGACUAUACUUUCAGGGAUCAGUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGU 420 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C +AAACCA:GA GA GAGA+G+AGC:UU::CUCC: GAGCGUGAA+CC: 421 GUAGAGCACCGAAAACCACGAGGAAGAGAGGUAGCGUUUUCUCCU-GAGCGUGAAGCCG- 478 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+ +U::G: GU+G:UU+ U:C+ACU:C::U GC:+UUGAUGAUCGUUC:U+: 479 ---GCUUUUUGGC-GUUGCUUCG-CUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCU 533 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CUCC U UU GGGA:U :GA :GGAG::AA:GC GUCUGA:UGG 534 CUCCGUAUU------GGGGAGUGAGA-GGGAGAGAACGCGGUCUGAGUGG 576 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz ----sequence: #8840,sp|AF020535.1|AF020535 Homo sapiens U3 small nuclear RNA (U3b2) gene, promoter region and complete sequence. ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAGUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGUGUAGAGCACCGAAAACCACGAGGAAGAGAGGUAGCGUUUUCUCCUGAGCGUGAAGCCGGCUUUUUGGCGUUGCUUCGCUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCUCUCCGUAUUGGGGAGUGAGAGGGAGAGAACGCGGUCUGAGUGG hit 102 : 361 576 (fwd) 100.46 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C:U:C+:+GAU+A U::UA++G+ UG+ +C++++::A U+U+U+:G:A:G: 361 AAGACUAUACUUUCAGGGAUCAGUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGU 420 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C +AAACCA:GA GA GAGA+G+AGC:UU::CUCC: GAGCGUGAA+CC: 421 GUAGAGCACCGAAAACCACGAGGAAGAGAGGUAGCGUUUUCUCCU-GAGCGUGAAGCCG- 478 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+ +U::G: GU+G:UU+ U:C+ACU:C::U GC:+UUGAUGAUCGUUC:U+: 479 ---GCUUUUUGGC-GUUGCUUCG-CUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCU 533 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CUCC U UU GGGA:U :GA :GGAG::AA:GC GUCUGA:UGG 534 CUCCGUAUU------GGGGAGUGAGA-GGGAGAGAACGCGGUCUGAGUGG 576 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum04.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum05.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum06.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum07.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum08.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum09.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum10.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum10.dat.fasta.gz ----sequence: #616,sp|AL157895.8|AL157895 Human DNA sequence from clone RP11-354E11 on chromosome 10 ----isReversed: 0 ----hitSequence: AAGACUGUGCUUUCAGGGAUCAUGUCUAUAGUUUGCCACUAGAGAAGUUUUUUUGAACAUGUAGUAGGGCACCAGAAGCACAAGGAAGAGGCACAGCCUUCUCUCCUGAGCAUGAAUCUGGCUCUUGGUCUUGCUUUGUUCCAGCUACCAUUUGCCAUUGAUUAUGUCCUUCUCUUCCUUCCAGAAAGUAAAAGGGAGAGAAUGCAGUCUGAGUGG hit 103 : 28499 28714 (fwd) 51.05 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CU:U:::U:C+:+GAU+AU:::UA++G+ UGC +C++++:::GU+UUU+:G:A::: 28499 AAGACUGUGCUUUCAGGGAUCAUGUCUAUAGUUUGCCACUAGAGAAGUUUUUUUGAACAU 28558 >>..-------------((((--------------((((((((((((,,,,,,,,,,,,, 61 gu..cAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucC 118 G: A++ ACC+ AA CA: A GA GAG C+CAGC+UUC:CUCC: GAGC UGAAUC 28559 GUagUAGGGCACCAGAAGCACAAGGAAGAGGCACAGCCUUCUCUCCU-GAGCAUGAAUCU 28617 <----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<- 119 gCGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccU 178 : GC+C U::G+ ++G+UUU UU+C++ U+C::UU+GC:+UUGAU AU 28618 G----GCUC-UUGGU-CUUGCUUUG-UUCCAGCUACCAUUUGCCAUUGAUUAUGUC---- 28666 -<<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 179 aucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 +U:::::UC+UU G :::::A A :GGAG:GAA+GCAGUCUGA:UG 28667 CUUCUCUUCCUUCCAGAAAGUAAAA----GGGAGAGAAUGCAGUCUGAGUGG 28714 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum10.dat.fasta.gz ----sequence: #5393,sp|AL627390.7|AL627390 Human DNA sequence from clone RP13-278H16 on chromosome X ----isReversed: 1 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUUGUUACUAGAGAAGUUUCUCUGAACGUGUAUAGCACUGAAAACCACAAAGAAGAGGUGCAGCAUUAUCUCCUAAGUGUAAAGCCGGCUCUUGAUGUUGCUUUGCUGCAACUGCCAUUUGCCAUUGAUGAUCGUUCUUUUCUUCCUUUGGGAGACUGGGAAGGAAAGGAUGCAAUCUGAGUGG hit 104 : 149172 148958 (rev) 65.29 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C:U:C+:+GAU+AUU::UA++G+ UG+ +C++++::AGU+U+U+:G:A:G: 26489 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUUGUUACUAGAGAAGUUUCUCUGAACGU 26548 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+ +AAACCA: A GA GAG GCAGC:U : UCC AG GU AA+CC: 26549 GUAUAGCACUGAAAACCACAAAGAAGAGGUGCAGCAUUAUCUCCU-AAGUGUAAAGCCG- 26606 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C U:: : GU+G:UUU U:C+ACU: ::UU+GC:+UUGAUGAUCGUUC:U 26607 ---GCUC-UUGAU-GUUGCUUUG-CUGCAACUGCCAUUUGCCAUUGAUGAUCGUUCUU-- 26658 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 ::C :UC+U UU+G+: G:: U :GA GGA : A:GCA UCUGA:UGG 26659 UUC-UUCCU-UUGGGA-GAC-UGGGA-AGGAAAGGAUGCAAUCUGAGUGG 26703 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum10.dat.fasta.gz ----sequence: #7515,sp|AP003113.1|AP003113 Homo sapiens genomic DNA, chromosome 8q23, clone:KB1747F8. ----isReversed: 0 ----hitSequence: AAGACUAUACUCUCAGGAAUCAUUUCUAUAGUUUUUUACUAGAGAAAUUUCUCUGAACGUGUAGAGCACUGGAAACCGUGAGGAGAAGCUGCCUUCUCUUCUGAGCAUGAAGUGAGCUCUCAGUGUUGCUUCUCUGCAACUGCCAUUUGCCAUUGAUGAUCGUUCUUCUCUUCCUCUGGGAGAGUAAAAGGGUACAGGAUGCAGUCUGAGU hit 105 : 93246 93456 (fwd) 59.43 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C:::C+:+ AU+A+U::UA++G+ U + +C++++::A+U+U+ +:G:::G: 93246 AAGACUAUACUCUCAGGAAUCAUUUCUAUAGUUUUUUACUAGAGAAAUUUCUCUGAACGU 93305 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+ +AAA C UGA GAGA GC+GC+U C: U C: GAGC UGAA++ 93306 GUAGAGCACUGGAAACC---GUGAGGAGAAGCUGCCUUCUCUUCU-GAGCAUGAAGUGA- 93360 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C U G: GU+G:UU+U U:C+ACU:C UU+GC +UUGAUGAUCGUU :U+: 93361 ---GCUC-UCAGU-GUUGCUUCU-CUGCAACUGCCAUUUGCCAUUGAUGAUCGUUCUUCU 93414 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CU:CCUCU GG:GA:UA: A :G A :G A+GCAGUCUGA G 93415 CUUCCUCUG------GGAGAGUAAAAGGGUACAGGAUGCAGUCUGA--GU 93456 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum10.dat.fasta.gz ----sequence: #7518,sp|AP003116.2|AP003116 Homo sapiens genomic DNA, chromosome 8q23, clone: KB1241F12. ----isReversed: 0 ----hitSequence: AAGACUAUACUCUCAGGAAUCAUUUCUAUAGUUUUUUACUAGAGAAAUUUCUCUGAACGUGUAGAGCACUGGAAACCGUGAGGAGAAGCUGCCUUCUCUUCUGAGCAUGAAGUGAGCUCUCAGUGUUGCUUCUCUGCAACUGCCAUUUGCCAUUGAUGAUCGUUCUUCUCUUCCUCUGGGAGAGUAAAAGGGUACAGGAUGCAGUCUGAGU hit 106 : 13755 13965 (fwd) 59.43 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C:::C+:+ AU+A+U::UA++G+ U + +C++++::A+U+U+ +:G:::G: 13755 AAGACUAUACUCUCAGGAAUCAUUUCUAUAGUUUUUUACUAGAGAAAUUUCUCUGAACGU 13814 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+ +AAA C UGA GAGA GC+GC+U C: U C: GAGC UGAA++ 13815 GUAGAGCACUGGAAACC---GUGAGGAGAAGCUGCCUUCUCUUCU-GAGCAUGAAGUGA- 13869 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C U G: GU+G:UU+U U:C+ACU:C UU+GC +UUGAUGAUCGUU :U+: 13870 ---GCUC-UCAGU-GUUGCUUCU-CUGCAACUGCCAUUUGCCAUUGAUGAUCGUUCUUCU 13923 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CU:CCUCU GG:GA:UA: A :G A :G A+GCAGUCUGA G 13924 CUUCCUCUG------GGAGAGUAAAAGGGUACAGGAUGCAGUCUGA--GU 13965 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum10.dat.fasta.gz ----sequence: #7819,sp|AP005327.2|AP005327 Homo sapiens genomic DNA, chromosome 18 clone:RP11-231N16, complete sequence. ----isReversed: 1 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCAUUACUAGAGAAGUUUCUCUGAAUGGGUAGAGCACUGGAAACCAUGAGGAGGAGGCACAGUGUUCUCUCCUGAGCAUGAAGCUGACUCUUGGUGUUGCUUCACUGCACCUGCCAUGUGCCACUGAUGAUUGUUCUUGUCUUCCUCUGGGAGAGUAAGACGGAGAGCAUGCAGUCUGAGUGC hit 107 : 127562 127348 (rev) 63.66 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU C+U:C+:+GAU+AUU::UA++G+ ++ +C++++::AGU+U+U+:G:A+G 34421 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCAUUACUAGAGAAGUUUCUCUGAAUGG 34480 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+ +AAA CA:GA GA GAG C+CAG U C:CUCC GAGC UGAA+C : 34481 GUAGAGCACUGGAAACCAUGAGGAGGAGGCACAGUGUUCUCUCCU-GAGCAUGAAGCUG- 34538 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 C+C U::G: G +G:UU+ U:C+ CU:C::U +G :++UGAUGAU GUUC:U+: 34539 ---ACUC-UUGGU-GUUGCUUCA-CUGCACCUGCCAUGUGCCACUGAUGAUUGUUCUUGU 34592 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CU:CCUCU GG:GA:UA:GA GGAG:G A CAGUCUGA:UG 34593 CUUCCUCUG------GGAGAGUAAGA-CGGAGAGCAUGCAGUCUGAGUGC 34635 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum10.dat.fasta.gz ----sequence: #7892,sp|AP005900.1|AP005900 Homo sapiens genomic DNA, chromosome 18p clone:RP11-931H21, complete sequence. ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCAUUACUAGAGAAGUUUCUCUGAAUGGGUAGAGCACUGGAAACCAUGAGGAGGAGGCACAGUGUUCUCUCCUGAGCAUGAAGCUGACUCUUGGUGUUGCUUCACUGCACCUGCCAUGUGCCACUGAUGAUUGUUCUUGUCUUCCUCUGGGAGAGUAAGACGGAGAGCAUGCAGUCUGAGUGC hit 108 : 88759 88973 (fwd) 63.66 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU C+U:C+:+GAU+AUU::UA++G+ ++ +C++++::AGU+U+U+:G:A+G 88759 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCAUUACUAGAGAAGUUUCUCUGAAUGG 88818 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+ +AAA CA:GA GA GAG C+CAG U C:CUCC GAGC UGAA+C : 88819 GUAGAGCACUGGAAACCAUGAGGAGGAGGCACAGUGUUCUCUCCU-GAGCAUGAAGCUG- 88876 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 C+C U::G: G +G:UU+ U:C+ CU:C::U +G :++UGAUGAU GUUC:U+: 88877 ---ACUC-UUGGU-GUUGCUUCA-CUGCACCUGCCAUGUGCCACUGAUGAUUGUUCUUGU 88930 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CU:CCUCU GG:GA:UA:GA GGAG:G A CAGUCUGA:UG 88931 CUUCCUCUG------GGAGAGUAAGA-CGGAGAGCAUGCAGUCUGAGUGC 88973 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum11.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum12.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum13.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum14.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum14.dat.fasta.gz ----sequence: #3301,sp|AL121839.3|CNS01DSQ Human chromosome 14 DNA sequence BAC R-747H7 of library RPCI-11 from chromosome 14 of Homo sapiens (Human) ----isReversed: 0 ----hitSequence: AAAAUUAUACUUUCAGCAAUCAUCUCUAUAGUUUGUUACUAGAGAAGCUUCUGUGAAUGUGUAGAGCACCGGAAACCACAAGGCAAAGGCUCAGCAUUCUCUCCUAAGCGCGAAGCUGGCUCCUGGUGUUGGUUGGCCGCAACUGCCAUUUGCCAUUGAUGAUCAUUCUUCUCUUCCUGUGGUAGAGGAAGAGGGAGAGAAUGCAGUUUGAGUGG hit 109 : 140802 141016 (fwd) 47.42 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AAA+ UAU:C+U:C+:: AU+ U:::UA++G+ UG+ +C++++:::G +U+ ::G:A+G: 140802 AAAAUUAUACUUUCAGCAAUCAUCUCUAUAGUUUGUUACUAGAGAAGCUUCUGUGAAUGU 140861 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C +AAACCA: A G AG C+CAGC:UUC:CUCC: AGCG GAA+C : 140862 GUAGAGCACCGGAAACCACAAGGCAAAGGCUCAGCAUUCUCUCCU-AAGCGCGAAGCUG- 140919 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+C :::G: GU+G UU+ C+ACU:C:::U+GC:+UUGAUGAUC UUC:U+ 140920 ---GCUC-CUGGU-GUUGGUUGG-CCGCAACUGCCAUUUGCCAUUGAUGAUCAUUCUUC- 140972 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 :C:UC+U U+GU:G:G A:GA :GGAG:GAA:GCAGU UGA:UGG 140973 --UCUUCCU-GUGGUAGAG--GAAGA-GGGAGAGAAUGCAGUUUGAGUGG 141016 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum14.dat.fasta.gz ----sequence: #3407,sp|AL136038.5|CNS01DVT Human chromosome 14 DNA sequence BAC C-2302E22 of library CalTech-D from chromosome 14 of Homo sapiens (Human) ----isReversed: 0 ----hitSequence: AAGACCAUAUUUUCAGGGAUCAUUUCUAUAGUUCAUUCAUUACUAGAGAAGUUUCUCUGAACAUGCAGGGCACCGCAAACCAUGAGGAAGAGGCACAGCAUUCUCUUCUGAGCCUGAAGCCAGCUCUUCUUGCUUCACUGCCAUUUGCCCUUCAUGAUCAUUCUCUUCCUGCAGGAGAGUAAGAAAGGAUGCAGUCUGAGUGG hit 110 : 13275 13477 (fwd) 38.61 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____....>>>>-->>>>>>-->>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcg....ucccUcugagucUuugaga 56 AA++C :U:+:U:C+:+GAU+AUU::UA++G+ ++ +C++++::AGU+U+U+:G: 13275 AAGACCAUAUUUUCAGGGAUCAUUUCUAUAGUUCAUUcauuACUAGAGAAGUUUCUCUGA 13334 >>>>>>-------------((((--------------((((((((((((,,,,,,,,,,, 57 aagagucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAau 116 A:+:G: ++CA+C CAAACCA:GA GA GAG C+CAGC:U C:CU:C GAGC UGAA+ 13335 ACAUGCAGGGCACCGCAAACCAUGAGGAAGAGGCACAGCAUUCUCUUCU-GAGCCUGAAG 13393 ,,<----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<< 117 cCgCGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuc 176 CC+ :C +:U::+G+UU+ U +C+::U:+ C:U AUGAUC U 13394 CCA---------GCUCUUCUUGCUUCACUGCCAUUUGCCCUU-------CAUGAUCAU-- 13435 <--<<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 177 cUaucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 U+:CU:CCU+++ GG:GA:UA G:A :G A:GCAGUCUGA:UGG 13436 -UCUCUUCCUGCA------GGAGAGUA----AGAA-AGGAUGCAGUCUGAGUGG 13477 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum14.dat.fasta.gz ----sequence: #3513,sp|AL161670.4|CNS01RHD Human chromosome 14 DNA sequence BAC R-804M7 of library RPCI-11 from chromosome 14 of Homo sapiens (Human) ----isReversed: 0 ----hitSequence: AAGACCAUAUUUUCAGGGAUCAUUUCUAUAGUUCAUUCAUUACUAGAGAAGUUUCUCUGAACAUGCAGGGCACCGCAAACCAUGAGGAAGAGGCACAGCAUUCUCUUCUGAGCCUGAAGCCAGCUCUUCUUGCUUCACUGCCAUUUGCCCUUCAUGAUCAUUCUCUUCCUGCAGGAGAGUAAGAAAGGAUGCAGUCUGAGUGG hit 111 : 161539 161741 (fwd) 38.61 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____....>>>>-->>>>>>-->>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcg....ucccUcugagucUuugaga 56 AA++C :U:+:U:C+:+GAU+AUU::UA++G+ ++ +C++++::AGU+U+U+:G: 161539 AAGACCAUAUUUUCAGGGAUCAUUUCUAUAGUUCAUUcauuACUAGAGAAGUUUCUCUGA 161598 >>>>>>-------------((((--------------((((((((((((,,,,,,,,,,, 57 aagagucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAau 116 A:+:G: ++CA+C CAAACCA:GA GA GAG C+CAGC:U C:CU:C GAGC UGAA+ 161599 ACAUGCAGGGCACCGCAAACCAUGAGGAAGAGGCACAGCAUUCUCUUCU-GAGCCUGAAG 161657 ,,<----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<< 117 cCgCGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuc 176 CC+ :C +:U::+G+UU+ U +C+::U:+ C:U AUGAUC U 161658 CCA---------GCUCUUCUUGCUUCACUGCCAUUUGCCCUU-------CAUGAUCAU-- 161699 <--<<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 177 cUaucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 U+:CU:CCU+++ GG:GA:UA G:A :G A:GCAGUCUGA:UGG 161700 -UCUCUUCCUGCA------GGAGAGUA----AGAA-AGGAUGCAGUCUGAGUGG 161741 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum14.dat.fasta.gz ----sequence: #3593,sp|AL355836.3|CNS05TCQ Human chromosome 14 DNA sequence BAC R-8L8 of library RPCI-11 from chromosome 14 of Homo sapiens (Human) ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCAUUACUAGAGAAGUUUCUCUGAAUGUGUAGAGCACCAGAAACUAUGAGGAGGAGGCACAGAGUUCUCUCCUGAGCAUGAAGCUGGCACUUGGUGUUGCUUUGCUGCAGCUGCCACUUACCAUUGGUGAUUGUUCUUGUCUUCCUCUUGGAGAGUAAGAGAAAGAGAAUGCAGUCUGAGAGG hit 112 : 118882 119096 (fwd) 71.91 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C+U:C+:+GAU+AUU::UA++G+ ++ +C++++::AGU+U+U+:G:A+G: 118882 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUUCAUUACUAGAGAAGUUUCUCUGAAUGU 118941 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C +AAAC: :GA GA GAG C+CAG: UUC:CU : GAGC UGAA+C : 118942 GUAGAGCACCAGAAACUAUGAGGAGGAGGCACAGAGUUCUCUCCU-GAGCAUGAAGCUG- 118999 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 G: C +::G: G++G:UUU U:C++CU:C::+U+:C:+UUG UGAU GUUC:U+: 119000 ---GCAC-UUGGU-GUUGCUUUG-CUGCAGCUGCCACUUACCAUUGGUGAUUGUUCUUGU 119053 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CU:CCUCUU GG:GA:UA:GA : AG:GAA :CAGUCUGA: :G 119054 CUUCCUCUU------GGAGAGUAAGA-GAAAGAGAAUGCAGUCUGAGAGG 119096 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum14.dat.fasta.gz ----sequence: #6701,sp|Z64431.1|HS119C3F H.sapiens CpG island DNA genomic Mse1 fragment, clone 119c3, forward read cpg119c3.ft1a . ----isReversed: 0 ----hitSequence: AGUACUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGUGUAGAGCACCGAAAACCACGAGGAAAAGAGGUAGCGUUUUCUCCUGAGCGUGAAGCCGGCUUUGUGGCGUNGCUUGNNUGNAACUGCCGACAGCCAUUGAUGAUCGUUCUUCUCUCCGAAUUGGGGAG hit 113 : 3 190 (fwd) 41.75 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 A+ +CUAU:C:U:C+:+GAU+AUU::UA++G+ UG+ +C++++::AGU+U+U+:G:A:G: 3 AGUACUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGU 62 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C +AAACCA+GA GA AGA+G+AGC UU++CUCC: GAGCGUGAA+CC: 63 GUAGAGCACCGAAAACCACGAGGAAAAGAGGUAGCGUUUUCUCCU-GAGCGUGAAGCCG- 120 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+ +:::G: GU +:UU+ U:+ ACU:C::: GC:+UUGAUGAUCGUUC 121 ---GCUUUGUGGC-GUNGCUUGN-NUGNAACUGCCGACAGCCAUUGAUGAUCGUUC---- 171 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 :UC::UC+ ::GG: GA : 172 UUCUCUCCG----AAUUGGG----GA-G---------------------- 190 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum14.dat.fasta.gz ----sequence: #7380,sp|Z56604.1|HS12E2R H.sapiens CpG island DNA genomic Mse1 fragment, clone 12e2, reverse read cpg12e2.rt1c . ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGCAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGUACGUGUAGAGCACCGAAAACCACGAGGAAGAGAGGUAGCGUUUUCUCCUGAGCGUGAAGCCGGCUUUCUGGCGUNGCUUGGCUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCUCUCCGUAUUGGGGAGUGAGAGGGAGAGAACGCGGUCUGAGUGG hit 114 : 2 218 (fwd) 92.17 bits ::::::<<<<<<<<-<<<.--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>> 1 aaacCUauccuucccagg.AUcauuucUAuaggAUgcgucccUcugagucUuugagaaag 59 AA++CUAU:C:U C+:+G AU+AUU::UA++G+ UG+ +C++++::AGU+U+U+:G A:G 2 AAGACUAUACUUUCAGGGcAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGUACG 61 >>>-------------((((--------------((((((((((((,,,,,,,,,,,,,< 60 agucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCg 119 :GU A+CA+C +AAACCA:GA GA GAGA+G+AGC:UU::CUCC: GAGCGUGAA+CC: 62 UGUAGAGCACCGAAAACCACGAGGAAGAGAGGUAGCGUUUUCUCCU-GAGCGUGAAGCCG 120 ----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<-- 120 CGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUa 179 GC+ +:::G: GU G:UU+ U:C ACU:C::: GC:+UUGAUGAUCGUUC:U+ 121 ----GCUUUCUGGC-GUNGCUUGG-CUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUC 174 <<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 180 ucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 :CUCC U UU GGGA:U :GA :GGAG::AA:GC GUCUGA:UGG 175 UCUCCGUAUU------GGGGAGUGAGA-GGGAGAGAACGCGGUCUGAGUGG 218 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum14.dat.fasta.gz ----sequence: #7627,sp|Z56643.1|HS133B12F H.sapiens CpG island DNA genomic Mse1 fragment, clone 133b12, forward read cpg133b12.ft1a . ----isReversed: 0 ----hitSequence: AAGACUAUACUNUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGUGUAGAGCACCGAAAACCACGAGGAAGAGAGGUAGCGUUUUCUCCUGAGCGUGAAGCCGGCUUUCUGGCGUUGCUUGGCUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCUCUCCGUAUUGGGGAGUGAGAGGGAGAGAACGCGGUCUGAGUGG hit 115 : 2 217 (fwd) 101.26 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C:+:C+:+GAU+AUU::UA++G+ UG+ +C++++::AGU+U+U+:G:+:G: 2 AAGACUAUACUNUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGU 61 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C +AAACCA:GA GA GAGA+G+AGC:UU::CUCC: GAGCGUGAA+CC: 62 GUAGAGCACCGAAAACCACGAGGAAGAGAGGUAGCGUUUUCUCCU-GAGCGUGAAGCCG- 119 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+ +:::G: GU+G:UU+ U:C+ACU:C::: GC:+UUGAUGAUCGUUC:U+: 120 ---GCUUUCUGGC-GUUGCUUGG-CUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCU 174 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CUCC U UU GGGA:U :GA :GGAG::AA:GC GUCUGA:UGG 175 CUCCGUAUU------GGGGAGUGAGA-GGGAGAGAACGCGGUCUGAGUGG 217 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum15.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum15.dat.fasta.gz ----sequence: #499,sp|BX295541.1|HS172N19 Homo sapiens chromosome X PAC RP1-172N19 map Xq13 markers PHKA1-DXS227 ----isReversed: 1 ----hitSequence: AGGGCUAUACUUUCAGGGGUAAUUUCUAUAGUUCAUUACUAGAGUAGUUUCUCUGAAUGUGUAGGGUGCCAGAAACCACAAGGAGGAGGCACAGCAUUCUCUAGUGAGUGUGAAGCCGGCUGUUGGUGUUGCUUCGCUGAAACUGCCAUUUGCCACUGAUAAUCGUUCUUCUUUUCCAUCAGGAGACUAAGAGGUAGAAAACGCAGUCUGAGUGG hit 116 : 105234 105020 (rev) 57.35 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 A++ CUAU:C+U:C+:+G U:AUU::UA++G+ ++ +C++++::AGU:U+U+:G:A+G: 71356 AGGGCUAUACUUUCAGGGGUAAUUUCUAUAGUUCAUUACUAGAGUAGUUUCUCUGAAUGU 71415 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU ++ +C +AAACCA: A GA GAG C+CAGC:UU :CU: : GAG GUGAA+CC: 71416 GUAGGGUGCCAGAAACCACAAGGAGGAGGCACAGCAUUCUCUAGU-GAGUGUGAAGCCG- 71473 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC++ U::G: GU+ :UU+ U: +ACU:C::UU+GC:++UGAU AUCGUUC:U+ 71474 ---GCUG-UUGGU-GUUGCUUCG-CUGAAACUGCCAUUUGCCACUGAUAAUCGUUCUUCU 71527 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 :U:CC U GG:G: UA:GA : :AG: AA:GCAGUCUGA:UGG 71528 UUUCCA------UCAGGAGACUAAGA-GGUAGAAAACGCAGUCUGAGUGG 71570 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum15.dat.fasta.gz ----sequence: #3453,sp|Z57913.1|HS21A8F H.sapiens CpG island DNA genomic Mse1 fragment, clone 21a8, forward read cpg21a8.ft1a . ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGCAAGUUUCUCUGAACGUGUAGAGCACCGAAAACCACGAGGAAGAGAGGUAGCGUUUUCUCCUGAGCGUGAAGCCGGCUUUCUGGNGUUGCUUGGNUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCUCUCCNNAUUGGGGAGUGAGAGGGAGAGAAACGCGGUCUGAGUGG hit 117 : 2 219 (fwd) 93.12 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->.>>>>>-->>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcu.gagucUuugagaaag 59 AA++CUAU:C:U:C+:+GAU+AUU::UA++G+ UG+ +C++++: :AGU+U+U+:G:A:G 2 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGcAAGUUUCUCUGAACG 61 >>>-------------((((--------------((((((((((((,,,,,,,,,,,,,< 60 agucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCg 119 :GU A+CA+C +AAACCA:GA GA GAGA+G+AGC:UU::CUCC: GAGCGUGAA+CC: 62 UGUAGAGCACCGAAAACCACGAGGAAGAGAGGUAGCGUUUUCUCCU-GAGCGUGAAGCCG 120 ----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<-- 120 CGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUa 179 GC+ +:::G+ GU+G:UU+ U:C+ACU+C::: GC:+UUGAUGAUCGUUC:U+ 121 ----GCUUUCUGGN-GUUGCUUGG-NUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUC 174 <<<<<<__________>>>>>>-->>>,)))))).))))))-------)))) 180 ucucccUcuuUUUuGuggggaaUaggaUgggagc.gaaggcaGUCUGAcugg 230 :CUCC+ UU +GGGA:U :GA :GGAG: :AA:GC GUCUGA:UGG 175 UCUCCNNAUU------GGGGAGUGAGA-GGGAGAgAAACGCGGUCUGAGUGG 219 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum15.dat.fasta.gz ----sequence: #4823,sp|Z60518.1|HS26F4F H.sapiens CpG island DNA genomic Mse1 fragment, clone 26f4, forward read cpg26f4.ft1b . ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUGCUAGAGAAGUUUCUCUGAACGUGUAGAGCACCGAAAACCACGAGGNAAAAGAGGUAGCGUUUUCUCCUGAGCGUGAAGCCGGCUUUGUGGCGUUGCUUGGCUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCUCUCCGUAUUGGGGAGUGAGAGGGAGAGAACGCGGUCUGAGUGG hit 118 : 2 218 (fwd) 88.70 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C:U:C+:+GAU+AUU::UA++G UG+ C++++::AGU+U+U+:G:A:G: 2 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUGCUAGAGAAGUUUCUCUGAACGU 61 >>-------------((((----.----------((((((((((((,,,,,,,,,,,,,< 61 gucAaaCAacccAAAccagGAUG.AUGAgacgcAgccuucgcucccaGAGCGUGAaucCg 119 GU A+CA+C +AAACCA:GA G A AGA+G+AGC:UU::CUCC: GAGCGUGAA+CC: 62 GUAGAGCACCGAAAACCACGAGGnAAAAGAGGUAGCGUUUUCUCCU-GAGCGUGAAGCCG 120 ----<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<-- 120 CGGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUa 179 GC+ +:::G: GU+G:UU+ U:C+ACU:C::: GC:+UUGAUGAUCGUUC:U+ 121 ----GCUUUGUGGC-GUUGCUUGG-CUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUC 174 <<<<<<__________>>>>>>-->>>,))))))))))))-------)))) 180 ucucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 :CUCC U UU GGGA:U :GA :GGAG::AA:GC GUCUGA:UGG 175 UCUCCGUAUU------GGGGAGUGAGA-GGGAGAGAACGCGGUCUGAGUGG 218 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum16.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum16.dat.fasta.gz ----sequence: #1564,sp|Z55710.1|HS59F6F H.sapiens CpG island DNA genomic Mse1 fragment, clone 59f6, forward read cpg59f6.ft1a . ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUCUUUGAACGUGUAGAGCACCGAAAACCACGAGGAAGAGAGGUAGCGUUUUCUCCUGAGCGUGAAGCCGGCUUUCUGGCGUUGCUUGGCUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCUCUCCGUAUUGGGGAGUGAGAGGGAGAGAACGCGGUCUGAGU hit 119 : 2 215 (fwd) 94.46 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C:U:C+:+GAU+AUU::UA++G+ UG+ +C++++::AGU+U+U+:G:A:G: 2 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUCUUUGAACGU 61 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C +AAACCA:GA GA GAGA+G+AGC:UU::CUCC: GAGCGUGAA+CC: 62 GUAGAGCACCGAAAACCACGAGGAAGAGAGGUAGCGUUUUCUCCU-GAGCGUGAAGCCG- 119 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+ +:::G: GU+G:UU+ U:C+ACU:C::: GC:+UUGAUGAUCGUUC:U+: 120 ---GCUUUCUGGC-GUUGCUUGG-CUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCU 174 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CUCC U UU GGGA:U :GA :GGAG::AA:GC GUCUGA:U 175 CUCCGUAUU------GGGGAGUGAGA-GGGAGAGAACGCGGUCUGAGU-- 215 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum16.dat.fasta.gz ----sequence: #4179,sp|Z63262.1|HS7H5R H.sapiens CpG island DNA genomic Mse1 fragment, clone 7h5, reverse read cpg7h5.rt1d . ----isReversed: 0 ----hitSequence: AGAUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUAUCUGAACGUGUAGAGCACCGAAAACCCCGAGGAAGAGAGGUAGCGUUUUCUCCUGAGCGUGAAGCCGGNUUUCUGGCGUUGCUUGGCUGNAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCUCUCCGUAUUGGNGAGUGAGAGGGAGAGAACGCGGUCUGAGUGG hit 120 : 1 214 (fwd) 82.37 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 A+A UAU:C:U:C+:+GAU+AUU::UA++G+ UG+ +C++++::AGU+U U+:G:A:G: 1 AGA--UAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUAUCUGAACGU 58 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C +AAACC::GA GA GAGA+G+AGC:UU::CUCC: GAGCGUGAA+CC: 59 GUAGAGCACCGAAAACCCCGAGGAAGAGAGGUAGCGUUUUCUCCU-GAGCGUGAAGCCG- 116 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 G + +:::G: GU++:UU+ U:++ACU:C::: C:+UUGAUGAUCGUUC:U+: 117 ---GNUUUCUGGC-GUUGCUUGG-CUGNAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCU 171 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CU C U UU G GA:U :GA :GGAG::AA:GC GUCUGA::GG 172 CUCCGUAUU------GGNGAGUGAGA-GGGAGAGAACGCGGUCUGAGUGG 214 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum16.dat.fasta.gz ----sequence: #5534,sp|Z66380.1|HS92A7R H.sapiens CpG island DNA genomic Mse1 fragment, clone 92a7, reverse read cpg92a7.rt1a . ----isReversed: 0 ----hitSequence: AGACUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGUGUAGAGCACCGAAAACCCCGAGGAAGAGAGGUAGCGUUUUCUCCUGAGCGUGAAGCCGGCUUUCUGGCGUNGCUUGGCUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCUCUCCGUAUUGGGGAGUGAGAGGGAGAGAACGCGGUCUGAGUGG hit 121 : 1 215 (fwd) 91.91 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 A ++CUAU:C:U:C+:+GAU+AUU::UA++G+ UG+ +C++++::AGU+U+U+:G:A:G: 1 A-GACUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGU 59 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C +AAACC::GA GA GAGA+G+AGC:UU::CUCC: GAGCGUGAA+CC: 60 GUAGAGCACCGAAAACCCCGAGGAAGAGAGGUAGCGUUUUCUCCU-GAGCGUGAAGCCG- 117 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+ +:::G: GU G:UU+ U:C ACU:C::: GC:+UUGAUGAUCGUUC:U+: 118 ---GCUUUCUGGC-GUNGCUUGG-CUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCU 172 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CUCC U UU GGGA:U :GA :GGAG::AA:GC GUCUGA::GG 173 CUCCGUAUU------GGGGAGUGAGA-GGGAGAGAACGCGGUCUGAGUGG 215 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum17.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum18.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum19.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum20.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum20.dat.fasta.gz ----sequence: #5488,sp|AJ009617.5|HSAJ9617 Homo sapiens chromosome 17 sequence from PAC RP1-149D14 and cosmid 40M01 ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGUGUAGAGCACCGAAAACCCCGAGGAAGAGAGGUAGCGUUUUCUCCUGAGCGUGAAGCCGGCUUUCUGGCGUUGCUUGGCUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCUCUCCGUAUUGGGGAGUGAGAGGGAGAGAACGCGGUCUGAGUGG hit 122 : 7742 7957 (fwd) 99.36 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C:U:C+:+GAU+AUU::UA++G+ UG+ +C++++::AGU+U+U+:G:A:G: 7742 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGU 7801 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C +AAACC::GA GA GAGA+G+AGC:UU::CUCC: GAGCGUGAA+CC: 7802 GUAGAGCACCGAAAACCCCGAGGAAGAGAGGUAGCGUUUUCUCCU-GAGCGUGAAGCCG- 7859 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+ +:::G: GU+G:UU+ U:C+ACU:C::: GC:+UUGAUGAUCGUUC:U+: 7860 ---GCUUUCUGGC-GUUGCUUGG-CUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCU 7914 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CUCC U UU GGGA:U :GA :GGAG::AA:GC GUCUGA::GG 7915 CUCCGUAUU------GGGGAGUGAGA-GGGAGAGAACGCGGUCUGAGUGG 7957 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum20.dat.fasta.gz ----sequence: #5488,sp|AJ009617.5|HSAJ9617 Homo sapiens chromosome 17 sequence from PAC RP1-149D14 and cosmid 40M01 ----isReversed: 1 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGUGCAGAGCACCGAAAACCACGAGGAAGAGAGGUAGCGUUUUCUCCUGAGCGUGAAGCCGGCUUUCUGGCGUUGCUUGGCUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCUCUCCGUAUUGGGGAGUGAGAGGGAGAGAACGCGGUCUGAGUGG hit 123 : 9966 9751 (rev) 100.48 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CU:U:C:U:C+:+GAU+AUU::UA++G+ UG+ +C++++::AGU+U+U+:G:A:G: 143644 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGU 143703 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 G: A+CA+C +AAACCA:GA GA GAGA+G+AGC:UU::CUCC: GAGCGUGAA+CC: 143704 GCAGAGCACCGAAAACCACGAGGAAGAGAGGUAGCGUUUUCUCCU-GAGCGUGAAGCCG- 143761 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+ +:::G: GU+G:UU+ U:C+ACU:C::: GC:+UUGAUGAUCGUUC:U+: 143762 ---GCUUUCUGGC-GUUGCUUGG-CUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCU 143816 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CUCC U UU GGGA:U :GA :GGAG::AA:GC GUCUGA:UGG 143817 CUCCGUAUU------GGGGAGUGAGA-GGGAGAGAACGCGGUCUGAGUGG 143859 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum21.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum21.dat.fasta.gz ----sequence: #2846,sp|AL121944.14|HSDJ313I6 Human DNA sequence from clone RP1-313I6 on chromosome 6. Contains a KIAA0036 pseudogene, olfactory receptor 2W2, 2B7, 2B8 and 1F12 pseudogenes (OR2W2P, OR2B7P, OR2B8 and OR1F12), the ZNF165 gene for zinc finger protein 165, two zinc finger protein pseudogenes, ESTs, STSs, GSSs and two CpG islands. ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUACAUUUCCGGGUAAUUUCUUUGAACAUGUGGAGCACCGGAAACCACCAGGAGGAGGCACAGCAUUUUCUCUGGAGCGUGAAGCCAGUUCUUGGUGUUGCUGCAUAGCAACUGCCAUUUGCCUUUGAUGAUCAUUCUUCUUUUCCUUUAGGAGAAUAAGAGGGGGAGAACCCAGUCUGAGGG hit 124 : 34347 34554 (fwd) 47.79 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:::U:C+:+GAU+A+U::UA A U + C + ::A+U+U+U+:G:A::: 34347 AAGACUAUACUUUCAGGGAUCAUUUCUACA---U-UU--CCGGGUAAUUUCUUUGAACAU 34400 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C +AAACCA: A GA GAG C+CAG :UU::C C: GAGCGUGAA+CC 34401 GUGGAGCACCGGAAACCACCAGGAGGAGGCACAGCAUUUUCUCUG-GAGCGUGAAGCCA- 34458 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 G +C U::G: GU+G:U + U :C+ACU:C::UU+ C UUUGAUGAUC UUC:U+U 34459 ---GUUC-UUGGU-GUUGCUGCA-UAGCAACUGCCAUUUGCCUUUGAUGAUCAUUCUUCU 34512 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 :U:CCU U+ GG:G:AUA:GA :G G::AA: CAGUCUGA: GG 34513 UUUCCUUUA------GGAGAAUAAGA-GGGGGAGAACCCAGUCUGAG-GG 34554 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum22.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum22.dat.fasta.gz ----sequence: #3918,sp|AL117334.29|HSJ687F11 Human DNA sequence from clone RP4-687F11 on chromosome 20 Contains the 5' end of the L3MBTL gene for l(3)mbt-like (Drosophila)(DKFZP434N061), a pseudogene similar to MMS2 and chicken CROC-1B and a putative CpG island. ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUGUAGUUCAUUAUUAGAGAGGUCUCUCUGAAUGAGUAGAGCACUAGAAACCACAGAAGGAGGCACAGUGGUCUCUCCUGAGCAUAAAGCUGGUUUUUGAUGUUGCUUUGCUGCAACUGCCAUUCGUCACUGAUGACUGUUUUCUUCCUCUGGGAGAGUAAGAGGGAGAGGACACUAUCUGAGUGU hit 125 : 54607 54817 (fwd) 38.64 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C+U:C+:+GAUCAU+::U ++:+ ++ +:++++::+GUCU+U+:G:A+G: 54607 AAGACUAUACUUUCAGGGAUCAUUUCUGUAGUUCAUUAUUAGAGAGGUCUCUCUGAAUGA 54666 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+ +AAA CA: A A GAG C+CAG:: C:CUCC: GAGC U AA+ C 54667 GUAGAGCACUAGAAACCAC-AGAAGGAGGCACAGUGGUCUCUCCU-GAGCAUAAAG-CU- 54722 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 : + +U:: : GU+G:UUU U:C+ACU: ::UU : ++UGAUGA GUU:: 54723 ---GGUUUUUGAU-GUUGCUUUG-CUGCAACUGCCAUUCGUCACUGAUGACUGUUUU--- 54774 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 C:UC+U U+G+:G G UA::A :GGAG:G ::C+ UCUGA:UG 54775 ---CUUCCU-CUGGGAGAG--UAAGA-GGGAGAGGACACUAUCUGAGUGU 54817 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum23.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum24.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum24.dat.fasta.gz ----sequence: #7234,sp|X14945.1|HSU3 Human gene for U3 small nuclear RNA ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGUGUAGAGCACCGAAAACCACGAGGAAGAGAGGUAGCGUUUUCUCCUGAGCGUGAAGCCGGCUUUCUGGCGUUGCUUGGCUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCUCUCCGUAUUGGGGAGUGAGAGGGAGAGAACGCGGUCUGAGUGG hit 126 : 538 753 (fwd) 102.14 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C:U:C+:+GAU+AUU::UA++G+ UG+ +C++++::AGU+U+U+:G:A:G: 538 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGU 597 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C +AAACCA:GA GA GAGA+G+AGC:UU::CUCC: GAGCGUGAA+CC: 598 GUAGAGCACCGAAAACCACGAGGAAGAGAGGUAGCGUUUUCUCCU-GAGCGUGAAGCCG- 655 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+ +:::G: GU+G:UU+ U:C+ACU:C::: GC:+UUGAUGAUCGUUC:U+: 656 ---GCUUUCUGGC-GUUGCUUGG-CUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCU 710 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CUCC U UU GGGA:U :GA :GGAG::AA:GC GUCUGA:UGG 711 CUCCGUAUU------GGGGAGUGAGA-GGGAGAGAACGCGGUCUGAGUGG 753 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum24.dat.fasta.gz ----sequence: #7538,sp|X14946.1|HSU3P Human pseudogene for U3 small nuclear RNA ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUGUAUAGUUCGUUACUAGAGAAGUUUCUCUGAAUGUGUAGAACACCAGAAACCACAAGGAGGAGGCGCAGCGUUCUCUCCUGAGCGUGAAGCCGGCUUUCUAGGCGUUGCUCAACUGCAACUGCAGUUUGCCAUUGAUGAUUGUUCUUCUCUUCGUUUGGGAGAGUAAGAGGCAAAGGAUGCAGUCUGAAUGG hit 127 : 230 446 (fwd) 74.95 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C+U:C+:+GAU+AUU::UA++G+ G+ +C++++::AGU+U+U+:G:A+G: 230 AAGACUAUACUUUCAGGGAUCAUUUGUAUAGUUCGUUACUAGAGAAGUUUCUCUGAAUGU 289 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU AACA+C +AAACCA A GA GAG CGCAGC U C: U C: GAGCGUGAA+CC: 290 GUAGAACACCAGAAACCACAAGGAGGAGGCGCAGCGUUCUCUCCU-GAGCGUGAAGCCG- 347 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+ +:::G+ GU+G:U U:C+ACU+C:::U+GC:+UUGAUGAU GUUC:U+: 348 ---GCUUUCUAGGCGUUGCUCAA-CUGCAACUGCAGUUUGCCAUUGAUGAUUGUUCUUCU 403 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CU:C U U + G:GA:UA:GA :G A :G A GCAGUCUGA UGG 404 CUUCGU------UUGGGAGAGUAAGA-GGCAAAGGAUGCAGUCUGAAUGG 446 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum25.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum25.dat.fasta.gz ----sequence: #1196,sp|M14061.1|HSUG3PE Human U3 small nuclear RNA gene. ----isReversed: 0 ----hitSequence: AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGUGUAGAGCACCGAAAACCACGAGGAAGAGAGGUAGCGUUUUCUCCUGAGCGUGAAGCCGGCUUUCUGGCGUUGCUUGGCUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCUCUCCGUAUUGGGGAGUGAGAGGGAGAGAACGCGGUCUGAGUGG hit 128 : 277 492 (fwd) 102.14 bits ::::::<<<<<<<<-<<<--<<<<<<--<<<<_____>>>>-->>>>>>-->>>>>>>>> 1 aaacCUauccuucccaggAUcauuucUAuaggAUgcgucccUcugagucUuugagaaaga 60 AA++CUAU:C:U:C+:+GAU+AUU::UA++G+ UG+ +C++++::AGU+U+U+:G:A:G: 277 AAGACUAUACUUUCAGGGAUCAUUUCUAUAGUGUGUUACUAGAGAAGUUUCUCUGAACGU 336 >>-------------((((--------------((((((((((((,,,,,,,,,,,,,<- 61 gucAaaCAacccAAAccagGAUGAUGAgacgcAgccuucgcucccaGAGCGUGAaucCgC 120 GU A+CA+C +AAACCA:GA GA GAGA+G+AGC:UU::CUCC: GAGCGUGAA+CC: 337 GUAGAGCACCGAAAACCACGAGGAAGAGAGGUAGCGUUUUCUCCU-GAGCGUGAAGCCG- 394 ---<<---<<<<<-<<<<<_______>>>>>->>>>>-->>>,,,,,,,,,,,,<<<--< 121 GGCgcgcaucugguguugguUuuuuUccuacUucacuUGgcuuuUGAUGAUCGUuccUau 180 GC+ +:::G: GU+G:UU+ U:C+ACU:C::: GC:+UUGAUGAUCGUUC:U+: 395 ---GCUUUCUGGC-GUUGCUUGG-CUGCAACUGCCGUCAGCCAUUGAUGAUCGUUCUUCU 449 <<<<<__________>>>>>>-->>>,))))))))))))-------)))) 181 cucccUcuuUUUuGuggggaaUaggaUgggagcgaaggcaGUCUGAcugg 230 CUCC U UU GGGA:U :GA :GGAG::AA:GC GUCUGA:UGG 450 CUCCGUAUU------GGGGAGUGAGA-GGGAGAGAACGCGGUCUGAGUGG 492 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum26.dat.fasta.gz done 1.65905e+10 nucs (frac lets thru so far=8.94197e-06, 2d-fracLetsThru=6.10075e-06). Filter report: done 1.65905e+10 nucs (frac lets thru so far=8.94197e-06, 2d-fracLetsThru=6.10075e-06). done 1.65905e+10 nucs (frac lets thru so far=8.94197e-06, 2d-fracLetsThru=6.10075e-06). CPU time: 870321.39u 383.26s 241:51:44.65 Elapsed: 245:33:46