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-U