Params: ./cmzasha --no-stderr --filter 180 11 Rfam/cm/RF00015.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00015_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00015_fwdinf_hmmtype1_advance_copy.bin Build: release Host: xmen.cs.washington.edu pid: 1572 ----cmFile: Rfam/cm/RF00015.cm (global) ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #20920,sp|AF270843.1|AF270843 Saccharomyces pastorianus unknown sequence. ----isReversed: 0 ----hitSequence: AUCCUUAUGCACGGGAAAUACGCAUAUCAGUGAGGAUUCGUCCGAGAUUGUGUUUUUGCUGGUUGAAAUUUAAUUAUAAACCAGACCGUCUCCUCAUGGUCUACUAUGGGUGUUCGCUUUUGAACACUUCAAGACUAUGUAGGGAAUUUUUGGAAUAUUUUCUCAU hit 0 : 940 1105 (fwd) 59.19 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUC UU GC A GGG AAUA:+:: ::CAGUGAGG UU +CCGAG::::+:UU UUGC 940 AUCCUUAUGC-ACGGGAAAUACGCAUAUCAGUGAGGAUUCGUCCGAGAUUGUGUUUUUGC 998 ,,<<<<_________......__>>>>,,,,,<<<<<<<<<<<<<<____.......... 61 UAgUugAAAACUAUU......CCcaAccgCCCgccuaagacgacauguua.......... 104 U+GU::AAA UA U CC::ACCG C :CC ::: G:C::+U+ 999 UGGUUGAAAUUUAAUuauaaaCCAGACCGUC-UCC-UCAUGGUCUACUAUggguguucgc 1056 ...........__>>>>>>>>>>>>>>,,,,,,,,,,,,<<<<___>>>> 105 ...........uauugucggcuuuggcAAUUUUUGGAAGcccuccaaggg 143 U ::G:C :::+GG:AAUUUUUGGAA ::: +C ::: 1057 uuuugaacacuUCAAGACUAUGUAGGGAAUUUUUGGAAUAUUUUC-UCAU 1105 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #59691,sp|D63682.1|D63682 Erythrobasidium hasegawianum U4 small nuclear RNA gene, complete sequence. ----isReversed: 0 ----hitSequence: AUCUUUGUGCUCGGGCACGCGAUGGCGACGUUGAAGGAAACUGAGUCCCAUCUAAUUGCUGGUUGCAAACUAAAUUCCACACUCUUCACUGCACUCUUCGGAGUCUUUGGGAAUUUCUGCCCGCCUAACGGC hit 1 : 100 231 (fwd) 25.66 bits :::::::::::::::::<<-..<<<<<-<<<_________________>>>>>>>>--.> 1 AuCUUUGCGCUAGGGGCaaU..aucguAgccAGUGAGGcUuuAaCCGAggcgcgauUA.u 57 AUCUUUG GC + GGGCA: :::G G:C UGA G AAC+GAG:C C:::UA : 100 AUCUUUGUGC-UCGGGCAC-gcGAUGGCGACGUUGAAGGA--AACUGAGUCCCAUCUAaU 155 >,,,,<<<<_________..__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>> 58 uGCUAgUugAAAACUAUU..CCcaAccgCCCgccuaagacgacauguuauauugucggcu 115 UGCU+GU : AAACUA CC: AC + ::C A+: +AC: U + :GU+ : 156 UGCUGGUUGCAAACUAAAuuCCACACUC---UUC--ACUGCACUCUUCG--GAGUCUU-- 206 >>>>>,,,,,,,,,,,,<<<<___>>>> 116 uuggcAAUUUUUGGAAGcccuccaaggg 143 UG::AAUUU+UG :CC + GG: 207 -UGGGAAUUUCUGCCC-GCCUAA-CGGC 231 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #68856,sp|U18778.1|SC9537 Saccharomyces cerevisiae chromosome V cosmids 9537, 9581, 9495, 9867, and lambda clone 5898. ----isReversed: 1 ----hitSequence: AUCCUUAUGCACGGGAAAUACGCAUAUCAGUGAGGAUUCGUCCGAGAUUGUGUUUUUGCUGGUUGAAAUUUAAUUAUAAACCAGACCGUCUCCUCAUGGUCAAUUCGGUGUUCGCUUUUGAAUACUUCAAGACUAUGUAGGGAAUUUUUGGAAUACCUUU hit 2 : 15676 15517 (rev) 63.89 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUC UU GC A GGG AAUA:+:: ::CAGUGAGG UU +CCGAG::::+:UU UUGC 50355 AUCCUUAUGC-ACGGGAAAUACGCAUAUCAGUGAGGAUUCGUCCGAGAUUGUGUUUUUGC 50413 ,,<<<<_________......__>>>>,,,,,<<<<<<<<<<<<<<____.......... 61 UAgUugAAAACUAUU......CCcaAccgCCCgccuaagacgacauguua.......... 104 U+GU::AAA UA U CC::ACCG C :CC+::::+:::AU + 50414 UGGUUGAAAUUUAAUuauaaaCCAGACCGUC-UCCUCAUGGUCAAUUCGGuguucgcuuu 50472 .....__>>>>>>>>...>>>>>>,,,,,,,,,,,,<<<<___>>>> 105 .....uauugucggc...uuuggcAAUUUUUGGAAGcccuccaaggg 143 UU:::+:: ::+GG:AAUUUUUGGAA +CCU+ 50473 ugaauACUUCAAGACuauGUAGGGAAUUUUUGGAAUACCUUU----- 50514 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #71108,sp|L22204.1|SCPSL1 Saccharomyces cerevisiae profilin synthetic lethal (PSL1) gene, complete cds. ----isReversed: 0 ----hitSequence: AUCCUUAUGCACGGGAAAUACGCAUAUCAGUGAGGAUUCGUCCGAGAUUGUGUUUUUGCUGGUUGAAAUUUAAUUAUAAACCAGACCGUCUCCUCAUGGUCAAUUCGGUGUUCGCUUUUGAAUACUUCAAGACUAUGUAGGGAAUUUUUGGAAUACCUUU hit 3 : 4781 4940 (fwd) 63.89 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUC UU GC A GGG AAUA:+:: ::CAGUGAGG UU +CCGAG::::+:UU UUGC 4781 AUCCUUAUGC-ACGGGAAAUACGCAUAUCAGUGAGGAUUCGUCCGAGAUUGUGUUUUUGC 4839 ,,<<<<_________......__>>>>,,,,,<<<<<<<<<<<<<<____.......... 61 UAgUugAAAACUAUU......CCcaAccgCCCgccuaagacgacauguua.......... 104 U+GU::AAA UA U CC::ACCG C :CC+::::+:::AU + 4840 UGGUUGAAAUUUAAUuauaaaCCAGACCGUC-UCCUCAUGGUCAAUUCGGuguucgcuuu 4898 .....__>>>>>>>>...>>>>>>,,,,,,,,,,,,<<<<___>>>> 105 .....uauugucggc...uuuggcAAUUUUUGGAAGcccuccaaggg 143 UU:::+:: ::+GG:AAUUUUUGGAA +CCU+ 4899 ugaauACUUCAAGACuauGUAGGGAAUUUUUGGAAUACCUUU----- 4940 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #71633,sp|M17238.1|SCSNR14A S.cerevisiae (U4-like) small nuclear RNA snR14 gene. ----isReversed: 0 ----hitSequence: AUCCUUAUGCACGGGAAAUACGCAUAUCAGUGAGGAUUCGUCCGAGAUUGUGUUUUUGCUGGUUGAAAUUUAAUUAUAAACCAGACCGUCUCCUCAUGGUCAAUUCGGUGUUCGCUUUUGAAUACUUCAAGACUAUGUAGGGAAUUUUUGGAAUACCUUU hit 4 : 314 473 (fwd) 63.89 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUC UU GC A GGG AAUA:+:: ::CAGUGAGG UU +CCGAG::::+:UU UUGC 314 AUCCUUAUGC-ACGGGAAAUACGCAUAUCAGUGAGGAUUCGUCCGAGAUUGUGUUUUUGC 372 ,,<<<<_________......__>>>>,,,,,<<<<<<<<<<<<<<____.......... 61 UAgUugAAAACUAUU......CCcaAccgCCCgccuaagacgacauguua.......... 104 U+GU::AAA UA U CC::ACCG C :CC+::::+:::AU + 373 UGGUUGAAAUUUAAUuauaaaCCAGACCGUC-UCCUCAUGGUCAAUUCGGuguucgcuuu 431 .....__>>>>>>>>...>>>>>>,,,,,,,,,,,,<<<<___>>>> 105 .....uauugucggc...uuuggcAAUUUUUGGAAGcccuccaaggg 143 UU:::+:: ::+GG:AAUUUUUGGAA +CCU+ 432 ugaauACUUCAAGACuauGUAGGGAAUUUUUGGAAUACCUUU----- 473 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #76725,sp|AL034382.1|SPBC428 S.pombe chromosome II cosmid c428. ----isReversed: 1 ----hitSequence: AUCUUUGUGCACGGGUAUUACGCUUAUCAGUGAGGAACUUUUCCUAGAUGGCGUUAUUGCUAGUUGAAAACUAUUACCCUGACCGCUCCAACUCUCGUUAAGAGUUUUGGGAAUAUUUGGAAACCAACU hit 5 : 26841 26713 (rev) 87.27 bits :::::::::::::::::<<-<<<<<-<<<_______..__________>>>>>>>>-->> 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGG..cUuuAaCCGAggcgcgauUAuu 58 AUCUUUG GC A GGG A+UA:::U ::CAGUGAGG CUUU +CC AG::G:::UUA+U 14415 AUCUUUGUGC-ACGGGUAUUACGCUUAUCAGUGAGGaaCUUU-UCCUAGAUGGCGUUAUU 14472 ,,,,<<<<_________..__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>> 59 GCUAgUugAAAACUAUU..CCcaAccgCCCgccuaagacgacauguuauauugucggcuu 116 GCUAGU::AAAACUAUU CC::ACCG ::C:AA+:C::++ U+A ::G: UU 14473 GCUAGUUGAAAACUAUUacCCUGACCG---CUCCAACUCUCGU--UAA-----GAGU-UU 14521 >>>>,,,,,,,,,,,,<<<<___>>>> 117 uggcAAUUUUUGGAAGcccuccaaggg 143 :G::AAU UUUGGAA CC++C 14522 UGGGAAUAUUUGGAAACCAACU----- 14543 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #77621,sp|X15491.1|SPSNU4 Yeast snu4 gene for small nuclear RNA U4 ----isReversed: 0 ----hitSequence: AUCUUUGUGCACGGGUAUUACGCUUAUCAGUGAGGAACUUUUCCUAGAUGGCGUUAUUGCUAGUUGAAAACUAUUACCCUGACCGCUCCAACUCUCGUUAAGAGUUUUGGGAAUAUUUGGAAACCAACU hit 6 : 209 337 (fwd) 87.27 bits :::::::::::::::::<<-<<<<<-<<<_______..__________>>>>>>>>-->> 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGG..cUuuAaCCGAggcgcgauUAuu 58 AUCUUUG GC A GGG A+UA:::U ::CAGUGAGG CUUU +CC AG::G:::UUA+U 209 AUCUUUGUGC-ACGGGUAUUACGCUUAUCAGUGAGGaaCUUU-UCCUAGAUGGCGUUAUU 266 ,,,,<<<<_________..__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>> 59 GCUAgUugAAAACUAUU..CCcaAccgCCCgccuaagacgacauguuauauugucggcuu 116 GCUAGU::AAAACUAUU CC::ACCG ::C:AA+:C::++ U+A ::G: UU 267 GCUAGUUGAAAACUAUUacCCUGACCG---CUCCAACUCUCGU--UAA-----GAGU-UU 315 >>>>,,,,,,,,,,,,<<<<___>>>> 117 uggcAAUUUUUGGAAGcccuccaaggg 143 :G::AAU UUUGGAA CC++C 316 UGGGAAUAUUUGGAAACCAACU----- 337 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #5158,sp|AC005719.2|AC005719 Drosophila melanogaster, chromosome 2L, region 38A5-38B4, BAC clone BACR48M05, complete sequence. ----isReversed: 1 ----hitSequence: AUCUUUGCGCAGAGGCGAUAUCGUAACCAAUGAAGUUCUACUGAGGUGCGAUUAUUGCUAGUUGAAAACUUUAACCAAUACCCCGCCAUGGGGACGUGAAAUACCGUCCACUACGGCAAUUUUUGGAAGCCCGAGAGGG hit 7 : 131802 131664 (rev) 126.48 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUCUUUGCGC AG GGC:AUAUCGUA:CCA+UGA G+U+U AC+GAGG:GCGAUUAU:GC 56540 AUCUUUGCGC-AGAGGCGAUAUCGUAACCAAUGAAGUUCU-ACUGAGGUGCGAUUAUUGC 56597 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA:UUGAAAACU+U CCAA:++CCCGCC :+G:+GAC:+G++AUA+:GUC+:C+: GGC 56598 UAGUUGAAAACUUUAACCAAUACCCCGCC-AUGGGGACGUGAAAUACCGUCCACUACGGC 56656 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 AAUUUUUGGAAGCCC: +:GGG 56657 AAUUUUUGGAAGCCCGA-GAGGG 56678 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #5171,sp|AC005811.10|AC005811 Drosophila melanogaster, chromosome 2L, region 39B1-39B3, P1 clone DS05527, complete sequence. ----isReversed: 1 ----hitSequence: AUCUUUGCGCAGUGGCAAUACCGUAACCAAUGAAGUCCUCCUGAGGUGCGGUUAUUGCUAGUUGAAAACUUUAACCAAUACCCCGCCAUGGGGACGUGAAAUACCGUCCACUACGGCAAUUUUUGGAAGCCCGAGAGGG hit 8 : 5801 5663 (rev) 123.94 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUCUUUGCGC AG GGCAAUA:CGUA:CCA+UGA G+ +U C+GAGG:GCG:UUAUUGC 67187 AUCUUUGCGC-AGUGGCAAUACCGUAACCAAUGAAGUCCU-CCUGAGGUGCGGUUAUUGC 67244 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA:UUGAAAACU+U CCAA:++CCCGCC :+G:+GAC:+G++AUA+:GUC+:C+: GGC 67245 UAGUUGAAAACUUUAACCAAUACCCCGCC-AUGGGGACGUGAAAUACCGUCCACUACGGC 67303 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 AAUUUUUGGAAGCCC: +:GGG 67304 AAUUUUUGGAAGCCCGA-GAGGG 67325 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #5800,sp|AC009910.5|AC009910 Drosophila melanogaster, chromosome 2L, region 25D-25E, BAC clone BACR35L07, complete sequence. ----isReversed: 0 ----hitSequence: AACCUUGUGCAGUGGCAACAUCGCAAGCAAUGAAGUUCCAACUGAGCUGCGAUUAUUGCUAGUUGAAAACUAAAACCAAUAUCUCGCCCAGCGUAAGGAUCUACGAUCUUUAAGCUAAGGCAAUUUUUUUAGGCCCCAAGUGGG hit 9 : 87034 87177 (fwd) 71.39 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A C UUG GC AG GGCAA AUCG:A: CA+UGA G+U+ AAC+GAG ::CGAUUAUUGC 87034 AACCUUGUGC-AGUGGCAACAUCGCAAGCAAUGAAGUUCCAACUGAGCUGCGAUUAUUGC 87092 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<..______.>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacau..guuaua.uugucggcuuu 117 UA:UUGAAAACUA CCAA:+ C CGCC :AG :A::: +U+ A :::U: CU:+ 87093 UAGUUGAAAACUAAAACCAAUAUCUCGCC-CAGCGUAAGGauCUACGAuCUUUAAGCUAA 87151 >>>,,,,,,,,,,,,<<<<___>>>> 118 ggcAAUUUUUGGAAGcccuccaaggg 143 GGCAAUUUUU A GCCC ++ GGG 87152 GGCAAUUUUUUUAGGCCCCAAGUGGG 87177 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #6417,sp|AC084532.1|AC084532 Caenorhabditis briggsae cosmid G22L08, complete sequence. ----isReversed: 0 ----hitSequence: AGCUUUGCGCUGGGGCGAUAACGUGACCAAUGAGGCUUUGCCGAGGUGCGUUUAUUGCUGGUUGAAAACUUUUCCCAAUUGCCCGCGAUGUCCCCUGAAACAUGGGUGACAUACGCAAUUUUUGAACGCCUCUAGGAGG hit 10 : 13028 13166 (fwd) 123.93 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC +GGGGC:AUA:CGU :CCA+UGAGGCUUU CCGAGG:GCG:UUAU:GC 13028 AGCUUUGCGC-UGGGGCGAUAACGUGACCAAUGAGGCUUU-GCCGAGGUGCGUUUAUUGC 13085 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 U+:UUGAAAACU+UUCCCAA: GCCCGC+ A:G :+:C:UG++A AU:G:+:+C:U++GC 13086 UGGUUGAAAACUUUUCCCAAUUGCCCGCG-AUG-UCCCCUGAAACAUGGGUGACAUACGC 13143 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 AAUUUUUG+A GCC::+++::GG 13144 AAUUUUUGAACGCCUCUAGGAGG 13166 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #6476,sp|AC084591.1|AC084591 Caenorhabditis briggsae cosmid G42B20, complete sequence. ----isReversed: 0 ----hitSequence: AGCUUUGCGCUGGGGCGAUAACGUGACCAAUGAGGCUUUGCCGAGGUGCGUUUAUUGCUGGUUGAAAACUUUUCCCAAUUGCCCGCGAUGUCCCCUGAAACAUGGGUGACAUACGCAAUUUUUGAACGCCUCUAGGAGG hit 11 : 18183 18321 (fwd) 123.93 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC +GGGGC:AUA:CGU :CCA+UGAGGCUUU CCGAGG:GCG:UUAU:GC 18183 AGCUUUGCGC-UGGGGCGAUAACGUGACCAAUGAGGCUUU-GCCGAGGUGCGUUUAUUGC 18240 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 U+:UUGAAAACU+UUCCCAA: GCCCGC+ A:G :+:C:UG++A AU:G:+:+C:U++GC 18241 UGGUUGAAAACUUUUCCCAAUUGCCCGCG-AUG-UCCCCUGAAACAUGGGUGACAUACGC 18298 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 AAUUUUUG+A GCC::+++::GG 18299 AAUUUUUGAACGCCUCUAGGAGG 18321 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #6476,sp|AC084591.1|AC084591 Caenorhabditis briggsae cosmid G42B20, complete sequence. ----isReversed: 1 ----hitSequence: AGCUUUGCGCUGGGGCGAUAACGUGACCAAUGAGGCUUUGCCGAGGUGCGUUUAUUGCUGGUUGAAAACUUUUCCCAAUUGCCCGCGAUGUCCCCUGAAACAUGGGUGACAUACGCAAUUUUUGAACGCCUCUAGGAGG hit 12 : 29419 29281 (rev) 123.93 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC +GGGGC:AUA:CGU :CCA+UGAGGCUUU CCGAGG:GCG:UUAU:GC 13786 AGCUUUGCGC-UGGGGCGAUAACGUGACCAAUGAGGCUUU-GCCGAGGUGCGUUUAUUGC 13843 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 U+:UUGAAAACU+UUCCCAA: GCCCGC+ A:G :+:C:UG++A AU:G:+:+C:U++GC 13844 UGGUUGAAAACUUUUCCCAAUUGCCCGCG-AUG-UCCCCUGAAACAUGGGUGACAUACGC 13901 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 AAUUUUUG+A GCC::+++::GG 13902 AAUUUUUGAACGCCUCUAGGAGG 13924 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #6706,sp|AC093099.1|AC093099 Drosophila melanogaster, chromosome 2L, region 39A-39D, BAC clone BACR34H23, complete sequence. ----isReversed: 1 ----hitSequence: AUCUUUGCGCAGUGGCAAUACCGUAACCAAUGAAGUCCUCCUGAGGUGCGGUUAUUGCUAGUUGAAAACUUUAACCAAUACCCCGCCAUGGGGACGUGAAAUACCGUCCACUACGGCAAUUUUUGGAAGCCCGAGAGGG hit 13 : 54500 54362 (rev) 123.94 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUCUUUGCGC AG GGCAAUA:CGUA:CCA+UGA G+ +U C+GAGG:GCG:UUAUUGC 108976 AUCUUUGCGC-AGUGGCAAUACCGUAACCAAUGAAGUCCU-CCUGAGGUGCGGUUAUUGC 109033 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA:UUGAAAACU+U CCAA:++CCCGCC :+G:+GAC:+G++AUA+:GUC+:C+: GGC 109034 UAGUUGAAAACUUUAACCAAUACCCCGCC-AUGGGGACGUGAAAUACCGUCCACUACGGC 109092 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 AAUUUUUGGAAGCCC: +:GGG 109093 AAUUUUUGGAAGCCCGA-GAGGG 109114 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #6946,sp|AC116967.2|AC116967 Dictyostelium discoideum chromosome 2 map 5481549-5500786 strain AX4, complete sequence. ----isReversed: 1 ----hitSequence: GUCUUUACGCUGGGACCAAAGCAGUAGGGCGUGACCGAUAAGGGAUCCACUGUUAGUGCUUUUUGCAAACUAUUCCACAACGCAGUCCGAAACAAUUCGGCCUGCAAUUUUUAAUUCUAUCCUAA hit 14 : 4907 4783 (rev) 15.64 bits :::::::::::::::::.<<-<<<<<-<<<_________________>>>>>>>>-->>, 1 AuCUUUGCGCUAGGGGC.aaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuG 59 UCUUU CGC +GGG C A ::G+AG : GUGA U+ A GA: C+C:: UA UG 14331 GUCUUUACGC-UGGGACcAAAGCAGUAGGGCGUGACCGAUA-AGGGAUCCACUGUUAGUG 14388 ,,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 60 CUAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 CU :U : AAACUAUUCC: A: + GC: ++ CGA:A +A :UCGG :G 14389 CUUUUUGCAAACUAUUCCACAA-C---GCA-GUC-CGAAA--CAA----UUCGGC--CUG 14434 >,,,,,,,,,,,,<<<<___>>>> 120 cAAUUUUUGGAAGcccuccaaggg 143 CAAUUUUU AA : ::+C :: : 14435 CAAUUUUU--AAUUCUAUC-CUAA 14455 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #7626,sp|AE003610.3|AE003610 Drosophila melanogaster chromosome 2L section 19 of 83 of the complete sequence. ----isReversed: 0 ----hitSequence: AACCUUGUGCAGUGGCAACAUCGCAAGCAAUGAAGUUCCAACUGAGCUGCGAUUAUUGCUAGUUGAAAACUAAAACCAAUAUCUCGCCCAGCGUAAGGAUCUACGAUCUUUAAGCUAAGGCAAUUUUUUUAGGCCCCAAGUGGG hit 15 : 130141 130284 (fwd) 71.39 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A C UUG GC AG GGCAA AUCG:A: CA+UGA G+U+ AAC+GAG ::CGAUUAUUGC 130141 AACCUUGUGC-AGUGGCAACAUCGCAAGCAAUGAAGUUCCAACUGAGCUGCGAUUAUUGC 130199 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<..______.>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacau..guuaua.uugucggcuuu 117 UA:UUGAAAACUA CCAA:+ C CGCC :AG :A::: +U+ A :::U: CU:+ 130200 UAGUUGAAAACUAAAACCAAUAUCUCGCC-CAGCGUAAGGauCUACGAuCUUUAAGCUAA 130258 >>>,,,,,,,,,,,,<<<<___>>>> 118 ggcAAUUUUUGGAAGcccuccaaggg 143 GGCAAUUUUU A GCCC ++ GGG 130259 GGCAAUUUUUUUAGGCCCCAAGUGGG 130284 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #7680,sp|AE003664.2|AE003664 Drosophila melanogaster chromosome 2L section 73 of 83 of the complete sequence. ----isReversed: 0 ----hitSequence: AUCUUUGCGCAGAGGCGAUAUCGUAACCAAUGAAGUUCUACUGAGGUGCGAUUAUUGCUAGUUGAAAACUUUAACCAAUACCCCGCCAUGGGGACGUGAAAUACCGUCCACUACGGCAAUUUUUGGAAGCCCGAGAGGG hit 16 : 78699 78837 (fwd) 126.48 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUCUUUGCGC AG GGC:AUAUCGUA:CCA+UGA G+U+U AC+GAGG:GCGAUUAU:GC 78699 AUCUUUGCGC-AGAGGCGAUAUCGUAACCAAUGAAGUUCU-ACUGAGGUGCGAUUAUUGC 78756 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA:UUGAAAACU+U CCAA:++CCCGCC :+G:+GAC:+G++AUA+:GUC+:C+: GGC 78757 UAGUUGAAAACUUUAACCAAUACCCCGCC-AUGGGGACGUGAAAUACCGUCCACUACGGC 78815 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 AAUUUUUGGAAGCCC: +:GGG 78816 AAUUUUUGGAAGCCCGA-GAGGG 78837 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #7685,sp|AE003669.4|AE003669 Drosophila melanogaster chromosome 2L section 78 of 83 of the complete sequence. ----isReversed: 1 ----hitSequence: AUCUUUGCGCAGUGGCAAUACCGUAACCAAUGAAGUCCUCCUGAGGUGCGGUUAUUGCUAGUUGAAAACUUUAACCAAUACCCCGCCAUGGGGACGUGAAAUACCGUCCACUACGGCAAUUUUUGGAAGCCCGAGAGGG hit 17 : 204840 204702 (rev) 123.94 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUCUUUGCGC AG GGCAAUA:CGUA:CCA+UGA G+ +U C+GAGG:GCG:UUAUUGC 69156 AUCUUUGCGC-AGUGGCAAUACCGUAACCAAUGAAGUCCU-CCUGAGGUGCGGUUAUUGC 69213 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA:UUGAAAACU+U CCAA:++CCCGCC :+G:+GAC:+G++AUA+:GUC+:C+: GGC 69214 UAGUUGAAAACUUUAACCAAUACCCCGCC-AUGGGGACGUGAAAUACCGUCCACUACGGC 69272 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 AAUUUUUGGAAGCCC: +:GGG 69273 AAUUUUUGGAAGCCCGA-GAGGG 69294 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #9821,sp|AF022972.1|AF022972 Caenorhabditis elegans cosmid F10D2, complete sequence. ----isReversed: 1 ----hitSequence: AGCUUUGCGCUGGGGCGAUAACGUGACCAAUGAGGCUUUGCCGAGGUGCGUUUAUUGCUGGUUGAAAACUUUUCCCAAUUGCCCGCGAUGACCUCUGAAACAUGGGUGCCAUACGCAAUUUUUGAACGCCUCUAGGAGG hit 18 : 10804 10666 (rev) 119.05 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC +GGGGC:AUA:CGU :CCA+UGAGGCUUU CCGAGG:GCG:UUAU:GC 22137 AGCUUUGCGC-UGGGGCGAUAACGUGACCAAUGAGGCUUU-GCCGAGGUGCGUUUAUUGC 22194 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 U+:UUGAAAACU+UUCCCAA: GCCCGC+ A:G :+:::UG++A AU:::+:+C:U++GC 22195 UGGUUGAAAACUUUUCCCAAUUGCCCGCG-AUG-ACCUCUGAAACAUGGGUGCCAUACGC 22252 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 AAUUUUUG+A GCC::+++::GG 22253 AAUUUUUGAACGCCUCUAGGAGG 22275 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #25406,sp|AF204671.1|AF204671 Leptomonas collosoma tRNA-Gly gene, partial sequence; and tRNA-Pro gene, complete sequence; and small nuclear RNA U4 gene, complete sequence. ----isReversed: 0 ----hitSequence: AGCCUUGCGCAGGGAGAUGUGAACGCAAGAACCUCAGUGAUUGUUCAUUUAGUGCUAUACUAAAAACUCCAGUACUCCUAUACGGGAAUAUUUGCAUCCACCAAGGGUG hit 19 : 434 542 (fwd) 15.76 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-.->>, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauU.AuuG 59 A+C UUGCGC AGGG A U U::: :::A GA CU+ A +GA::::::A U A+UG 434 AGCCUUGCGC-AGGGAGA-UGUGAACGCAA--GAACCUC--AGUGAUUGUUCAUUuAGUG 487 ,,,<<<<_________....__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>> 60 CUAgUugAAAACUAUU....CCcaAccgCCCgccuaagacgacauguuauauugucggcu 115 CUA: ACUA CC ++: ::C: + +UA 488 CUAU------ACUAAAaacuCCAGUA-----CUCC--------U--AUA----------- 515 >>>>>,,,,,,,,,,,,<<<<___>>>> 116 uuggcAAUUUUUGGAAGcccuccaaggg 143 :G::AAU UUUG A C:C: ++:G:G 516 -CGGGAAUAUUUGCAUCCACCAAGGGUG 542 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #37194,sp|AF326336.1|AF326336 Crithidia fasciculata U4 snRNA, complete sequence. ----isReversed: 0 ----hitSequence: AGCCUUGCGCAGGGAGAUGUGAACGCAAGAACCUCCGGUGAUUGUUCACUUAGUGCUCAACUAAAACUCCAGUACUCCUAUUACAGGGAACAUUUGAUCCUGCCACGGGCA hit 20 : 2 112 (fwd) 11.34 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-.->>, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauU.AuuG 59 A+C UUGCGC AGGG A U:U::: :::A GA CU+ +GA::::::A:U A+UG 2 AGCCUUGCGC-AGGGAGA-UGUGAACGCAA--GAACCUCC-GGUGAUUGUUCACUuAGUG 56 ,,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 60 CUAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 CU : ::AAAACU C:: :++ :CC+ + UUA C +GG 57 CUCAACUAAAACU----CCAGUAC---UCCU----A------UUA------C-----AGG 88 >,,,,,,,,,,,,<<<<___>>>> 120 cAAUUUUUGGAAGcccuccaaggg 143 :AA UUUG+ ::C: C+:G:: 89 GAACAUUUGAUCCUGCCACGGGCA 112 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----sequence: #13573,sp|L22250.1|ALSNUC Ascaris lumbricoides small nuclear RNA (snRNA) U4-1 gene. ----isReversed: 0 ----hitSequence: AGCUUUGCGCAGAGGCGAUAACGUGACCAAUGAGGCUCAGCCGAGGUGCGUUUAUUGCUGGUUGAAAACUUUCACCCAAUUGCCCGCCGCGGCGCCUGAAACAUGGCGGCCGUACGAAUUUUUGAACGCCCUGAAGGG hit 21 : 171 308 (fwd) 108.75 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC AG GGC:AUA:CGU :CCA+UGAGGCU++ CCGAGG:GCG:UUAU:GC 171 AGCUUUGCGC-AGAGGCGAUAACGUGACCAAUGAGGCUCA-GCCGAGGUGCGUUUAUUGC 228 ,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 61 UAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 U+:UUGAAAACU+U CCCAA: GCCCGC ::G +::C:UG++A AU:G::++C::+ G 229 UGGUUGAAAACUUUCaCCCAAUUGCCCGCC-GCG-GCGCCUGAAACAUGGCGGCCGUACG 286 >,,,,,,,,,,,,<<<<___>>>> 120 cAAUUUUUGGAAGcccuccaaggg 143 AAUUUUUG+A GCCCU + AGGG 287 -AAUUUUUGAACGCCCUGA-AGGG 308 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----sequence: #15526,sp|AY007789.1|AY007789 Leishmania tarentolae spliced leader RNA gene, partial sequence; U4 snRNA, snoRNA, tRNA-Pro, tRNA-Thr, snoRNA, and tRNA-Gly genes, complete sequence. ----isReversed: 1 ----hitSequence: AGCCUUGCGCAGGGAGAUGUGAACGCAAGAACCUCAGGUGAUUGUUCACUUAGUGCUGAACUAAAGACUCCAUCACUCCUAUUGCAGGGAAUAUUUGAACCACCAAGGGUG hit 22 : 386 276 (rev) 20.84 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-.->>, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauU.AuuG 59 A+C UUGCGC AGGG A U:U::: :::A GA CU++ +GA::::::A:U A+UG 1288 AGCCUUGCGC-AGGGAGA-UGUGAACGCAA--GAACCUCA-GGUGAUUGUUCACUuAGUG 1342 ,,,<<<<_________...__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>> 60 CUAgUugAAAACUAUU...CCcaAccgCCCgccuaagacgacauguuauauugucggcuu 116 CU+: ACUA CCA+:++ :CC+ + UU+ C 1343 CUGA------ACUAAAgacUCCAUCAC---UCCU----A------UUG------C----- 1372 >>>>,,,,,,,,,,,,<<<<___>>>> 117 uggcAAUUUUUGGAAGcccuccaaggg 143 +GG:AAU UUUG+A C:C: ++:G:G 1373 AGGGAAUAUUUGAAC-CACCAAGGGUG 1398 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----sequence: #43515,sp|Z78012.1|CEC52E4 Caenorhabditis elegans cosmid C52E4 ----isReversed: 0 ----hitSequence: AGCUUUGCGCUGGGGCGAUAACGUGACCAAUGAGGCUUUGCCGAGGUGCGUUUAUUGCUGGUUGAAAACUUUUCCCAAUUGCCCGCGAUGUCCCCUGAAACAUGGGUGGCAUACGCAAUUUUUGAACGCCUCUAGGAGG hit 23 : 16121 16259 (fwd) 124.25 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC +GGGGC:AUA:CGU :CCA+UGAGGCUUU CCGAGG:GCG:UUAU:GC 16121 AGCUUUGCGC-UGGGGCGAUAACGUGACCAAUGAGGCUUU-GCCGAGGUGCGUUUAUUGC 16178 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 U+:UUGAAAACU+UUCCCAA: GCCCGC+ A:G :+:C:UG++A AU:G:+:GC:U++GC 16179 UGGUUGAAAACUUUUCCCAAUUGCCCGCG-AUG-UCCCCUGAAACAUGGGUGGCAUACGC 16236 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 AAUUUUUG+A GCC::+++::GG 16237 AAUUUUUGAACGCCUCUAGGAGG 16259 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----sequence: #44428,sp|Z74039.1|CEK03B8 Caenorhabditis elegans cosmid K03B8 ----isReversed: 1 ----hitSequence: AGCUUUGCGCUGGGGCGAUAACGUGACCAAUGAGGCUUUGCCGAGGUGCGUUUAUUGCUGGUUGAAAACUUUUCCCAAUUGCCCGCGAUGUCCCCUGAAACAUGGGUGGCAUACGCAAUUUUUGAACGCCUCCAGGAGG hit 24 : 1549 1411 (rev) 124.74 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC +GGGGC:AUA:CGU :CCA+UGAGGCUUU CCGAGG:GCG:UUAU:GC 27584 AGCUUUGCGC-UGGGGCGAUAACGUGACCAAUGAGGCUUU-GCCGAGGUGCGUUUAUUGC 27641 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 U+:UUGAAAACU+UUCCCAA: GCCCGC+ A:G :+:C:UG++A AU:G:+:GC:U++GC 27642 UGGUUGAAAACUUUUCCCAAUUGCCCGCG-AUG-UCCCCUGAAACAUGGGUGGCAUACGC 27699 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 AAUUUUUG+A GCC::C++::GG 27700 AAUUUUUGAACGCCUCCAGGAGG 27722 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----sequence: #45029,sp|X51382.1|CESNU41 Caenorhabditis elegans DNA encoding U4-1 snRNA ----isReversed: 0 ----hitSequence: AGCUUUGCGCUGGGGCGAUAACGUGACCAAUGAGGCUUUGCGAGGUGCGUUUAUUGCUGGUUGAAAACUUUUCCCAAUUGCCCGCGAUGUCCCCUGAAACAUGGGUGGCAUACGCAAUUUUUGAACNCUCUAGGAGG hit 25 : 183 319 (fwd) 112.53 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC +GGGGC:AUA:CGU :CCA+UGAGGCUU + CGAGG:GCG:UUAU:GC 183 AGCUUUGCGC-UGGGGCGAUAACGUGACCAAUGAGGCUU--UGCGAGGUGCGUUUAUUGC 239 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 U+:UUGAAAACU+UUCCCAA: GCCCGC+ A:G :+:C:UG++A AU:G:+:GC:U++GC 240 UGGUUGAAAACUUUUCCCAAUUGCCCGCG-AUG-UCCCCUGAAACAUGGGUGGCAUACGC 297 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 AAUUUUUG+A C::+++::G 298 AAUUUUUGAAC-NCUCUAGGAGG 319 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----sequence: #45030,sp|X51383.1|CESNU42 Caenorhabditis elegans DNA encoding U4-2 snRNA ----isReversed: 0 ----hitSequence: AGCUUUGCGCUGGGGCGAUAACGUGACCAAUGAGGCUUUGCCGAGGUGCGUUUAUUGCUGGUUGAAAACUUUUCCCAAUUGCCCGCGAUGUCCCCUGAAACAUGGGUGGCAUACGCAAUUUUUGAACGCCUCUAGGAGG hit 26 : 153 291 (fwd) 124.25 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC +GGGGC:AUA:CGU :CCA+UGAGGCUUU CCGAGG:GCG:UUAU:GC 153 AGCUUUGCGC-UGGGGCGAUAACGUGACCAAUGAGGCUUU-GCCGAGGUGCGUUUAUUGC 210 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 U+:UUGAAAACU+UUCCCAA: GCCCGC+ A:G :+:C:UG++A AU:G:+:GC:U++GC 211 UGGUUGAAAACUUUUCCCAAUUGCCCGCG-AUG-UCCCCUGAAACAUGGGUGGCAUACGC 268 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 AAUUUUUG+A GCC::+++::GG 269 AAUUUUUGAACGCCUCUAGGAGG 291 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----sequence: #45031,sp|X51384.1|CESNU43 Caenorhabditis elegans DNA encoding U4-3 snRNA ----isReversed: 0 ----hitSequence: AGCUUUGCGCUGGGGCGAUAACGUGACCAAUGAGGCUUUGCCGAGGUGCGUUUAUUGCUGGUUGAAAACUUUUCCCAAUUGCCCGCGAUGUCCCCUGAAACAUGGGUGGCAUACGCAAUUUUUGAACGCCUCUAGGAGG hit 27 : 287 425 (fwd) 124.25 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC +GGGGC:AUA:CGU :CCA+UGAGGCUUU CCGAGG:GCG:UUAU:GC 287 AGCUUUGCGC-UGGGGCGAUAACGUGACCAAUGAGGCUUU-GCCGAGGUGCGUUUAUUGC 344 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 U+:UUGAAAACU+UUCCCAA: GCCCGC+ A:G :+:C:UG++A AU:G:+:GC:U++GC 345 UGGUUGAAAACUUUUCCCAAUUGCCCGCG-AUG-UCCCCUGAAACAUGGGUGGCAUACGC 402 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 AAUUUUUG+A GCC::+++::GG 403 AAUUUUUGAACGCCUCUAGGAGG 425 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----sequence: #45156,sp|Z74042.1|CET11F9 Caenorhabditis elegans cosmid T11F9 ----isReversed: 0 ----hitSequence: AGCUUUGCGCUGGGGCGAUAACGUGACCAAUGAGGCUUUGCCGAGGUGCGUUUAUUGCUGGUUGAAAACUUUUCCCAAUUGCCCGCGAUGUCCCCUGAAACAUGGGUGGCAUACGCAAUUUUUGAACGCCUCUAGGAGG hit 28 : 20147 20285 (fwd) 124.25 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC +GGGGC:AUA:CGU :CCA+UGAGGCUUU CCGAGG:GCG:UUAU:GC 20147 AGCUUUGCGC-UGGGGCGAUAACGUGACCAAUGAGGCUUU-GCCGAGGUGCGUUUAUUGC 20204 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 U+:UUGAAAACU+UUCCCAA: GCCCGC+ A:G :+:C:UG++A AU:G:+:GC:U++GC 20205 UGGUUGAAAACUUUUCCCAAUUGCCCGCG-AUG-UCCCCUGAAACAUGGGUGGCAUACGC 20262 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 AAUUUUUG+A GCC::+++::GG 20263 AAUUUUUGAACGCCUCUAGGAGG 20285 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----sequence: #45156,sp|Z74042.1|CET11F9 Caenorhabditis elegans cosmid T11F9 ----isReversed: 1 ----hitSequence: AGCUUUGCGCUGGGGCGAUAACGUGACCAAUGAGGCUUUGCCGAGGUGCGUUUAUUGCUGGUUGAAAACUUUUCCCAAUUGCCCGCGAUGUCCCCUGAAACAUGGGUGGCAUACGCAAUUUUUGAAAGCCUCUAGGAGG hit 29 : 30433 30295 (rev) 126.84 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC +GGGGC:AUA:CGU :CCA+UGAGGCUUU CCGAGG:GCG:UUAU:GC 7282 AGCUUUGCGC-UGGGGCGAUAACGUGACCAAUGAGGCUUU-GCCGAGGUGCGUUUAUUGC 7339 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 U+:UUGAAAACU+UUCCCAA: GCCCGC+ A:G :+:C:UG++A AU:G:+:GC:U++GC 7340 UGGUUGAAAACUUUUCCCAAUUGCCCGCG-AUG-UCCCCUGAAACAUGGGUGGCAUACGC 7397 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 AAUUUUUG+AAGCC::+++::GG 7398 AAUUUUUGAAAGCCUCUAGGAGG 7420 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----sequence: #45378,sp|X07828.1|CEU4 Caenorhabditis elegans U4 small nuclear RNA ----isReversed: 0 ----hitSequence: AGCUUUGCGCUGGGGCGAUAACGUGACCAAUGAGGCUUUGCCGAGGUGCGUUUAUUGCUGGUUGAAAACUUUUCCCAAUUGCCCGCGAUGUCCCCUGAAACAUGGGUGGCAUACGCAAUUUUUGAACGCCUCUAGGAGG hit 30 : 1 139 (fwd) 124.25 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC +GGGGC:AUA:CGU :CCA+UGAGGCUUU CCGAGG:GCG:UUAU:GC 1 AGCUUUGCGC-UGGGGCGAUAACGUGACCAAUGAGGCUUU-GCCGAGGUGCGUUUAUUGC 58 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 U+:UUGAAAACU+UUCCCAA: GCCCGC+ A:G :+:C:UG++A AU:G:+:GC:U++GC 59 UGGUUGAAAACUUUUCCCAAUUGCCCGCG-AUG-UCCCCUGAAACAUGGGUGGCAUACGC 116 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 AAUUUUUG+A GCC::+++::GG 117 AAUUUUUGAACGCCUCUAGGAGG 139 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz ----sequence: #68,sp|K03095.1|DM4 D. melanogaster U4 small nuclear RNA. ----isReversed: 0 ----hitSequence: AGCUUAGCGCAGUGGCAAUACCGUAACCAAUGAAGCCUCCCUGAGGUGCGGUUAUUGCUAGUUGAAAACUUUAACCAACCCACGCCAUGGGACGUGAAAUACCGUCCACUACGGCAAUUUUUGGAAGCCCUUACGAGGG hit 31 : 1 139 (fwd) 114.47 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUU GCGC AG GGCAAUA:CGUA:CCA+UGA GC U C+GAGG:GCG:UUAUUGC 1 AGCUUAGCGC-AGUGGCAAUACCGUAACCAAUGAAGCCUC-CCUGAGGUGCGGUUAUUGC 58 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UAGUUGAAAACU+U CCAAC +C CGCC :+G +GAC:+G++AUA+:GUC++C+: GGC 59 UAGUUGAAAACUUUAACCAAC-CCACGCC-AUG-GGACGUGAAAUACCGUCCACUACGGC 115 ,,,,,,,,,,,,<<<<__._>>>> 121 AAUUUUUGGAAGcccucc.aaggg 143 AAUUUUUGGAAGCCCU++ +AGGG 116 AAUUUUUGGAAGCCCUUAcGAGGG 139 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz ----sequence: #4638,sp|D00042.1|DMU4NR1 Drosophila melanogaster U4 small nuclear RNA gene (U4-1). ----isReversed: 0 ----hitSequence: AACAGUGCUGAGCUCAUCAUCGUAACCAAUGAAGUUCUACUGAGGUGCGAUUAUUGCUAGUUGAAAACUUUAACCAAUACCCCGCCAUGGGGACGUGAAAUACCGUCCACUACGGCAAUUUUUGGAAGCCCGAGAGGG hit 32 : 513 650 (fwd) 90.86 bits :::::::::::::::::<<-.<<<<<-<<<_________________>>>>>>>>-->>, 1 AuCUUUGCGCUAGGGGCaaU.aucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuG 59 A C G GC +G G :AU AUCGUA:CCA+UGA G+U+U AC+GAGG:GCGAUUAU:G 513 AAC--AGUGC-UGAGCUCAUcAUCGUAACCAAUGAAGUUCU-ACUGAGGUGCGAUUAUUG 568 ,,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 60 CUAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 CUA:UUGAAAACU+U CCAA:++CCCGCC :+G:+GAC:+G++AUA+:GUC+:C+: GG 569 CUAGUUGAAAACUUUAACCAAUACCCCGCC-AUGGGGACGUGAAAUACCGUCCACUACGG 627 >,,,,,,,,,,,,<<<<___>>>> 120 cAAUUUUUGGAAGcccuccaaggg 143 CAAUUUUUGGAAGCCC: +:GGG 628 CAAUUUUUGGAAGCCCGA-GAGGG 650 ----endhit ----hitSequence: AUCUUUGCGCAGAGGCGAUAUCGUAACCAAUGAAGUUCUACUGAGGUGCGAUUAUUGCUAGUUGAAAACUUUAACCAAUACCCCGCCAUGGGGACGUGAAAUACCGUCCACUACGGCAAUUUUUGGAAGCCCGAGAGGG hit 33 : 321 459 (fwd) 126.48 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUCUUUGCGC AG GGC:AUAUCGUA:CCA+UGA G+U+U AC+GAGG:GCGAUUAU:GC 321 AUCUUUGCGC-AGAGGCGAUAUCGUAACCAAUGAAGUUCU-ACUGAGGUGCGAUUAUUGC 378 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA:UUGAAAACU+U CCAA:++CCCGCC :+G:+GAC:+G++AUA+:GUC+:C+: GGC 379 UAGUUGAAAACUUUAACCAAUACCCCGCC-AUGGGGACGUGAAAUACCGUCCACUACGGC 437 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 AAUUUUUGGAAGCCC: +:GGG 438 AAUUUUUGGAAGCCCGA-GAGGG 459 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz ----sequence: #4639,sp|D00043.1|DMU4NR2 Drosophila melanogaster U4 small nuclear RNA gene (U4-2). ----isReversed: 0 ----hitSequence: AUCUUUGCGCAGUGGCAAUACCGUAACCAAUGAAGUCCUCCUGAGGUGCGGUUAUUGCUAGUUGAAAACUUUAACCAAUACCCCGCCAUGGGGACGUGAAAUACCGUCCACUACGGCAAUUUUUGGAAGCCCGAGAGGG hit 34 : 320 458 (fwd) 123.94 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUCUUUGCGC AG GGCAAUA:CGUA:CCA+UGA G+ +U C+GAGG:GCG:UUAUUGC 320 AUCUUUGCGC-AGUGGCAAUACCGUAACCAAUGAAGUCCU-CCUGAGGUGCGGUUAUUGC 377 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA:UUGAAAACU+U CCAA:++CCCGCC :+G:+GAC:+G++AUA+:GUC+:C+: GGC 378 UAGUUGAAAACUUUAACCAAUACCCCGCC-AUGGGGACGUGAAAUACCGUCCACUACGGC 436 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 AAUUUUUGGAAGCCC: +:GGG 437 AAUUUUUGGAAGCCCGA-GAGGG 458 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz ----sequence: #11337,sp|Z46971.2|LMLAPGN Leishmania mexicana MBAP gene for membrane-bound acid phosphatase ----isReversed: 1 ----hitSequence: AGCCUUGCGCAGGGAGAUGUGAACGCAAGAACCUCAGGUGAUUGUUCACUUAGUGCUGAACUAAAGACUCCAUUACUCCUAUUGCAGGGAAUAUUUGAUCCCACCACGGG hit 35 : 6456 6347 (rev) 21.73 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-.->>, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauU.AuuG 59 A+C UUGCGC AGGG A U:U::: :::A GA CU++ +GA::::::A:U A+UG 369 AGCCUUGCGC-AGGGAGA-UGUGAACGCAA--GAACCUCA-GGUGAUUGUUCACUuAGUG 423 ,,,<<<<_________...__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>> 60 CUAgUugAAAACUAUU...CCcaAccgCCCgccuaagacgacauguuauauugucggcuu 116 CU+: ACUA CCA+:++ :CC+ + UU+ C 424 CUGA------ACUAAAgacUCCAUUAC---UCCU----A------UUG------C----- 453 >>>>,,,,,,,,,,,,<<<<___>>>> 117 uggcAAUUUUUGGAAGcccuccaaggg 143 +GG:AAU UUUG+ CCC:CCA:GGG 454 AGGGAAUAUUUGAU--CCCACCACGGG 478 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz ----sequence: #11712,sp|AJ245951.1|LSE245951 Leptomonas seymouri tRNA-Gly, tRNA-Pro and U4 snRNA genes ----isReversed: 0 ----hitSequence: AGCCUUGCGCAGGGAGAUGUGAACGCAAGAACCUCCGGUGAUUGUUCACUUAGUGCUUAACUAAAAACUCCAGUACUCCUAUCACAGGGAAUAUUUGAUCCUACCAAGG hit 36 : 444 552 (fwd) 17.42 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-.->>, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauU.AuuG 59 A+C UUGCGC AGGG A U:U::: :::A GA CU+ +GA::::::A:U A+UG 444 AGCCUUGCGC-AGGGAGA-UGUGAACGCAA--GAACCUCC-GGUGAUUGUUCACUuAGUG 498 ,.,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>> 60 C.UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuug 118 C UA::U AAAACU C A::++ :CC+ +U +G 499 CuUAACUAAAAACU----CCAGUAC---UCCU-----------AUCAC----------AG 530 >>,,,,,,,,,,,,<<<<___>>>> 119 gcAAUUUUUGGAAGcccuccaaggg 143 G:AAU UUUG+ CC: CC :GG 531 GGAAUAUUUGAU--CCUACC-AAGG 552 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz ----sequence: #11899,sp|X97621.1|LTMEDRNA5 Leishmania tarentolae DNA for mini-exon and U4 snRNA gene ----isReversed: 1 ----hitSequence: AGCCUUGCGCAGGGAGAUGUGAACGCAAGAACCUCAGGUGAUUGUUCACUUAGUGCUGAACUAAAGACUCCAUCACUCCUAUUGCAGGGAAUAUUUGAACCACCAAGGGUG hit 37 : 386 276 (rev) 20.84 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-.->>, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauU.AuuG 59 A+C UUGCGC AGGG A U:U::: :::A GA CU++ +GA::::::A:U A+UG 160 AGCCUUGCGC-AGGGAGA-UGUGAACGCAA--GAACCUCA-GGUGAUUGUUCACUuAGUG 214 ,,,<<<<_________...__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>> 60 CUAgUugAAAACUAUU...CCcaAccgCCCgccuaagacgacauguuauauugucggcuu 116 CU+: ACUA CCA+:++ :CC+ + UU+ C 215 CUGA------ACUAAAgacUCCAUCAC---UCCU----A------UUG------C----- 244 >>>>,,,,,,,,,,,,<<<<___>>>> 117 uggcAAUUUUUGGAAGcccuccaaggg 143 +GG:AAU UUUG+A C:C: ++:G:G 245 AGGGAAUAUUUGAAC-CACCAAGGGUG 270 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz ----sequence: #16480,sp|Z98547.2|PFMAL3P3 Plasmodium falciparum MAL3P3 ----isReversed: 0 ----hitSequence: AUCUUUGCGGGAGGGGCAGUAUCGCUGUAAAUGACGACUAACGGAUACGCGAUUAUUGCUAGUUGAAAACUACUCCAAUUCCCGUCUCGAUGCUUGAAAAAGCAGAGAGCAAUUUUUGUAGCCUUUCUUUAUAAAGG hit 38 : 38134 38270 (fwd) 74.84 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUCUUUGCG AGGGGCA:UAUCG: G::A+UGA G U+ AC GA::C:CGAUUA:UGC 38134 AUCUUUGCGGGAGGGGCAGUAUCGCUGUAAAUGACGACUA-ACGGAUACGCGAUUAUUGC 38192 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA:UUGAAAACUA UC CAA: +CC G: +::::C: G++A :G:::: :C 38193 UAGUUGAAAACUACUC-CAAUUCCC-GUCU--CGAUGCUUGAAA--AAGCAGA---GAGC 38243 ,,,,,,,,,,,,<<<<__....._>>>> 121 AAUUUUUGGAAGcccucc.....aaggg 143 AAUUUUUG AGCC:U+C AA:GG 38244 AAUUUUUG-UAGCCUUUCuuuauAAAGG 38270 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz ----sequence: #17921,sp|X13840.1|PPU4SNR Physarum polycephalum U4 small nuclear RNA ----isReversed: 0 ----hitSequence: UUUGCGCUUGGGGCAAUAUUAUAGCGCGUGACCGAAAGGGAUGCAUAAUUAUUGCUAGUUGAAAACUAAUCUAAUGGCUGCGGUGACCCCUCGUGGUCAGGCUGCAAUUUUUGAAAAAGCU hit 39 : 1 121 (fwd) 69.26 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 UUUGCGCU+GGGGCAAUAU::+AGC: GUGA C +AA GA:GC+::AUUAUUGC 1 ---UUUGCGCUUGGGGCAAUAUUAUAGCGCGUGA--CCGAAAGGGAUGCAUAAUUAUUGC 55 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA:UU:AAAACUA UC :AA: G C GC+ ++G ++:C:++ U+ +:G:+ U+ C 56 UAGUUGAAAACUAAUC-UAAU-GGCUGCG-GUG-ACCCCUCGUGGUCAGGC-----UG-C 105 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 AAUUUUUG+AA ++CU 106 AAUUUUUGAAAAAGCU------- 121 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz ----sequence: #22506,sp|M25777.1|TBURNAC Trypanosoma small nuclear RNA (uRNA C) gene. ----isReversed: 0 ----hitSequence: AGCCUUGCGCAGGGAGGUGUGAACGCAAGAUCCUCAGGUGAUUGUUCACUAGUGCAAUACUAUAUCCGGUACUCCUUCGGGGAAAGUUUGCUACCCACCACGGG hit 40 : 131 234 (fwd) 37.94 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+C UUGCGC AGGG : U:U::: :::A GA CU++ +GA::::::A:UA+:GC 131 AGCCUUGCGC-AGGGAGG-UGUGAACGCAA--GAUCCUCA-GGUGAUUGUUCACUAGUGC 185 ,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 61 UAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 A: ACUAU CC+++: ::C: UU :G: 186 AAU------ACUAUAuCCGGUA-----CUCC-----------UUC------------GGG 211 >,,,,,,,,,,,,<<<<___>>>> 120 cAAUUUUUGGAAGcccuccaaggg 143 :AA UUUG A CCC:CCA:GGG 212 GAAAGUUUGCUA-CCCACCACGGG 234 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz ----sequence: #24915,sp|X58844.1|TTU41 T.thermophila U4.1 snRNA ----isReversed: 0 ----hitSequence: ACCUCGCGACAGGGGCAAUAUAGCAGCAAGUGACGGUUAACUGAUGCGCUAUUAUUGCUAGUUGAAAACUACUUCAAUAAGUGGAAACGACGCUUGCGUCGGGUCCCAAUUUCUGGAAGGUCGUAUGAC hit 41 : 2 130 (fwd) 91.48 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A C U GCG +AGGGGCAAUAU:G:AGC:AGUGA G UU+ AC+GA:GC:C:AUUAUUGC 2 ACC-UCGCGACAGGGGCAAUAUAGCAGCAAGUGACGGUUA-ACUGAUGCGCUAUUAUUGC 59 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA:UUGAAAACUA U CAA:+ G:+ +A:ACGAC: +UU+ :GUCGG: U+:C 60 UAGUUGAAAACUACUU-CAAUAA---GUG-GAAACGACG-CUUG---CGUCGGG--UCCC 108 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 AAUUU+UGGAAG::C:++ :G:: 109 AAUUUCUGGAAGGUCGUA-UGAC 130 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mam.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/mam.dat.fasta.gz ----sequence: #7155,sp|AC097268.10|AC097268 Pan troglodytes BAC RP43-43O8 (Roswell Park Cancer Institute) complete sequence. ----isReversed: 1 ----hitSequence: AGCUUUGUGCAGUGGCAGUAUCGUAGCCAGUGAGGUUUAUCGGAGGUGUGAUCACUGCUAAUUGAAAACUUUUCUAUAAAGGAACUGGUCUGUAGUUAAAAAAAAAAAAUCAGUGUCACAAAGGACAAGGAAAUAUGCAACAUGUAAUCUU hit 42 : 121408 121258 (rev) 43.58 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUG GC AG GGCA:UAUC UA CCAGUGAGG+UU+ +C GAGG G GAU A:UGC 119871 AGCUUUGUGC-AGUGGCAGUAUCGUAGCCAGUGAGGUUUA-UCGGAGGUGUGAUCACUGC 119928 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<____................ 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguua................ 104 UA:U :AAAACU+UUC : A:+G ::C+ G:::: ::GUUA 119929 UAAUUGAAAACUUUUCUAUAAAGG--AACU--GGUCUGUAGUUAaaaaaaaaaaaucagu 119984 ..__>>>>>>>>>>>>>>,,,,,,,,,,,,<<<<___>>>> 105 ..uauugucggcuuuggcAAUUUUUGGAAGcccuccaaggg 143 A:: ::::C +G::AAU U G AA :::++A::: 119985 guCACAAAGGACA-AGGAAAUAU--GCAA-CAUGUAAUCUU 120021 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #4600,sp|AC012104.6|AC012104 Mus musculus chromosome , clone CT7-478J15, complete sequence. ----isReversed: 1 ----hitSequence: AGCUUUGCGCAGUGGCAGUAUCGUAGCCAAUGAGGUUUAUCCGAGGCGCGAUUAUUGCUAAACUGAAUUAGCUCCUGAGCAGGCCAACUGCCUUCUACAUGAGCCCAAGUCUCGCCCGAGCUA hit 43 : 122955 122833 (rev) 41.60 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC AG GGCA:UAUCGUAGCCA+UGAGG+UU+ +CCGAGGCGCGAUUA:UGC 1419 AGCUUUGCGC-AGUGGCAGUAUCGUAGCCAAUGAGGUUUA-UCCGAGGCGCGAUUAUUGC 1476 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA: ACU + :C+ G:+: AG:C+ ::UG U U:: +G: :+:C 1477 UAA------ACUGAAUUAGCUCCU--GAGC-AGGCCAACUGCCUUCUACAUGA---GCCC 1524 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 AA U U G G++CU A 1525 AAGUCUCGCCCGAGCU--A---- 1541 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #4703,sp|AC068665.3|AC068665 Mus musculus chromosome 5 clone RP23-426K16 strain C57BL6/J, complete sequence. ----isReversed: 1 ----hitSequence: AGCUUUGUGCAGUGGCAGUACUGUAGGUAGGUUUAUCUGAGGCGCGAUUAUUGCUAAUUGAAAAUUGGGAUACAUAUAUUUCAAUUCAUAGUAACCUGUGGUGACUGGCCACUAUAUAAAAUAGUAUAG hit 44 : 182336 182208 (rev) 17.87 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUG GC AG GGCA:UA GUAG :A GG+UU+ +C+GA: CGC UUA:UGC 23602 AGCUUUGUGC-AGUGGCAGUACUGUAGGUA----GGUUUA-UCUGAGGCGCGAUUAUUGC 23655 ,,<<<<______..._____>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>.>> 61 UAgUugAAAACU...AUUCCcaAccgCCCgccuaagacgacauguuauauugucggc.uu 116 UA:U :AAAA U AU C : A: ::: : ::::A:A: ++ :U:U:::: : 23656 UAAUUGAAAAUUgggAUAC-AUAU-----AUUUCAAUUCAUAGUAAC--CUGUGGUGaCU 23707 >>>>,,,,,,,,,,,,<<<<___>>>> 117 uggcAAUUUUUGGAAGcccuccaaggg 143 :::A U U U +AA ++ ++++ 23708 GGCCACUAUAUAAAAUAGUAUAG---- 23730 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #4792,sp|AC079245.35|AC079245 Mus musculus chromosome 9 clone rp23-426k2 strain C57BL/6J, complete sequence. ----isReversed: 1 ----hitSequence: AGCUUUGCGUAGUGGCAAUAUCAUAGCCAAUGAGGUUUAUCCAAGGGGCAAUUAUUGCUAAUUAAAGGCAACUCUUUAAAAAACAAAUAAGCAUAUAUAUAUAUAUAUAUAUAUGUGUGUGUGUGUGUGUGUG hit 45 : 173972 173840 (rev) 22.02 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCG AG GGCAAUAU :UA:CCA+UGAGG+UU+ +CC AGG:G: AUUAUUGC 39127 AGCUUUGCGU-AGUGGCAAUAUCAUAGCCAAUGAGGUUUA-UCCAAGGGGCAAUUAUUGC 39184 ,,<<<<__..._________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>> 61 UAgUugAA...AACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuu 117 UA:UU AA AACU UU AA:++ :::U:AG :::: +UAUA:::: U:U 39185 UAAUUAAAggcAACUCUUUAAAAAAC---AAAUAAG---CAUAUAUAUAUAUA----UAU 39234 >>>,,,,,,,,,,,,<<<<___>>>> 118 ggcAAUUUUUGGAAGcccuccaaggg 143 ::: AU U UG G: ::+ +:: : 39235 AUAUAUGUGUGUGUGUGUGU-GUGUG 39259 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #4840,sp|AC084070.57|AC084070 Mus musculus chromosome 5 clone rp23-268d19 strain C57BL/6J, complete sequence. ----isReversed: 0 ----hitSequence: AGCUUUGCGCAGUGGCAGUAUCGUAGCCAAUGAGGUUUAUCUGAGGCGCGAUUAUUGCAAUUGAAAAACCCUCACGGUCAGCCCCUUUUGCAGCUUUGAUUGGUUGUAACUGCUUAGAAG hit 46 : 331438 331557 (fwd) 47.24 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC AG GGCA:UAUCGUAGCCA+UGAGG+UU+ +C+GAGGCGCGAUUA:UGC 331438 AGCUUUGCGC-AGUGGCAGUAUCGUAGCCAAUGAGGUUUA-UCUGAGGCGCGAUUAUUGC 331495 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 A : AAAAC U C : +GCCC: :U +G ++ + U: : 331496 AAUUGAAAAACCCUCACGGUCAGCCCCUUU---------UGCAG--C---------UUUG 331535 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 A U UUG AA C: :+ A: :G 331536 AUUGGUUGUAA-CUGCUUAGAAG 331557 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #4856,sp|AC084322.17|AC084322 Mus musculus chromosome 5 clone rp23-376e18 strain C57BL/6J, complete sequence. ----isReversed: 0 ----hitSequence: AGCUUUGCGCAGUGGCAGUAUCGUAGCCAAUGAGGUUUAUCUGAGGCGCGAUUAUUGCAAUUGAAAAACCCUCACGGUCAGCCCCUUUUGCAGCUUUGAUUGGUUGUAACUGCUUAGAAG hit 47 : 25559 25678 (fwd) 47.24 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC AG GGCA:UAUCGUAGCCA+UGAGG+UU+ +C+GAGGCGCGAUUA:UGC 25559 AGCUUUGCGC-AGUGGCAGUAUCGUAGCCAAUGAGGUUUA-UCUGAGGCGCGAUUAUUGC 25616 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 A : AAAAC U C : +GCCC: :U +G ++ + U: : 25617 AAUUGAAAAACCCUCACGGUCAGCCCCUUU---------UGCAG--C---------UUUG 25656 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 A U UUG AA C: :+ A: :G 25657 AUUGGUUGUAA-CUGCUUAGAAG 25678 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #5328,sp|AC108950.4|AC108950 Mus musculus chromosome 9 clone RP23-458E21, complete sequence. ----isReversed: 0 ----hitSequence: AGCUUUGCGUAGUGGCAAUAUCAUAGCCAAUGAGGUUUAUCCAAGGGGCAAUUAUUGCUAAUUAAAGGCAACUCUUUAAAAAACAAAUAAGCAUAUAUAUAUAUAUAUAUAUAUGUGUGUGUGUGUGUGUGUG hit 48 : 100524 100656 (fwd) 22.02 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCG AG GGCAAUAU :UA:CCA+UGAGG+UU+ +CC AGG:G: AUUAUUGC 100524 AGCUUUGCGU-AGUGGCAAUAUCAUAGCCAAUGAGGUUUA-UCCAAGGGGCAAUUAUUGC 100581 ,,<<<<__..._________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>> 61 UAgUugAA...AACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuu 117 UA:UU AA AACU UU AA:++ :::U:AG :::: +UAUA:::: U:U 100582 UAAUUAAAggcAACUCUUUAAAAAAC---AAAUAAG---CAUAUAUAUAUAUA----UAU 100631 >>>,,,,,,,,,,,,<<<<___>>>> 118 ggcAAUUUUUGGAAGcccuccaaggg 143 ::: AU U UG G: ::+ +:: : 100632 AUAUAUGUGUGUGUGUGUGU-GUGUG 100656 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #5425,sp|AC112662.7|AC112662 Mus musculus, clone RP23-467F2, complete sequence. ----isReversed: 0 ----hitSequence: AGUUUUGAUCAGUGGCAAAAUGGAAAUCAGUGAGCUUUACCUGACGGUUGAUUAUUGCUCACUGAAAACAAUUGUAUAAAUCCACACCAAUAGUAUCAGGAUGGAAACAGAAUAGACAAGCAAACUAAGCAACUCAUUCAUGU hit 49 : 49134 49276 (fwd) 12.73 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+ UUUG C AG GGCAA AU :A AGUGAG +UU+ C+GA : AUUAUUGC 49134 AGUUUUGAUC-AGUGGCAAAAUGGAAAUCAGUGAGCUUUA-CCUGACGGUUGAUUAUUGC 49191 ,,<<<<_________..__>>>>,,,,,<<<<<<<<<<<<<<____..__>>>>>>>>>> 61 UAgUugAAAACUAUU..CCcaAccgCCCgccuaagacgacauguua..uauugucggcuu 116 U ::U:AAAAC AUU :A:: +C C:C : :::: :C :G+U+ A: G: :::: 49192 UCACUGAAAACAAUUguAUAAAU-CCACACCAAUAGUAUCAGGAUGgaAACAGAAUAGAC 49250 >>>>,,,,,,,,,,,,<<<<___>>>> 117 uggcAAUUUUUGGAAGcccuccaaggg 143 : G:AA U G AA :C:U+C A:G: 49251 AAGCAAACUAAGCAACUCAUUC-AUGU 49276 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #5434,sp|AC113004.13|AC113004 Mus musculus, clone RP23-250M13, complete sequence. ----isReversed: 0 ----hitSequence: AGCUUUGUGUAGUAGCCAUAUUGUAGCCAGUGAGGUUUAUCUGAGGCAAAAUUAUUGCUAAUUGAAAUUCUUCCCAAUACAUUGCCGCAACAACUUGCAAUACAGUCGGCAUUGACAAUUGUUGGCAGGAUGUAUGGAGACUAAAUAAC hit 50 : 176261 176409 (fwd) 63.86 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUG G AG GC:AUAU: +AGCCAGUGAGG+UU+ +C+GAGGC+ :AUUAU:GC 176261 AGCUUUGUGU-AGUAGCCAUAUUGUAGCCAGUGAGGUUUA-UCUGAGGCAAAAUUAUUGC 176318 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA:UUGAA A U UUCCCAA:++ G C :::AC AC:+G +AUA+:GU GG:::UG C 176319 UAAUUGAA-AUUCUUCCCAAUACAUUGCC-GCAACAACUUGCAAUACAGUCGGCAUUGAC 176376 ,,,,,,,,,,,,<<<<__.........._>>>> 121 AAUUUUUGGAAGcccucc..........aaggg 143 AAUU UUGG AG: ::++ A:: : 176377 AAUUGUUGGCAGGAUGUAuggagacuaaAUAAC 176409 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #5444,sp|AC113127.6|AC113127 Mus musculus, clone RP23-352H13, complete sequence. ----isReversed: 1 ----hitSequence: AGCUUUGCACAGCAGCAGUAUCGUAGCCAAUGAGGCUUAUCCAAGGCAGGAUUAUUGUUAAUUGAAAACUGUUUUUCUUUUGUGCUGUAUUUAUUUAUUUAUUUAUUUAUUCAUUCAUUCAUUCAUUCAUUUUUUAUAGCAACAAAGACU hit 51 : 162233 162084 (rev) 24.06 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGC C AG GCA:UAUC +AGCCA+UGAGGCUU+ +CC AGGC+ GAUUA:UG 23569 AGCUUUGCAC-AGCAGCAGUAUCGUAGCCAAUGAGGCUUA-UCCAAGGCAGGAUUAUUGU 23626 ,,<<<<_________..__>>>>,,,,,<<<<<<<<<<<<<<____.............. 61 UAgUugAAAACUAUU..CCcaAccgCCCgccuaagacgacauguua.............. 104 UA: :AAAACU UU C: : :+ ::G::: :A UUA 23627 UAAUUGAAAACUGUUuuUCUUUU-----GUG-CUGUAUUUA-UUUAuuuauuuauuuauu 23679 __>>>>>>>>>>>>>>.,,,,,,,,,,,,<<<<___>>>> 105 uauugucggcuuuggc.AAUUUUUGGAAGcccuccaaggg 143 A U: :::C::U+: AUUUUU + AG :: +A:: 23680 CA-UUCAUUCAUUCAUuCAUUUUUUAUAGCAACAAAGACU 23718 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #5469,sp|AC114005.5|AC114005 Mus musculus chromosome 8 clone RP23-179L18, complete sequence. ----isReversed: 1 ----hitSequence: AGCUUUUCGCAGUGGCAGUAUCGUAGCCAAUGAGGUUUAUCCGAGGCACAAUUAUUGCUAACUGAAAGAUUUAAAGAAAGAAAGUGAAAAAGAUCUCAGAAGAUGGAAAAACCUCCUAUGCUCAUAGAUC hit 52 : 70581 70452 (rev) 32.74 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUU CGC AG GGCA:UAU G+AGCCA+UGAGG+UU+ +CCGAGGC+C AUUA:UGC 144152 AGCUUUUCGC-AGUGGCAGUAUCGUAGCCAAUGAGGUUUA-UCCGAGGCACAAUUAUUGC 144209 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>.>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauuguc.ggcuuugg 119 UA::U:AAA U+U :A:: ::+ :::::GA:A +++ A U:UC :::::U+: 144210 UAACUGAAAGAUUUA--AAGA-----AAG-AAAGUGAAA--AAG-A-UCUCaGAAGAUGG 144257 >,,,,,,,,,,,,<<<<___>>>> 120 cAAUUUUUGGAAGcccuccaaggg 143 :AA +U A : :: A:: : 144258 AAAAACCUCCUAUGCUCAUAGAUC 144281 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #5618,sp|AC117206.3|AC117206 Mus musculus chromosome 5 clone RP23-260L17, complete sequence. ----isReversed: 0 ----hitSequence: AGCUUUCCAUAGUGGAAUUAUUGCAGCCAGUGAGGUUUAUCUGAGGCGUGGUUAUUGCUAAUUGAAAUUAUAGAUGCUGUCCAAUUGUUUUAUAGUAUUUUACCCACACCUUUUUCAAAAGGACUUCCAGAAAAUA hit 53 : 840 975 (fwd) 20.60 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUU C AG GG A+UA :AGCCAGUGAGG+UU+ +C+GAGGC: UUA+UGC 840 AGCUUUCCAU-AGUGGAAUUAUUGCAGCCAGUGAGGUUUA-UCUGAGGCGUGGUUAUUGC 897 ,,<<<<_________.......__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>> 61 UAgUugAAAACUAUU.......CCcaAccgCCCgccuaagacgacauguuauauugucgg 113 UA:UUGAA A UAU CCAA: : :U:+:::G:::+ U+ +:::C:: 898 UAAUUGAA-AUUAUAgaugcugUCCAAU-----UGUUUUAUAGUAUUUUAC-CCACACCU 950 >>>>>>>,,,,,,,,,,,,<<<<___>>>> 114 cuuuggcAAUUUUUGGAAGcccuccaaggg 143 :+:U: :AA +U AG+ ++++ 951 UUUUCAAAAGGACUUCCAGAAAAUA----- 975 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #6022,sp|AC122057.3|AC122057 Mus musculus chromosome 9 clone RP24-468F14, complete sequence. ----isReversed: 1 ----hitSequence: AUCUGCUCUUAGUUGUAGUAUCAUAGCUAAUGAGGUUUAUCCUAGGCACAAUUAUUGCUAAUUAAAAACUUUUCCCAAUACCCUGCCGUGACAACUUGCAGUACACUCAGCAAUUGGCAAUUUUUUACAGUCUCUACAGAGA hit 54 : 85081 84940 (rev) 64.65 bits ::::::::::.:::::::<<-<<<<<-<<<_________________>>>>>>>>-->>, 1 AuCUUUGCGC.UAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuG 59 AUC UGC C UAG G A:UAU :+AGC:A+UGAGG+UU+ +CC A:GC+: AUUA:UG 84735 AUC--UGCUCuUAGUUGUAGUAUCAUAGCUAAUGAGGUUUA-UCCUAGGCACAAUUAUUG 84791 ,,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>.>>>> 60 CUAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggc.uuug 118 CUA:UU AAAACU+UUCC AA:++CC GCC ::GA A :+G ++UA+: U GC ::UG 84792 CUAAUUAAAAACUUUUCCCAAUACCCUGCC-GUGACAACUUGCAGUACACUCAGCaAUUG 84850 >>,,,,,,,,,,,,<<<<__._>>>> 119 gcAAUUUUUGGAAGcccucc.aaggg 143 GCAAUUUUU + AG:C::++ A::G: 84851 GCAAUUUUUUACAGUCUCUAcAGAGA 84876 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #6055,sp|AC122241.4|AC122241 Mus musculus chromosome 15 clone RP23-146M20, complete sequence. ----isReversed: 0 ----hitSequence: AGCUUUGUGCAGUGGCAGGCUUGUAGCCGAUGAGGUUUAUCUGAGGGCGUGAUUAUUUCUAAUUGAAAACUUCAUUACUUAUUCAGGAUUGCUUACUCUAUUUGAAGGUCAUAUUUCCUUAAAUUCUAAGAGAUUUUUGAAG hit 55 : 105098 105239 (fwd) 29.06 bits :::::::::::::::::<<-<<<<<-<<<_________________.>>>>>>>>-->>, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGA.ggcgcgauUAuuG 59 A+CUUUG GC AG GGCA: U UAGCC +UGAGG+UU+ +C+GA GGCG A UA:U 105098 AGCUUUGUGC-AGUGGCAGGCUUGUAGCCGAUGAGGUUUA-UCUGAgGGCGUGAUUAUUU 105155 ,,,<<<<_________..__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>... 60 CUAgUugAAAACUAUU..CCcaAccgCCCgccuaagacgacauguuauauugucggc... 114 CUA:U :AAAACU+ C: A: + : + A+: C :::U+U+ U::: G : 105156 CUAAUUGAAAACUUCAuuACUUAUUC---AGG-AUUGCUUACUCUAU-UUGAAGGUCaua 105210 .>>>>>>,,,,,,,,,,,,<<<<___>>>> 115 .uuuggcAAUUUUUGGAAGcccuccaaggg 143 +U + :AA UU+U + AG::::+ :::: 105211 uUUCCUUAAAUUCUAAGAGAUUUUU-GAAG 105239 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #7487,sp|AC132684.3|AC132684 Mus musculus chromosome 9 clone RP23-277L20, complete sequence. ----isReversed: 0 ----hitSequence: CGCAUGCGCAGUGGCAGUAUCGUAGCCAAUGAGGUUUAUUGGAGGCACGAUUAUUGCUAAUUGAAAGAAAGCAAACUGAGAAAGUCAUGGAUAACAAACAUGGAUAAGAAGUCUGUAGUCUGUGCUUCAG hit 56 : 128360 128489 (fwd) 18.82 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 +C UGCGC AG GGCA:UAUCG+AGCCA+UGAGG+UU+ + GAGGC+CGAUUA:UGC 128360 CGC-AUGCGC-AGUGGCAGUAUCGUAGCCAAUGAGGUUUA-UUGGAGGCACGAUUAUUGC 128416 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA:UUGAAA A CAA: :: : : :G: +G + A+ :C: : :U :: 128417 UAAUUGAAA--GAAAG-CAAA-----CUG-AGAAAGUCAUGGAUAACAAACAUGGAUAAG 128467 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 AA U+UG A C: C :G 128468 AA-GUCUGUAGUCUGUGCUUCAG 128489 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #7644,sp|AE014182.1|AE014182 Mus musculus piebald deletion region section 10 of 11 of the complete sequence. ----isReversed: 1 ----hitSequence: AGCUUUGUGCAGUGGCAGUUAUCGUAGCCAAUGAGGUUUAUCUGAGGCGUGAUUAUUGCUAGCUGAAGACUUUUCCCAGCCUCUGUCAUUAUACCAAAAUAGUUAAGAUGAUAAACACGGAAGCUUGCUUUAUG hit 57 : 364170 364037 (rev) 54.07 bits :::::::::::::::::<<-.<<<<<-<<<_________________>>>>>>>>-->>, 1 AuCUUUGCGCUAGGGGCaaU.aucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuG 59 A+CUUUG GC AG GGCA:U AUC UAGCCA+UGAGG+UU+ +C+GAGGCG GAUUA:UG 35860 AGCUUUGUGC-AGUGGCAGUuAUCGUAGCCAAUGAGGUUUA-UCUGAGGCGUGAUUAUUG 35917 ,,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 60 CUAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 CUAG:UGAA ACU+UUCCCA:C :CU++ A::A: +++A :U::G UG: 35918 CUAGCUGAAGACUUUUCCCAGC-----CUCUGUCAUUAUACCAAAAUAGUUAAGA--UGA 35970 >,,,,,,,,,,,,<<<<___>>>> 120 cAAUUUUUGGAAGcccuccaaggg 143 AA + GGAAGC ::C :: G 35971 UAAACAC-GGAAGCUUGCUUUAUG 35993 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #23796,sp|AL355176.10|AL355176 Mouse DNA sequence from clone RP21-505L19 on chromosome 5 ----isReversed: 1 ----hitSequence: AGCUUUAUACAUUGGUAGUGUUAUAGCCAGUGAUGUUUAUCUGAGGUGCAAUUAUAGCUAACUGAAAACUUUUCUGGAUACCCUGCUGUUAUAACUUGAAAUAUAGUUGGCAUUGGCAAUUUUUGAUAGUUUCUAUGGAAA hit 58 : 130740 130600 (rev) 66.50 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUU C A GG :U U::UA CCAGUGA G+UU+ +C+GAGG G::A UA: GC 20610 AGCUUUAUAC-AUUGGUAGUGUUAUAGCCAGUGAUGUUUA-UCUGAGGUGCAAUUAUAGC 20667 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA::: AAAACU+UUC :::++CC GC: :::A: AC:UG++AUAU:GU :G:::U:GC 20668 UAACUGAAAACUUUUCUGGAUACCCUGCU-GUUAUAACUUGAAAUAUAGUUGGCAUUGGC 20726 ,,,,,,,,,,,,<<<<__._>>>> 121 AAUUUUUGGAAGcccucc.aaggg 143 AAUUUUUG+ AG::::++ +:::: 20727 AAUUUUUGAUAGUUUCUAuGGAAA 20750 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #23801,sp|AL359381.8|AL359381 Mouse DNA sequence from clone CT7-87K14 on chromosome 17 ----isReversed: 1 ----hitSequence: AGCUUUUCACAGUGGCAGUAUUGUAGCCAAUGAGGUUUAUCCAAGGCAAGAUUAUUGCUAAUUGAGAACAUUUCUCCUCCACGUGUGUGCAUGGCAGCCAUCUCCUUGCUGUCUGUGUUGAGUCACUGAUAAUAUAGUGAAAUUUCCAUAC hit 59 : 43846 43696 (rev) 23.49 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUU C C AG GGCA:UAU +AGCCA+UGAGG+UU+ +CC AGGC+ AUUA:UGC 59072 AGCUUUUCAC-AGUGGCAGUAUUGUAGCCAAUGAGGUUUA-UCCAAGGCAAGAUUAUUGC 59129 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<____................ 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguua................ 104 UA: GA AAC +UUC C : :C ::G:+: CAUG A 59130 UAAUUGAGAACAUUUCUCCUC-----CAC-GUGUGUGCAUGGCAgccaucuccuugcugu 59183 ...__>>>>>>>>>>>>>>,,,,,,,,,,,,<<<<___>>>> 105 ...uauugucggcuuuggcAAUUUUUGGAAGcccuccaaggg 143 U UUG :+:C::UG: AAU U GAA :::UCC A::: 59184 cugUGUUG-AGUCACUGAUAAUAUAGUGAA-AUUUCC-AUAC 59222 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #24990,sp|AL670851.6|AL670851 Mouse DNA sequence from clone RP23-414J20 on chromosome 4 ----isReversed: 1 ----hitSequence: AGCUUUGCGAAUUGGCUGUAUUGUAGUCCAUGAGGUUUAUCCGAGGCGCAAUUAUUGCUAAUUGAAAACUUUUCCCAAUACCCUGCCAUGAUGACUUGAAAUAAAGUCGGCAUUGGCAAUUUUUGACAGUCUCUACUGAGAC hit 60 : 159966 159825 (rev) 101.11 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCG A GGC :UAU:GUAG C +UGAGG+UU+ +CCGAG CGC:AUUA: GC 48117 AGCUUUGCGA-AUUGGCUGUAUUGUAGUCCAUGAGGUUUA-UCCGAGGCGCAAUUAUUGC 48174 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA:UUGAAAACU+UUCCCAA:++CC GCC A:GA:GAC: G++AUA :GUC:GC:UUGGC 48175 UAAUUGAAAACUUUUCCCAAUACCCUGCC-AUGAUGACUUGAAAUAAAGUCGGCAUUGGC 48233 ,,,,,,,,,,,,<<<<__..._>>>> 121 AAUUUUUGGAAGcccucc...aaggg 143 AAUUUUUG+ A ::CUC +AG:: 48234 AAUUUUUGACA-GUCUCUacuGAGAC 48258 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #25391,sp|AL691413.5|AL691413 Mouse DNA sequence from clone RP23-309E11 on chromosome 11 ----isReversed: 1 ----hitSequence: AGCUUUGAGCACUAGCUAUAACCUGUCUUCUCUGAGGUGCAAUUGUUGCUAAUUGAAUUAUCCCAAUACCUUACCACGAUGACUUGAAAUAUAGUCAGCAUUGACAAUUCCUGAUAGUCUCUAUAGAGA hit 61 : 109845 109717 (rev) 26.00 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUG GC A GC AUA :CC GU CUU +C+GAGG:GC AUU U GC 54203 AGCUUUGAGC-ACUAGCUAUA-----ACCUGU----CUUC-UCUGAGGUGCAAUUGUUGC 54251 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA:UUGAA U+ UCCCAA:++C : C A:GA:GAC:UG++AUAU:GUC:GC:UUG : 54252 UAAUUGAA---UUAUCCCAAUACCUUACC-ACGAUGACUUGAAAUAUAGUCAGCAUUGAC 54307 ,,,,,,,,,,,,<<<<__._>>>> 121 AAUUUUUGGAAGcccucc.aaggg 143 AAUU +UG+ AG:C::++ A::G: 54308 AAUUCCUGAUAGUCUCUAuAGAGA 54331 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #25854,sp|AL732620.14|AL732620 Mouse DNA sequence from clone RP23-167G19 on chromosome 2 ----isReversed: 1 ----hitSequence: AGCUUUGCGUAGUGGCAGUAUUGUAGCCAGUGAGGUUUAUCUGAGGCAUGAUUAUUGCUAAUUGAAAACUUUCCCCAAUACCCUGUCAUGACUACCUGCAGUACAGUCAGCAUUGGCAAUUUCUGACAGUCUUUAUGGAGA hit 62 : 2320 2180 (rev) 100.34 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCG AG GGCA:UAU +AGCCAGUGAGG+UU+ +C+GAGGC+ AUUA:UGC 227797 AGCUUUGCGU-AGUGGCAGUAUUGUAGCCAGUGAGGUUUA-UCUGAGGCAUGAUUAUUGC 227854 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA:UUGAAAACU+U CCCAA:++CC G:C A:GA AC:+G ++UA+:GU GC:UUG:C 227855 UAAUUGAAAACUUUCCCCAAUACCCUGUC-AUGACUACCUGCAGUACAGUCAGCAUUGGC 227913 ,,,,,,,,,,,,<<<<__._>>>> 121 AAUUUUUGGAAGcccucc.aaggg 143 AAUUU+UG+ AG:C::++ +::G: 227914 AAUUUCUGACAGUCUUUAuGGAGA 227937 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #26156,sp|AL805952.11|AL805952 Mouse DNA sequence from clone RP23-125H10 on chromosome 4 ----isReversed: 0 ----hitSequence: AUUUGCACAGCAGCAAUGCUGUAGCCAGUGAAGUAUAUCUGGAGAACUACUGCUAGUUGAAAACUUUCUCCAAAUUCUUAAGGAUGCUCUUCCUCGUAGAUUUGGAGAAUGAAGGCCCUUGCC hit 63 : 38808 38930 (fwd) 13.93 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A UUUGC C AG GCA U: : +A:C AGUGA G+ U+ +C G:+ : :UA UGC 38808 A--UUUGCAC-AGCAGCAAUGCUGUAGCCAGUGAAGUAUA-UC---UGGAGAACUACUGC 38860 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA UUGAAAACU+U CCAA ::C :A::+ : :++UU +: : +::U: G:: 38861 UAGUUGAAAACUUUCUCCAAA-----UUCUUAAGGAUGCUCUUCCUCGUA-GAUUUGGAG 38914 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 AAU GAA ::C C G:: 38915 AAU-----GAA-GGCCCU-UGCC 38930 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #26454,sp|AL833781.5|AL833781 Mouse DNA sequence from clone RP23-447J12 on chromosome 4 ----isReversed: 1 ----hitSequence: AGCUUUGCGCAGUGGCAGUAUAGUAGCCAAUGAGGCUUAUCCAAGGCGCGUUUAUUGCUAAUUGAAAACUUAAAAUAUGGAGAGAACCCCUGGGUAUUUACUAUACAGUUAGAUUAACUCUAUUUAGUUAGUCACAG hit 64 : 39540 39404 (rev) 42.21 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC AG GGCA:UA GUAGCCA+UGAGGCUU+ +CC AGGCGC UUA:UGC 126161 AGCUUUGCGC-AGUGGCAGUAUAGUAGCCAAUGAGGCUUA-UCCAAGGCGCGUUUAUUGC 126218 ,,<<<<_________.......__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>> 61 UAgUugAAAACUAUU.......CCcaAccgCCCgccuaagacgacauguuauauugucgg 113 UA:U::AAAACU+ ::A:C+CC G + A: ::A +UA A U::+ 126219 UAAUUGAAAACUUAAaauauggAGAGAACCCCUGGG-UAU-UUACU--AUACA-GUUAGA 126273 >>>>>>>,,,,,,,,,,,,<<<<___>>>> 114 cuuuggcAAUUUUUGGAAGcccuccaaggg 143 :U ++ C AUUU AG::::+C :::: 126274 UUAACUCUAUUU-----AGUUAGUC-ACAG 126297 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #26678,sp|AL844867.3|AL844867 Mouse DNA sequence from clone RP23-17B8 on chromosome X ----isReversed: 1 ----hitSequence: AGCUUUGUCCAGUGUCAGUAUCAUAGCCAGUGAGGUUUAUCCAAAGAAUGAUUAUUGCUAAUAGAUAGCUAGAGCUUUAGGCGAGUAUCAAGGCAUCCAUACGUCUGGGAAUGAUUAUAAUAUCCUUUGAC hit 65 : 78490 78360 (rev) 21.41 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUG C AG G CA:UAUC:+A C AGUGAGG+UU+ +CC A G +:GAUUA:UGC 96767 AGCUUUGUCC-AGUGUCAGUAUCAUAGCCAGUGAGGUUUA-UCCAAAGAAUGAUUAUUGC 96824 ,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 61 UAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 UA:U :A A CUA C : A: C+ A : :+ : :++U : : +: : U+G 96825 UAAUAGAUAGCUAGAgCUUUAG-----GCG-AGUAUCAAGGCAUC--CAUACGUC--UGG 96874 >,,,,,,,,,,,,<<<<___>>>> 120 cAAUUUUUGGAAGcccuccaaggg 143 AAU UU AA ::C + G:: 96875 GAAUGAUUAUAAUAUCCUU-UGAC 96897 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #26997,sp|AL928715.10|AL928715 Mouse DNA sequence from clone RP23-373D16 on chromosome 2 ----isReversed: 1 ----hitSequence: AGCUUGGCACAGUGGCAGUAUUGUAGCCAAUGAAGUUUAUCAGAGGUGCAAUUAUUACUAAUGGGAAGUUUGAACCAAUAUACUCUCUCCAAAACCCACUCAUUCUAUAGAAAUUCUUGCCAACGAGAAUUCCAUAUAUGAACCCCAGGGUAC hit 66 : 3810 3658 (rev) 22.51 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUU GC C AG GGCA:UAU:GUA CCA+UGA G+UU+ +C GAGG GC:AUUA:U C 133056 AGCUUGGCAC-AGUGGCAGUAUUGUAGCCAAUGAAGUUUA-UCAGAGGUGCAAUUAUUAC 133113 ,,<<<<_________..__>>>>,,,,,<<<<<<<<<<<<<<____.......__>>>>> 61 UAgUugAAAACUAUU..CCcaAccgCCCgccuaagacgacauguua.......uauuguc 111 UA:U:: AA U+ C ::A:++ C ::C:: : C+ : U++U AU : + 133114 UAAUGGGAAGUUUGAacCAAUAUACUCUCUCCAAAACCCACUCAUUcuauagaAAUUCUU 133173 >>>>>>>>>,,,,,,,,,,,,<<<<__..._>>>> 112 ggcuuuggcAAUUUUUGGAAGcccucc...aaggg 143 G : ::G::AAUU + + A : ::CC +:: : 133174 GCCAACGAGAAUUCCAUAUAUGAACCCcagGGUAC 133208 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #76728,sp|M10328.1|MMUR57S Mouse 5.7S U4 small nuclear RNA type a. ----isReversed: 0 ----hitSequence: AGCUUUGCGCAGUGGCAGUAUCGUAGCCAAUGAGGUUUAUCCGAGGCGCGAUUAUUGCUAAUUGAAAACUUUUCCCAAUACCCCGCCAUGACGACUUGAAAUAUAGUCGGCAUUGGCAAUUUUUGACAGUCUCUACGGAGA hit 67 : 2 142 (fwd) 130.89 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC AG GGCA:UAUCGUAGCCA+UGAGG+UU+ +CCGAGGCGCGAUUA:UGC 2 AGCUUUGCGC-AGUGGCAGUAUCGUAGCCAAUGAGGUUUA-UCCGAGGCGCGAUUAUUGC 59 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA:UUGAAAACU+UUCCCAA:++CCCGCC A:GACGAC:UG++AUAU:GUCGGC:UUGGC 60 UAAUUGAAAACUUUUCCCAAUACCCCGCC-AUGACGACUUGAAAUAUAGUCGGCAUUGGC 118 ,,,,,,,,,,,,<<<<__._>>>> 121 AAUUUUUGGAAGcccucc.aaggg 143 AAUUUUUG+ AG:C::++ +::G: 119 AAUUUUUGACAGUCUCUAcGGAGA 142 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #76729,sp|M18004.1|MMUR57T Mouse 5.7S U4 small nuclear RNA type b. ----isReversed: 0 ----hitSequence: AGCUUUGCGCAGUGGCAGUAUCGUAGCCAAUGAGGUUUAUCCGAGGCGCGAUUAUUGCUAAUUGAAAACUUUUCCCAAUACCCCGCCGUGACGACUUGCAAUAUAGUCGGCAUUGGCAAUUUUUGACAGUCUCUACGGAGA hit 68 : 2 142 (fwd) 129.24 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC AG GGCA:UAUCGUAGCCA+UGAGG+UU+ +CCGAGGCGCGAUUA:UGC 2 AGCUUUGCGC-AGUGGCAGUAUCGUAGCCAAUGAGGUUUA-UCCGAGGCGCGAUUAUUGC 59 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA:UUGAAAACU+UUCCCAA:++CCCGCC ::GACGAC:UG +AUAU:GUCGGC::UGGC 60 UAAUUGAAAACUUUUCCCAAUACCCCGCC-GUGACGACUUGCAAUAUAGUCGGCAUUGGC 118 ,,,,,,,,,,,,<<<<__._>>>> 121 AAUUUUUGGAAGcccucc.aaggg 143 AAUUUUUG+ AG:C::++ +::G: 119 AAUUUUUGACAGUCUCUAcGGAGA 142 ----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: #2285,sp|AB023028.1|AB023028 Arabidopsis thaliana genomic DNA, chromosome 5, TAC clone:K20J1. ----isReversed: 1 ----hitSequence: AUCUUUGCGCUUGGGGCAAUGACGCAGCUAAUGAGGUUCUAACCGAGGCGCGUCUAUUGCUGGUUGAAAACUAUUUCCAAACCCCCUCCUAGGCCU hit 69 : 96 1 (rev) 48.08 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUCUUUGCGCU+GGGGCAAU::CG:AGC:A+UGAGG+U+UAACCGA:GC:CG::UAUUGC 36148 AUCUUUGCGCUUGGGGCAAUGACGCAGCUAAUGAGGUUCUAACCGAGGCGCGUCUAUUGC 36207 ,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 61 UAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 U+GUU:AAAACUAUU CC:AACC+CC :C U++ 36208 UGGUUGAAAACUAUUuCCAAACCCCCUCC-------------UAG--------------- 36239 >,,,,,,,,,,,,<<<<___>>>> 120 cAAUUUUUGGAAGcccuccaaggg 143 : CCU 36240 G-------------CCU------- 36243 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #2591,sp|AB026295.2|AB026295 Oryza sativa (japonica cultivar-group) genomic DNA, chromosome 6, clone:P0681F10. ----isReversed: 1 ----hitSequence: AUCUUUGCGCUUGGGGCAAUGACGCAGCUUAUGAGGUUAUACCGAGGCGCGUCAAUUGCUGGUUGAAAACUAUUUCCAAACCCCCUCUUUGGCCCACCCGGGCCACUGAGAAUUUCUGGAAGGGCUCUCUCUCUUCGGAGAGAGUAAAGCC hit 70 : 157499 157349 (rev) 91.41 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUCUUUGCGCU+GGGGCAAU::CG:AGC: +UGAGG+U U ACCGA:GC:CG:: AUUGC 12873 AUCUUUGCGCUUGGGGCAAUGACGCAGCUUAUGAGGUUAU-ACCGAGGCGCGUCAAUUGC 12931 ,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 61 UAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 U+GUU:AAAACUAUU CC:AACC+C ::CU :G:C::: :::G:C: UG: 12932 UGGUUGAAAACUAUUuCCAAACCCC--CUCUUUGGCCCAC--------CCGGGCCACUGA 12981 >,,,,,,,,,,,,<<<<__.................._>>>> 120 cAAUUUUUGGAAGcccucc..................aaggg 143 :AAUUU+UGGAAG::CUC AAG:: 12982 GAAUUUCUGGAAGGGCUCUcucucuucggagagaguaAAGCC 13023 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #8693,sp|AC005405.1|AC005405 BAC F18A17 from chromosome V containing TINY at 60.5 cM, complete sequence. ----isReversed: 1 ----hitSequence: AUCUUUGCGCUUGGGGCAAUGACGCAGCUAAUGAGGUCUUAACCGAGGCGCGUCUAUUGCUGGUUGAAAACUAUUUCCAAACCCCCUCCUAGGCCUAAGCUUGUCUAGGGCCUUCGAGAAUUUCUGGAAGGGCUCCCUUCGGGGUAAAGCC hit 71 : 5525 5375 (rev) 119.67 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUCUUUGCGCU+GGGGCAAU::CG:AGC:A+UGAGG+ UUAACCGA:GC:CG::UAUUGC 88838 AUCUUUGCGCUUGGGGCAAUGACGCAGCUAAUGAGGUCUUAACCGAGGCGCGUCUAUUGC 88897 ,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 61 UAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 U+GUU:AAAACUAUU CC:AACC+C ::C::AG:C: :A:+UU+ :U: :G:CU::G: 88898 UGGUUGAAAACUAUUuCCAAACCCC--CUCCUAGGCCUAAGCUUG-UCUAGGGCCUUCGA 88954 >,,,,,,,,,,,,<<<<__.........._>>>> 120 cAAUUUUUGGAAGcccucc..........aaggg 143 :AAUUU+UGGAAG::CUCC AAG:: 88955 GAAUUUCUGGAAGGGCUCCcuucgggguaAAGCC 88988 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #8969,sp|AC009322.1|AC009322 Arabidopsis thaliana chromosome I BAC F18B13 genomic sequence, complete sequence. ----isReversed: 0 ----hitSequence: AGCUAGUGCUAUAAUGACGCAGCUAAUGAGGUACUAACCGAGGCGCGUCUAUUGCUGGUUGAAAACUAUUUCCAAACCCCCUCAUGGGCCUGGGCUUGACCUAUGGCCUUUGAGAAUUUCUGGAAGGGCUCCCUUCGGGGUAAAGCC hit 72 : 17890 18036 (fwd) 84.98 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+C U G GCUA AAU::CG:AGC:A+UGAGG+ +UAACCGA:GC:CG::UAUUGC 17890 AGC-UAGUGCUA----UAAUGACGCAGCUAAUGAGGUACUAACCGAGGCGCGUCUAUUGC 17944 ,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 61 UAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 U+GUU:AAAACUAUU CC:AACC+C ::C:::G:C: ::+UU+ :: :G:C:::G: 17945 UGGUUGAAAACUAUUuCCAAACCCC--CUCAUGGGCCUGGGCUUGACCUAUGGCCUUUGA 18002 >,,,,,,,,,,,,<<<<__.........._>>>> 120 cAAUUUUUGGAAGcccucc..........aaggg 143 :AAUUU+UGGAAG::CUCC AAG:: 18003 GAAUUUCUGGAAGGGCUCCcuucgggguaAAGCC 18036 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #9031,sp|AC011717.6|AC011717 Arabidopsis thaliana chromosome 1 BAC F19K16 genomic sequence, complete sequence. ----isReversed: 1 ----hitSequence: AGCUAGUGCUAUAAUGACGCAGCUAAUGAGGUACUAACCGAGGCGCGUCUAUUGCUGGUUGAAAACUAUUUCCAAACCCCCUCAUGGGCCUGGGCUUGACCUAUGGCCUUUGAGAAUUUCUGGAAGGGCUCCCUUCGGGGUAAAGCC hit 73 : 23054 22908 (rev) 84.98 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+C U G GCUA AAU::CG:AGC:A+UGAGG+ +UAACCGA:GC:CG::UAUUGC 88248 AGC-UAGUGCUA----UAAUGACGCAGCUAAUGAGGUACUAACCGAGGCGCGUCUAUUGC 88302 ,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 61 UAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 U+GUU:AAAACUAUU CC:AACC+C ::C:::G:C: ::+UU+ :: :G:C:::G: 88303 UGGUUGAAAACUAUUuCCAAACCCC--CUCAUGGGCCUGGGCUUGACCUAUGGCCUUUGA 88360 >,,,,,,,,,,,,<<<<__.........._>>>> 120 cAAUUUUUGGAAGcccucc..........aaggg 143 :AAUUU+UGGAAG::CUCC AAG:: 88361 GAAUUUCUGGAAGGGCUCCcuucgggguaAAGCC 88394 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #9081,sp|AC015986.4|AC015986 Arabidopsis thaliana chromosome 1 BAC T2E12 genomic sequence, complete sequence. ----isReversed: 1 ----hitSequence: AUCUUUGCGCUUGUGCAAAAUGACGCAGCUAAUGAGGUCUUAGUCUAAUACUGGUUGAAAACUAUUUCCAAACAUCUUCCUAGGCCUAGGCUUAUUUUGGACUUUCUAGAAUUUGUGGAAGUGCAUC hit 74 : 23477 23351 (rev) 30.54 bits :::::::::::::::.::<<-<<<<<-<<<_________________>>>>>>>>-->>, 1 AuCUUUGCGCUAGGG.GCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuG 59 AUCUUUGCGCU+G G A U CG AG::A+UGAGG+ UU A::C UA U 11753 AUCUUUGCGCUUGUGcAAAAUGACGCAGCUAAUGAGGUCUU-----AGUC-----UAAUA 11802 ,,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>.>>> 60 CUAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggc.uuu 117 CU+GUU:AAAACUAUU CC:AAC+ C :: ::AG:C: :::+UUA ::: :G:C U:: 11803 CUGGUUGAAAACUAUUuCCAAACAUC--UUCCUAGGCCUAGGCUUA--UUUUGGACuUUC 11858 >>>,,,,,,,,,,,,<<<<___>>>> 118 ggcAAUUUUUGGAAGcccuccaaggg 143 ::AAUUU UGGAAG +C++C 11859 UAGAAUUUGUGGAAGUGCAUC----- 11879 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #9082,sp|AC016041.5|AC016041 Genomic sequence for Arabidopsis thaliana BAC F27J15 from chromosome I, complete sequence. ----isReversed: 0 ----hitSequence: AUCUUUGCGCUUGGGGCAAUGACGCAGCUAAUGAGGUUCUAACCGAGGCGCGUCUAUUGCUGGUUGAAAACUAUUUCCAAACCCCCUCCUGGGCCUAAGCUUGUCUUGGGCCUUCGAGAAUUUCUGGAAGGGCUCCCUUCGGGGUAAAGCC hit 75 : 932 1082 (fwd) 120.96 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUCUUUGCGCU+GGGGCAAU::CG:AGC:A+UGAGG+U+UAACCGA:GC:CG::UAUUGC 932 AUCUUUGCGCUUGGGGCAAUGACGCAGCUAAUGAGGUUCUAACCGAGGCGCGUCUAUUGC 991 ,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 61 UAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 U+GUU:AAAACUAUU CC:AACC+C ::C:::G:C: :A:+UU+ :U: :G:C:::G: 992 UGGUUGAAAACUAUUuCCAAACCCC--CUCCUGGGCCUAAGCUUG-UCUUGGGCCUUCGA 1048 >,,,,,,,,,,,,<<<<__.........._>>>> 120 cAAUUUUUGGAAGcccucc..........aaggg 143 :AAUUU+UGGAAG::CUCC AAG:: 1049 GAAUUUCUGGAAGGGCUCCcuucgggguaAAGCC 1082 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #9085,sp|AC016447.5|AC016447 Arabidopsis thaliana chromosome 1 BAC T22E19 genomic sequence, complete sequence. ----isReversed: 1 ----hitSequence: AUCUUUGCGCUUGUGCAAAAUGACGCAGCUAAUGAGGUCUUAGUCUAAUACUGGUUGAAAACUAUUUCCAAACAUCUUCCUAGGCCUAGGCUUAUUUUGGACUUUCUAGAAUUUGUGGAAGUGCAUC hit 76 : 224 98 (rev) 30.54 bits :::::::::::::::.::<<-<<<<<-<<<_________________>>>>>>>>-->>, 1 AuCUUUGCGCUAGGG.GCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuG 59 AUCUUUGCGCU+G G A U CG AG::A+UGAGG+ UU A::C UA U 107593 AUCUUUGCGCUUGUGcAAAAUGACGCAGCUAAUGAGGUCUU-----AGUC-----UAAUA 107642 ,,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>.>>> 60 CUAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggc.uuu 117 CU+GUU:AAAACUAUU CC:AAC+ C :: ::AG:C: :::+UUA ::: :G:C U:: 107643 CUGGUUGAAAACUAUUuCCAAACAUC--UUCCUAGGCCUAGGCUUA--UUUUGGACuUUC 107698 >>>,,,,,,,,,,,,<<<<___>>>> 118 ggcAAUUUUUGGAAGcccuccaaggg 143 ::AAUUU UGGAAG +C++C 107699 UAGAAUUUGUGGAAGUGCAUC----- 107719 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #9093,sp|AC016827.7|AC016827 Arabidopsis thaliana chromosome III BAC F17A9 genomic sequence, complete sequence. ----isReversed: 1 ----hitSequence: AUCUUUGCGCUUGGGGCAAUGACGCAGCUAAUGAGGUACUAACCGAGGCGCGUCUAUUGCUGGUUGAAAACUAUUUCCAAACCCCCUCCUGGGCCUAAGCUUGUCUUGGGCCUUCGAGAAUUUCUGGAAGGGCUCCCUUUGGGGUAAAGCC hit 77 : 17430 17280 (rev) 117.82 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUCUUUGCGCU+GGGGCAAU::CG:AGC:A+UGAGG+ +UAACCGA:GC:CG::UAUUGC 72713 AUCUUUGCGCUUGGGGCAAUGACGCAGCUAAUGAGGUACUAACCGAGGCGCGUCUAUUGC 72772 ,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 61 UAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 U+GUU:AAAACUAUU CC:AACC+C ::C:::G:C: :A:+UU+ :U: :G:C:::G: 72773 UGGUUGAAAACUAUUuCCAAACCCC--CUCCUGGGCCUAAGCUUG-UCUUGGGCCUUCGA 72829 >,,,,,,,,,,,,<<<<__.........._>>>> 120 cAAUUUUUGGAAGcccucc..........aaggg 143 :AAUUU+UGGAAG::CUCC AAG:: 72830 GAAUUUCUGGAAGGGCUCCcuuugggguaAAGCC 72863 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #9254,sp|AC068901.8|AC068901 Arabidopsis thaliana chromosome 1 BAC F1O3 genomic sequence, complete sequence. ----isReversed: 1 ----hitSequence: AUCGGCGCUUGGGGCACUGAUGCAAAUAGUGAUAUUUUAACUGAGGCACGUCUAUUACUUGCUGGUUGAAAACUGUUUCUAAACUUUCUCUUCGAUUUGGGCUUGGGUUUGGGCUUGAACCACGGCCUUUGAAUUUUUUUCCAAAGAUUC hit 78 : 66902 66753 (rev) 23.10 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>--.... 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUA.... 56 AUC GCGCU+GGGGCA:U:: G:A ::AGUGA +UUUAAC+GA:: :C ::UA 7364 AUC--GGCGCUUGGGGCACUGAUGCAAAUAGUGAUAUUUUAACUGAGGCACGUCUAuuac 7421 >>,,,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<____........... 57 uuGCUAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguua........... 104 :UGCU+GUU:AAAACU UU C :AAC C :C: ::GA: ::: +UU+ 7422 UUGCUGGUUGAAAACUGUUuCUAAACUUUC-UCU-UCGAUUUGGGCUUGgguuugggcuu 7479 __>>>>>>>>>>>>>>,,,,,,,,,,,,<<<<___>>>> 105 uauugucggcuuuggcAAUUUUUGGAAGcccuccaaggg 143 A ::: :GC::U:G:A UUUUU A +++U+C 7480 GAACCACGGCCUUUGAAUUUUUUUCCAAAGAUUC----- 7513 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #9264,sp|AC069160.7|AC069160 Arabidopsis thaliana chromosome 1 BAC T9I1 genomic sequence, complete sequence. ----isReversed: 0 ----hitSequence: AUCUUUGCGCUUGGGGCAAUGACAUAGCUAAUGAGGUUUUAAACGAGACGCGUCUAUUGAUGGUUGACAACCAUUUCCACAACCCCAUCCUAGGCCUAAGCUUGUCUUUGGCCUUUGAGAAUUUCGAGACCAACACUAG hit 79 : 78990 79128 (fwd) 70.46 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUCUUUGCGCU+GGGGCAAU::C:UAG :A+UGAGG+UUUAA CGA: CG:G::UAUUG 78990 AUCUUUGCGCUUGGGGCAAUGACAUAGCUAAUGAGGUUUUAAACGAGACGCGUCUAUUGA 79049 ,,<<<<_________..__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>> 61 UAgUugAAAACUAUU..CCcaAccgCCCgccuaagacgacauguuauauugucggcuuug 118 U+GUUGA AAC AUU C CAACC+C ::C::AG:C: :A:+UU+ :U: :G:CU::G 79050 UGGUUGACAACCAUUucCACAACCCC--AUCCUAGGCCUAAGCUUG-UCUUUGGCCUUUG 79106 >>,,,,,,,,,,,,<<<<___>>>> 119 gcAAUUUUUGGAAGcccuccaaggg 143 ::AAUUU+ G+ A C ::C+ :: G 79107 AGAAUUUC-GAGA-CCAACA-CUAG 79128 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #9285,sp|AC069556.4|AC069556 Genomic Sequence For Arabidopsis thaliana Clone T1G16 From Chromosome V, complete sequence. ----isReversed: 0 ----hitSequence: AUCUUUGCGCUUGGGGCAAUGACGCAGCUAAUGAGGUAUUAACCGAGGCGCGUCUAUUGCUGGUUGAAAACUAUUUCCAAACCCCCUCCUAGGCCUAAGCUUGUCUUGGGCCUCUGAGAAUUUCUGGAAGAGCUCC hit 80 : 53184 53319 (fwd) 116.50 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUCUUUGCGCU+GGGGCAAU::CG:AGC:A+UGAGG+ UUAACCGA:GC:CG::UAUUGC 53184 AUCUUUGCGCUUGGGGCAAUGACGCAGCUAAUGAGGUAUUAACCGAGGCGCGUCUAUUGC 53243 ,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 61 UAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 U+GUU:AAAACUAUU CC:AACC+C ::C: AG:C: :A:+UU+ :U: :G:CU :G: 53244 UGGUUGAAAACUAUUuCCAAACCCC--CUCCUAGGCCUAAGCUUG-UCUUGGGCCUCUGA 53300 >,,,,,,,,,,,,<<<<___>>>> 120 cAAUUUUUGGAAGcccuccaaggg 143 :AAUUU+UGGAAG++CUCC 53301 GAAUUUCUGGAAGAGCUCC----- 53319 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #9896,sp|AC137830.6|AC137830 Medicago truncatula clone mth2-33g10, complete sequence. ----isReversed: 1 ----hitSequence: AUCUUUGUGUUUGGGGGCAAUGACACAGCUAACGAGCUUUUAACCAAGGCGUGUCUAUUGCUGCUGGUUGAAAACUAUUUUCAAAUCCCUUCUUAAGCUUAAGACAACUCAAGUCUUUGAGAAUUACUGGAAGGACUCCCUUUAAAGUAAAGUC hit 81 : 101635 101482 (rev) 73.15 bits ::::::::::::.:::::<<-<<<<<-<<<_________________>>>>>>>>-->>, 1 AuCUUUGCGCUA.GGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuG 59 AUCUUUG G U+ GGGGCAAU::C::AGC:A+ GAG +UUUAACC A:GC::G::UAUUG 12221 AUCUUUGUGUUUgGGGGCAAUGACACAGCUAACGAGCUUUUAACCAAGGCGUGUCUAUUG 12280 ,,...,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>> 60 CU...AgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggcu 115 CU +:UU:AAAACUAUU C:AA:C+C ::CU:A: C:::A: +A :U:::G :U 12281 CUgcuGGUUGAAAACUAUUuUCAAAUCCC--UUCUUAAGCUUAAGACAA--CUCAAGUCU 12336 >>>>>,,,,,,,,,,,,<<<<__.........._>>>> 116 uuggcAAUUUUUGGAAGcccucc..........aaggg 143 :UG::AAUU +UGGAAG::CUCC AAG:: 12337 UUGAGAAUUACUGGAAGGACUCCcuuuaaaguaAAGUC 12374 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #99395,sp|AP003760.4|AP003760 Oryza sativa (japonica cultivar-group) genomic DNA, chromosome 1, BAC clone:OSJNBb0063G05. ----isReversed: 1 ----hitSequence: AUCUUUGCGCUUGGGGCAAUGACGCAGCUAGUGAGGUAAUACCGAGGCGCGUCAAUUGCUGGUUGAAAACUAUUUCCAAACCCCCUCUUUGGCCCGUCAGGGCCACUGAGAAUUUCUGGAAGGGCUCCUUCUCUUCGGGGAGGGUAAAGCC hit 82 : 10053 9903 (rev) 97.16 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUCUUUGCGCU+GGGGCAAU::CG:AGC:AGUGAGG+ U ACCGA:GC:CG:: AUUGC 172629 AUCUUUGCGCUUGGGGCAAUGACGCAGCUAGUGAGGUAAU-ACCGAGGCGCGUCAAUUGC 172687 ,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 61 UAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 U+GUU:AAAACUAUU CC:AACC+C ::CU :G:C::+ U A ::G:C: UG: 172688 UGGUUGAAAACUAUUuCCAAACCCC--CUCUUUGGCCCG---UCA-----GGGCCACUGA 172737 >,,,,,,,,,,,,<<<<__.................._>>>> 120 cAAUUUUUGGAAGcccucc..................aaggg 143 :AAUUU+UGGAAG::CUCC AAG:: 172738 GAAUUUCUGGAAGGGCUCCuucucuucggggaggguaAAGCC 172779 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #100144,sp|AP006099.1|AP006099 Lotus corniculatus var. japonicus genomic DNA, chromosome 5, clone:LjT03D07, TM0180a. ----isReversed: 0 ----hitSequence: AUCUUUGCGCUUGGGGCAAUGACGCAGCUUAUGAGGUUCUAACCGAGGCGCGUCUAUUGCUGGUUGAAAACUAUUUCCAAACCCCCUCUUAGGCCUGGGUUCACCCCUGGCCUUCGAGAAUUUCUGGAAGGGCUCCCUUUGGGGUAAAGCU hit 83 : 69439 69589 (fwd) 108.40 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUCUUUGCGCU+GGGGCAAU::CG:AGC: +UGAGG+U+UAACCGA:GC:CG::UAUUGC 69439 AUCUUUGCGCUUGGGGCAAUGACGCAGCUUAUGAGGUUCUAACCGAGGCGCGUCUAUUGC 69498 ,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 61 UAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 U+GUU:AAAACUAUU CC:AACC+C ::C :AG:C: ::: U A ::: :G:CU: G: 69499 UGGUUGAAAACUAUUuCCAAACCCC--CUCUUAGGCCUGGGUUCA-CCCCUGGCCUUCGA 69555 >,,,,,,,,,,,,<<<<__.........._>>>> 120 cAAUUUUUGGAAGcccucc..........aaggg 143 :AAUUU+UGGAAG :CUCC AAG: 69556 GAAUUUCUGGAAGGGCUCCcuuugggguaAAGCU 69589 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #101415,sp|AC002131.1|ATAC2131 Arabidopsis thaliana chromosome 1 BAC F12F1 sequence, complete sequence. ----isReversed: 0 ----hitSequence: AUCUUUGCGCUUGGGGCAAUGACGCAGCUAAUGAGGUCUUAACCGAGGCGCGUCUAUUGCUGGUUGAAAACUAUUUCCAAACCCCCUCCUAGGCCUAAGCUUGUCUUGGGCCUUCGAGAAUUUCUGGAAGGGUUCCCUUCGGGGUAAAGC hit 84 : 107603 107752 (fwd) 118.02 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUCUUUGCGCU+GGGGCAAU::CG:AGC:A+UGAGG+ UUAACCGA:GC:CG::UAUUGC 107603 AUCUUUGCGCUUGGGGCAAUGACGCAGCUAAUGAGGUCUUAACCGAGGCGCGUCUAUUGC 107662 ,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 61 UAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 U+GUU:AAAACUAUU CC:AACC+C ::C::AG:C: :A:+UU+ :U: :G:CU::G: 107663 UGGUUGAAAACUAUUuCCAAACCCC--CUCCUAGGCCUAAGCUUG-UCUUGGGCCUUCGA 107719 >,,,,,,,,,,,,<<<<__........._>>>> 120 cAAUUUUUGGAAGcccucc.........aaggg 143 :AAUUU+UGGAAG: :UCC AA: : 107720 GAAUUUCUGGAAGGGUUCCcuucgggguAAAGC 107752 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #101505,sp|AF007270.1|ATAF7270 Arabidopsis thaliana BAC F2P16, complete sequence. ----isReversed: 1 ----hitSequence: AUCUUUGCGCUUGGGGCAAUGACGCAGCUAAUGAGGUCUUAACCGAGGCGCGUCUAUUGCUGGUUGAAAACUAUUUCCAAACCCCCUCCUAGGCCUAAGCUUGUCUUGGGCCUUCGAGAAUUUCUGGAAGAGCUCC hit 85 : 95661 95526 (rev) 119.59 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUCUUUGCGCU+GGGGCAAU::CG:AGC:A+UGAGG+ UUAACCGA:GC:CG::UAUUGC 15286 AUCUUUGCGCUUGGGGCAAUGACGCAGCUAAUGAGGUCUUAACCGAGGCGCGUCUAUUGC 15345 ,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 61 UAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 U+GUU:AAAACUAUU CC:AACC+C ::C::AG:C: :A:+UU+ :U: :G:CU::G: 15346 UGGUUGAAAACUAUUuCCAAACCCC--CUCCUAGGCCUAAGCUUG-UCUUGGGCCUUCGA 15402 >,,,,,,,,,,,,<<<<___>>>> 120 cAAUUUUUGGAAGcccuccaaggg 143 :AAUUU+UGGAAG++CUCC 15403 GAAUUUCUGGAAGAGCUCC----- 15421 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #103562,sp|AJ505691.1|ATH505691 Arabidopsis thaliana partial putative U4.1 small nuclear RNA (U4.1 snRNA gene), clone Ath-188a, 5' end incomplete ----isReversed: 0 ----hitSequence: GGCAAUGACGCAGCUAAUGAGGUCUUAACCGAGGCGCGUCUAUUGCUGGUUGAAAACUAUUUCCAAACCCCCUCCUAGGCCUAAGCUUGUCUUGGGCCUUCGAGAAUUUCUGGAAGGGUUCCCUUCGGGGUAAAGC hit 86 : 1 136 (fwd) 73.26 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 GGCAAU::CG:AGC:A+UGAGG+ UUAACCGA:GC:CG::UAUUGC 1 --------------GGCAAUGACGCAGCUAAUGAGGUCUUAACCGAGGCGCGUCUAUUGC 46 ,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 61 UAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 U+GUU:AAAACUAUU CC:AACC+C ::C::AG:C: :A:+UU+ :U: :G:CU::G: 47 UGGUUGAAAACUAUUuCCAAACCCC--CUCCUAGGCCUAAGCUUG-UCUUGGGCCUUCGA 103 >,,,,,,,,,,,,<<<<__........._>>>> 120 cAAUUUUUGGAAGcccucc.........aaggg 143 :AAUUU+UGGAAG: :UCC AA: : 104 GAAUUUCUGGAAGGGUUCCcuucgggguAAAGC 136 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #103563,sp|AJ505692.1|ATH505692 Arabidopsis thaliana partial putative U4.1 small nuclear RNA (U4.1 snRNA gene), clone Ath-188b, 5' end incomplete ----isReversed: 0 ----hitSequence: CAAUGACGCAGCUAAUGAGGUUCUAACCGAGGCGCGUCUAUUGCUGGUUGAAAACUAUUUCCAAACCCCCUCCUGGGCCUAAGCUUGUCUUGGGCCUUCGAGAAUUUCUGGAAGGGCUCCCUUCGGGGUAAAGCC hit 87 : 1 135 (fwd) 69.72 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 CAAU::CG:AGC:A+UGAGG+U+UAACCGA:GC:CG::UAUUGC 1 ----------------CAAUGACGCAGCUAAUGAGGUUCUAACCGAGGCGCGUCUAUUGC 44 ,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 61 UAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 U+GUU:AAAACUAUU CC:AACC+C ::C:::G:C: :A:+UU+ :U: :G:C:::G: 45 UGGUUGAAAACUAUUuCCAAACCCC--CUCCUGGGCCUAAGCUUG-UCUUGGGCCUUCGA 101 >,,,,,,,,,,,,<<<<__.........._>>>> 120 cAAUUUUUGGAAGcccucc..........aaggg 143 :AAUUU+UGGAAG::CUCC AAG:: 102 GAAUUUCUGGAAGGGCUCCcuucgggguaAAGCC 135 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #119574,sp|X67145.1|ATU41SN A.thaliana U4.1 snRNA gene ----isReversed: 0 ----hitSequence: AUCUUUGCGCUUGGGGCAAUGACGCAGCUAAUGAGGUUCUAACCGAGGCGCGUCUAUUGCUGGUUGAAAACUAUUUCCAAACCCCCUCCUAGGCCUAAGCUUGUCUUAGGCCUUCGAGAAUUUCUGGAAGGGCUCCCUUUGGGGUAAAGCC hit 88 : 194 344 (fwd) 123.34 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUCUUUGCGCU+GGGGCAAU::CG:AGC:A+UGAGG+U+UAACCGA:GC:CG::UAUUGC 194 AUCUUUGCGCUUGGGGCAAUGACGCAGCUAAUGAGGUUCUAACCGAGGCGCGUCUAUUGC 253 ,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 61 UAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 U+GUU:AAAACUAUU CC:AACC+C ::C::AG:C:::A:+UU+ :U:::G:CU::G: 254 UGGUUGAAAACUAUUuCCAAACCCC--CUCCUAGGCCUAAGCUUG-UCUUAGGCCUUCGA 310 >,,,,,,,,,,,,<<<<__.........._>>>> 120 cAAUUUUUGGAAGcccucc..........aaggg 143 :AAUUU+UGGAAG::CUCC AAG:: 311 GAAUUUCUGGAAGGGCUCCcuuugggguaAAGCC 344 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #119577,sp|X67146.1|ATU42SN A.thaliana U4.2 snRNA gene ----isReversed: 0 ----hitSequence: AUCUUUGCGCUUGGGGCAAUGACGCAGCUAAUGAGGUACUAACCGAGGCGCGUCUAUUGCUGGUUGAAAACUAUUUCCAAACCCCCUCCUGGGCCUAAGCUUGUCUUGGGCCUUCGAGAAUUUCUGGAAGGGCUCCCUUUGGGUAAAGCC hit 89 : 296 445 (fwd) 118.16 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUCUUUGCGCU+GGGGCAAU::CG:AGC:A+UGAGG+ +UAACCGA:GC:CG::UAUUGC 296 AUCUUUGCGCUUGGGGCAAUGACGCAGCUAAUGAGGUACUAACCGAGGCGCGUCUAUUGC 355 ,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 61 UAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 U+GUU:AAAACUAUU CC:AACC+C ::C:::G:C: :A:+UU+ :U: :G:C:::G: 356 UGGUUGAAAACUAUUuCCAAACCCC--CUCCUGGGCCUAAGCUUG-UCUUGGGCCUUCGA 412 >,,,,,,,,,,,,<<<<__........._>>>> 120 cAAUUUUUGGAAGcccucc.........aaggg 143 :AAUUU+UGGAAG::CUCC AAG:: 413 GAAUUUCUGGAAGGGCUCCcuuuggguaAAGCC 445 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #119585,sp|X67147.1|ATU43SN A.thaliana U4.3 snRNA pseudogene ----isReversed: 0 ----hitSequence: AUCGUUGCGCUUGGACAAUGACACAUCUAAUGAGGUUCUAACCGAGAUGCGUCUAUGCUGGUUGAAAACUAUUUCUAAACCCCCUCCUAACCCUAAGUUUGUCUUGGGCCUUGGAGAAUUUUUGUAUUUCCUUUGGGU hit 90 : 239 376 (fwd) 71.00 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUC UUGCGC + GG CAAU::C::A :A+UGAGG+U+UAACCGA: ::G::UA UGC 239 AUCGUUGCGC-UUGGACAAUGACACAUCUAAUGAGGUUCUAACCGAGAUGCGUCUA-UGC 296 ,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 61 UAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 U+GUU:AAAACUAUU C :AACC+C ::C::A: C: :A: UU+ :U: :G :U::G: 297 UGGUUGAAAACUAUUuCUAAACCCC--CUCCUAACCCUAAGUUUG-UCUUGGGCCUUGGA 353 >,,,,,,,,,,,,<<<<___>>>> 120 cAAUUUUUGGAAGcccuccaaggg 143 :AAUUUUUG A :CC:+ :GG: 354 GAAUUUUUGUAUUUCCUUU-GGGU 376 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #158266,sp|AY198655.1|AY198655 Arabidopsis thaliana sequence flanking Ds3 end of Ds-EnhancerTrap insertion from line ET2049. ----isReversed: 1 ----hitSequence: AGCUAAUGAGGUACUAACCGAGGCGCGUCUAUUGCUGGUUGAAAACUAUUUCCAAACCCCCUCAUGGGCCUGGGCUUGACCUAUGGCCUUUGAGAAUUUCUGGAAGGGCUCCCUUCGGGGUAAAGCC hit 91 : 478 352 (rev) 30.14 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CU AAU:: GUA C:A ACCGA:GCGC ::UAUUGC 1 AGCU-------------AAUGAGGUA-CUA-----------ACCGAGGCGCGUCUAUUGC 35 ,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 61 UAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 U+GUU:AAAACUAUU CC:AACC+C ::C:::G:C: ::+UU+ :: :G:C:::G: 36 UGGUUGAAAACUAUUuCCAAACCCC--CUCAUGGGCCUGGGCUUGACCUAUGGCCUUUGA 93 >,,,,,,,,,,,,<<<<__.........._>>>> 120 cAAUUUUUGGAAGcccucc..........aaggg 143 :AAUUU+UGGAAG::CUCC AAG:: 94 GAAUUUCUGGAAGGGCUCCcuucgggguaAAGCC 127 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #182775,sp|X71485.1|CRRNAU4A C.reinhardtii U4 snRNA ----isReversed: 0 ----hitSequence: AUCCUUGCGCUUGGGGCAGUGUCGCAGACUGUGAGGUCUAACCGAGUCGCGACAGUGCCAGUUGAAAACUUAUUCCAUCCCCGUCGGUCGUCGUUCUUCGGAACGCUUCCGCAAUUUCUGUCGGGCCUUUUGGC hit 92 : 1 134 (fwd) 58.79 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUC UUGCGCU+GGGGCA:U:UCG:AG:C GUGAGG+ U+ ACCGAG:C:CGA: A:UGC 1 AUCCUUGCGCUUGGGGCAGUGUCGCAGACUGUGAGGUCUA-ACCGAGUCGCGAC-AGUGC 58 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 AG UGAAAACU+ U CCA CC+C G: ::: +:: ++UU + ::+ ::: :C 59 CAGUUGAAAACUUAUUCCAUCCCC--GUC-GGUCGUCGUUCUU---CGGAACGCUUCCGC 112 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 AAUUU+UG G:CC + GG: 113 AAUUUCUGUCGGGCCUUU-UGGC 134 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #202810,sp|X15931.1|PSSNU4A Pea U4 snRNA (clone pPSUN4.1) ----isReversed: 0 ----hitSequence: AUCUUUGCGCUUGGGGCAAUGACGCAGCUAGUGAGGUACUAACCGAGGCGCGUCUAUUGCUGGUUGAAAACUAUUUCCAAACCCCCUCUUGGGCCUGGGCUUUGCUUGGGCCUUUGAGAAUUUCUGGAAGGGCUCCCUCUGGGUAAAGCC hit 93 : 1 150 (fwd) 115.06 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUCUUUGCGCU+GGGGCAAU::CG:AGC:AGUGAGG+ +UAACCGA:GC:CG::UAUUGC 1 AUCUUUGCGCUUGGGGCAAUGACGCAGCUAGUGAGGUACUAACCGAGGCGCGUCUAUUGC 60 ,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 61 UAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 U+GUU:AAAACUAUU CC:AACC+C ::C :+G:+:::::G U U :::::+:C+:UG: 61 UGGUUGAAAACUAUUuCCAAACCCC--CUC-UUGGGCCUGGGCUUUGCUUGGGCCUUUGA 117 >,,,,,,,,,,,,<<<<__........._>>>> 120 cAAUUUUUGGAAGcccucc.........aaggg 143 :AAUUU+UGGAAG::CUCC AAG:: 118 GAAUUUCUGGAAGGGCUCCcucuggguaAAGCC 150 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #202811,sp|X15932.1|PSSNU4B Pea U4 snRNA (clone pPSU4.2) ----isReversed: 0 ----hitSequence: AUCUUUGCGCUUGGGGCAAUGACGCAGCUAGUGAGGUUCUAACCGAGGUGCGUCUAUUGCUGGUUGAAAACUAUUUCCAAACCCCCUCUUAGGCUUGAGGCAACUCAAGCCUUUGAGAAUUUUUGGAAGGACUCCCUUAGGGUAAAGUC hit 94 : 1 149 (fwd) 126.33 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUCUUUGCGCU+GGGGCAAU::CG:A C:AGUGAGG+U+UAACCGA:G :CG::UAUUGC 1 AUCUUUGCGCUUGGGGCAAUGACGCAGCUAGUGAGGUUCUAACCGAGGUGCGUCUAUUGC 60 ,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 61 UAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 U+GUU:AAAACUAUU CC:AACC+C ::CU:AG:C:::A:G +A :U:::G:CU:UG: 61 UGGUUGAAAACUAUUuCCAAACCCC--CUCUUAGGCUUGAGGCAA--CUCAAGCCUUUGA 116 >,,,,,,,,,,,,<<<<__........._>>>> 120 cAAUUUUUGGAAGcccucc.........aaggg 143 :AAUUUUUGGAAG::CUCC AAG:: 117 GAAUUUUUGGAAGGACUCCcuuaggguaAAGUC 149 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #202812,sp|X15933.1|PSSNU4C Pea U4 snRNA (clone pPSU4.3) ----isReversed: 0 ----hitSequence: AUCUUUGCGCUUGGGGCAAUGACGCAGCUAGUGAGGUUCUAACCGAGGCGCGUCUAUUGCUGGUUGAAAACUAUUUCCAAACCCCCUCUUAGGCUUGAGGUAACUCAAGCCUUUGAGAAUUUCUGGAAGGGCUCCCUUAGGGUAAAGUC hit 95 : 1 149 (fwd) 128.35 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUCUUUGCGCU+GGGGCAAU::CG:AGC:AGUGAGG+U+UAACCGA:GC:CG::UAUUGC 1 AUCUUUGCGCUUGGGGCAAUGACGCAGCUAGUGAGGUUCUAACCGAGGCGCGUCUAUUGC 60 ,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 61 UAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 U+GUU:AAAACUAUU CC:AACC+C ::CU:AG:C:::A:GU+A :U:::G:CU:UG: 61 UGGUUGAAAACUAUUuCCAAACCCC--CUCUUAGGCUUGAGGUAA--CUCAAGCCUUUGA 116 >,,,,,,,,,,,,<<<<__........._>>>> 120 cAAUUUUUGGAAGcccucc.........aaggg 143 :AAUUU+UGGAAG: CUCC AAG : 117 GAAUUUCUGGAAGGGCUCCcuuaggguaAAGUC 149 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #212198,sp|X07112.1|VFU4A Vicia faba U4A small nuclear RNA ----isReversed: 0 ----hitSequence: AUCUUUGCGCUUGGGGCAAUGACGUAGCUAGUGAGGUUCUAACCGAGGCGCGUCUAUUGCUGGUUGAAAACUAUUUGCCAAACCCCUCUUAGGCUUGGGCUUGGGUUCAAGCCUUUGAGAAUUUCUGGAAGGACUCCCUUUGGGGUAAAGUC hit 96 : 1 152 (fwd) 124.22 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUCUUUGCGCU+GGGGCAAU::CGUAGC:AGUGAGG+U+UAACCGA:GCGCG::UAUUGC 1 AUCUUUGCGCUUGGGGCAAUGACGUAGCUAGUGAGGUUCUAACCGAGGCGCGUCUAUUGC 60 ,,<<<<_________..__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>> 61 UAgUugAAAACUAUU..CCcaAccgCCCgccuaagacgacauguuauauugucggcuuug 118 U+GUU:AAAACUAUU CC:AACC+ ::CU:AG:C:::::+UU+ :::::G:CU:UG 61 UGGUUGAAAACUAUUugCCAAACCC---CUCUUAGGCUUGGGCUUGGGUUCAAGCCUUUG 117 >>,,,,,,,,,,,,<<<<__.........._>>>> 119 gcAAUUUUUGGAAGcccucc..........aaggg 143 ::AAUUU+UGGAAG::CUCC AAG:: 118 AGAAUUUCUGGAAGGACUCCcuuugggguaAAGUC 152 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pln.dat.fasta.gz ----sequence: #212199,sp|X07113.1|VFU4B Vicia faba U4B small nuclear RNA ----isReversed: 0 ----hitSequence: AUCUUUGCGCUUGGGGCAAUGACGUAGCUAGUGAGGUUCUAACCGAGGCGCGUCUAUUGCUGGUUGAAAACUAUUUCUAAACCCCCUCUUAGGCUUGAGUUUAACUCAAGCCUUUGAGAAUUUCUGGAAGGACUCCUUCGGGGUAAAGUC hit 97 : 1 150 (fwd) 125.03 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 AUCUUUGCGCU+GGGGCAAU::CGUAGC:AGUGAGG+U+UAACCGA:GCGCG::UAUUGC 1 AUCUUUGCGCUUGGGGCAAUGACGUAGCUAGUGAGGUUCUAACCGAGGCGCGUCUAUUGC 60 ,,<<<<_________.__>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 61 UAgUugAAAACUAUU.CCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 U+GUU:AAAACUAUU C :AACC+C ::CU:AG:C:::A: UUA A:U:::G:CU:UG: 61 UGGUUGAAAACUAUUuCUAAACCCC--CUCUUAGGCUUGAGUUUA-ACUCAAGCCUUUGA 117 >,,,,,,,,,,,,<<<<__........._>>>> 120 cAAUUUUUGGAAGcccucc.........aaggg 143 :AAUUU+UGGAAG::CUCC AAG:: 118 GAAUUUCUGGAAGGACUCCuucgggguaAAGUC 150 ----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: #1527,sp|AC131886.5|AC131886 Rattus norvegicus 4 BAC CH230-53A1 (Children's Hospital Oakland Research Institute) complete sequence. ----isReversed: 0 ----hitSequence: AGCUUUGCGCAGUGGCAGUAUCGUAGCCUAUGAGGUUUAUCCGAGGCGCGAUUAUUGCUAAUUGAAAACUUUUCCCUAAAGAGAAAUUAAGUACCUCAUCUAAGACUCCUUUAGAUGCAAUAGAGCAUAGUUUGUAAGCUCCACAAAU hit 98 : 52109 52256 (fwd) 60.30 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC AG GGCA:UAUCGUAGCC +UGAGG+UU+ +CCGAGGCGCGAUUA:UGC 52109 AGCUUUGCGC-AGUGGCAGUAUCGUAGCCUAUGAGGUUUA-UCCGAGGCGCGAUUAUUGC 52166 ,,<<<<_________..__>>>>,,,,,<<<<<<<<<<<<<<____......__>>>>>> 61 UAgUugAAAACUAUU..CCcaAccgCCCgccuaagacgacauguua......uauugucg 112 UA:UU:AAAACU+UU C :AA:+G ::: A : C+:C U+U+A U U G:+G 52167 UAAUUGAAAACUUUUccCUAAAGAGAAAUUA-AGUACCUCAUCUAAgacuccUUUAGAUG 52225 >>>>>>>>,,,.,,,,,,,,,<<<<___>>>> 113 gcuuuggcAAU.UUUUGGAAGcccuccaaggg 143 : U+::: AU UUUG AAG : C : 52226 CAAUAGAGCAUaGUUUGUAAGCUCCAC-AAAU 52256 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/rod.dat.fasta.gz ----sequence: #13732,sp|K00782.1|RN4A Rat U4 small nuclear RNA. ----isReversed: 0 ----hitSequence: AACUUUGCAGUGGCAGUAUCGUAGCCAAUGAGGUUUAUCCGAGGCGCGAUUAUUGCUAAUUGAAAACUUUUCCCAAUACCCCGCCGUGACGACUUGAAAUAUAGUCGGCAUUGGCAAUUUUUGUCUCUACGGAGA hit 99 : 2 136 (fwd) 108.43 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A CUUUGC AG GGCA:UAUCGUAGCCA+UGAGG+UU+ +CCGAGGCGCGAUUA:UGC 2 AACUUUGC---AGUGGCAGUAUCGUAGCCAAUGAGGUUUA-UCCGAGGCGCGAUUAUUGC 57 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA:UUGAAAACU+UUCCCAA:++CCCGCC ::GACGAC:UG++AUAU:GUCGGC::UGGC 58 UAAUUGAAAACUUUUCCCAAUACCCCGCC-GUGACGACUUGAAAUAUAGUCGGCAUUGGC 116 ,,,,,,,,,,,,<<<<__._>>>> 121 AAUUUUUGGAAGcccucc.aaggg 143 AAUUUUUG :C::++ +::G: 117 AAUUUUUG----UCUCUAcGGAGA 136 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/rod.dat.fasta.gz ----sequence: #21450,sp|M26115.1|RNUGPSA Rat U4-1 small nuclear RNA pseudogene. ----isReversed: 0 ----hitSequence: AGACUUUGCGCAGUGGCAGUAUCGUAGCCAAUGAGGUUUAUCCGAGGCGCGAUUAUUGCUAAUUGAAACAUAAUAGGUUACACAGACAAUUAAU hit 100 : 29 122 (fwd) 21.53 bits ::.:::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>, 1 Au.CUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuG 59 A+ CUUUGCGC AG GGCA:UAUCGUAGCCA+UGAGG+UU+ +CCGAGGCGCGAUUA:UG 29 AGaCUUUGCGC-AGUGGCAGUAUCGUAGCCAAUGAGGUUUA-UCCGAGGCGCGAUUAUUG 86 ,,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>> 60 CUAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuugg 119 CUA:UU:AAA C :AA:+G G::: + ::: 87 CUAAUUGAAA------CAUAAUAG---GUUA-----------CAC------------AGA 114 >,,,,,,,,,,,,<<<<___>>>> 120 cAAUUUUUGGAAGcccuccaaggg 143 CAAUU AA U 115 CAAUU-----AA----U------- 122 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/rod.dat.fasta.gz ----sequence: #21451,sp|M26116.1|RNUGPSB Rat U4-2 small nuclear RNA pseudogene. ----isReversed: 0 ----hitSequence: AGCUUUGCGCAGUGGCAGUAUCGUAGCCAAUGAGGUUUAUCCGAGGCGCGAUUAUUGCUAAUUGAAAACUUAAAGAAAAGUAGUCAAUAGAAU hit 101 : 15 107 (fwd) 35.38 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC AG GGCA:UAUCGUAGCCA+UGAGG+UU+ +CCGAGGCGCGAUUA:UGC 15 AGCUUUGCGC-AGUGGCAGUAUCGUAGCCAAUGAGGUUUA-UCCGAGGCGCGAUUAUUGC 72 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA:UU:AAAACU+ :AA: G U++ C 73 UAAUUGAAAACUUAAAGAAAA-----G--------------UAG--------------UC 99 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 AAU AG+ +U 100 AAU-------AGA-AU------- 107 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/rod.dat.fasta.gz ----sequence: #21452,sp|M26117.1|RNUGPSC Rat U4-3 small nuclear RNA pseudogene. ----isReversed: 0 ----hitSequence: AGCUUUGCGCAGUGGCAGUAUCGUAGCCAAUGAGGUUUAUCCGAGGCGCGAUUAUUGCUAAUUGAAAGUCAACAUUAGGGCUGGAGAGAUA hit 102 : 1 91 (fwd) 21.74 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC AG GGCA:UAUCGUAGCCA+UGAGG+UU+ +CCGAGGCGCGAUUA:UGC 1 AGCUUUGCGC-AGUGGCAGUAUCGUAGCCAAUGAGGUUUA-UCCGAGGCGCGAUUAUUGC 58 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA:UU +AA: G:C: A+ + UUA :G:C 59 UAAUU------------GAAA-----GUCA-AC-A------UUA------------GGGC 81 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 UGGA G+++U A 82 ------UGGA-GAGAU--A---- 91 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/rod.dat.fasta.gz ----sequence: #21453,sp|M26118.1|RNUGPSD Rat U4-4 small nuclear RNA pseudogene. ----isReversed: 0 ----hitSequence: AGCUUUGCGCAGUGGCAGUAUCGUAGCCAAUGAGGUUUAUUCAAGGUGCCAUUACUGCUAAUUGAAAACUAUUAUUAUCAGAGAAAACAGGU hit 103 : 31 122 (fwd) 15.55 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC AG GGCA:UAU GUA CCA+UGAGG+UU+ + C AGG GC AUUA:UGC 31 AGCUUUGCGC-AGUGGCAGUAUCGUAGCCAAUGAGGUUUA-UUCAAGGUGCCAUUACUGC 88 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA:U :AAAACUAUU : A: : + A : 89 UAAUUGAAAACUAUUA-UUAU-----C--------------AGA---------------G 113 ,,,,,,,,,,,,<<<<___>>>> 121 AAUUUUUGGAAGcccuccaaggg 143 AA AA ++ U 114 AA-------AACAGGU------- 122 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/rod.dat.fasta.gz ----sequence: #21532,sp|K00477.1|RNURU4A Rat U4a small nuclear RNA (snRNA). ----isReversed: 0 ----hitSequence: AGCUUUGCGCAGUGGCAGUAUCGUAGCCAAUGAGGUUUAUCCGAGGCGCGAUUAUUGCUAAUUGAAAACUUUUCCCAAUACCCCGCCGUGACGACUUGCAAUAUAGUCGGCAUUGGCAAUUUUUGACAGUCUCUACGGAGA hit 104 : 2 142 (fwd) 129.24 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC AG GGCA:UAUCGUAGCCA+UGAGG+UU+ +CCGAGGCGCGAUUA:UGC 2 AGCUUUGCGC-AGUGGCAGUAUCGUAGCCAAUGAGGUUUA-UCCGAGGCGCGAUUAUUGC 59 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA:UUGAAAACU+UUCCCAA:++CCCGCC ::GACGAC:UG +AUAU:GUCGGC::UGGC 60 UAAUUGAAAACUUUUCCCAAUACCCCGCC-GUGACGACUUGCAAUAUAGUCGGCAUUGGC 118 ,,,,,,,,,,,,<<<<__._>>>> 121 AAUUUUUGGAAGcccucc.aaggg 143 AAUUUUUG+ AG:C::++ +::G: 119 AAUUUUUGACAGUCUCUAcGGAGA 142 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/rod.dat.fasta.gz ----sequence: #21533,sp|K00478.1|RNURU4B Rat U4b small nuclear RNA (snRNA). ----isReversed: 0 ----hitSequence: AGCUUUGCGCAGUGGCAGUAUCGUAGCCAAUGAGGUUUAUCCGAGGCGCGAUUAUUGCUAAUUGAAAACUUUUCCCAAUACCCCGCCGUGACGACUUGCAAUAUAGUCGGCAUUGGCAAUUUUUGACAGUCUCUACGGAGA hit 105 : 2 142 (fwd) 129.24 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC AG GGCA:UAUCGUAGCCA+UGAGG+UU+ +CCGAGGCGCGAUUA:UGC 2 AGCUUUGCGC-AGUGGCAGUAUCGUAGCCAAUGAGGUUUA-UCCGAGGCGCGAUUAUUGC 59 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA:UUGAAAACU+UUCCCAA:++CCCGCC ::GACGAC:UG +AUAU:GUCGGC::UGGC 60 UAAUUGAAAACUUUUCCCAAUACCCCGCC-GUGACGACUUGCAAUAUAGUCGGCAUUGGC 118 ,,,,,,,,,,,,<<<<__._>>>> 121 AAUUUUUGGAAGcccucc.aaggg 143 AAUUUUUG+ AG:C::++ +::G: 119 AAUUUUUGACAGUCUCUAcGGAGA 142 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/rod.dat.fasta.gz ----sequence: #21534,sp|K00479.1|RNURU4C Rat U4c small nuclear RNA (snRNA). ----isReversed: 0 ----hitSequence: AGCUUUGCGCAGUGGCAGUAUCGUAGCCAAUGAGGUUUAUCCGAGGCGCGAUUAUUGCUAAUUGAAAACUUUUCCCAAUACCCCGCCAUGACGACUUGAAAUAUAGUCGGCAUUGGCAAUUUUUGACAGUCUCUACGGAGA hit 106 : 2 142 (fwd) 130.89 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC AG GGCA:UAUCGUAGCCA+UGAGG+UU+ +CCGAGGCGCGAUUA:UGC 2 AGCUUUGCGC-AGUGGCAGUAUCGUAGCCAAUGAGGUUUA-UCCGAGGCGCGAUUAUUGC 59 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA:UUGAAAACU+UUCCCAA:++CCCGCC A:GACGAC:UG++AUAU:GUCGGC:UUGGC 60 UAAUUGAAAACUUUUCCCAAUACCCCGCC-AUGACGACUUGAAAUAUAGUCGGCAUUGGC 118 ,,,,,,,,,,,,<<<<__._>>>> 121 AAUUUUUGGAAGcccucc.aaggg 143 AAUUUUUG+ AG:C::++ +::G: 119 AAUUUUUGACAGUCUCUAcGGAGA 142 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----sequence: #42594,sp|M14136.1|GGU4BX Chicken U4X and U4B small nuclear RNA genes. ----isReversed: 0 ----hitSequence: AGCUUUGCGCAGUGGCAGUAUCGUAGCCAAUGAGGUUAAUCCGAGGCGCGAUUAUUGCUAAUUGAAAACUUUUCCCAAUACCCCGCCAUGACGACUUGAAAUAUAGUCGGCAUUGGCAAUUUUUGACAGUCUCUACGGAGA hit 107 : 1141 1281 (fwd) 127.81 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC AG GGCA:UAUCGUAGCCA+UGAGG+U + +CCGAGGCGCGAUUA:UGC 1141 AGCUUUGCGC-AGUGGCAGUAUCGUAGCCAAUGAGGUUAA-UCCGAGGCGCGAUUAUUGC 1198 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA:UUGAAAACU+UUCCCAA:++CCCGCC A:GACGAC:UG++AUAU:GUCGGC:UUGGC 1199 UAAUUGAAAACUUUUCCCAAUACCCCGCC-AUGACGACUUGAAAUAUAGUCGGCAUUGGC 1257 ,,,,,,,,,,,,<<<<__._>>>> 121 AAUUUUUGGAAGcccucc.aaggg 143 AAUUUUUG+ AG:C::++ +::G: 1258 AAUUUUUGACAGUCUCUAcGGAGA 1281 ----endhit ----hitSequence: AGCUUUGCGCAGUGGCAGUAUCGUAGCCAAUGAGGUUUAUCCGAGGCGCGAUUAUUGCUAGUUGAAAACUUUUCCCAAUACCCCGCCAUGACGACUUGAAAUAUAGUCGGCAUUGGCAAUUUUUGAGAGCCUCCCCGGAGG hit 108 : 535 675 (fwd) 135.02 bits :::::::::::::::::<<-<<<<<-<<<_________________>>>>>>>>-->>,, 1 AuCUUUGCGCUAGGGGCaaUaucguAgccAGUGAGGcUuuAaCCGAggcgcgauUAuuGC 60 A+CUUUGCGC AG GGCA:UAUCGUAGCCA+UGAGG+UU+ +CCGAGGCGCGAUUA:UGC 535 AGCUUUGCGC-AGUGGCAGUAUCGUAGCCAAUGAGGUUUA-UCCGAGGCGCGAUUAUUGC 592 ,,<<<<___________>>>>,,,,,<<<<<<<<<<<<<<______>>>>>>>>>>>>>> 61 UAgUugAAAACUAUUCCcaAccgCCCgccuaagacgacauguuauauugucggcuuuggc 120 UA:UUGAAAACU+UUCCCAA:++CCCGCC A:GACGAC:UG++AUAU:GUCGGC:UUGGC 593 UAGUUGAAAACUUUUCCCAAUACCCCGCC-AUGACGACUUGAAAUAUAGUCGGCAUUGGC 651 ,,,,,,,,,,,,<<<<__._>>>> 121 AAUUUUUGGAAGcccucc.aaggg 143 AAUUUUUG+ AGCC::CC +::GG 652 AAUUUUUGAGAGCCUCCCcGGAGG 675 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----sequence: #42713,sp|K00474.1|GGURU4A Chicken U4a small nuclear RNA (snRNA). ----isReversed: