Params: ./cmzasha --no-stderr --filter 380 20 Rfam/cm/RF00030.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00030_greedy_forwardinf_cfsqp_cycling_Saureus_0MM.bin hmm data/TryAllCm/RF00030_forwardinf_hmmtype1_Saureus_0MM.bin Build: release Host: bicycle.cs.washington.edu pid: 28810 ----hmm-from-cmFileName: Rfam/cm/RF00030.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-greedy-node 380 20.00 Rfam/cm/RF00030.cm forward-alg-inf 100000 cycling-node cfsqp-elim-gauss 0 1 Build: release Host: recycle.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Saureus_0mm.mm --cm2hmm-set-greedy-node 380 20.00 Rfam/cm/RF00030.cm forward-alg-inf 100000 cycling-node cfsqp-elim-gauss 0 1 Build: release Host: recycle.cs.washington.edu ----hmm-from-cmFileName: Rfam/cm/RF00030.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Saureus_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00030.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Saureus_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00030.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----cmFile: Rfam/cm/RF00030.cm (global) ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #43303,sp|AY090593.1|AY090593 Arxiozyma telluris RNase MRP snRNA (NME1) gene, partial sequence. ----isReversed: 0 ----hitSequence: GACCUGGUCGUAUGCGGAAAACGUAAUGAGAUUUAAAAAUUUAUAAAAUUGUUUAAAUAGACUCAUUAAUUGUCCAUUUUUAUGGGUAAUUGUUGUCCCAUCUCCUCCCUCGUGGGUGGGAUAGAUGGUGUUUUUUCGGUAUUGGAGUUCCUUUAUAUUAUAUAUAUGUAUGAACUCUAAAUCAUAGUUAUGACGAUUGCUCUUUAACAACAUGAUGUACAUUUAUGUGUGUAUCAUAGUUAUUGAGUAACCCAAUGGAGCU hit 0 : 1 262 (fwd) 78.92 bits ((((((,,,,,<<<<<<<----------<<<<<<______>>>>>>-------->>>>>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaauUUauguacucAaaacUAUGCuUuG 60 - ------------------------------------------------------------ - >,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<<<<_ 61 gGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAauuu 120 GACCUG :UCG UAUGCGG:AAACGUAAUGAGAUUUAAAA+UUU 1 ----------------GACCUG-GUCG-UAUGCGGAAAACGUAAUGAGAUUUAAAAAUUU 42 ____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<--------<<< 121 UUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUgccg 180 UAAAA+UGUUUAAAU ACUCAUUAA::: +::: UUUU :::+ U AUUG :: 43 AUAAAAUUGUUUAAAUAGACUCAUUAAUUG--UCCA----UUUU-UAUGGGUAAUUG-UU 94 <----<<<<___>>>>--.....->>>>>>>>>>>>>>>>>>>>,,,,,,,,,,,<<<<< 181 caCCugggaccuuuuuuu.....AgcgggguguugguguguguuUCGGUAcuGGAaucca 235 ++CC : : CCU : : + +::++:::U GGU::: :::UCGGUA+UGGA:U:C: 95 GUCCCAUCUCCUCCCUCGugggu-GGGAUAGAU-GGUGUU-UUUUCGGUAUUGGAGUUCC 151 <_...._____.......>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----..... 236 aa....uUUUU.......uuggauUcuAAACCAUAGUUAUgacGauUGcucUuUc..... 279 :+ UU U+ ::G:A:UCUAAA CAUAGUUAUGACGAUUGCUCUUU 152 UUuauaUUAUAuauauguAUGAACUCUAAAUCAUAGUUAUGACGAUUGCUCUUUAacaac 211 ....................<<<_____>>>--->>>::::::::::::::: 280 ....................cguuuuuggcgaUugagUAACCCAAUGGAGCU 311 : U U G :AUUGAGUAACCCAAUGGAGCU 212 augauguacauuuaugugugUAUCAUA-GUUAUUGAGUAACCCAAUGGAGCU 262 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #43304,sp|AY090594.1|AY090594 Kluyveromyces africanus RNase MRP snRNA (NME1) gene, partial sequence. ----isReversed: 0 ----hitSequence: GGAGUGUUUUACUCAAGUAUGCUUUGGGUUGAAAGUCUCCCACCUGUCAAUGUGCGGAAACGUAGUGAGAUUUAAAAAUUUAAAUUGUUUAAAUCAACUCACUAAGAAUUGGGAAGAUUCUCUUCUCUUUUCUUCACUACCUGGGACUAUCUUUGUCCCGGUGCUUUUCGGUACUGGAGUCUUUAUAGACUCUAAACCAUAGUUAUGACGAUUGCUUUGUUUUCAUUGUUUUUCUCAUGGGAAAACACGAGAACAAGGUAACCCAAUGGAGCU hit 1 : 2 274 (fwd) 151.79 bits ((((((,,,,,<<<<<<<----------<<<<<<______>>>>>>-------->>>>>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaauUUauguacucAaaacUAUGCuUuG 60 GGAGUG UUU UACUC AA UAUGCUUUG 2 ---------------------------GGAGUG--UUU---UACUC--AAGUAUGCUUUG 27 >,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<<<<_ 61 gGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAauuu 120 GGUU GAAAGUCUCC +ACCUG U::: U UG:::AAA CGUA:UGAGAUUUAAAA+U 28 GGUU-GAAAGUCUCC-CACCUG-UCAA-UGUGCGGAAA-CGUAGUGAGAUUUAAAAAU-- 80 ____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<.----.<<<<<--------< 121 UUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucg.uUuU.gcacuUcUuaUUgc 178 UUAA A+UGUUUAAAUCAACUCA:UAAGA+ +::+G::G UU U :::+:U+UU+UU C 81 UUAA-AUUGUUUAAAUCAACUCACUAAGAA--UUGGGAAGaUUCUcUUCUCUUUUCUU-C 136 <<<----<<<<___>>>>--->>>>>>>>>>>>>>>>>>>>,,,,,,,,,,,<<<<<<__ 179 cgcaCCugggaccuuuuuuuAgcgggguguugguguguguuUCGGUAcuGGAauccaaau 238 ++ ACCUGG AC+ U UUU :+::: ::U+:: UUUCGGUACUGGA:UC: U 137 ACUACCUGGGACUAUCUUU------GUCCC-GGUGCU--UUUCGGUACUGGAGUCU---U 184 ____>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----.......<<<____..... 239 UUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUc.......cguuuuu..... 286 U U :GA:UCUAAACCAUAGUUAUGACGAUUGC::U U ::UUU+U 185 UAU---AGACUCUAAACCAUAGUUAUGACGAUUGCUUUGUUuucauugUUUUUCUcaugg 241 ........._>>>--->>>::::::::::::::: 287 .........ggcgaUugagUAACCCAAUGGAGCU 311 + ::A ::GUAACCCAAUGGAGCU 242 gaaaacacgA-GAACAAGGUAACCCAAUGGAGCU 274 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #43305,sp|AY090595.1|AY090595 Kluyveromyces delphensis RNase MRP snRNA (NME1) gene, partial sequence. ----isReversed: 0 ----hitSequence: UUAACCUUCAUAUCUGCUUCGGGUCGAAAGUCUCCCACCUGGUCGUAUGCGGAAAACGUAAUGAGAUUUAAAAAUUUAUUUAAAAUGUUUAAAUCAACUCAUUGGAAAGCUAGCUCUUUCCCACAGUCCUGGGCUGUUUAAUAAACUCCCAGUCGUAUCUUUUCGGUACUGAGGCCCCAGAAAUGGGUUUCAAACCAUAGUUAUGACGAUUGCGGUUUUGCAGAAUUUUAGUAUUCUGGAUAACCGUAACCCAAUGGGGGCU hit 2 : 6 267 (fwd) 120.62 bits ((((((,,,,,<<<<<<<----------<<<<<<______>>>>>>-------->>>>>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaauUUauguacucAaaacUAUGCuUuG 60 U+A:C UU+ A++U UGCUU+G 6 -------UUAACC----------------------UUC----------AUAUCUGCUUCG 26 >,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<<<<. 61 gGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAauu. 119 :GU GAAAGUCUCC +ACCUG :UCG UAUGCGG:AAACG AAUGAGAUUUAAAAAUU 27 GGUC-GAAAGUCUCC-CACCUG-GUCG-UAUGCGGAAAACGUAAUGAGAUUUAAAAAUUu 82 _____.>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<--------< 120 uUUAa.aaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUgc 178 +UU A AAUGUUUAAAUCAACUCAUU +:A: : U UCUU ++: 83 AUUUAa-AAUGUUUAAAUCAACUCAUUGGAAA--G-------CUAG----CUCUUUCCCA 128 <<<----<<<<___>>>>--->>>>>>>>>>>>>>>>..>>>>,,,,,,,,,,,<<<<<< 179 cgcaCCugggaccuuuuuuuAgcgggguguuggugug..uguuUCGGUAcuGGAauccaa 236 ::++CCU::G ++U U::U ::: ++++ +GU+++ ::U:UCGGUACUG++::CC 129 CAGUCCUGGGCUGUUUAAU---AAACUCCC-AGUCGUauCUUUUCGGUACUGAGGCCC-- 182 _.._____>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----............<<< 237 a..uUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUc............cgu 282 U GG::U++AAACCAUAGUUAUGACGAUUGC::UUU ::U 183 -caGAAAU--GGGUUUCAAACCAUAGUUAUGACGAUUGCGGUUUUgcagaauuuuagUAU 239 _____>>>--->>>::::::::::::.::: 283 uuuuggcgaUugagUAACCCAAUGGA.GCU 311 U U G:: ::GUAACCCAAUGG+ GCU 240 UCU--GGAUAACCGUAACCCAAUGGGgGCU 267 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #43306,sp|AY090596.1|AY090596 Kluyveromyces lactis RNase MRP snRNA (NME1) gene, partial sequence. ----isReversed: 0 ----hitSequence: AUCGUCACUGAUCGAAGCUUACAUAAGGAACGGAUUUUAUCUGUUCAAUUGAAAUGAUAUCAUUUCUAUAGCUUUGGGUAGAAAGUCUCCGACCAGUCCGUAAGCGGAAACGUAAUGAGAUUUAAAAACUUUUCAAAUGUUUAAAUCAACUCAUUAAUCGUGUUGGUUUUCUGUCACGGUUUCUAUCCAGAGGCUGUUUUAGAAGCCUCUGUGUCUUGGGUACUGAAGUAUUUCUUUACUUUAAACGAAAGUUAUGACGAUUGCCCGAGCGUUUUUAUCUCUUUUUUUGUUACUUCUGUUUACAGGGGUGAUUAGGGAGGAGGUAGCUUGGGUAACCCAAUGGAGCU hit 3 : 15 361 (fwd) 152.19 bits ((((((,,,,,<<<<<<<----------<<<<<<_._____>>>>>>.--------.... 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaa.uUUauguacuc.AaaacUAU.... 54 AUCGUCACUGAUCGAAGCUUACA AA GGA::G:A UUUAU:U::UC A++ ++AU 15 AUCGUCACUGAUCGAAGCUUACAUAA-GGAACGGAuUUUAUCUGUUCaAUUGAAAUgaua 73 ...........>>>>>>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<< 55 ...........GCuUuGgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGua 103 GCUUUGGGU+ GAAAGUCUCC GACC+G U:CG UA+GCG:AAA CGUA 74 ucauuucuauaGCUUUGGGUA-GAAAGUCUCC-GACCAG-UCCG-UAAGCGGAAA-CGUA 128 <<<<<<<<<<<<<<<<_____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<--- 104 aUGaGAUUUAAAAauuuUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUu 163 AUGAGAUUUAAAAA:U UU +A:AUGUUUAAAUCAACUCAUUAA:++ + U:G+ UUU 129 AUGAGAUUUAAAAACU-UUUCAAAUGUUUAAAUCAACUCAUUAAUCG--UGUUGG--UUU 183 -<<<<<--------<<<<----<<<<___>>>>--->>>>>>>>>>>>>>>>>>>>,,,, 164 UgcacuUcUuaUUgccgcaCCugggaccuuuuuuuAgcgggguguugguguguguuUCGG 223 U +++U + UU ::: +CC G:G:C+ :U:U :::G++++ +U:U :U GG 184 U-CUGUCACGGUU-UCUAUCCAGAGGCUGUUUUA---GAAGCCUC-UGUGUC---UUGGG 234 ,,,,,,,<<<<<<______>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----.... 224 UAcuGGAauccaaauUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUc.... 279 UACUG+A:U: UU U :A:U+UAAAC A AGUUAUGACGAUUGC:C + C 235 UACUGAAGUAU---UUCU---UUACUUUAAACGAAAGUUAUGACGAUUGCCCGAGCguuu 288 ......<<<____..................................._>>>--->>>:: 280 ......cguuuuu...................................ggcgaUugagUA 298 C::UUUU G::G UUG:GUA 289 uuaucuCUUUUUUuguuacuucuguuuacaggggugauuagggaggagGUAGCUUGGGUA 348 ::::::::::::: 299 ACCCAAUGGAGCU 311 ACCCAAUGGAGCU 349 ACCCAAUGGAGCU 361 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #43307,sp|AY090597.1|AY090597 Saccharomyces barnettii RNase MRP snRNA (NME1) gene, partial sequence. ----isReversed: 0 ----hitSequence: AUGCUCUGGGCAUGAAAGUCUCCCACCUGACCGUAUGCGGAAAACGCAGUGAGAUUUAAAAAUUUUUACAAUGUUUAAAUCAACUCACUUGGACGUAUCUGUUUUGCAUAUUCUCUCUCUCUCUGCACCCUUUGGGUACCUAGAGUGGGAGGAUUGUUGAAUUGUACGUCUAGUAUUGUCCUGGCAAGUUUAAUACUUGACAGUGUAUAUUUCGGUAUUGGGACCUUGUUAGGUCCUAAACGAUAGUUAUGACGAUUGCCUAAUAUUUUUCUUAUUAGGUAACCCAAUGGAGCU hit 4 : 1 294 (fwd) 123.81 bits ((((((,,,,,<<<<<<<----------<<<<<<______>>>>>>-------->>>>>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaauUUauguacucAaaacUAUGCuUuG 60 AUGCU+UG 1 ----------------------------------------------------AUGCUCUG 8 >,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<<<<_ 61 gGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAauuu 120 GG + GAAAGUCUCC +ACCUG ::CG UAUGCG::AAACG:A:UGAGAUUUAAAAAUUU 9 GGCAUGAAAGUCUCC-CACCUG-ACCG-UAUGCGGAAAACGCAGUGAGAUUUAAAAAUUU 65 ____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----................ 121 UUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuU................ 164 UUA+ AAUGUUUAAAUCAACUCA:U:+GA: G+:::U: UUUU 66 UUAC-AAUGUUUAAAUCAACUCACUUGGAC--GUAUCUG-UUUUgcauauucucucucuc 121 .......................................<<<<<--------.<<<<--- 165 .......................................gcacuUcUuaUUg.ccgcaCC 184 ::::+ C U+U G ::+++CC 122 ucugcacccuuuggguaccuagagugggaggauuguugaAUUGUACGUCUAGuAUUGUCC 181 -<<<<___>>>>--->>>>>>>>>>>>>>>>>>>>,,,,,,,,,,,<<<<<<______>> 185 ugggaccuuuuuuuAgcgggguguugguguguguuUCGGUAcuGGAauccaaauUUUUuu 244 U:::A +UU:::U ::+:::: :G:::+U:UUUCGGUA+UGG+A:C: U UU 182 UGGCAAGUUUAAU----ACUUGAC-AGUGUAUAUUUCGGUAUUGGGACCU---UGUU--- 230 >>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<_____>>>--->>>:::::::: 245 ggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuuggcgaUugagUAACCCAA 304 :G:U+CUAAAC AUAGUUAUGACGAUUGC:: +U :+UUU+U :AUU::GUAACCCAA 231 AGGUCCUAAACGAUAGUUAUGACGAUUGCCUAAUAUUUUUCU---UAUUAGGUAACCCAA 287 ::::::: 305 UGGAGCU 311 UGGAGCU 288 UGGAGCU 294 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #43308,sp|AY090598.1|AY090598 Saccharomyces bayanus RNase MRP snRNA (NME1) gene, partial sequence. ----isReversed: 0 ----hitSequence: AUCGUCACUAAUCGAAGCUUACAAAAAUGGAGUAAAGGAAUUUUUCUUCUUACUCAAUAUUAAUGCUUUGGGUUGAAAGUCUCCCACCAAUUCAUAUGCGGAAAACGUAAUGAGAUUUAAAAAAUUUAAAUUCUUUAAAUCAACUCAUUAAGAGAAAUAUCUUUAGAUAUUUCUCUUCUUGACCCAGUACUCUGUUACAGGAGCGCUGGUGUUUUCUUCGGUACUGGAUUCCUUAUAUAUGGAAUCUAAACCAUAGUUAUGACGAUUGCUCUUUCCCAUGCUGGAUCGAGUAACCCAAUGGAGCU hit 5 : 1 305 (fwd) 219.29 bits ((((((,,,,,<<<<<<<--------.--<<<<<<_........._____>>>>>>.--- 1 auCgucAcUgAuCgAaGCUUaCAAAA.UGgagugaa.........uUUauguacuc.Aaa 49 AUCGUCACU+AUCGAAGCUUACAAAA UGGAGU::A +UU ::ACUC A+A 1 AUCGUCACUAAUCGAAGCUUACAAAAaUGGAGUAAAggaauuuuuCUUC-UUACUCaAUA 59 ----->>>>>>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<< 50 acUAUGCuUuGgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGA 109 + +AUGCUUUGGGUU GAAAGUCUCC +ACC+ UUC: UAUG:GGAAAACGUAAUGAGA 60 UUAAUGCUUUGGGUU-GAAAGUCUCC-CACCAA-UUCA-UAUGCGGAAAACGUAAUGAGA 115 <<<<<<<<<<_____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<< 110 UUUAAAAauuuUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacu 169 UUUAAAA++U UUAA ++U+UUUAAAUCAACUCAUUAAG:: :::::UC UUU G:::U 116 UUUAAAAAAU-UUAA-AUUCUUUAAAUCAACUCAUUAAGAG--AAAUAUC-UUUAGAUAU 170 --------<<<<----<<<<___>>>>--->>>>>>>>>>>>>>>>>>>>,,,,,,,,,, 170 UcUuaUUgccgcaCCugggaccuuuuuuuAgcgggguguugguguguguuUCGGUAcuGG 229 U+ U+UU+ ::+ACC :G+AC++U+U: +::+G:::U GG:::::::UUCGGUACUGG 171 UUCUCUUC-UUGACCCAGUACUCUGUUAC-AGGAGCGCU-GGUGUUUUCUUCGGUACUGG 227 ,<<<<<<_..._____>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<____ 230 Aauccaaa...uUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuu 286 A:UCC U U U GGA:UCUAAACCAUAGUUAUGACGAUUGCUCUUUCC::U + 228 AUUCC---uuaUAUAU--GGAAUCUAAACCAUAGUUAUGACGAUUGCUCUUUCCCAUGC- 281 _>>>--->>>::::::::::::::: 287 ggcgaUugagUAACCCAAUGGAGCU 311 ::GAU GAGUAACCCAAUGGAGCU 282 -UGGAUCGAGUAACCCAAUGGAGCU 305 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #43309,sp|AY090599.1|AY090599 Saccharomyces castellii RNase MRP snRNA (NME1) gene, partial sequence. ----isReversed: 0 ----hitSequence: CACCAAUUCAUAUGCGGAAAACGUAAUAAGAUUUAAAAAUUUUAAAUUGUUUAAAUCAACUUAUUAAGAAAGUUUUACAUUUUCUUCUAGACCUAGGAUGUCUUUGCAUGUCCUGGUGUUAUCUUCGGUACUGAGAUCGAAAGUUAUUUGGAUCUUAAACGAUAGUCAUGACGAUUGCUUUUCCUUUUUAACAAGGUAAGUAACCCAAUGGAGCU hit 6 : 1 215 (fwd) 99.44 bits ((((((,,,,,<<<<<<<----------<<<<<<______>>>>>>-------->>>>>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaauUUauguacucAaaacUAUGCuUuG 60 - ------------------------------------------------------------ - >,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<<<<_ 61 gGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAauuu 120 +ACC+ UUC: UAUG:GGAAAACGUAAU:AGAUUUAAAA+UU 1 ----------------CACCAA-UUCA-UAUGCGGAAAACGUAAUAAGAUUUAAAAAUU- 41 ____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<--------<<< 121 UUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUgccg 180 UUAA A+UGUUUAAAUCAACU:AUUAAG:: ::U: UU :U+UU+UU+ : 42 UUAA-AUUGUUUAAAUCAACUUAUUAAGAA--AGUU----UUAC----AUUUUCUUC-UA 89 <----<<<<___>>>>--->>>>>>>>>>>>>>>>>>>>,,,,,,,,,,,<<<<<<____ 181 caCCugggaccuuuuuuuAgcgggguguugguguguguuUCGGUAcuGGAauccaaauUU 240 +ACCU:GG+++U+UU:+ :+:+++U GGU:U::::UUCGGUACUG++AUC+AAA UU 90 GACCUAGGAUGUCUUUGC---AUGUCCU-GGUGUUAUCUUCGGUACUGAGAUCGAAAGUU 145 __>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----.<<<_____>>>--->>>::: 241 UUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUc.cguuuuuggcgaUugagUAA 299 UUU+GAU++UAAAC AUAGU AUGACGAUUGCU:UU C ::UU + :: U:AGUAA 146 AUUUGGAUCUUAAACGAUAGUCAUGACGAUUGCUUUUCCuUUUUAAC--AAGGUAAGUAA 203 :::::::::::: 300 CCCAAUGGAGCU 311 CCCAAUGGAGCU 204 CCCAAUGGAGCU 215 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #43310,sp|AY090600.1|AY090600 Saccharomyces dairenensis RNase MRP snRNA (NME1) gene, partial sequence. ----isReversed: 0 ----hitSequence: AUCGUCACUGAUCGAAGCUUACAAAAUUGGAGUUCUCAUUUCAUUCAUUGAAUGAAAUGAACUGAACUCAUCACUAUGCUUUGGGUUGAAAGUCUCCCACCAGGUCAUAUGCGGAAAACGUAAUAAGAUUUAAAAAUUUUAAAAUCUUUAAAUCAACUUAUUAAAGUUUGAAAAAGCUAUCAUCAGAUUGUUUUUUCUUACUUUCCCGACUUGAAUCUUCUUUGAAUGAUUCAAUGUUUUCUUCGGUAUCGAGAUCCCCUUUUCAAUGGAUCUCAAACCAUAGUCAUGACGAUUGCUGUACAAAAUUACAUUUGUUUGUCAUUUGUAUGGUAACCCAAUGGAGCU hit 7 : 1 345 (fwd) 181.84 bits ((((((,,,,,<<<<<<<--------.--<<<<<<_..____.................. 1 auCgucAcUgAuCgAaGCUUaCAAAA.UGgagugaa..uUUa.................. 39 AUCGUCACUGAUCGAAGCUUACAAAA UGGAGU+: UUU 1 AUCGUCACUGAUCGAAGCUUACAAAAuUGGAGUUCUcaUUU-cauucauugaaugaaaug 59 ..._>>>>>>-------->>>>>>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>> 40 ...uguacucAaaacUAUGCuUuGgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGga 96 U:+ACUCA++ACUAUGCUUUGGGUU GAAAGUCUCC +ACC+G :UC: UAUG:GG: 60 aacUGAACUCAUCACUAUGCUUUGGGUU-GAAAGUCUCC-CACCAG-GUCA-UAUGCGGA 115 ,,,,,<<<<<<<<<<<<<<<<<<_____>>>>->>>>>>>--->>>>>>>,<<<--<<<< 97 AAACGuaaUGaGAUUUAAAAauuuUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcuc 156 AAACGUAAU:AGAUUUAAAAAUU UUAA AAU+UUUAAAUCAACU:AUUAA:::UUG::: 116 AAACGUAAUAAGAUUUAAAAAUU-UUAA-AAUCUUUAAAUCAACUUAUUAAAGUUUGAAA 173 <<<<----............<<<<<--------<<<<----<<<<___.>>>>--->>>> 157 gucguUuU............gcacuUcUuaUUgccgcaCCugggaccu.uuuuuuAgcgg 203 ::: U U ::+::U+ UU+ ::+AC UG:++C+U :UU +::+ 174 AAG-CUAUcaucagauuguuUUUUCUUACUUUC-CCGACUUGAAUCUUc--UUU--GAAU 227 >>>>>>>>>>>>>>>>,,,,,,,,,,,<<<<<<______>>>>>>,,,,,,,,,,,,,,, 204 gguguugguguguguuUCGGUAcuGGAauccaaauUUUUuuggauUcuAAACCAUAGUUA 263 ::+:: ::::::U:::UCGGUA+ G++AUCC::+UUU +::GGAU+++AAACCAUAGU A 228 GAUUC-AAUGUUUUCUUCGGUAUCGAGAUCCCCUUUUCAAUGGAUCUCAAACCAUAGUCA 286 ,))))))--<<<----............<<<_____>>>--->>>::::::::::::::: 264 UgacGauUGcucUuUc............cguuuuuggcgaUugagUAACCCAAUGGAGCU 311 UGACGAUUGC: U+ ::: U+ ::: U :GUAACCCAAUGGAGCU 287 UGACGAUUGCUGUACAaaauuacauuugUUUGUCA-UUUGUAUGGUAACCCAAUGGAGCU 345 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #43311,sp|AY090601.1|AY090601 Saccharomyces cerevisiae var. diastaticus RNase MRP snRNA (NME1) gene, partial sequence. ----isReversed: 0 ----hitSequence: AUCGUCACAAAUCGAAGCUUACAAAAUGGAGUAAAAUUUUUUUUACUCAGUAAUAUGCUUUGGGUUGAAAGUCUCCCACCAAUUCGUAUGCGGAAAACGUAAUGAGAUUUAAAAAUUUUAAAUUGUUUAAAUCAACUCAUUAAGGAGGAUGCCCUUGGGUAUUCUGCUUCUUGACCUGGUACCUCUAUUGCAGGGUACUGGUGUUUUCUUCGGUACUGGAUUCCGUUUGUAUGGAAUCUAAACCAUAGUUAUGACGAUUGCUCUUUCCCGUGCUGGAUCGAGUA hit 8 : 1 284 (fwd) 196.12 bits ((((((,,,,,<<<<<<<----------<<<<<<_..._____>>>>>>-------->>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaa...uUUauguacucAaaacUAUGCu 57 AUCGUCAC +AUCGAAGCUUACAAAAUGGAGU::A UUU+ ::ACUCA +A+UAUGCU 1 AUCGUCACAAAUCGAAGCUUACAAAAUGGAGUAAAauuUUUU-UUACUCAGUAAUAUGCU 59 >>>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<< 58 UuGgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAa 117 UUGGGUU GAAAGUCUCC +ACC+ UUCG UAUGCGGAAAACGUAAUGAGAUUUAAAA+ 60 UUGGGUU-GAAAGUCUCC-CACCAA-UUCG-UAUGCGGAAAACGUAAUGAGAUUUAAAAA 115 <<_____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<-------- 118 uuuUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUg 177 UU UUAA A+UGUUUAAAUCAACUCAUUAAG:: G:::G:C UU G: :UUCU++UU 116 UU-UUAA-AUUGUUUAAAUCAACUCAUUAAGGA--GGAUGCC-CUUGGGUAUUCUGCUU- 169 <<<<----<<<<___.>>>>--->>>>>>>>>>>>>>>>>>>>,,,,,,,,,,,<<<<<< 178 ccgcaCCugggaccu.uuuuuuAgcgggguguugguguguguuUCGGUAcuGGAauccaa 236 C:: ACCUGG:ACCU U:UU+ ::GG: :U G:U:::U::UUCGGUACUGGA:UCC 170 CUUGACCUGGUACCUcUAUUG--CAGGGUACU-GGUGUUUUCUUCGGUACUGGAUUCC-- 224 _..._____>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<_____>>>--- 237 a...uUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuuggcgaUu 293 U U U GGA:UCUAAACCAUAGUUAUGACGAUUGCUCUUUCC: U + :GAU 225 -guuUGUAU--GGAAUCUAAACCAUAGUUAUGACGAUUGCUCUUUCCCGUGC--UGGAUC 279 >>>::::::::::::::: 294 gagUAACCCAAUGGAGCU 311 GAGUA 280 GAGUA------------- 284 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #43312,sp|AY090602.1|AY090602 Saccharomyces globosus RNase MRP snRNA (NME1) gene, partial sequence. ----isReversed: 0 ----hitSequence: AUCGUCACUUAUCGAAGCUUACACAAAGAGUCUAUUAGAUUCAAAUUAUGCUUUGGGCUGAAAGUCUCCCACCUGUUCAUAUGCGGAAAACGUAAUGAGAUUUAAAAAUUUUUAAAUUCUUUAAAUCAACUCAUUAGGUUGGUCCUUUUUGGAUCAAUCUGCUGACCUAGGAUUCACUUUGUUGAUUUCCUAGUGUUUUCUUCGGUAUAGAAAUGUUUUUACAUUUCAAACCAUAGUUAUGACGAUUGCUUUUAUCCUUUUCUUUUGAUUGGAUGAAGUAACCCAAUGGAGCU hit 9 : 17 309 (fwd) 209.46 bits ((((((,,,,,<<<<<<<--------.--<<<<<<______>>>>>>-------->>>>> 1 auCgucAcUgAuCgAaGCUUaCAAAA.UGgagugaauUUauguacucAaaacUAUGCuUu 59 AUCGUCACU AUCGAAGCUUACA AA GA:U:: UU ::A:UC AAA UAUGCUUU 17 AUCGUCACUUAUCGAAGCUUACACAAa--GAGUCU-AUU--AGAUUC-AAAUUAUGCUUU 70 >>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<<<< 60 GgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAauu 119 GGG U GAAAGUCUCC +ACCUG UUC: UAUG:GGAAAACGUAAUGAGAUUUAAAA+UU 71 GGGCU-GAAAGUCUCC-CACCUG-UUCA-UAUGCGGAAAACGUAAUGAGAUUUAAAAAUU 126 _____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<--------<< 120 uUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUgcc 179 UUUAA A+U+UUUAAAUCAACUCAUUA+G : G:UC:U UUUU :::UC UG : 127 UUUAA-AUUCUUUAAAUCAACUCAUUAGGUU--GGUCCU--UUUU--GGAUCAAUCUG-C 178 <<----<<<<___.>>>>--->>>>>>>>>>>>>>>>>>>>,,,,,,,,,,,<<<<<<__ 180 gcaCCugggaccu.uuuuuuAgcgggguguugguguguguuUCGGUAcuGGAauccaaau 238 :+ACCU:GG++++ +UU:+U +::+:::+U +G:GU:U: UUCGGUA+ G+AAU+: U 179 UGACCUAGGAUUCaCUUUGU-UGAUUUCCU-AGUGUUUUCUUCGGUAUAGAAAUGU---U 233 ____>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<____......_>>>-- 239 UUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuu......ggcgaU 292 UUU :+AUU++AAACCAUAGUUAUGACGAUUGCU:UU C::UUU+ +::GAU 234 UUU---ACAUUUCAAACCAUAGUUAUGACGAUUGCUUUUAUCCUUUUCuuuugaUUGGAU 290 ->>>::::::::::::::: 293 ugagUAACCCAAUGGAGCU 311 :AGUAACCCAAUGGAGCU 291 GAAGUAACCCAAUGGAGCU 309 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #43313,sp|AY090603.1|AY090603 Saccharomyces kluyveri RNase MRP snRNA (NME1) gene, partial sequence. ----isReversed: 0 ----hitSequence: AUCGUCACUGAUCGAAGCUUACAAAAGGAUUCCCUCAGGAAUCACCAAUGCUUUGGGUUGAAAGUCUCCCACCUGGCCGUAUGCGGAAAACGCAAUGAGAUUUAAAAAUUUUUAAAACUGUUUAAAUCAACUCAUUAGAGAUGCGAUAGUGUCUCUGUUGUCCCGGAAGAUUUACUCUUCUGGUGUUUUCUUCGGUAUGGAAGUCUUAUUGACUUCAAACCAUAGUUAUGACGAUUGUCCCUGCUUUUUGUAGGGGUA hit 10 : 1 258 (fwd) 156.27 bits ((((((,,,,,<<<<<<<----------<<<<<<______>>>>>>-------->>>>>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaauUUauguacucAaaacUAUGCuUuG 60 AUCGUCACUGAUCGAAGCUUACAAAA GGA:U:: +U+A ::A:UC A C+AUGCUUUG 1 AUCGUCACUGAUCGAAGCUUACAAAA-GGAUUCC-CUCA-GGAAUC--ACCAAUGCUUUG 55 >,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<<<<_ 61 gGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAauuu 120 GGUU GAAAGUCUCC +ACCUG ::CG UAUGCG::AAACG:AAUGAGAUUUAAAA+UUU 56 GGUU-GAAAGUCUCC-CACCUG-GCCG-UAUGCGGAAAACGCAAUGAGAUUUAAAAAUUU 111 ____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<--------<<< 121 UUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUgccg 180 UUAAAA+UGUUUAAAUCAACUCAUU:+::: :::+ +U U U UG ++ 112 UUAAAACUGUUUAAAUCAACUCAUUAGAGA--UGCG----AUAG-----UGUCUCUG-UU 159 <----<<<<___>>>>--->>>>>>>>>>>>>>>>>>>>,,,,,,,,,,,<<<<<<____ 181 caCCugggaccuuuuuuuAgcgggguguugguguguguuUCGGUAcuGGAauccaaauUU 240 ++CC :::A UU::: +++U+U GGU+::::::UCGGUA+ G+A:UC UU 160 GUCCCGGAAGAUUUAC------UCUUCU-GGUGUUUUCUUCGGUAUGGAAGUC----UUA 208 __>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<_____>>>--->>>:::: 241 UUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuuggcgaUugagUAAC 300 UU GA:U++AAACCAUAGUUAUGACGAUUG::C U C::UUU ::G G::UA 209 UU---GACUUCAAACCAUAGUUAUGACGAUUGUCCCUG-CUUUUUG-UAG---GGGUA-- 258 ::::::::::: 301 CCAAUGGAGCU 311 - ----------- - ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #43314,sp|AY090604.1|AY090604 Saccharomyces norbensis RNase MRP snRNA (NME1) gene, partial sequence. ----isReversed: 0 ----hitSequence: AUCGUCACAAAUCGAAGCUUACAAAAUGGAGUAAAAUUUUUUUUACUCAGUAAUAUGCUUUGGGUUGAAAGUCUCCCACCAAUUCGUAUGCGGAAAACGUAAUGAGAUUUAAAAAUUCUAAAUUGUUUAAAUCAACUCAUUAAGGAGGAUGCCCUUGGGUAUUCUGCUUCUUGACCUGGUACCUCUAUUGCAGGGUACUGGUGUUUUCUUCGGUACUGGAUUCCGUUUGUAUGGAAUCUAAACCAUAGUUAUGACGAUUGCUCUUUCCCGUGCUGGAUCGAGUAACCCAAUGGAGCU hit 11 : 1 297 (fwd) 224.73 bits ((((((,,,,,<<<<<<<----------<<<<<<_..._____>>>>>>-------->>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaa...uUUauguacucAaaacUAUGCu 57 AUCGUCAC +AUCGAAGCUUACAAAAUGGAGU::A UUU+ ::ACUCA +A+UAUGCU 1 AUCGUCACAAAUCGAAGCUUACAAAAUGGAGUAAAauuUUUU-UUACUCAGUAAUAUGCU 59 >>>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<< 58 UuGgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAa 117 UUGGGUU GAAAGUCUCC +ACC+ UUCG UAUGCGGAAAACGUAAUGAGAUUUAAAA+ 60 UUGGGUU-GAAAGUCUCC-CACCAA-UUCG-UAUGCGGAAAACGUAAUGAGAUUUAAAAA 115 <<_____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<-------- 118 uuuUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUg 177 UU UAA A+UGUUUAAAUCAACUCAUUAAG:: G:::G:C UU G: :UUCU++UU 116 UU-CUAA-AUUGUUUAAAUCAACUCAUUAAGGA--GGAUGCC-CUUGGGUAUUCUGCUU- 169 <<<<----<<<<___.>>>>--->>>>>>>>>>>>>>>>>>>>,,,,,,,,,,,<<<<<< 178 ccgcaCCugggaccu.uuuuuuAgcgggguguugguguguguuUCGGUAcuGGAauccaa 236 C:: ACCUGG:ACCU U:UU+ ::GG: :U G:U:::U::UUCGGUACUGGA:UCC 170 CUUGACCUGGUACCUcUAUUG--CAGGGUACU-GGUGUUUUCUUCGGUACUGGAUUCC-- 224 _..._____>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<_____>>>--- 237 a...uUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuuggcgaUu 293 U U U GGA:UCUAAACCAUAGUUAUGACGAUUGCUCUUUCC: U + :GAU 225 -guuUGUAU--GGAAUCUAAACCAUAGUUAUGACGAUUGCUCUUUCCCGUGC--UGGAUC 279 >>>::::::::::::::: 294 gagUAACCCAAUGGAGCU 311 GAGUAACCCAAUGGAGCU 280 GAGUAACCCAAUGGAGCU 297 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #43315,sp|AY090605.1|AY090605 Saccharomyces pastorianus RNase MRP snRNA (NME1) gene, partial sequence. ----isReversed: 0 ----hitSequence: AUCGUCACUAAUCGAAGCUUACAAAAAUGGAGUAAAGGAAUUUUUUCCUCACUCAAUAAUAAUGCUUUGGGUUGAAAGUCUCCCACCAAUUCAUAUGCGGAAAACGUAAUGAGAUUUAAAAAAUUUAAAUUCUUUAAAUCAACUCAUUAAGAGGAAUAUCUUUGGAUAUUUUUCUUCUUGACCUGGCACCUCUAUUACAGGAGUGCUGGUGUUUUCUUCGGUACUGGAUUCCUUAUAUAUGGAAUCUAAACCAUAGUUAUGACGAUUGCUCUUUCCCAUGCUGGAUUGAGUAACCCAAUGGAGCU hit 12 : 1 305 (fwd) 226.48 bits ((((((,,,,,<<<<<<<--------.--<<<<<<_....____..._>>>>>>.----- 1 auCgucAcUgAuCgAaGCUUaCAAAA.UGgagugaa....uUUa...uguacuc.Aaaac 51 AUCGUCACU+AUCGAAGCUUACAAAA UGGAGU::A UUU+ +::ACUC A+AA 1 AUCGUCACUAAUCGAAGCUUACAAAAaUGGAGUAAAggaaUUUUuucCUCACUCaAUAAU 60 --->>>>>>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<< 52 UAUGCuUuGgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUU 111 +AUGCUUUGGGUU GAAAGUCUCC +ACC+ UUC: UAUG:GGAAAACGUAAUGAGAUU 61 AAUGCUUUGGGUU-GAAAGUCUCC-CACCAA-UUCA-UAUGCGGAAAACGUAAUGAGAUU 116 <<<<<<<<_____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<-- 112 UAAAAauuuUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUc 171 UAAAA++U UUAA ++U+UUUAAAUCAACUCAUUAAG:: G::::UC UUU G:::UU+ 117 UAAAAAAU-UUAA-AUUCUUUAAAUCAACUCAUUAAGAG--GAAUAUC-UUUGGAUAUUU 171 ------<<<<----<<<<___.>>>>--->>>>>>>>>>>>>>>>>>>>,,,,,,,,,,, 172 UuaUUgccgcaCCugggaccu.uuuuuuAgcgggguguugguguguguuUCGGUAcuGGA 230 UU+UU+ ::+ACCUGG ACCU U UU +::+G:::U GG::::U::UUCGGUACUGGA 172 UUCUUC-UUGACCUGGCACCUcUAUUAC-AGGAGUGCU-GGUGUUUUCUUCGGUACUGGA 228 <<<<<<_..._____>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<_____ 231 auccaaa...uUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuug 287 :UCC U U U GGA:UCUAAACCAUAGUUAUGACGAUUGCUCUUUCC::U + 229 UUCC---uuaUAUAU--GGAAUCUAAACCAUAGUUAUGACGAUUGCUCUUUCCCAUGC-- 281 >>>--->>>::::::::::::::: 288 gcgaUugagUAACCCAAUGGAGCU 311 ::GAUUGAGUAACCCAAUGGAGCU 282 UGGAUUGAGUAACCCAAUGGAGCU 305 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #43316,sp|AY090606.1|AY090606 Saccharomyces servazzii RNase MRP snRNA (NME1) gene, partial sequence. ----isReversed: 0 ----hitSequence: AUCGUCACUAAUCGAAGCUUGCACAAUUGGAGUUGUUUUGACUCAGAAUUAAAGCUUUGGGGAAAGUCUCCGACCUGAACGUAUGCGGAAAACGUAAUGAGAUUUAAAAAUUAUUUACAAUGUUUAAAUAGACUCAUUAGUCAAUUCAUUGUUUAUUCGAUGGAUUGAUUGUUGUCCCAUCUCCCUUGCGUGGGAUAGAUGGUGUUUCUUCGGUACUGGGAUCUCUUUUUUUAUAGAUCCUAAACCAUAGUUAUGACGAUUGCUCUUUGAUUUUUUUUCAUUGAGUAACCCAAUGGAGCU hit 13 : 1 300 (fwd) 205.38 bits ((((((,,,,,<<<<<<<--------.--<<<<<<______>>>>>>--------.>>>> 1 auCgucAcUgAuCgAaGCUUaCAAAA.UGgagugaauUUauguacucAaaacUAU.GCuU 58 AUCGUCACU+AUCGAAGCUU CA AA UGGAGU UUU ACUCA AA UA GCUU 1 AUCGUCACUAAUCGAAGCUUGCACAAuUGGAGUUG-UUU--UGACUCAGAAUUAAaGCUU 57 >>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<<< 59 uGgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAau 118 UGG GGAAAGUCUCC GACCUG ::CG UAUGCG::AAACGUAAUGAGAUUUAAAAAU 58 UGG---GGAAAGUCUCC-GACCUG-AACG-UAUGCGGAAAACGUAAUGAGAUUUAAAAAU 111 <._____.>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<.----..<<<<<---- 119 u.uUUAa.aaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucg.uUuU..gcacuUcUu 173 U UUUA AAUGUUUAAAU ACUCAUUA+::: :UC:U:G UU U G :++ +U+ 112 UaUUUA-c-AAUGUUUAAAUAGACUCAUUAGUCA--AUUCAUUGuUUAUucGAUGGAUUG 167 ----<<<<----<<<<___>>>>--->>>>>>>>>>>>>>>>>>>>,,,,,,,,,,,<<< 174 aUUgccgcaCCugggaccuuuuuuuAgcgggguguugguguguguuUCGGUAcuGGAauc 233 AUUG ::++CC : : CC+ : :+U +::+++: U :G:GU: :::UCGGUACUGG+AUC 168 AUUG-UUGUCCCAUCUCCCUUGCGU-GGGAUAGAU-GGUGUU-UCUUCGGUACUGGGAUC 223 <<<______>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<_____>>>--- 234 caaauUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuuggcgaUu 293 :::+UUUUU:::GAU+CUAAACCAUAGUUAUGACGAUUGCUCUUU :::UUUU :::AUU 224 UCUUUUUUUAUAGAUCCUAAACCAUAGUUAUGACGAUUGCUCUUUGAUUUUUU-UUCAUU 282 >>>::::::::::::::: 294 gagUAACCCAAUGGAGCU 311 GAGUAACCCAAUGGAGCU 283 GAGUAACCCAAUGGAGCU 300 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #43317,sp|AY090607.1|AY090607 Saccharomyces unisporus RNase MRP snRNA (NME1) gene, partial sequence. ----isReversed: 0 ----hitSequence: GACCUGAUCGUAUGCGGAAAACGUAAUGAGAUUUAAAAAUUAUUUACAAUGUUUAAAUAGACUCAUUAAUCGAUUUUUUUGUGUAUUCAAUGGAUCGAUUGUUGUCCCAUCUCCCAUGUGUGGGAUAGGUGGUGUUUCUUCGGUAAUGGGAUUUUUUUUGAAUCCUAAACCAUAGUUAUGACGAUUGCUCUUUGAUUUAGUUCAUUGAGUAACCCAAUGGAGCU hit 14 : 1 224 (fwd) 102.14 bits ((((((,,,,,<<<<<<<----------<<<<<<______>>>>>>-------->>>>>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaauUUauguacucAaaacUAUGCuUuG 60 - ------------------------------------------------------------ - >,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<<<<. 61 gGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAauu. 119 GACCUG :UCG UAUGCGG:AAACGUAAUGAGAUUUAAAAAUU 1 ----------------GACCUG-AUCG-UAUGCGGAAAACGUAAUGAGAUUUAAAAAUUa 42 _____.>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<.....----<<<<<---- 120 uUUAa.aaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucg.....uUuUgcacuUcUu 173 UUUA AAUGUUUAAAU ACUCAUUAA::: :U:+U:+ UU :++ + + 43 UUUA-c-AAUGUUUAAAUAGACUCAUUAAUCG--AUUUUUUUguguaUUCA-AUGGAUCG 97 ----<<<<----<<<<___>>>>--->>>>>>>>>>>>>>>>>>>>,,,,,,,,,,,<<< 174 aUUgccgcaCCugggaccuuuuuuuAgcgggguguugguguguguuUCGGUAcuGGAauc 233 AUUG ::++CC : : CC+ : :+U +::+++: U :G+:U: :::UCGGUA UGG+AU: 98 AUUG-UUGUCCCAUCUCCCAUGUGU-GGGAUAGGU-GGUGUU-UCUUCGGUAAUGGGAUU 153 <<<______>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----.<<<_____>>>-- 234 caaauUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUc.cguuuuuggcgaU 292 : UUUUU ::AU+CUAAACCAUAGUUAUGACGAUUGCUCUUU :+U UU :AU 154 U---UUUUU--GAAUCCUAAACCAUAGUUAUGACGAUUGCUCUUUGaUUUAGUU---CAU 205 ->>>::::::::::::::: 293 ugagUAACCCAAUGGAGCU 311 UGAGUAACCCAAUGGAGCU 206 UGAGUAACCCAAUGGAGCU 224 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #43318,sp|AY090608.1|AY090608 Torulaspora delbrueckii RNase MRP snRNA (NME1) gene, partial sequence. ----isReversed: 0 ----hitSequence: AUCGUCACUGUUCGAAGCUUGCAAAACUGGAGUGGUUCAUACACUCAAUCAAUGCUUUGGGUAGAAAGUCUCCGACCAGACCGUAUGCGGAAAACGUAAUGAGAUUUAAAAAUUUUACAAUCUUUAAAUCAACUCAUUAAGUGGACUGGGGAUACUUGUAUUUUCAGCCCGCUUUCCAACCUGUAUACUCCUUUGAGUUGCAGUGCUUUUCGGUAUGGGAAUCUCGCUAGAUUUCAAACCAUAGUUAUGACGAUUGUUCAGUUUUUGCUGAAUAACCCAAUGGAGCU hit 15 : 17 303 (fwd) 200.54 bits ((((((,,,,,<<<<<<<--------.--<<<<<<______>>>>>>-------->>>>> 1 auCgucAcUgAuCgAaGCUUaCAAAA.UGgagugaauUUauguacucAaaacUAUGCuUu 59 AUCGUCACUG UCGAAGCUU CAAAA UGGAGU: UU+AU :ACUC AA+C+AUGCUUU 17 AUCGUCACUGUUCGAAGCUUGCAAAAcUGGAGUGG-UUCAUACACUC-AAUCAAUGCUUU 74 >>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<<<< 60 GgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAauu 119 GGGU+ GAAAGUCUCC GACC+G ::CG UAUGCG::AAACGUAAUGAGAUUUAAAAAUU 75 GGGUA-GAAAGUCUCC-GACCAG-ACCG-UAUGCGGAAAACGUAAUGAGAUUUAAAAAUU 130 _____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<........----<<<<<-- 120 uUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucg........uUuUgcacuUc 171 UUA+ AAU+UUUAAAUCAACUCAUUAAG:+ G: :G+:G +UUU:CA:: C 131 -UUAC-AAUCUUUAAAUCAACUCAUUAAGUG--GACUGGGGauacuuguAUUUUCAGC-C 185 ------<<<<----<<<<___.>>>>--->>>>>>>>>>>>>>>>>>>>,,,,,,,,,,, 172 UuaUUgccgcaCCugggaccu.uuuuuuAgcgggguguugguguguguuUCGGUAcuGGA 230 ++UU :C+ ACCUG ++ CU UUU G:::UG: :+U: : :UUCGGUA+ GGA 186 CGCUU-UCCAACCUGUAUACUc--CUUU---GAGUUGC-AGUGCU--UUUCGGUAUGGGA 236 <<<<<<_._____>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<_____>> 231 auccaaa.uUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuuggc 289 AUC: U :GAUU++AAACCAUAGUUAUGACGAUUG:UC GUUUUU GC 237 AUCU---cGCU----AGAUUUCAAACCAUAGUUAUGACGAUUGUUC----AGUUUUU-GC 284 >--->>>::::::::::::::: 290 gaUugagUAACCCAAUGGAGCU 311 GA:UAACCCAAUGGAGCU 285 U---GAAUAACCCAAUGGAGCU 303 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #43319,sp|AY090609.1|AY090609 Zygosaccharomyces rouxii RNase MRP snRNA (NME1) gene, partial sequence. ----isReversed: 0 ----hitSequence: AUCGUCAAUUUUCGAAGCCUGCAAAAGGGAUGGGUACCCCCAUUCAAAUAAUAUGCUUUGGGAUGAAAGUCUCCGACCUGACAACUUGCGGAAAACGCAAUGAGAUUUAAAAGUUUCAAAAUGUUUAAAUCAACUCAUUAAGUAGAUGGUUAUUCGAUUAUCUGCUUUGCCACCUAGAUCGUCACAGAUGGUCUAGUGCUUUUCGGUAUGGGAAACCAUUGUGGUUUCCAAACCAUAGUUAUGACGAUUGCUCAAGGAUUAUCCUUUGAGUA hit 16 : 1 272 (fwd) 152.46 bits ((((((,,,,,<<<<<<<----------<<<<<<_.._____>>>>>>.-------->>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaa..uUUauguacuc.AaaacUAUGCu 57 AUCGUCA+U UCGAAGC U CAAAA GG::U:: + + ::A::C AA+A+UAUGCU 1 AUCGUCAAUUUUCGAAGCCUGCAAAA-GGGAUGGGuaCCC--CCAUUCaAAUAAUAUGCU 57 >>>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<< 58 UuGgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAa 117 UUGGG U GAAAGUCUCC GACCUG :::: UG::::AAACG:AAUGAGAUUUAAAA: 58 UUGGGAU-GAAAGUCUCC-GACCUG-ACAA-CUUGCGGAAAACGCAAUGAGAUUUAAAAG 113 <<_____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<-------- 118 uuuUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUg 177 UU U AA A:UGUUUAAAUCAACUCAUU:AG:+ G: +GU: +UU G:++:UCU++UU 114 UU-UCAA-AAUGUUUAAAUCAACUCAUUAAGUA--GAUGGUU-AUUCGAUUAUCUGCUUU 168 <<<<----<<<<___.>>>>--->>>>>>>>>>>>>>>>>>>>,,,,,,,,,,,<<<<<< 178 ccgcaCCugggaccu.uuuuuuAgcgggguguugguguguguuUCGGUAcuGGAauccaa 236 ++CACCU::++C+U :: + ++:++:U :GU+ : :UUCGGUA+ GGAA+CC 169 -GCCACCUAGAUCGUc--ACAG---AUGGUCU-AGUGCU--UUUCGGUAUGGGAAACC-- 217 ______>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<_____>>>--->>> 237 auUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuuggcgaUugag 296 UU U GG+UUC+AAACCAUAGUUAUGACGAUUGCUC + :+U U+ : UUGAG 218 -AUUGU--GGUUUCCAAACCAUAGUUAUGACGAUUGCUCAAGGAUUAUC----CUUUGAG 270 ::::::::::::::: 297 UAACCCAAUGGAGCU 311 UA 271 UA------------- 272 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #68437,sp|U16248.1|SC16248 Saccharomyces cerevisiae C-type cyclin (UME3) gene, complete cds. ----isReversed: 1 ----hitSequence: AUCGUCACAAAUCGAAGCUUACAAAAUGGAGUAAAAUUUUUUUUACUCAGUAAUAUGCUUUGGGUUGAAAGUCUCCCACCAAUUCGUAUGCGGAAAACGUAAUGAGAUUUAAAAAUUUUAAAUUGUUUAAAUCAACUCAUUAAGGAGGAUGCCCUUGGGUAUUCUGCUUCUUGACCUGGUACCUCUAUUGCAGGGUACUGGUGUUUUCUUCGGUACUGGAUUCCGUUUGUAUGGAAUCUAAACCAUAGUUAUGACGAUUGCUCUUUCCCGUGCUGGAUCGAGUAACCCAAUGGAGCU hit 17 : 846 550 (rev) 226.70 bits ((((((,,,,,<<<<<<<----------<<<<<<_..._____>>>>>>-------->>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaa...uUUauguacucAaaacUAUGCu 57 AUCGUCAC +AUCGAAGCUUACAAAAUGGAGU::A UUU+ ::ACUCA +A+UAUGCU 1819 AUCGUCACAAAUCGAAGCUUACAAAAUGGAGUAAAauuUUUU-UUACUCAGUAAUAUGCU 1877 >>>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<< 58 UuGgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAa 117 UUGGGUU GAAAGUCUCC +ACC+ UUCG UAUGCGGAAAACGUAAUGAGAUUUAAAA+ 1878 UUGGGUU-GAAAGUCUCC-CACCAA-UUCG-UAUGCGGAAAACGUAAUGAGAUUUAAAAA 1933 <<_____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<-------- 118 uuuUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUg 177 UU UUAA A+UGUUUAAAUCAACUCAUUAAG:: G:::G:C UU G: :UUCU++UU 1934 UU-UUAA-AUUGUUUAAAUCAACUCAUUAAGGA--GGAUGCC-CUUGGGUAUUCUGCUU- 1987 <<<<----<<<<___.>>>>--->>>>>>>>>>>>>>>>>>>>,,,,,,,,,,,<<<<<< 178 ccgcaCCugggaccu.uuuuuuAgcgggguguugguguguguuUCGGUAcuGGAauccaa 236 C:: ACCUGG:ACCU U:UU+ ::GG: :U G:U:::U::UUCGGUACUGGA:UCC 1988 CUUGACCUGGUACCUcUAUUG--CAGGGUACU-GGUGUUUUCUUCGGUACUGGAUUCC-- 2042 _..._____>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<_____>>>--- 237 a...uUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuuggcgaUu 293 U U U GGA:UCUAAACCAUAGUUAUGACGAUUGCUCUUUCC: U + :GAU 2043 -guuUGUAU--GGAAUCUAAACCAUAGUUAUGACGAUUGCUCUUUCCCGUGC--UGGAUC 2097 >>>::::::::::::::: 294 gagUAACCCAAUGGAGCU 311 GAGUAACCCAAUGGAGCU 2098 GAGUAACCCAAUGGAGCU 2115 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #70718,sp|Z14231.1|SCNME1G S.cerevisiae NME1 gene encoding RNA component of RNase MRP. ----isReversed: 0 ----hitSequence: AUCGUCACAAAUCGAAGCUUACAAAAUGGAGUAAAAUUUUUUUUACUCAGUAAUAUGCUUUGGGUUGAAAGUCUCCCACCAAUUCGUAUGCGGAAAACGUAAUGAGAUUUAAAAAUUUUAAAUUGUUUAAAUCAACUCAUUAAGGAGGAUGCCCUUGGGUAUUCUGCUUCUUGACCUGGUACCUCUAUUGCAGGGUACUGGUGUUUUCUUCGGUACUGGAUUCCGUUUGUAUGGAAUCUAAACCAUAGUUAUGACGAUUGCUCUUUCCCGUGCUGGAUCGAGUAACCCAAUGGAGCU hit 18 : 289 585 (fwd) 226.70 bits ((((((,,,,,<<<<<<<----------<<<<<<_..._____>>>>>>-------->>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaa...uUUauguacucAaaacUAUGCu 57 AUCGUCAC +AUCGAAGCUUACAAAAUGGAGU::A UUU+ ::ACUCA +A+UAUGCU 289 AUCGUCACAAAUCGAAGCUUACAAAAUGGAGUAAAauuUUUU-UUACUCAGUAAUAUGCU 347 >>>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<< 58 UuGgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAa 117 UUGGGUU GAAAGUCUCC +ACC+ UUCG UAUGCGGAAAACGUAAUGAGAUUUAAAA+ 348 UUGGGUU-GAAAGUCUCC-CACCAA-UUCG-UAUGCGGAAAACGUAAUGAGAUUUAAAAA 403 <<_____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<-------- 118 uuuUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUg 177 UU UUAA A+UGUUUAAAUCAACUCAUUAAG:: G:::G:C UU G: :UUCU++UU 404 UU-UUAA-AUUGUUUAAAUCAACUCAUUAAGGA--GGAUGCC-CUUGGGUAUUCUGCUU- 457 <<<<----<<<<___.>>>>--->>>>>>>>>>>>>>>>>>>>,,,,,,,,,,,<<<<<< 178 ccgcaCCugggaccu.uuuuuuAgcgggguguugguguguguuUCGGUAcuGGAauccaa 236 C:: ACCUGG:ACCU U:UU+ ::GG: :U G:U:::U::UUCGGUACUGGA:UCC 458 CUUGACCUGGUACCUcUAUUG--CAGGGUACU-GGUGUUUUCUUCGGUACUGGAUUCC-- 512 _..._____>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<_____>>>--- 237 a...uUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuuggcgaUu 293 U U U GGA:UCUAAACCAUAGUUAUGACGAUUGCUCUUUCC: U + :GAU 513 -guuUGUAU--GGAAUCUAAACCAUAGUUAUGACGAUUGCUCUUUCCCGUGC--UGGAUC 567 >>>::::::::::::::: 294 gagUAACCCAAUGGAGCU 311 GAGUAACCCAAUGGAGCU 568 GAGUAACCCAAUGGAGCU 585 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #74511,sp|Z71300.1|SCYNL024C S.cerevisiae chromosome XIV reading frame ORF YNL024c ----isReversed: 0 ----hitSequence: AUCGUCACAAAUCGAAGCUUACAAAAUGGAGUAAAAUUUUUUUUACUCAGUAAUAUGCUUUGGGUUGAAAGUCUCCCACCAAUUCGUAUGCGGAAAACGUAAUGAGAUUUAAAAAUUUUAAAUUGUUUAAAUCAACUCAUUAAGGAGGAUGCCCUUGGGUAUUCUGCUUCUUGACCUGGUACCUCUAUUGCAGGGUACUGGUGUUUUCUUCGGUACUGGAUUCCGUUUGUAUGGAAUCUAAACCAUAGUUAUGACGAUUGCUCUUUCCCGUGCUGGAUCGAGUAACCCAAUGGAGCU hit 19 : 312 608 (fwd) 226.70 bits ((((((,,,,,<<<<<<<----------<<<<<<_..._____>>>>>>-------->>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaa...uUUauguacucAaaacUAUGCu 57 AUCGUCAC +AUCGAAGCUUACAAAAUGGAGU::A UUU+ ::ACUCA +A+UAUGCU 312 AUCGUCACAAAUCGAAGCUUACAAAAUGGAGUAAAauuUUUU-UUACUCAGUAAUAUGCU 370 >>>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<< 58 UuGgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAa 117 UUGGGUU GAAAGUCUCC +ACC+ UUCG UAUGCGGAAAACGUAAUGAGAUUUAAAA+ 371 UUGGGUU-GAAAGUCUCC-CACCAA-UUCG-UAUGCGGAAAACGUAAUGAGAUUUAAAAA 426 <<_____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<-------- 118 uuuUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUg 177 UU UUAA A+UGUUUAAAUCAACUCAUUAAG:: G:::G:C UU G: :UUCU++UU 427 UU-UUAA-AUUGUUUAAAUCAACUCAUUAAGGA--GGAUGCC-CUUGGGUAUUCUGCUU- 480 <<<<----<<<<___.>>>>--->>>>>>>>>>>>>>>>>>>>,,,,,,,,,,,<<<<<< 178 ccgcaCCugggaccu.uuuuuuAgcgggguguugguguguguuUCGGUAcuGGAauccaa 236 C:: ACCUGG:ACCU U:UU+ ::GG: :U G:U:::U::UUCGGUACUGGA:UCC 481 CUUGACCUGGUACCUcUAUUG--CAGGGUACU-GGUGUUUUCUUCGGUACUGGAUUCC-- 535 _..._____>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<_____>>>--- 237 a...uUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuuggcgaUu 293 U U U GGA:UCUAAACCAUAGUUAUGACGAUUGCUCUUUCC: U + :GAU 536 -guuUGUAU--GGAAUCUAAACCAUAGUUAUGACGAUUGCUCUUUCCCGUGC--UGGAUC 590 >>>::::::::::::::: 294 gagUAACCCAAUGGAGCU 311 GAGUAACCCAAUGGAGCU 591 GAGUAACCCAAUGGAGCU 608 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #74512,sp|Z71301.1|SCYNL025C S.cerevisiae chromosome XIV reading frame ORF YNL025c ----isReversed: 0 ----hitSequence: AUCGUCACAAAUCGAAGCUUACAAAAUGGAGUAAAAUUUUUUUUACUCAGUAAUAUGCUUUGGGUUGAAAGUCUCCCACCAAUUCGUAUGCGGAAAACGUAAUGAGAUUUAAAAAUUUUAAAUUGUUUAAAUCAACUCAUUAAGGAGGAUGCCCUUGGGUAUUCUGCUUCUUGACCUGGUACCUCUAUUGCAGGGUACUGGUGUUUUCUUCGGUACUGGAUUCCGUUUGUAUGGAAUCUAAACCAUAGUUAUGACGAUUGCUCUUUCCCGUGCUGGAUCGAGUAACCCAAUGGAGCU hit 20 : 2229 2525 (fwd) 226.70 bits ((((((,,,,,<<<<<<<----------<<<<<<_..._____>>>>>>-------->>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaa...uUUauguacucAaaacUAUGCu 57 AUCGUCAC +AUCGAAGCUUACAAAAUGGAGU::A UUU+ ::ACUCA +A+UAUGCU 2229 AUCGUCACAAAUCGAAGCUUACAAAAUGGAGUAAAauuUUUU-UUACUCAGUAAUAUGCU 2287 >>>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<< 58 UuGgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAa 117 UUGGGUU GAAAGUCUCC +ACC+ UUCG UAUGCGGAAAACGUAAUGAGAUUUAAAA+ 2288 UUGGGUU-GAAAGUCUCC-CACCAA-UUCG-UAUGCGGAAAACGUAAUGAGAUUUAAAAA 2343 <<_____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<-------- 118 uuuUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUg 177 UU UUAA A+UGUUUAAAUCAACUCAUUAAG:: G:::G:C UU G: :UUCU++UU 2344 UU-UUAA-AUUGUUUAAAUCAACUCAUUAAGGA--GGAUGCC-CUUGGGUAUUCUGCUU- 2397 <<<<----<<<<___.>>>>--->>>>>>>>>>>>>>>>>>>>,,,,,,,,,,,<<<<<< 178 ccgcaCCugggaccu.uuuuuuAgcgggguguugguguguguuUCGGUAcuGGAauccaa 236 C:: ACCUGG:ACCU U:UU+ ::GG: :U G:U:::U::UUCGGUACUGGA:UCC 2398 CUUGACCUGGUACCUcUAUUG--CAGGGUACU-GGUGUUUUCUUCGGUACUGGAUUCC-- 2452 _..._____>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<_____>>>--- 237 a...uUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuuggcgaUu 293 U U U GGA:UCUAAACCAUAGUUAUGACGAUUGCUCUUUCC: U + :GAU 2453 -guuUGUAU--GGAAUCUAAACCAUAGUUAUGACGAUUGCUCUUUCCCGUGC--UGGAUC 2507 >>>::::::::::::::: 294 gagUAACCCAAUGGAGCU 311 GAGUAACCCAAUGGAGCU 2508 GAGUAACCCAAUGGAGCU 2525 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/mam.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/mam.dat.fasta.gz ----sequence: #35603,sp|Z18244.1|BTDISLPR Bos taurus displacement-loop region. ----isReversed: 0 ----hitSequence: GCCUGUUUCCUAGGCUACAUACGGAGGACUAGUUCCUUGUUUGCGCCUAGGGGAAAGUCCCCGGACCGUGGGCAGAGAGUGCCACGUGCCCGUGCACGUAGACUUCCCCUGCUUCUCACGACUAAACCCGCCAAGAAGCGAUCCUACCCUGGGGGUGGGGAAGCCGAGCGGCGUGUUGCGGGGUGUCAUCCGUCAGCUUCUAAUAGUUACGCAGGCAGUGCCUCCAUGCGCACCAACCUCACGGGGCU hit 21 : 725 972 (fwd) 36.30 bits ((((((,,,,,<<<<<<<----------<<<<<<______>>>>>>--------..>>>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaauUUauguacucAaaacUAU..GCuU 58 ::C::: U :C:A:GCU++ +A+ ::::GA +U GU:::: + U+U GC:U 725 GCCUGU-UU--CCUAGGCUACAUAC---GGAGGA-CUA--GUUCCU---UGUUUgcGCCU 772 >>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<<< 59 uGgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAau 118 :G: GGAAAGUC+CCGGACC G::C:G+ +G:G:: :::UG: 773 AGG---GGAAAGUCCCCGGACCGUGGGCAGAGAGUGCC-----ACGUGC----------- 813 <_____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<--------< 119 uuUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUgc 178 :CA:::A:ACUU:C:C+:C UU U CAC+ CU A + C 814 --CCGU----------------GCACGUAGACUUCCCCUGC-UUCU-CACGACUAAAC-C 852 <<<----.......<<<<___>>>>--...........->>>>>>>>>>>>>>>>>>>>, 179 cgcaCCu.......gggaccuuuuuuu...........AgcgggguguugguguguguuU 220 CGC +++ ::+ACC+U+::++ AGCGG+GUGUUG:+G:G:GU: 853 CGCCAAGaagcgauCCUACCCUGGGGGuggggaagccgAGCGGCGUGUUGCGGGGUGUCA 912 ,,,,,,,,,,<<<<<<______>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----< 221 CGGUAcuGGAauccaaauUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUcc 280 ++ C G ++ AUAGUUA :::G:: +:U: C 913 UCCGUCAG----------------------CUUCUAAUAGUUACGCAGGC-AGUG----C 945 <<_____>>>--->>>::::::::::::::: 281 guuuuuggcgaUugagUAACCCAAUGGAGCU 311 :U U G:G :A: AACC A+GG+GCU 946 CUCCAU-GCG---CACCAACCUCACGGGGCU 972 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mam.dat.fasta.gz ----sequence: #36402,sp|Z25280.1|BTMRPRNA B.taurus RNase MRP gene, complete CDS ----isReversed: 0 ----hitSequence: GCCUGUUUCCUAGGCUACAUACGGAGGACUAGUUCCUUGUUUGCGCCUAGGGGAAAGUCCCCGGACCGUGGGCAGAGAGUGCCACGUGCCCGUGCACGUAGACUUCCCCUGCUUCUCACGACUAAACCCGCCAAGAAGCGAUCCUACCCUGGGGGUGGGGAAGCCGAGCGGCGUGUUGCGGGGUGUCAUCCGUCAGCUUCUAAUAGUUACGCAGGCAGUGCCUCCAUGCGCACCAACCUCACGGGGCU hit 22 : 716 963 (fwd) 36.30 bits ((((((,,,,,<<<<<<<----------<<<<<<______>>>>>>--------..>>>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaauUUauguacucAaaacUAU..GCuU 58 ::C::: U :C:A:GCU++ +A+ ::::GA +U GU:::: + U+U GC:U 716 GCCUGU-UU--CCUAGGCUACAUAC---GGAGGA-CUA--GUUCCU---UGUUUgcGCCU 763 >>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<<< 59 uGgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAau 118 :G: GGAAAGUC+CCGGACC G::C:G+ +G:G:: :::UG: 764 AGG---GGAAAGUCCCCGGACCGUGGGCAGAGAGUGCC-----ACGUGC----------- 804 <_____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<--------< 119 uuUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUgc 178 :CA:::A:ACUU:C:C+:C UU U CAC+ CU A + C 805 --CCGU----------------GCACGUAGACUUCCCCUGC-UUCU-CACGACUAAAC-C 843 <<<----.......<<<<___>>>>--...........->>>>>>>>>>>>>>>>>>>>, 179 cgcaCCu.......gggaccuuuuuuu...........AgcgggguguugguguguguuU 220 CGC +++ ::+ACC+U+::++ AGCGG+GUGUUG:+G:G:GU: 844 CGCCAAGaagcgauCCUACCCUGGGGGuggggaagccgAGCGGCGUGUUGCGGGGUGUCA 903 ,,,,,,,,,,<<<<<<______>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----< 221 CGGUAcuGGAauccaaauUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUcc 280 ++ C G ++ AUAGUUA :::G:: +:U: C 904 UCCGUCAG----------------------CUUCUAAUAGUUACGCAGGC-AGUG----C 936 <<_____>>>--->>>::::::::::::::: 281 guuuuuggcgaUugagUAACCCAAUGGAGCU 311 :U U G:G :A: AACC A+GG+GCU 937 CUCCAU-GCG---CACCAACCUCACGGGGCU 963 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mam.dat.fasta.gz ----sequence: #37465,sp|L22578.1|BTURNA Bos taurus small nuclear RNA gene. ----isReversed: 0 ----hitSequence: GCCUGUUUCCUAGGCUACAUACGGAGGACUAGUUCCUUGUUUGCGCCUAGGGGAAAGUCCCCGGACCGUGGGCAGAGAGUGCCACGUGCCCGUGCACGUAGACUUCCCCUGCUUCUCACGACUAAACCCGCCAAGAAGCGAUCCUACCCUGGGGGUGGGGAAGCCGAGCGGCGUGUUGCGGGGUGUCAUCCGUCAGCUUCUAAUAGUUACGCAGGCAGUGCCUCCAUGCGCACCAACCUCACGGGGCU hit 23 : 716 963 (fwd) 36.30 bits ((((((,,,,,<<<<<<<----------<<<<<<______>>>>>>--------..>>>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaauUUauguacucAaaacUAU..GCuU 58 ::C::: U :C:A:GCU++ +A+ ::::GA +U GU:::: + U+U GC:U 716 GCCUGU-UU--CCUAGGCUACAUAC---GGAGGA-CUA--GUUCCU---UGUUUgcGCCU 763 >>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<<< 59 uGgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAau 118 :G: GGAAAGUC+CCGGACC G::C:G+ +G:G:: :::UG: 764 AGG---GGAAAGUCCCCGGACCGUGGGCAGAGAGUGCC-----ACGUGC----------- 804 <_____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<--------< 119 uuUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUgc 178 :CA:::A:ACUU:C:C+:C UU U CAC+ CU A + C 805 --CCGU----------------GCACGUAGACUUCCCCUGC-UUCU-CACGACUAAAC-C 843 <<<----.......<<<<___>>>>--...........->>>>>>>>>>>>>>>>>>>>, 179 cgcaCCu.......gggaccuuuuuuu...........AgcgggguguugguguguguuU 220 CGC +++ ::+ACC+U+::++ AGCGG+GUGUUG:+G:G:GU: 844 CGCCAAGaagcgauCCUACCCUGGGGGuggggaagccgAGCGGCGUGUUGCGGGGUGUCA 903 ,,,,,,,,,,<<<<<<______>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----< 221 CGGUAcuGGAauccaaauUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUcc 280 ++ C G ++ AUAGUUA :::G:: +:U: C 904 UCCGUCAG----------------------CUUCUAAUAGUUACGCAGGC-AGUG----C 936 <<_____>>>--->>>::::::::::::::: 281 guuuuuggcgaUugagUAACCCAAUGGAGCU 311 :U U G:G :A: AACC A+GG+GCU 937 CUCCAU-GCG---CACCAACCUCACGGGGCU 963 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #25779,sp|AL732506.10|AL732506 Mouse DNA sequence from clone RP23-195K8 on chromosome 4 ----isReversed: 1 ----hitSequence: GCCUGUUUCCUAGGCUACAUACGAGGGACAUGUUCCUUAUCCUUUCGCCUAGGGGAAAGUCCCCGGACCACGGGCAGAGAGUGCCGCGUGCACACGCGCGUAGACUUCCCCCGCAAGUCACUGUUAGCCCGCCAAGAAGCGACCCCUCCGGGGCGAGCUGAGCGGCGUGCAGCGGGGCGUCAUCCGUCAGCUCACAUAGUGACGCAGGCAGUGCGACCUGGCUCGCACCAACCACACGGGGCU hit 24 : 107206 106964 (rev) 34.46 bits ((((((,,,,,<<<<<<<----------<<<<<<______>>>>>>--------.>>>>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaauUUauguacucAaaacUAU.GCuUu 59 ::C::: U :C:A:GCU++ +A+ ::G:GA + U GU:C:: A+ CU+U GC:U: 71387 GCCUGU-UU--CCUAGGCUACAUAC---GAGGGA-CAU--GUUCCUUAUCCUUUcGCCUA 71437 >>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<<<< 60 GgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAauu 119 G: GGAAAGUC+CCGGACC+ G::C:G+ +G:G:: ::::G: 71438 GG---GGAAAGUCCCCGGACCACGGGCAGAGAGUGCC-----GCGUGC------------ 71477 _____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<--------<< 120 uUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUgcc 179 A+ :C::::A:ACUU C:C::C + U CAC U UUA + CC 71478 -ACAC----------------GCGCGUAGACUUCCCCCGC-AAGU-CAC-UGUUAGC-CC 71516 <<----......<<<<___>>>>--.....->>>>.>>>>>>>>>>>>>>>>,,,,,,,, 180 gcaCCu......gggaccuuuuuuu.....Agcgg.gguguugguguguguuUCGGUAcu 227 GC +++ ::::+C+:::: + AGCGG GUG+ G::G:G GU: ++ C 71517 GCCAAGaagcgaCCCCUCCGGGGCGagcugAGCGGc-GUGCAGCGGGGCGUCAUCCGUCA 71575 ,,,<<<<<<______>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<____. 228 GGAauccaaauUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuu. 286 G ++ AC AUAGU A :::G:: +:U: CG: U 71576 G----------------------CUCAC-AUAGUGACGCAGGC-AGUG----CGACCU-g 71606 .._>>>--->>>::::::::::::::: 287 ..ggcgaUugagUAACCCAAUGGAGCU 311 :CG :A: AACC A+GG+GCU 71607 gc-UCG---CACCAACCACACGGGGCU 71629 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #66769,sp|J03151.1|MMMRP Mouse mitochondrial RNA-processing endoribonuclease RNA gene. ----isReversed: 0 ----hitSequence: GCCUGUUUCCUAGGCUACAUACGAGGGACAUGUUCCUUAUCCUUUCGCCUAGGGGAAAGUCCCCGGACCACGGGCAGAGAGUGCCGCGUGCACACGCGCGUAGACUUCCCCCGCAAGUCACUGUUAGCCCGCCAAGAAGCGACCCCUCCGGGGCGAGCUGAGCGGCGUGCAGCGGGGCGUCAUCCGUCAGCUCACAUAGUGACGCAGGCAGUGCGACCUGGCUCGCACCAACCACACGGGGCU hit 25 : 859 1101 (fwd) 34.46 bits ((((((,,,,,<<<<<<<----------<<<<<<______>>>>>>--------.>>>>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaauUUauguacucAaaacUAU.GCuUu 59 ::C::: U :C:A:GCU++ +A+ ::G:GA + U GU:C:: A+ CU+U GC:U: 859 GCCUGU-UU--CCUAGGCUACAUAC---GAGGGA-CAU--GUUCCUUAUCCUUUcGCCUA 909 >>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<<<< 60 GgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAauu 119 G: GGAAAGUC+CCGGACC+ G::C:G+ +G:G:: ::::G: 910 GG---GGAAAGUCCCCGGACCACGGGCAGAGAGUGCC-----GCGUGC------------ 949 _____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<--------<< 120 uUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUgcc 179 A+ :C::::A:ACUU C:C::C + U CAC U UUA + CC 950 -ACAC----------------GCGCGUAGACUUCCCCCGC-AAGU-CAC-UGUUAGC-CC 988 <<----......<<<<___>>>>--.....->>>>.>>>>>>>>>>>>>>>>,,,,,,,, 180 gcaCCu......gggaccuuuuuuu.....Agcgg.gguguugguguguguuUCGGUAcu 227 GC +++ ::::+C+:::: + AGCGG GUG+ G::G:G GU: ++ C 989 GCCAAGaagcgaCCCCUCCGGGGCGagcugAGCGGc-GUGCAGCGGGGCGUCAUCCGUCA 1047 ,,,<<<<<<______>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<____. 228 GGAauccaaauUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuu. 286 G ++ AC AUAGU A :::G:: +:U: CG: U 1048 G----------------------CUCAC-AUAGUGACGCAGGC-AGUG----CGACCU-g 1078 .._>>>--->>>::::::::::::::: 287 ..ggcgaUugagUAACCCAAUGGAGCU 311 :CG :A: AACC A+GG+GCU 1079 gc-UCG---CACCAACCACACGGGGCU 1101 ----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/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: #20242,sp|J05014.1|RNSR72R Rat gene for small nuclear 7-2 RNA. ----isReversed: 0 ----hitSequence: GCCUGUUUCCUAGGCUACGUACGGGGGACCUUGUUCCUUAUCCUUUCGCCUAGGGGAAAGUCCCCGGACCAUGGGCAGAGAGUGCCGCGUGCACACGCGCGUAGGCUUCCCCCGCAAGUCACUGUUAGCCCGCCAAGAAGCGACCCCUCCGGGGCGAGCUGAGCGGCGUGCGGCGGGGUGUCAUCCGUCAGUUCUCCUAGUGACGCAGGCAGUGCGACCUUGUACGCACCAACCACACGGGGCU hit 26 : 15 258 (fwd) 32.06 bits ((((((,,,,,<<<<<<<----------<<<<<<______>>>>>>--------.>>>>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaauUUauguacucAaaacUAU.GCuUu 59 ::C::: U :C:A:GCU++ +A+ ::G:GA + U+ GU:C:: A+ CU+U GC:U: 15 GCCUGU-UU--CCUAGGCUACGUAC---GGGGGA-CCUU-GUUCCUUAUCCUUUcGCCUA 66 >>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<<<< 60 GgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAauu 119 G: GGAAAGUC+CCGGACC+ G::C:G+ +G:G:: ::::G: 67 GG---GGAAAGUCCCCGGACCAUGGGCAGAGAGUGCC-----GCGUGC------------ 106 _____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<--------<< 120 uUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUgcc 179 A+ :C::::A::CUU:C:C::C + U CAC U UUA + CC 107 -ACAC----------------GCGCGUAGGCUUCCCCCGC-AAGU-CAC-UGUUAGC-CC 145 <<----......<<<<___>>>>--.....->>>>.>>>>>>>>>>>>>>>>,,,,,,,, 180 gcaCCu......gggaccuuuuuuu.....Agcgg.gguguugguguguguuUCGGUAcu 227 GC +++ ::::+C+:::: + AGCGG GUG+ G::G:G:G:: ++ C 146 GCCAAGaagcgaCCCCUCCGGGGCGagcugAGCGGc-GUGCGGCGGGGUGUCAUCCGUCA 204 ,,,<<<<<<______>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<____. 228 GGAauccaaauUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuu. 286 G U+ CC UAGU A :::G:: +:U: CG: UU 205 G----------------------UUCUCC-UAGUGACGCAGGC-AGUG----CGACCUUg 236 _>>>--->>>::::::::::::::: 287 ggcgaUugagUAACCCAAUGGAGCU 311 +:CG :A: AACC A+GG+GCU 237 UACG---CACCAACCACACGGGGCU 258 ----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: #51567,sp|D30745.1|XLMRPRNA Xenopus laevis MRP RNA gene. ----isReversed: 0 ----hitSequence: ACCUGAAGUCUAGGCAACGUACGGGAGACGUAGUUCUUCAAUCACAUGACGCCUAGGGGAAAGUCCCCGGAUCUCGGGUAGAAAGUGCCGUGCGCUACUAUGGCGUGCAAUAAUCCCGCCCUGCUGUCCAUAUCAACCCGCCAAGAAGCUCCCAGAGCCGAGCGGCUUGGAUUAGGGCGGGAUCUCUCAUCAGUCACCAUAGUAACUCAGGUAGCGCGGCAACGUCCACGCUAACUAAACGGGGCU hit 27 : 2851 3096 (fwd) 21.55 bits ((((((,,,,,<<<<<<<----------<<<<<<______>>>>>>.--------...>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaauUUauguacuc.AaaacUAU...GC 56 A:C::: + UC:A:GC ++ +A+ ::G:GA + UA GU:C:: AA+ + AU GC 2851 ACCUGA-AG--UCUAGGCAACGUAC---GGGAGA-CGUA-GUUCUUcAAUCACAUgacGC 2902 >>>>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<< 57 uUuGgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAA 116 :U:GG GGAAAGUC+CCGGA CU G::::G+A+G:::: :+::G::A 2903 CUAGG---GGAAAGUCCCCGGAUCUCGGGUAGAAAGUGCC-----GUGCGCUA------- 2947 <<<_____>>>>->>>>>>>--->>>>>>>...,<<<--<<<<<<<<----<<<<<---- 117 auuuUUAaaaaUGUUUAAAUCAACuCAuua...AgacuUgcucgucguUuUgcacuUcUu 173 UA ::C::+: A:+C :C:C:::G U G::C:U U 2948 ----CUA---------------UGGCGUGCaauAAUC--CCGCCCUG-CU-GUCCAUAUC 2984 ----<<<<----..<<<<___>>>>--->>>>..>>>>>>>>>>>>>>>>,,,,,,,,,, 174 aUUgccgcaCCu..gggaccuuuuuuuAgcgg..gguguugguguguguuUCGGUAcuGG 229 A + CCGC +++ ::::CC :::: +AGCGG :G::UU:::G:G:G+: ++ A+ 2985 AAC-CCGCCAAGaaGCUCCCAGAGCCGAGCGGcuUGGAUUAGGGCGGGAUCUCUCAUCA- 3042 ,<<<<<<______>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<____._> 230 AauccaaauUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuu.gg 288 + ACCAUAGU A :::G:U +::: :G: + +: 3043 ---------------------GUCACCAUAGUAACUCAGGU-AGCG----CGGCAACgUC 3076 >>--->>>::::::::::::::: 289 cgaUugagUAACCCAAUGGAGCU 311 C: :::UAAC AA+GG+GCU 3077 CA---CGCUAACUAAACGGGGCU 3096 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----sequence: #51853,sp|Z11844.1|XLRNMRP X.laevis DNA for RNase MRP RNA component. ----isReversed: 0 ----hitSequence: ACCUGAAGUCUAGGCAACGUACGGGAGACGUAGUUCUUCAAUCACAUGACGCCUAGGGGAAAGUCCCCGGAUCUCGGGUAGAAAGUGCCGUGCGCUACUAUGGCGUGCAAUAAUCCCGCCCUGCUGUCCAUAUCAACCCGCUAAGAAGCUCCCAGAGCCGAGCGGCUUGGAUUAGGGCGGGAUCUCUCAUCAGUCACCAUAGUAACUCAGGUAGCGCGGCAACGUCCACGCUAACUAAACGGGGCU hit 28 : 506 751 (fwd) 22.24 bits ((((((,,,,,<<<<<<<----------<<<<<<______>>>>>>.--------...>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaauUUauguacuc.AaaacUAU...GC 56 A:C::: + UC:A:GC ++ +A+ ::G:GA + UA GU:C:: AA+ + AU GC 506 ACCUGA-AG--UCUAGGCAACGUAC---GGGAGA-CGUA-GUUCUUcAAUCACAUgacGC 557 >>>>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<< 57 uUuGgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAA 116 :U:GG GGAAAGUC+CCGGA CU G::::G+A+G:::: :+::G::A 558 CUAGG---GGAAAGUCCCCGGAUCUCGGGUAGAAAGUGCC-----GUGCGCUA------- 602 <<<_____>>>>->>>>>>>--->>>>>>>...,<<<--<<<<<<<<----<<<<<---- 117 auuuUUAaaaaUGUUUAAAUCAACuCAuua...AgacuUgcucgucguUuUgcacuUcUu 173 UA ::C::+: A:+C :C:C:::G U G::C:U U 603 ----CUA---------------UGGCGUGCaauAAUC--CCGCCCUG-CU-GUCCAUAUC 639 ----<<<<----..<<<<___>>>>--->>>>..>>>>>>>>>>>>>>>>,,,,,,,,,, 174 aUUgccgcaCCu..gggaccuuuuuuuAgcgg..gguguugguguguguuUCGGUAcuGG 229 A + CCGC++++ ::::CC :::: +AGCGG :G::UU:::G:G:G+: ++ A+ 640 AAC-CCGCUAAGaaGCUCCCAGAGCCGAGCGGcuUGGAUUAGGGCGGGAUCUCUCAUCA- 697 ,<<<<<<______>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<____._> 230 AauccaaauUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuu.gg 288 + ACCAUAGU A :::G:U +::: :G: + +: 698 ---------------------GUCACCAUAGUAACUCAGGU-AGCG----CGGCAACgUC 731 >>--->>>::::::::::::::: 289 cgaUugagUAACCCAAUGGAGCU 311 C: :::UAAC AA+GG+GCU 732 CA---CGCUAACUAAACGGGGCU 751 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum01.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum04.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum05.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum06.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum06.dat.fasta.gz ----sequence: #7886,sp|AF334829.1|AF334829 Homo sapiens mitochondrial RNA-processing endoribonuclease RNA (RMRP) gene, complete sequence. ----isReversed: 0 ----hitSequence: GCCUGUAUCCUAGGCUACACACUGAGGACUCUGUUCCUCUCCUUUCCGCCUAGGGGAAAGUCCCCGGACCUCGGGCAGAGAGUGCCACGUGCAUACGCACGUAGACAUUCCCCGCUUCCCACUCCAAAGUCCGCCAAGAAGCGUAUCCCGCUGAGCGGCGUGGCGCGGGGGCGUCAUCCGUCAGCUCCCUCUAGUUACGCAGGCAGUGCGUGUCCGCGCACCAACCACACGGGGCU hit 29 : 134546 134781 (fwd) 50.14 bits ((((((,,,,,<<<<<<<----------<<<<<<______>>>>>>--------..>>>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaauUUauguacucAaaacUAU..GCuU 58 ::C::: +U :C:A:GCU++ A+ ::::GA +U++ GU:::: + CU+U GC:U 134546 GCCUGU-AU--CCUAGGCUACACAC---UGAGGA-CUCU-GUUCCU-CUCCUUUccGCCU 134596 >>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<<< 59 uGgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAau 118 :G: GGAAAGUC+CCGGACCU G::C:G+ +G:G:: :::UG: 134597 AGG---GGAAAGUCCCCGGACCUCGGGCAGAGAGUGCC-----ACGUGC----------- 134637 <_____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<--------< 119 uuUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUgc 178 UA+ :CA:::A:AC+U+C:C::C UU :CAC C A U C 134638 --AUAC----------------GCACGUAGACAUUCCCCGC-UUC-CCACUCCAAAGU-C 134676 <<<----..<<<<___>>>>--->>>>>>>>>>>>>>>>.>>>>,,,,,,,,,,,<<<<< 179 cgcaCCu..gggaccuuuuuuuAgcgggguguuggugug.uguuUCGGUAcuGGAaucca 235 CGC +++ :: ++ ::U+AGCGG GUG:+G::G:G +GU: ++ C G 134677 CGCCAAGaaGCGUAUCCCGCUGAGCGGCGUGGCGCGGGGgCGUCAUCCGUCAG------- 134729 <______>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<_____>>>--->> 236 aauUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuuggcgaUuga 295 ++ C UAGUUA :::G:: +:U: CGU U++ GCG :A 134730 ---------------CUCCCUCUAGUUACGCAGGC-AGUG----CGUGUCC-GCG---CA 134765 >::::::::::::::: 296 gUAACCCAAUGGAGCU 311 : AACC A+GG+GCU 134766 CCAACCACACGGGGCU 134781 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum07.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum07.dat.fasta.gz ----sequence: #2544,sp|AF458223.1|AF458223 Homo sapiens RNase MRP RNA component, complete sequence. ----isReversed: 0 ----hitSequence: GCCUGUAUCCUAGGCUACACACUGAGGACUCUGUUCCUCCCCUUUCCGCCUAGGGGGAAGUCCCCGGACCUCGGGCAGAGAGUGCCACGUGCAUACGCACGUAGACAUUCCCCGCUUCCCACUCCAAAGUCCGCCAAGAAGCGUAUCCCGCUGAGCGGCGUGGCGCGGGGGCGUCAUCCGUCAGCUCCCUCUAGUUACGCAGGCAGUGCGUGUCCGCGCACCAACCACACGGGGCU hit 30 : 14 249 (fwd) 45.46 bits ((((((,,,,,<<<<<<<----------<<<<<<______>>>>>>--------..>>>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaauUUauguacucAaaacUAU..GCuU 58 ::C::: +U :C:A:GCU++ A+ ::::GA +U++ GU:::: + CU+U GC:U 14 GCCUGU-AU--CCUAGGCUACACAC---UGAGGA-CUCU-GUUCCU-CCCCUUUccGCCU 64 >>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<<< 59 uGgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAau 118 :G: GG AAGUC+CCGGACCU G::C:G+ +G:G:: :::UG: 65 AGG---GGGAAGUCCCCGGACCUCGGGCAGAGAGUGCC-----ACGUGC----------- 105 <_____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<--------< 119 uuUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUgc 178 UA+ :CA:::A:AC+U+C:C::C UU :CAC C A U C 106 --AUAC----------------GCACGUAGACAUUCCCCGC-UUC-CCACUCCAAAGU-C 144 <<<----..<<<<___>>>>--->>>>>>>>>>>>>>>>.>>>>,,,,,,,,,,,<<<<< 179 cgcaCCu..gggaccuuuuuuuAgcgggguguuggugug.uguuUCGGUAcuGGAaucca 235 CGC +++ :: ++ ::U+AGCGG GUG:+G::G:G +GU: ++ C G 145 CGCCAAGaaGCGUAUCCCGCUGAGCGGCGUGGCGCGGGGgCGUCAUCCGUCAG------- 197 <______>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<_____>>>--->> 236 aauUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuuggcgaUuga 295 ++ C UAGUUA :::G:: +:U: CGU U++ GCG :A 198 ---------------CUCCCUCUAGUUACGCAGGC-AGUG----CGUGUCC-GCG---CA 233 >::::::::::::::: 296 gUAACCCAAUGGAGCU 311 : AACC A+GG+GCU 234 CCAACCACACGGGGCU 249 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum07.dat.fasta.gz ----sequence: #2545,sp|AF458224.1|AF458224 Homo sapiens cell line Coriell GM05893 RNase MRP RNA component gene, complete sequence. ----isReversed: 0 ----hitSequence: GCCUGUAUCCUAGGCUACACACUGAGGACUCUGUUCCUCCCCUUUCCGCCUAGGGGAAAGUCCCCGGACCUCGGGCAGAGAGUGCCACGUGCAUACGCACGUAGACAUUCCCCGCUUCCCACUCCAAAGUCCGCCAAGAAGCGUAUCCCGCUGAGCGGCGUGGCGCGGGGGCGUCAUCCGUCAGCUCCCUCUAGUUACGCAGGCAGUGCGUGUCCGCGCACCAACCACACGGGGCU hit 31 : 560 795 (fwd) 49.97 bits ((((((,,,,,<<<<<<<----------<<<<<<______>>>>>>--------..>>>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaauUUauguacucAaaacUAU..GCuU 58 ::C::: +U :C:A:GCU++ A+ ::::GA +U++ GU:::: + CU+U GC:U 560 GCCUGU-AU--CCUAGGCUACACAC---UGAGGA-CUCU-GUUCCU-CCCCUUUccGCCU 610 >>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<<< 59 uGgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAau 118 :G: GGAAAGUC+CCGGACCU G::C:G+ +G:G:: :::UG: 611 AGG---GGAAAGUCCCCGGACCUCGGGCAGAGAGUGCC-----ACGUGC----------- 651 <_____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<--------< 119 uuUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUgc 178 UA+ :CA:::A:AC+U+C:C::C UU :CAC C A U C 652 --AUAC----------------GCACGUAGACAUUCCCCGC-UUC-CCACUCCAAAGU-C 690 <<<----..<<<<___>>>>--->>>>>>>>>>>>>>>>.>>>>,,,,,,,,,,,<<<<< 179 cgcaCCu..gggaccuuuuuuuAgcgggguguuggugug.uguuUCGGUAcuGGAaucca 235 CGC +++ :: ++ ::U+AGCGG GUG:+G::G:G +GU: ++ C G 691 CGCCAAGaaGCGUAUCCCGCUGAGCGGCGUGGCGCGGGGgCGUCAUCCGUCAG------- 743 <______>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<_____>>>--->> 236 aauUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuuggcgaUuga 295 ++ C UAGUUA :::G:: +:U: CGU U++ GCG :A 744 ---------------CUCCCUCUAGUUACGCAGGC-AGUG----CGUGUCC-GCG---CA 779 >::::::::::::::: 296 gUAACCCAAUGGAGCU 311 : AACC A+GG+GCU 780 CCAACCACACGGGGCU 795 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum07.dat.fasta.gz ----sequence: #2546,sp|AF458225.1|AF458225 Homo sapiens cell line Coriell GM03626A RNase MRP RNA component gene, complete sequence. ----isReversed: 0 ----hitSequence: GCCUGUAUCCUAGGCUACACACUGAGGACUCUGUUCCUCCCCUUUCCGCCUAGGGGGAAGUCCCCGGACCUCGGGCAGAGAGUGCCACGUGCAUACGCACGUAGACAUUCCCCGCUUCCCACUCCAAAGUCCGCCAAGAAGCGUAUCCCGCUGAGCGGCGUGGCGCGGGGGCGUCAUCCGUCAGCUCCCUCUAGUUACGCAGGCAGUGCGUGUCCGCGCACCAACCACACGGGGCU hit 32 : 560 795 (fwd) 45.46 bits ((((((,,,,,<<<<<<<----------<<<<<<______>>>>>>--------..>>>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaauUUauguacucAaaacUAU..GCuU 58 ::C::: +U :C:A:GCU++ A+ ::::GA +U++ GU:::: + CU+U GC:U 560 GCCUGU-AU--CCUAGGCUACACAC---UGAGGA-CUCU-GUUCCU-CCCCUUUccGCCU 610 >>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<<< 59 uGgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAau 118 :G: GG AAGUC+CCGGACCU G::C:G+ +G:G:: :::UG: 611 AGG---GGGAAGUCCCCGGACCUCGGGCAGAGAGUGCC-----ACGUGC----------- 651 <_____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<--------< 119 uuUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUgc 178 UA+ :CA:::A:AC+U+C:C::C UU :CAC C A U C 652 --AUAC----------------GCACGUAGACAUUCCCCGC-UUC-CCACUCCAAAGU-C 690 <<<----..<<<<___>>>>--->>>>>>>>>>>>>>>>.>>>>,,,,,,,,,,,<<<<< 179 cgcaCCu..gggaccuuuuuuuAgcgggguguuggugug.uguuUCGGUAcuGGAaucca 235 CGC +++ :: ++ ::U+AGCGG GUG:+G::G:G +GU: ++ C G 691 CGCCAAGaaGCGUAUCCCGCUGAGCGGCGUGGCGCGGGGgCGUCAUCCGUCAG------- 743 <______>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<_____>>>--->> 236 aauUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuuggcgaUuga 295 ++ C UAGUUA :::G:: +:U: CGU U++ GCG :A 744 ---------------CUCCCUCUAGUUACGCAGGC-AGUG----CGUGUCC-GCG---CA 779 >::::::::::::::: 296 gUAACCCAAUGGAGCU 311 : AACC A+GG+GCU 780 CCAACCACACGGGGCU 795 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum07.dat.fasta.gz ----sequence: #2547,sp|AF458226.1|AF458226 Homo sapiens cell line Coriell GM03625C RNase MRP RNA component gene, complete sequence. ----isReversed: 0 ----hitSequence: GCCUGUAUCCUAGGCUACACACUGAGGACUCUGUUCCUCCCCUUUCCGCCUAGGGGGAAGUCCCCGGACCUCGGGCAGAGAGUGCCACGUGCAUACGCACGUAGACAUUCCCCGCUUCCCACUCCAAAGUCCGCCAAGAAGCGUAUCCCGCUGAGCGGCGUGGCGCGGGGGCGUCAUCCGUCAGCUCCCUCUAGUUACGCAGGCAGUGCGUGUCCGCGCACCAACCACACGGGGCU hit 33 : 560 795 (fwd) 45.46 bits ((((((,,,,,<<<<<<<----------<<<<<<______>>>>>>--------..>>>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaauUUauguacucAaaacUAU..GCuU 58 ::C::: +U :C:A:GCU++ A+ ::::GA +U++ GU:::: + CU+U GC:U 560 GCCUGU-AU--CCUAGGCUACACAC---UGAGGA-CUCU-GUUCCU-CCCCUUUccGCCU 610 >>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<<< 59 uGgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAau 118 :G: GG AAGUC+CCGGACCU G::C:G+ +G:G:: :::UG: 611 AGG---GGGAAGUCCCCGGACCUCGGGCAGAGAGUGCC-----ACGUGC----------- 651 <_____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<--------< 119 uuUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUgc 178 UA+ :CA:::A:AC+U+C:C::C UU :CAC C A U C 652 --AUAC----------------GCACGUAGACAUUCCCCGC-UUC-CCACUCCAAAGU-C 690 <<<----..<<<<___>>>>--->>>>>>>>>>>>>>>>.>>>>,,,,,,,,,,,<<<<< 179 cgcaCCu..gggaccuuuuuuuAgcgggguguuggugug.uguuUCGGUAcuGGAaucca 235 CGC +++ :: ++ ::U+AGCGG GUG:+G::G:G +GU: ++ C G 691 CGCCAAGaaGCGUAUCCCGCUGAGCGGCGUGGCGCGGGGgCGUCAUCCGUCAG------- 743 <______>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<_____>>>--->> 236 aauUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuuggcgaUuga 295 ++ C UAGUUA :::G:: +:U: CGU U++ GCG :A 744 ---------------CUCCCUCUAGUUACGCAGGC-AGUG----CGUGUCC-GCG---CA 779 >::::::::::::::: 296 gUAACCCAAUGGAGCU 311 : AACC A+GG+GCU 780 CCAACCACACGGGGCU 795 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum07.dat.fasta.gz ----sequence: #2548,sp|AF458227.1|AF458227 Homo sapiens cell line Coriell GM01671 RNase MRP RNA component gene, complete sequence. ----isReversed: 0 ----hitSequence: GCCUGUAUCCUAGGCUACACACUGAGGACUCUGUUCCUCCCCUUUCCGCCUAGGGGGAAGUCCCCGGACCUCGGGCAGAGAGUGCCACGUGCAUACGCACGUAGACAUUCCCCGCUUCCCACUCCAAAGUCCGCCAAGAAGCGUAUCCCGCUGAGCGGCGUGGCGCGGGGGCGUCAUCCGUCAGCUCCCUCUAGUUACGCAGGCAGUGCGUGUCCGCGCACCAACCACACGGGGCU hit 34 : 560 795 (fwd) 45.46 bits ((((((,,,,,<<<<<<<----------<<<<<<______>>>>>>--------..>>>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaauUUauguacucAaaacUAU..GCuU 58 ::C::: +U :C:A:GCU++ A+ ::::GA +U++ GU:::: + CU+U GC:U 560 GCCUGU-AU--CCUAGGCUACACAC---UGAGGA-CUCU-GUUCCU-CCCCUUUccGCCU 610 >>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<<< 59 uGgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAau 118 :G: GG AAGUC+CCGGACCU G::C:G+ +G:G:: :::UG: 611 AGG---GGGAAGUCCCCGGACCUCGGGCAGAGAGUGCC-----ACGUGC----------- 651 <_____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<--------< 119 uuUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUgc 178 UA+ :CA:::A:AC+U+C:C::C UU :CAC C A U C 652 --AUAC----------------GCACGUAGACAUUCCCCGC-UUC-CCACUCCAAAGU-C 690 <<<----..<<<<___>>>>--->>>>>>>>>>>>>>>>.>>>>,,,,,,,,,,,<<<<< 179 cgcaCCu..gggaccuuuuuuuAgcgggguguuggugug.uguuUCGGUAcuGGAaucca 235 CGC +++ :: ++ ::U+AGCGG GUG:+G::G:G +GU: ++ C G 691 CGCCAAGaaGCGUAUCCCGCUGAGCGGCGUGGCGCGGGGgCGUCAUCCGUCAG------- 743 <______>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<_____>>>--->> 236 aauUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuuggcgaUuga 295 ++ C UAGUUA :::G:: +:U: CGU U++ GCG :A 744 ---------------CUCCCUCUAGUUACGCAGGC-AGUG----CGUGUCC-GCG---CA 779 >::::::::::::::: 296 gUAACCCAAUGGAGCU 311 : AACC A+GG+GCU 780 CCAACCACACGGGGCU 795 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum08.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum09.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum10.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum10.dat.fasta.gz ----sequence: #2358,sp|AL357874.13|AL357874 Human DNA sequence from clone RP11-331F9 on chromosome 9 ----isReversed: 1 ----hitSequence: GCCUGUAUCCUAGGCUACACACUGAGGACUCUGUUCCUCCCCUUUCCGCCUAGGGGAAAGUCCCCGGACCUCGGGCAGAGAGUGCCACGUGCAUACGCACGUAGACAUUCCCCGCUUCCCACUCCAAAGUCCGCCAAGAAGCGUAUCCCGCUGAGCGGCGUGGCGCGGGGGCGUCAUCCGUCAGCUCCCUCUAGUUACGCAGGCAGUGCGUGUCCGCGCACCAACCACACGGGGCU hit 35 : 66113 65878 (rev) 49.97 bits ((((((,,,,,<<<<<<<----------<<<<<<______>>>>>>--------..>>>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaauUUauguacucAaaacUAU..GCuU 58 ::C::: +U :C:A:GCU++ A+ ::::GA +U++ GU:::: + CU+U GC:U 22216 GCCUGU-AU--CCUAGGCUACACAC---UGAGGA-CUCU-GUUCCU-CCCCUUUccGCCU 22266 >>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<<< 59 uGgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAau 118 :G: GGAAAGUC+CCGGACCU G::C:G+ +G:G:: :::UG: 22267 AGG---GGAAAGUCCCCGGACCUCGGGCAGAGAGUGCC-----ACGUGC----------- 22307 <_____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<--------< 119 uuUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUgc 178 UA+ :CA:::A:AC+U+C:C::C UU :CAC C A U C 22308 --AUAC----------------GCACGUAGACAUUCCCCGC-UUC-CCACUCCAAAGU-C 22346 <<<----..<<<<___>>>>--->>>>>>>>>>>>>>>>.>>>>,,,,,,,,,,,<<<<< 179 cgcaCCu..gggaccuuuuuuuAgcgggguguuggugug.uguuUCGGUAcuGGAaucca 235 CGC +++ :: ++ ::U+AGCGG GUG:+G::G:G +GU: ++ C G 22347 CGCCAAGaaGCGUAUCCCGCUGAGCGGCGUGGCGCGGGGgCGUCAUCCGUCAG------- 22399 <______>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<_____>>>--->> 236 aauUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuuggcgaUuga 295 ++ C UAGUUA :::G:: +:U: CGU U++ GCG :A 22400 ---------------CUCCCUCUAGUUACGCAGGC-AGUG----CGUGUCC-GCG---CA 22435 >::::::::::::::: 296 gUAACCCAAUGGAGCU 311 : AACC A+GG+GCU 22436 CCAACCACACGGGGCU 22451 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum11.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum12.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum13.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum14.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum15.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum16.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum17.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum18.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum19.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum20.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum21.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum22.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum23.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum23.dat.fasta.gz ----sequence: #4817,sp|M29916.1|HSMRP Human mitochondrial RNA-processing endoribonuclease RNA (mrp) gene; complete cds. ----isReversed: 0 ----hitSequence: GCCUGUAUCCUAGGCUACACACUGAGGACUCUGUUCCUCCCCUUUCCGCCUAGGGGAAAGUCCCCGGACCUCGGGCAGAGAGUGCCACGUGCAUACGCACGUAGACAUUCCCCGCUUCCCACUCCAAAGUCCGCCAAGAAGCGUAUCCCGCUGAGCGGCGUGGCGCGGGGGCGUCAUCCGUCAGCUCCCUCUAGUUACGCAGGCAGUGCGUGUCCGCGCACCAACCACACGGGGCU hit 36 : 758 993 (fwd) 49.97 bits ((((((,,,,,<<<<<<<----------<<<<<<______>>>>>>--------..>>>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaauUUauguacucAaaacUAU..GCuU 58 ::C::: +U :C:A:GCU++ A+ ::::GA +U++ GU:::: + CU+U GC:U 758 GCCUGU-AU--CCUAGGCUACACAC---UGAGGA-CUCU-GUUCCU-CCCCUUUccGCCU 808 >>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<<< 59 uGgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAau 118 :G: GGAAAGUC+CCGGACCU G::C:G+ +G:G:: :::UG: 809 AGG---GGAAAGUCCCCGGACCUCGGGCAGAGAGUGCC-----ACGUGC----------- 849 <_____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<--------< 119 uuUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUgc 178 UA+ :CA:::A:AC+U+C:C::C UU :CAC C A U C 850 --AUAC----------------GCACGUAGACAUUCCCCGC-UUC-CCACUCCAAAGU-C 888 <<<----..<<<<___>>>>--->>>>>>>>>>>>>>>>.>>>>,,,,,,,,,,,<<<<< 179 cgcaCCu..gggaccuuuuuuuAgcgggguguuggugug.uguuUCGGUAcuGGAaucca 235 CGC +++ :: ++ ::U+AGCGG GUG:+G::G:G +GU: ++ C G 889 CGCCAAGaaGCGUAUCCCGCUGAGCGGCGUGGCGCGGGGgCGUCAUCCGUCAG------- 941 <______>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<_____>>>--->> 236 aauUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuuggcgaUuga 295 ++ C UAGUUA :::G:: +:U: CGU U++ GCG :A 942 ---------------CUCCCUCUAGUUACGCAGGC-AGUG----CGUGUCC-GCG---CA 977 >::::::::::::::: 296 gUAACCCAAUGGAGCU 311 : AACC A+GG+GCU 978 CCAACCACACGGGGCU 993 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum23.dat.fasta.gz ----sequence: #4824,sp|X51867.1|HSMRPRNA H.sapiens MRP RNA gene encoding the RNA component of RNase MRP ----isReversed: 0 ----hitSequence: GCCUGUAUCCUAGGCUACACACUGAGGACUCUGUUCCUCCCCUUUCCGCCUAGGGGAAAGUCCCCGGACCUCGGGCAGAGAGUGCCACGUGCAUACGCACGUAGACAUUCCCCGCUUCCCACUCCAAAGUCCGCCAAGAAGCGUAUCCCGCUGAGCGGCGUGGCGCGGGGGCGUCAUCCGUCAGCUCCCUCUAGUUACGCAGGCAGUGCGUGUCCGCGCACCAACCACACGGGGCU hit 37 : 729 964 (fwd) 49.97 bits ((((((,,,,,<<<<<<<----------<<<<<<______>>>>>>--------..>>>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaauUUauguacucAaaacUAU..GCuU 58 ::C::: +U :C:A:GCU++ A+ ::::GA +U++ GU:::: + CU+U GC:U 729 GCCUGU-AU--CCUAGGCUACACAC---UGAGGA-CUCU-GUUCCU-CCCCUUUccGCCU 779 >>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<<< 59 uGgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAau 118 :G: GGAAAGUC+CCGGACCU G::C:G+ +G:G:: :::UG: 780 AGG---GGAAAGUCCCCGGACCUCGGGCAGAGAGUGCC-----ACGUGC----------- 820 <_____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<--------< 119 uuUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUgc 178 UA+ :CA:::A:AC+U+C:C::C UU :CAC C A U C 821 --AUAC----------------GCACGUAGACAUUCCCCGC-UUC-CCACUCCAAAGU-C 859 <<<----..<<<<___>>>>--->>>>>>>>>>>>>>>>.>>>>,,,,,,,,,,,<<<<< 179 cgcaCCu..gggaccuuuuuuuAgcgggguguuggugug.uguuUCGGUAcuGGAaucca 235 CGC +++ :: ++ ::U+AGCGG GUG:+G::G:G +GU: ++ C G 860 CGCCAAGaaGCGUAUCCCGCUGAGCGGCGUGGCGCGGGGgCGUCAUCCGUCAG------- 912 <______>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<_____>>>--->> 236 aauUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuuggcgaUuga 295 ++ C UAGUUA :::G:: +:U: CGU U++ GCG :A 913 ---------------CUCCCUCUAGUUACGCAGGC-AGUG----CGUGUCC-GCG---CA 948 >::::::::::::::: 296 gUAACCCAAUGGAGCU 311 : AACC A+GG+GCU 949 CCAACCACACGGGGCU 964 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum24.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum24.dat.fasta.gz ----sequence: #1566,sp|M29212.1|HSRRTH Human Th RNA, complete cds. ----isReversed: 0 ----hitSequence: GCCUGUAUCCUAGGCUACACACUGAGGACUCUGUUCCUCCCCUUUCCGCCUAGGGGAAAGUCCCCGGACCUCGGGCAGAGAGUGCCACGUGCAUACGCACGUAGACAUUCCCCGCUUCCCACUCCAAAGUCCGCCAAGAAGCGAUUCCCGCUGAGCGGCGUGGCGCGGGGGCGUCAUCCGUCAGCUCCCUCUAGUUACGCAGGCAGUGCGUGUCCGCGCACCUACCACACGGGGCU hit 38 : 14 249 (fwd) 47.05 bits ((((((,,,,,<<<<<<<----------<<<<<<______>>>>>>--------..>>>> 1 auCgucAcUgAuCgAaGCUUaCAAAAUGgagugaauUUauguacucAaaacUAU..GCuU 58 ::C::: +U :C:A:GCU++ A+ ::::GA +U++ GU:::: + CU+U GC:U 14 GCCUGU-AU--CCUAGGCUACACAC---UGAGGA-CUCU-GUUCCU-CCCCUUUccGCCU 64 >>>,,,,,,,,,,,,,,,,,,,,,,<<<<_____>>>>,,,,,<<<<<<<<<<<<<<<<< 59 uGgGUUGGAAAGUCUCCGgACCUGGuuCgGUAUGcGgaAAACGuaaUGaGAUUUAAAAau 118 :G: GGAAAGUC+CCGGACCU G::C:G+ +G:G:: :::UG: 65 AGG---GGAAAGUCCCCGGACCUCGGGCAGAGAGUGCC-----ACGUGC----------- 105 <_____>>>>->>>>>>>--->>>>>>>,<<<--<<<<<<<<----<<<<<--------< 119 uuUUAaaaaUGUUUAAAUCAACuCAuuaAgacuUgcucgucguUuUgcacuUcUuaUUgc 178 UA+ :CA:::A:AC+U+C:C::C UU :CAC C A U C 106 --AUAC----------------GCACGUAGACAUUCCCCGC-UUC-CCACUCCAAAGU-C 144 <<<----..<<<<___>>>>--->>>>>>>>>>>>>>>>.>>>>,,,,,,,,,,,<<<<< 179 cgcaCCu..gggaccuuuuuuuAgcgggguguuggugug.uguuUCGGUAcuGGAaucca 235 CGC +++ :: +++++ ::U+AGCGG GUG:+G::G:G +GU: ++ C G 145 CGCCAAGaaGCGAUUCCCGCUGAGCGGCGUGGCGCGGGGgCGUCAUCCGUCAG------- 197 <______>>>>>>,,,,,,,,,,,,,,,,))))))--<<<----<<<_____>>>--->> 236 aauUUUUuuggauUcuAAACCAUAGUUAUgacGauUGcucUuUccguuuuuggcgaUuga 295 ++ C UAGUUA :::G:: +:U: CGU U++ GCG :A 198 ---------------CUCCCUCUAGUUACGCAGGC-AGUG----CGUGUCC-GCG---CA 233 >::::::::::::::: 296 gUAACCCAAUGGAGCU 311 : ACC A+GG+GCU 234 CCUACCACACGGGGCU 249 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/hum25.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/hum26.dat.fasta.gz done 1.65905e+10 nucs (frac lets thru so far=9.51175e-06, 2d-fracLetsThru=5.05505e-06). Filter report: done 1.65905e+10 nucs (frac lets thru so far=0.00323421, 2d-fracLetsThru=0.00171256). Filter report: done 5.36572e+07 nucs (frac lets thru so far=0.00294099, 2d-fracLetsThru=0.00295175). done 1.65905e+10 nucs (frac lets thru so far=9.51175e-06, 2d-fracLetsThru=5.05505e-06). CPU time: 898431.39u 1498.38s 249:58:49.77 Elapsed: 252:19:53