Params: ./cmzasha --no-stderr --filter 450 20 Rfam/cm/RF00009.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_5.0/RF00009_forwardinf_hmmtype1_Ecoli_0MM.bin 2struct-str data/TryAllCm_5.0/RF00009_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left,126,140,154,81,196 2struct-str data/TryAllCm_5.0/RF00009_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-left,125,126,139,140,153,154,80,81,195,196 Build: release Host: tricycle.cs.washington.edu pid: 1778 ----hmm-from-cmFileName: Rfam/cm/RF00009.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00009.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00009.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----hmm-from-cmFileName: Rfam/cm/RF00009.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00009.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00009.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-left,126/remember-left,140/remember-left,154/remember-left,81/remember-left,196 ----hmm-from-cmFileName: Rfam/cm/RF00009.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00009.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00009.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-left,125/remember-left,126/remember-left,139/remember-left,140/remember-left,153/remember-left,154/remember-left,80/remember-left,81/remember-left,195/remember-left,196 ----cmFile: Rfam/cm/RF00009.cm (global) ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #16102,sp|AF186214.1|AF186214 Arxiozyma telluris RNase P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: CUCCUUCUUCCCGCUCCUGGUUCUACGCGGCGUGCGCUGUACCACCAUCGGUGGUUAUGGCGCUUACCCCGUGAGGGGGGCUUGGGGAACCGAGUCUAGCGUUGUUAUAAGAAAUCAAUCUUUUGGAUCCAGCCAGGGUCCUCUAGCAGAAAAGGGGGAUGGGGCUCUCUUGGGCUCUCCCCUCCACGCCUGCGGGAUUCUGAUGGGAAUGACAACGGUCGGUCCAUUUGACUUUAUCAUUACGAUGGUUCUAGUCGUGUUAUGGUAAAGGUCUGUUGAGUGCAAUUGUAGAGCAAAUUGAUUCAAUUUGAA hit 0 : 53 364 (fwd) 47.73 bits :::::::::::[[[[,,,,,<<<<---------.<<.<<<_____>>>>>---------> 1 GCGGAaGGAAGcuCauUgUAacguucAccagca.Ga.gugcUugucacuCaacuaacaua 58 CUC:UU U+:C::++ C G + :A G:G + C:CU:+AC+A+CAU: 53 -----------CUCCUUCUUCCCGCUCCUGGUUcUAcGCGGCGUGCGCUGUACCACCAUC 101 >>>,,,,,,,,,,,,,,,,,,(((((,,,,,,<<<<<_____>>>>><<<<<<<____>> 59 cgugGGGAAGGUCUGAGAaACaggcCAauuauugCcCgUGAAGgGcaucaccggGGAAcc 118 :G: + + G:C +UUA :CCCGUGA GGG: :::::GGGGAACC 102 GGU--------------GGUUAUGGCGCUUA--CCCCGUGA-GGGG-GGCUUGGGGAACC 143 >>>>>,..<<<<<<<____________................................. 119 ggugau..cgguGucAUCAGAAAUccA................................. 143 :::::U CG:UG::AU+AGAAAUC+A 144 GAGUCUagCGUUGUUAUAAGAAAUCAAucuuuuggauccagccaggguccucuagcagaa 203 _______________....................................________> 144 acgguugagcuggcu....................................AUGGGAAug 167 A+GG+ GA+++GGCU AUGGGAAU: 204 AAGGGGGAUGGGGCUcucuugggcucuccccuccacgccugcgggauucugAUGGGAAUG 263 >>>>>>))))),,............................................... 168 gCaccgGgccuUu............................................... 180 :CA:CGG:C U+ 264 ACAACGGUCGGUCcauuugacuuuaucauuacgaugguucuagucguguuaugguaaagg 323 .,,,,,,,,,,,,,,,,,]]]]<<<<<....______>>>>>::::::::::: 181 .CUGUUGAGUGCAAUgGuuGagcugag....uuaggCcucagAACCCAAUcag 228 CUGUUGAGUGCAAU GU:GAGC::A: U+A :U::GAA 324 uCUGUUGAGUGCAAUUGUAGAGCAAAUugauUCA---AUUUGAA--------- 364 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #16103,sp|AF186215.1|AF186215 Clavispora lusitaniae RNase P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: GUUCGCCCCAUCCCUCCCCGUGCGUCUUUCGGGGCGCGCGGGGCGAAAGAAUGCUCCUGAGAGCUUCCUGGGCGGAAAUAUUUCCGCCGGGCGUCGCCAUCAGAAAUUCAGCAGGCUAUGCUUGCAUGGGAGGCGGCGCGGAUGGUUGGUCUCUCACAAUGUGGAGAGGCUGUUGAGUGCAAUUUGCGGCCCUGGCA hit 1 : 1 197 (fwd) 29.19 bits :::::::::::[[[[,,,,,<<<<---------<<<<<_____>>>>>--------->>> 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagugcUugucacuCaacuaacauacg 60 - ------------------------------------------------------------ - >,,,,,,,,,,,,,,,,,,(....((((,,,,,,.......................... 61 ugGGGAAGGUCUGAGAaACa....ggcCAauuau.......................... 90 +++C: ::CC + + 1 ---------------GUUCGccccAUCCCUCCCCgugcgucuuucggggcgcgcggggcg 45 ......<<<<<_____>>>>>.....<<<<<<<____>>>>>>>,..<<<<<<<______ 91 ......ugCcCgUGAAGgGca.....ucaccggGGAAccggugau..cgguGucAUCAGA 137 +GC:C UGA G:GC+ :+:::::+ A :::::+:+ CG::G:CAUCAGA 46 aaagaaUGCUCCUGA-GAGCUuccugGGCGGAAAUAUUUCCGCCGggCGUCGCCAUCAGA 104 ______._______________________>>>>>>>.)))).),,.............. 138 AAUccA.acgguugagcuggcuAUGGGAAuggCaccg.Ggcc.uUu.............. 180 AAU+CA ++GG U+ GCU+GC AUGGGA G:C::CG GG:: :UU 105 AAUUCAgCAGGCUAUGCUUGC-AUGGGA--GGCGGCGcGGAUgGUUggucucucacaaug 161 ........,,,,,,,,,,,,,,,,,]]]]<<<<<______>>>>>::::::::::: 181 ........CUGUUGAGUGCAAUgGuuGagcugaguuaggCcucagAACCCAAUcag 228 CUGUUGAGUGCAAU + +G+ C U G A 162 uggagaggCUGUUGAGUGCAAUUUGCGGCC----CUG-------GCA--------- 197 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #16104,sp|AF186216.1|AF186216 Clavispora opuntiae RNase P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: GUUCUCCCCAUCCCUCUCUGGGUGCUUCUGCAUUCAGAGCGAUAUAAUGCUCUUGAGAGCUUCCUGGGCGUAGAUAGUUACGCCGGGCGUCGCCAUCAGAAAAACAGCAGAGCUACGCUUUGCAUGGGAGGCGGCGCGGAUGGUUGGUCUUUCAAUACGAGGAAAGGCUGUUGAGUGCAAUUUGCGGCCUUUGGCA hit 2 : 1 196 (fwd) 28.41 bits :::::::::::[[[[,,,,,<<<<---------<<<<<_____>>>>>--------->>> 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagugcUugucacuCaacuaacauacg 60 - ------------------------------------------------------------ - >,,,,,,,,,,,,,,,,,,(....((((,,,,,,.......................... 61 ugGGGAAGGUCUGAGAaACa....ggcCAauuau.......................... 90 +++C: ::CC + U U 1 ---------------GUUCUccccAUCCCUCUCUgggugcuucugcauucagagcgauau 45 ..<<<<<_____>>>>>.....<<<<<<<____>>>>>>>,..<<<<<<<__________ 91 ..ugCcCgUGAAGgGca.....ucaccggGGAAccggugau..cgguGucAUCAGAAAUc 141 +GC:C+UGA G:GC+ :+:::::+ A :::::+:+ CG::G:CAUCAGAAA 46 aaUGCUCUUGA-GAGCUuccugGGCGUAGAUAGUUACGCCGggCGUCGCCAUCAGAAAAA 104 __..._______________________>>>>>>>.))))..),,............... 142 cA...acgguugagcuggcuAUGGGAAuggCaccg.Ggcc..uUu............... 180 CA +G U+ ++ U+GC AUGGGA G:C::CG GG:: :U 105 CAgcaGAGCUACGCUUUGC-AUGGGA--GGCGGCGcGGAUggUUGgucuuucaauacgag 161 ......,,,,,,,,,,,,,,,,,]]]]<<<<<______>>>>>::::::::::: 181 ......CUGUUGAGUGCAAUgGuuGagcugaguuaggCcucagAACCCAAUcag 228 CUGUUGAGUGCAAU + +G+ C UU+G G A 162 gaaaggCUGUUGAGUGCAAUUUGCGGCC----UUUG------GCA--------- 196 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #16105,sp|AF186217.1|AF186217 Kluyveromyces polysporus RNase P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: CAGCAGUUCUCUCUUCGUAAGAAGAGAGAUUGUGUUACCCUUCGUAACACAUUACCCGUGAGGGAACUAUUAGGUGGAAACCUAGUUAGCUUUGUCGUCAUAAGUGAUCAACGUCUUUCCCCUCGAUUUAUUUUCGGCGGGCGAAUGACGGAUGGGAACGGCGAUAGUUACAAUGUUUGACGUAUCACGUGAUAUUAUCACAAGGUAUGGUCUGUUGAGUGCAAUCGUAGGACCCCGGUUGUUAUCUACAACCGGUUGAA hit 3 : 6 265 (fwd) 32.72 bits :::::::::::[[[[,,,,,<<<<---------<<<<<_____>>>>>--------->>> 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagugcUugucacuCaacuaacauacg 60 AG UU U CU + A +A 6 ---------------------------------CAGCAGUUCUCUCUUCGUAAGAA---- 28 >,,,,,,,,,,,,,,,,,,(.....((((,,,,,,<<<<<_____>>>>>..<<<<<<<_ 61 ugGGGAAGGUCUGAGAaACa.....ggcCAauuauugCcCgUGAAGgGca..ucaccggG 113 GA +G UG+G +AC: :::CA+ U U:CCCGUGA GGG:A :::::G:G 29 ----GAGAGAUUGUGUUACCcuucgUAACACAU--UACCCGUGA-GGGAAcuAUUAGGUG 81 ___>>>>>>>,.....<<<<<<<____________............_____________ 114 GAAccggugau.....cgguGucAUCAGAAAUccA............acgguugagcugg 156 GAA:C:::::U ::::GUCAU+AG AUC+A + +UU+ + U G 82 GAAACCUAGUUagcuuUGUCGUCAUAAGUGAUCAAcgucuuuccccuCGAUUUAUUUUCG 141 __.............________>>>>>>>))))...),,.................... 157 cu.............AUGGGAAuggCaccgGgcc...uUu.................... 180 ++ AUGGGAA+GGC::::G::: :+U 142 GCgggcgaaugacggAUGGGAACGGCGAUAGUUAcaaUGUuugacguaucacgugauauu 201 ...............,,,,,,,,,,,,,,,,,]]]]<<<<<....____.....__>>>> 181 ...............CUGUUGAGUGCAAUgGuuGagcugag....uuag.....gCcuca 216 CUGUUGAGUGCAAU+GU+G++C:::G UUA+ CC::: 202 aucacaagguaugguCUGUUGAGUGCAAUCGUAGGACCCCGguugUUAUcuacaACCGGU 261 .>::::::::::: 217 .gAACCCAAUcag 228 GAA 262 uGAA--------- 265 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #16106,sp|AF186218.1|AF186218 Kluyveromyces thermotolerans RNase P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: ACACAGCGAGACAACAAUCGCCAGGGGCUUCGGCCCUGAUUCUCGUGAGAGAAGCCGCUGGAAAGCGGUUGUGGGCGCUGUCAUCAGAAAUACACAUGUUGGCCGGCGCUAUCGCCGCACCAAUGUGAUGGGAAAGGCAGCGGAUGUCUCGUUUGACUUUGCCUUAGGGUAAAGGUCUGUUGAGUGCAAUGGUAGGAGGCCGCUUUAUGGUGGCCAA hit 4 : 3 219 (fwd) 54.54 bits :::::::::::[[[[,,,,,<<<<---------<<<<<_____>>>>>--------->>> 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagugcUugucacuCaacuaacauacg 60 - ------------------------------------------------------------ - >,,,,,,,,,,,,,,,,,,(...((((,,,,,,.....................<<<<<_ 61 ugGGGAAGGUCUGAGAaACa...ggcCAauuau.....................ugCcCg 96 A+ACA :G:CAA +AU U:C:CG 3 ---------------ACACAgcgAGACAACAAUcgccaggggcuucggcccugaUUCUCG 47 ____>>>>><<<<<<<____>>>>>>>,.....<<<<<<<____________._______ 97 UGAAGgGcaucaccggGGAAccggugau.....cgguGucAUCAGAAAUccA.acgguug 150 UGA G:G:A ::C:::GGAA:::G:: U CG:UGUCAUCAGAAAU CA A G+U G 48 UGA-GAGAA-GCCGCUGGAAAGCGGU-UgugggCGCUGUCAUCAGAAAUACAcAUGUUGG 104 ________.................________>>>>>>>...))))..),,........ 151 agcuggcu.................AUGGGAAuggCaccg...Ggcc..uUu........ 180 +++ GCU AUGGGAA GGCA:CG G:C: UUU 105 CCGGCGCUaucgccgcaccaaugugAUGGGAAAGGCAGCGgauGUCUcgUUUgacuuugc 164 ..............,,,,,,,,,,,,,,,,,]]]]<<<<<..______>>>>>::::::: 181 ..............CUGUUGAGUGCAAUgGuuGagcugag..uuaggCcucagAACCCAA 224 CUGUUGAGUGCAAUGGU+G++ ::: UUA+G ::: AA 165 cuuaggguaaagguCUGUUGAGUGCAAUGGUAGGAGGCCGcuUUAUGGUGGCCAA----- 219 :::: 225 Ucag 228 - ---- - ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #16107,sp|AF186219.1|AF186219 Pichia canadensis RNase P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: UCUGUAUUUUACCUGCCUACAAAAGGAGGAGUCCCCGGCGGACUUCCUCAGUAUUCGCAGGUGGGAAAUUCGGUGAAAUCGCUCUGCCCACCAGGGAAAAGGUAAAACUCUCCCUGGUCCUUGGAAGGACUUGUCCUUCUGAGUCUCGUGAGAGAUGCCAAGCGUGGAGACGCUAGGGUGGUCGCCAUAAGAAACUUCAACAGGUCACACUGUUAUGGGAGGCGCCACGGGCAGUUGGUCCCUUUGCAUCCAGAAGGAAGCUUUGGGGCUGUUGAGUGCAAUAUACAGAGCGCUAGAAGGAGUCCUUCCUUCUACGCGUAA hit 5 : 13 333 (fwd) 64.70 bits :::::::::::[[[[.,,,,,<<<<.---------.<<<<<..._____......>>>>> 1 GCGGAaGGAAGcuCa.uUgUAacgu.ucAccagca.Gagug...cUugu......cacuC 48 :::: +U+U+AC:U +C++CA++A GAG:: C++G ::CUC 13 -----------UCUGuAUUUUACCUgCCUACAAAAgGAGGAgucCCCGGcggacuUCCUC 61 ---------.>>>>,,,,,,,,,,,,,,,,,.,(....((((,,,,,,............ 49 aacuaacau.acgugGGGAAGGUCUGAGAaA.Ca....ggcCAauuau............ 90 A + + C A:GU GGGAA++UC+G+GAAA C: G:CCA+ ++ 62 AGUAUUCG-cAGGU-GGGAAAUUCGGUGAAAuCGcucuGCCCACCAGGgaaaagguaaaa 119 ...................................<<<<<_____>>>>>..<<<<<<<_ 91 ...................................ugCcCgUGAAGgGca..ucaccggG 113 ::C:CGUGA G:G:: ::A:CG:G 120 cucucccugguccuuggaaggacuuguccuucugaGUCUCGUGA-GAGAUgcCAAGCGUG 178 ___>>>>>>>,..<<<<<<<________.____._______________________>>> 114 GAAccggugau..cgguGucAUCAGAAA.UccA.acgguugagcuggcuAUGGGAAuggC 169 GA :CG:U::+ G :G:CAU+AGAAA U+CA ++GGU + CUG AUGGGA G:C 179 GAGACGCUAGGguGGUCGCCAUAAGAAAcUUCAaCAGGUCACACUGUU-AUGGGA--GGC 235 >>>>.)))).),,................................,,,,,,,,,,,,,,, 170 accg.Ggcc.uUu................................CUGUUGAGUGCAAUg 195 : C GG:C :UU CUGUUGAGUGCAAU 236 GCCAcGGGCaGUUggucccuuugcauccagaaggaagcuuuggggCUGUUGAGUGCAAUA 295 ,,]]]]<<<<<.................______>>>>>::::::::::: 196 GuuGagcugag.................uuaggCcucagAACCCAAUcag 228 + ::::::G: UA :C::AA 296 UACAGAGCGCUagaaggaguccuuccuuCUA---CGCGUAA--------- 333 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #16108,sp|AF186220.1|AF186220 Pichia guilliermondii RNase P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: GUUCUCUCCGUCCACGGAGGCAGGUUUCUGCCUUCGCACAAAAUGCUCCUGAGAGCGUCCUGGCGCGAAAGCGCCGGGCAGGGCCAUCAGAAAUCAGUCGAGUUUACUUGGCAUGGGAGGCUCUGCGGACGGUUGGUCAUGUGUAUGAACAUGGCUAUUGAGUGCAAUAUGCGAACCUUGAA hit 6 : 1 182 (fwd) 37.84 bits :::::::::::[[[[,,,,,<<<<---------<<<<<_____>>>>>--------->>> 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagugcUugucacuCaacuaacauacg 60 - ------------------------------------------------------------ - >,,,,,,,,,,,,,,,,,,(....((((,,,,,,........................<< 61 ugGGGAAGGUCUGAGAaACa....ggcCAauuau........................ug 92 +++C: G:CCA+ A :G 1 ---------------GUUCUcuccGUCCACGGAGgcagguuucugccuucgcacaaaaUG 45 <<<_____>>>>>..<<<<<<<____>>>>>>>,<<<<<<<____________.______ 93 CcCgUGAAGgGca..ucaccggGGAAccggugaucgguGucAUCAGAAAUccA.acgguu 149 C:C UGA G:GC: ::::CG:G AA:CG::::+C:G:G:CAUCAGAAAUC++ + GUU 46 CUCCUGA-GAGCGucCUGGCGCGAAAGCGCCGGGCAGGGCCAUCAGAAAUCAGuCGAGUU 104 _________________>>>>>>>.))))..),,...................,,,,,,, 150 gagcuggcuAUGGGAAuggCaccg.Ggcc..uUu...................CUGUUGA 187 A+ UGGC AUGGGA G:C:C:G GG:C :U CU UUGA 105 UACUUGGC-AUGGGA--GGCUCUGcGGACggUUGgucauguguaugaacauggCUAUUGA 161 ,,,,,,,,,,]]]]<<<<<______>>>>>::::::::::: 188 GUGCAAUgGuuGagcugaguuaggCcucagAACCCAAUcag 228 GUGCAAU + +GA+C U+ GAA 162 GUGCAAUAUGCGAAC----CUU-------GAA--------- 182 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #16109,sp|AF186221.1|AF186221 Pichia mississippiensis RNase P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: ACCUGCCCACAAAAGGAGCUCCGUGCUCAGAAUUACGCAGGUGGGAAAUUCGGUGGUUCACGCUGUCCAACAUUACCCUUUCUCUUGAGAGAUCCUGGCGAGGAAUCGCUGGGUGCGGCCAUAAGAAAUCAGCCCCCUAAAAAGGGCAUGGGAGGCUGCACGGACAGUUGGUCCUUGGAAAGAGGGCUAUUGAGUGCAAUAUACAGACUGGGGGCUUUGGCCCCUGGAA hit 7 : 4 232 (fwd) 83.22 bits :::::::::::[[[[,,,,,<<<<.---------.<<<<<_____>>>>>---------. 1 GCGGAaGGAAGcuCauUgUAacgu.ucAccagca.GagugcUugucacuCaacuaacau. 57 AC:U +C +CA++A GAG +++GU CUCA + + + 4 --------------------ACCUgCCCACAAAAgGAGC-UCCGUG-CUCAGAAUUACGc 41 >>>>,,,,,,,,,,,,,,,,,,(....((((,,,,,,.....<<<<<_____>>>>>.<< 58 acgugGGGAAGGUCUGAGAaACa....ggcCAauuau.....ugCcCgUGAAGgGca.uc 107 A:GU GGGAA++UC+G+G+++CA G:CCAA + U +:C:C+UGA G:G:+ :: 42 AGGU-GGGAAAUUCGGUGGUUCAcgcuGUCCAACAUUacccuUUCUCUUGA-GAGAUcCU 99 <<<<<____>>>>>>>,<<<<<<<____________._______________________ 108 accggGGAAccggugaucgguGucAUCAGAAAUccA.acgguugagcuggcuAUGGGAAu 166 ::CG:GGAA:CG::::+:G::G:CAU+AGAAAUC++ +C U++A +GGC AUGGGA 100 GGCGAGGAAUCGCUGGGUGCGGCCAUAAGAAAUCAGcCCCCUAAAAAGGGC-AUGGGA-- 156 >>>>>>>.))))..),,................,,,,,,,,,,,,,,,,,]]]]<<<<<. 167 ggCaccg.Ggcc..uUu................CUGUUGAGUGCAAUgGuuGagcugag. 206 G:C::C: GG:C UU CU UUGAGUGCAAU + + ++C G:G 157 GGCUGCAcGGACagUUGguccuuggaaagagggCUAUUGAGUGCAAUAUACAGACUGGGg 216 ..______>>>>.>::::::::::: 207 ..uuaggCcuca.gAACCCAAUcag 228 UU+GGCC:C GAA 217 gcUUUGGCCCCUgGAA--------- 232 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #16110,sp|AF186222.1|AF186222 Pichia strasburgensis RNase P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: AAGUCUGUAUUUACCUGCCUACACAAGGGGCCCUCUUCCCCCAGAGGGACCCAGCAGGAGCAGGUGGGAAAUUCGGUGGUACACGCCGCCCAUUAAUUUCUCUCUUGAGAGAGUCCAGGCGAGGAAUCGCUAGGGUGUUGCCAUAAGAAAUUCAGUCCGCCUAGCGGGCAUGGGAGGCUUCACGGGCGGUUGGUCCCUAGUGCAAAACUUUCGCGCUAGGAGGCUUUUGAGUGCAAUAUACAGACCGCCUAGUGGUUCCUUGGGAUCAUCUGGGCGGAACGCGAUACC hit 8 : 10 297 (fwd) 86.18 bits :::::::::::[[[[,,,,,<<<<.---------<<<<<._____..........>>>>> 1 GCGGAaGGAAGcuCauUgUAacgu.ucAccagcaGagug.cUugu..........cacuC 48 AAG::::U +U+AC:U +C++CA +AG:G:: CU+ U ::C:C 10 --------AAGUCUGUAUUUACCUgCCUACACAAGGGGCcCUCUUcccccagaggGACCC 61 ---------.>>>>,,,,,,,,,,,,,,,,,,(....((((,,,,,,..<<<<<_____> 49 aacuaacau.acgugGGGAAGGUCUGAGAaACa....ggcCAauuau..ugCcCgUGAAG 101 A C + A:GU GGGAA++UC+G+G++ACA G:CCA+U+AU ::C:C+UGA G 62 AGCAGGAG-cAGGU-GGGAAAUUCGGUGGUACAcgccGCCCAUUAAUuuCUCUCUUGA-G 118 >>>>..<<<<<<<____>>>>>>>,.<<<<<<<____________.._____________ 102 gGca..ucaccggGGAAccggugau.cgguGucAUCAGAAAUccA..acgguugagcugg 156 :G:: ::::CG:GGAA:CG::::+ :G G:CAU+AGAAAU+CA +CG U++++ GG 119 AGAGucCAGGCGAGGAAUCGCUAGGgUGUUGCCAUAAGAAAUUCAguCCGCCUAGCG-GG 177 __________>>>>>>>.))))..),,...............................,, 157 cuAUGGGAAuggCaccg.Ggcc..uUu...............................CU 182 C AUGGGA G:C C: GG:C UU CU 178 C-AUGGGA--GGCUUCAcGGGCggUUGgucccuagugcaaaacuuucgcgcuaggaggCU 234 ,,,,,,,,,,,,,,,]]]]<<<<<...................______>>>>>:::::: 183 GUUGAGUGCAAUgGuuGagcugag...................uuaggCcucagAACCCA 223 +UUGAGUGCAAU + ::::C:G:: U++G ::C:GAAC C+ 235 UUUGAGUGCAAUAUACAGACCGCCuagugguuccuugggaucaUCUG--GGCGGAACGCG 292 ::::: 224 AUcag 228 AU+++ 293 AUACC 297 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #16111,sp|AF186223.1|AF186223 Saccharomyces pastorianus RNase P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: ACCUGUUUGCAAAAGGGCCUGCCCACGCGGGUCAUCUUAUUUAUCAGGUGGGAAAUUCGGUGGAACACAGUGGAGCCUUGCCUUCCGGGCCAUUGUCUCUGGCAGUGGCCCCUGCUCGUGAGAGAAGAAACUUGCUGGGGAACCAGUCUUUACCGACCGUUGCUAUCAGAAAUUGAACGGGGCCCGGUCCCGCCGGGCCUCGAUGGGAACGGCAACGGUUGUUCCGUUUGACUUGUCGCCCGCCACGGCGCGCUGCAAGGUCUGUUGAGUGCAAUCGUAGGACGCCAUUCGUGGCGAACCCGA hit 9 : 9 311 (fwd) 92.31 bits :::::::::::[[[[,,,,,<<<<.---------.<<<<<._____..>>>>>------- 1 GCGGAaGGAAGcuCauUgUAacgu.ucAccagca.Gagug.cUugu..cacuCaacuaac 55 AC:U U++ CA++A G:+: C++ :+:CA+CU+A 9 --------------------ACCUgUUUGCAAAAgGGCCUgCCCACgcGGGUCAUCUUAU 48 --...>>>>,,,,,,,,,,,,,,,,,,(.....((((,,,,,,................. 56 au...acgugGGGAAGGUCUGAGAaACa.....ggcCAauuau................. 90 +U A:GU GGGAA++UC+G+G+AACA G::C +U + 49 UUaucAGGU-GGGAAAUUCGGUGGAACAcagugGAGCCUUGCCuuccgggccauugucuc 107 .............<<<<<_____>>>>>.....<<<<<<<____>>>>>>>,.......< 91 .............ugCcCgUGAAGgGca.....ucaccggGGAAccggugau.......c 125 U C:CGUGA G:G A :::C:GGGGAACC:G:::U C 108 uggcaguggccccUGCUCGUGA-GAGAAgaaacUUGCUGGGGAACCAGUCUUuaccgacC 166 <<<<<<____________......._______________....________>>>>>>>. 126 gguGucAUCAGAAAUccA.......acgguugagcuggcu....AUGGGAAuggCaccg. 173 G:UG::AUCAGAAAU+ A +CGGU GC GG++ AUGGGAA+::CA:CG 167 GUUGCUAUCAGAAAUUGAacggggcCCGGUCCCGCCGGGCcucgAUGGGAACGGCAACGg 226 ..))))..),,................................,,,,,,,,,,,,,,,,, 174 ..Ggcc..uUu................................CUGUUGAGUGCAAUgGu 197 G::C UUU CUGUUGAGUGCAAU+GU 227 uuGUUCcgUUUgacuugucgcccgccacggcgcgcugcaagguCUGUUGAGUGCAAUCGU 286 ]]]]<<<<<______>>>>>::::::::::: 198 uGagcugaguuaggCcucagAACCCAAUcag 228 +G++C::::UU G ::::GAACCC+A 287 AGGACGCCAUUCG--UGGCGAACCCGA---- 311 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #16112,sp|AF186224.1|AF186224 Saccharomyces dairenensis RNase P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: ACAGUGAUGAUUCCUACGUUUUAAGAACCUGUUUACAGAAGGAGGAUAACACUUUAGUGCUUUUCUCAUAUAAGUUCAGGUGGGAAAUUCGGUGAAACACAGCGGAACCAACAACAUCUACCAAGGUGUCGUUGCCCUCCCCAAGCCUAGACGGUGUCUUCUUCUAGGAGGAGCUUAAGUCCAGGUCCUUCCCGUGAGGGCAGUUUUCUUUGCAAUUUUAAAUUUUACUGGGGAACCGGUCUGCCUAAAAAUUGCCAUUGAAGAAUUUAUUGGGACGUCGUUAGCAGAAAUUCACAGAGACCUCUUUCAAAGAAAUUGGUCCCUGAUGGGAACAGCGACGGUAGUUCCAUUUGACUUGUGGUGUGAAAUAAUAUCGACCAUAAGGUCUGUUGAGUGCAAUCGUAGGACAGAUUUGAUUUGAAAAUCUGAACCCGAUCCC hit 10 : 6 444 (fwd) 89.48 bits :::::::::::[[[[...,,,,,...<<<<.---------.<<<<<....._____.... 1 GCGGAaGGAAGcuCa...uUgUA...acgu.ucAccagca.Gagug.....cUugu.... 43 +C+G++ A ::C: UU+UA AC:U U+++CAG+A GAG : CUU 6 ACAGUGAUGAUUCCUacgUUUUAagaACCUgUUUACAGAAgGAGGAuaacaCUUUAgugc 65 ..>>>>>---------.>>>>,,,,,,,,,,,,,,,,,,(......((((,,,,,,.... 44 ..cacuCaacuaacau.acgugGGGAAGGUCUGAGAaACa......ggcCAauuau.... 90 : CUCA++UAA +U A:GU GGGAA++UC+G+GAAACA ::C AA +A+ 66 uuUUCUCAUAUAAGUUcAGGU-GGGAAAUUCGGUGAAACAcagcggAACCAACAACaucu 124 ............................................................ - ............................................................ - 125 accaaggugucguugcccuccccaagccuagacggugucuucuucuaggaggagcuuaag 184 .........<<<<<_____>>>>>......................<<<<<<<____>>> 91 .........ugCcCgUGAAGgGca......................ucaccggGGAAccg 119 U:CCCGUGA GGG:A ::AC:GGGGAACC: 185 uccagguccUUCCCGUGA-GGGCAguuuucuuugcaauuuuaaauuUUACUGGGGAACCG 243 >>>>,................................<<<<<<<____________.... 120 gugau................................cgguGucAUCAGAAAUccA.... 143 GU::+ CG::GU:A CAGAAAU+CA 244 GUCUGccuaaaaauugccauugaagaauuuauugggaCGUCGUUAGCAGAAAUUCAcaga 303 ............._______________________>>>>>>>..))))...),,..... 144 .............acgguugagcuggcuAUGGGAAuggCaccg..Ggcc...uUu..... 180 + UUG++C + AUGGGAA+:GC::CG G:: UUU 304 gaccucuuucaaaGAAAUUGGUCCCUG-AUGGGAACAGCGACGguAGUUccaUUUgacuu 362 .............................,,,,,,,,,,,,,,,,,]]]]<<<<<...._ 181 .............................CUGUUGAGUGCAAUgGuuGagcugag....u 207 CUGUUGAGUGCAAU+GU:G::C:GA: U 363 guggugugaaauaauaucgaccauaagguCUGUUGAGUGCAAUCGUAGGACAGAUuugaU 422 ___.__>>>>>::::::::::: 208 uag.gCcucagAACCCAAUcag 228 U+G :UC:GAACCC+AUC++ 423 UUGaAAAUCUGAACCCGAUCCC 444 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #16113,sp|AF186225.1|AF186225 Saccharomyces servazzii RNase P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: ACACAGAGGAUCGAUAAUGACCAGGAACUGUAACAGGUUCUGUUUCCUCGUGAGAGGGGCUUGGGGAACCGAGUCUGGCGUUGCUAUAAGAAAUCUACAGCGUUGUUCGUUACUUGUAACGUGGCAACCCUGAUGGGAAUGGUAACGGAUGAUCCAUUUGACGUACUGCUACCACUUGUGAUAGCGGUAAGGUCUGUUGAGUGCAAUCGUAGAGCAAAUGUUCGCAUUUGAA hit 11 : 3 234 (fwd) 53.49 bits :::::::::::[[[[,,,,,<<<<---------<<<<<_____>>>>>--------->>> 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagugcUugucacuCaacuaacauacg 60 - ------------------------------------------------------------ - >,,,,,,,,,,,,,,,,,,(...((((,,,,,,..........................< 61 ugGGGAAGGUCUGAGAaACa...ggcCAauuau..........................u 91 A+ACA G::C AU+AU : 3 ---------------ACACAgagGAUCGAUAAUgaccaggaacuguaacagguucuguuU 47 <<<<_____>>>>><<<<<<<____>>>>>>>,...<<<<<<<____________.____ 92 gCcCgUGAAGgGcaucaccggGGAAccggugau...cgguGucAUCAGAAAUccA.acgg 147 :C:CGUGA G:G:: ::::GGGGAACC:::: CG:U ::AU+AGAAAUC A A G 48 CCUCGUGA-GAGGG-GCUUGGGGAACCGAGU-CuggCGUUGCUAUAAGAAAUCUAcAGCG 104 ___________...................________>>>>>>>...))))..),,... 148 uugagcuggcu...................AUGGGAAuggCaccg...Ggcc..uUu... 180 UUG +C++ + AUGGGAAU:: A:CG G::C UUU 105 UUGUUCGUUACuuguaacguggcaacccugAUGGGAAUGGUAACGgauGAUCcaUUUgac 164 ...............................,,,,,,,,,,,,,,,,,]]]]<<<<<.__ 181 ...............................CUGUUGAGUGCAAUgGuuGagcugag.uu 208 CUGUUGAGUGCAAU+GU+GAGC::A: UU 165 guacugcuaccacuugugauagcgguaagguCUGUUGAGUGCAAUCGUAGAGCAAAUgUU 224 ____>>>>>::::::::::: 209 aggCcucagAACCCAAUcag 228 GC:U::GAA 225 C-GCAUUUGAA--------- 234 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #16114,sp|AF186226.1|AF186226 Saccharomyces unisporus RNase P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: ACACAGAGGAUCAAUUAUCAAAGACCAGGAACUGUAAAGGGUUCUGUUUCCUCGUGAGAGGGGCUUGGGGAACCGAGUUUGGCGUUGUUAUAAGAAAUCAACAGGGUUUGGUUUGGCAUUUUUCGAAGUGGUUGGCCGAACUCUGAUGGGAAUGGCAACGGAUGAUCCAUUUGACGUAUCACUAUUAACAAGUGAUAAGGUCUGUUGAGUGCAAUCGUAGAGCAAAUGGUAACACAUUUGAA hit 12 : 3 244 (fwd) 62.21 bits :::::::::::[[[[,,,,,<<<<---------<<<<<_____>>>>>--------->>> 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagugcUugucacuCaacuaacauacg 60 - ------------------------------------------------------------ - >,,,,,,,,,,,,,,,,,,(...((((,,,,,,........................... 61 ugGGGAAGGUCUGAGAaACa...ggcCAauuau........................... 90 A+ACA G::CAAUUAU 3 ---------------ACACAgagGAUCAAUUAUcaaagaccaggaacuguaaaggguucu 47 ...<<<<<_____>>>>><<<<<<<____>>>>>>>,...<<<<<<<____________. 91 ...ugCcCgUGAAGgGcaucaccggGGAAccggugau...cgguGucAUCAGAAAUccA. 143 ::C:CGUGA G:G:: ::::GGGGAACC:::: U CG:UGU:AU+AGAAAUC+A 48 guuUCCUCGUGA-GAGGG-GCUUGGGGAACCGAGU-UuggCGUUGUUAUAAGAAAUCAAc 104 _______________............................________>>>>>>>.. 144 acgguugagcuggcu............................AUGGGAAuggCaccg.. 173 A GGUU +G U+G++ AUGGGAAU:GCA:CG 105 AGGGUUUGGUUUGGCauuuuucgaagugguuggccgaacucugAUGGGAAUGGCAACGga 164 .))))..),,.............................,,,,,,,,,,,,,,,,,]]]] 174 .Ggcc..uUu.............................CUGUUGAGUGCAAUgGuuGag 201 G::C UUU CUGUUGAGUGCAAU+GU+GAG 165 uGAUCcaUUUgacguaucacuauuaacaagugauaagguCUGUUGAGUGCAAUCGUAGAG 224 <<<<<.____.__>>>>>::::::::::: 202 cugag.uuag.gCcucagAACCCAAUcag 228 C::A: UA C:U::GAA 225 CAAAUgGUAAcACAUUUGAA--------- 244 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #16115,sp|AF186227.1|AF186227 Saccharomyces castellii RNase P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: ACAGCGACGACUCCUACGACUUAGAGACCUGUUUACACAAGGAGGGUACCCUCCCUCAACCAACAGGUGGGAAAUUCGGUGAAACACAGUGGAAUCAUUCCUUCCAGCCUGGGCUCGCUUCCUUCGGGAAGCUAGGCUCAGGUCUUUCCGUGAGGACAGCCUAGCCGGGGACCGGUCUGCCUGGACGUUGUUAUCAGAAAUUCACACGGGUAACCGUGAUGGGAAAGCAACGAGUGUUUUAUUUGACGGGCUUCUGUUUACACAGUGGUCCAGUCUGUUGAGUGCAAUCGUAGGACAUGCCCUAGGGCUUGAACCCGAUACC hit 13 : 8 329 (fwd) 107.24 bits :::::::::::[[[[.....,,,,,.<<<<.---------<<<<<_____>>>>>----- 1 GCGGAaGGAAGcuCa.....uUgUA.acgu.ucAccagcaGagugcUugucacuCaacua 53 +C+G + A ::C: UU A AC:U U+++CA +AG:::G U C:::C +C A 8 ACAGCGACGACUCCUacgacUUAGAgACCUgUUUACACAAGGAGGGUAC-CCUCCCUCAA 66 ----.>>>>,,,,,,,,,,,,,,,,,,(......((((,,,,,,................ 54 acau.acgugGGGAAGGUCUGAGAaACa......ggcCAauuau................ 90 +CA+ A:GU GGGAA++UC+G+GAAACA :: CA+U U 67 CCAAcAGGU-GGGAAAUUCGGUGAAACAcaguggAAUCAUUCCUuccagccugggcucgc 125 ..........................<<<<<_____>>>>>...<<<<<<<____>>>>> 91 ..........................ugCcCgUGAAGgGca...ucaccggGGAAccggu 121 U::CCGUGA GG::A :::CCGGGGA CCGG: 126 uuccuucgggaagcuaggcucaggucUUUCCGUGA-GGACAgccUAGCCGGGGA-CCGGU 183 >>,......<<<<<<<____________._______________________>>>>>>>. 122 gau......cgguGucAUCAGAAAUccA.acgguugagcuggcuAUGGGAAuggCaccg. 173 ::+ CG:UGU:AUCAGAAAU+CA ACGG+U+A+C++G AUGGGAA :GCA:CG 184 CUGccuggaCGUUGUUAUCAGAAAUUCAcACGGGUAACCGUG--AUGGGAA-AGCAACGa 240 ..))))..),,..............................,,,,,,,,,,,,,,,,,]] 174 ..Ggcc..uUu..............................CUGUUGAGUGCAAUgGuuG 199 G :: UUU CUGUUGAGUGCAAU+GU:G 241 guGUUUuaUUUgacgggcuucuguuuacacagugguccaguCUGUUGAGUGCAAUCGUAG 300 ]]<<<<<.______>>>>>::::::::::: 200 agcugag.uuaggCcucagAACCCAAUcag 228 ::C:::: UA G ::::GAACCC+AU+++ 301 GACAUGCcCUA-GGGCUUGAACCCGAUACC 329 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #16116,sp|AF186228.1|AF186228 Saccharomycopsis fibuligera RNase P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: UCUGGUAUCCUACGGGAUAGUCCAGGACUAUUGGAUUUAAUUCCAAAUGCUCCUGAGAGCUCCAUAGAGCGGAAGCUCUGGACGAAGCCAUCAGAAAAAUCGCUUACUUGUGAAGUGAUGGGCCACUCUACUUCGGAGUGGCUCAAUGGAAGCGGCUUCGUGGACAGUUGGCUUAGGCCGCCCUCAGGGGCGGUUUGAGCUGUUAAGUGCAAUACACAGACAUUGUGCA hit 14 : 15 243 (fwd) 21.11 bits :::::::::::[[[[,,,,,<<<<---------<<<<<_____>>>>>--------->>> 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagugcUugucacuCaacuaacauacg 60 :::: U U 15 -----------UCUGGUAUC---------------------------------------- 23 >,,,,,,,,,,,,,,,,,,(.....((((,,,,,,..................<<<<<__ 61 ugGGGAAGGUCUGAGAaACa.....ggcCAauuau..................ugCcCgU 97 +AC: G:CCA + U +GC:C U 24 ---------------CUACGggauaGUCCAGGACUauuggauuuaauuccaaaUGCUCCU 68 ___>>>>>..<<<<<<<____>>>>>>>,<<<<<<<____________..........._ 98 GAAGgGca..ucaccggGGAAccggugaucgguGucAUCAGAAAUccA...........a 144 GA G:GC+ :A::G:GGAA:C::U: CG::G:CAUCAGAAA A 69 GA-GAGCUccAUAGAGCGGAAGCUCUGGACGAAGCCAUCAGAAAAAUCgcuuacuugugA 127 ______________..................________>>>>>>>.)))).),,.... 145 cgguugagcuggcu..................AUGGGAAuggCaccg.Ggcc.uUu.... 180 +G+++ +G+ CU AUGG+A +G:C::CG GG:C :UU 128 AGUGAUGGGCCACUcuacuucggaguggcucaAUGGAAGCGGCUUCGuGGACaGUUggcu 187 ..........................,,,,,,,,,,,,,,,,,]]]]<<<<<______>> 181 ..........................CUGUUGAGUGCAAUgGuuGagcugaguuaggCcu 214 CUGUU AGUGCAAU ::::C: UU 188 uaggccgcccucaggggcgguuugagCUGUUAAGUGCAAUACACAGACA---UUG----- 239 >>>::::::::::: 215 cagAACCCAAUcag 228 :G A 240 -UGCA--------- 243 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #16117,sp|AF186229.1|AF186229 Torulaspora delbrueckii RNase P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: UCCUACGAUUUAGAAACCUGUUUGCUAACGGAGUCUCAGGGCUCACACUAAUAGCAGGUGGGAAAUUCGGUGAAUCACUGCGGAACCCGACAGAGCCUAACAAGCUUUGUCGACCGGUUGCCUUGGCGACUUUUCCGUGAGGAGGGCCUGGGGAACCAGGCUCAUAUGGUCAUUGUCACAAGAAAUCAACUCGGUAGUCCUGUACUAUCGAGGAUGGGAAGGCAAUGGACGUUCCGUUUAACUUGAUCUCAUCAAGGUUUGUUGAGUGCAAUCGUAGGACGGUCUUAGACCUGAA hit 15 : 1 295 (fwd) 84.83 bits :::::::::::[[[[...,,,,,...<<<<.---------.<<<<<_____>>>>>---- 1 GCGGAaGGAAGcuCa...uUgUA...acgu.ucAccagca.GagugcUugucacuCaacu 52 ::C: +U+UA AC:U U++ C+++ GAG :++ G : CUCA ++ 1 -----------UCCUacgAUUUAgaaACCUgUUUGCUAACgGAGUCUCAG-GGCUCACAC 48 -----..>>>>,,,,,,,,,,,,,,,,,,(.....((((,,,,,,............... 53 aacau..acgugGGGAAGGUCUGAGAaACa.....ggcCAauuau............... 90 +A+++ A:GU GGGAA++UC+G+GAA+CA G::C + + 49 UAAUAgcAGGU-GGGAAAUUCGGUGAAUCAcugcgGAACCCGACAgagccuaacaagcuu 107 ........................<<<<<_____>>>>><<<<<<<____>>>>>>>,.. 91 ........................ugCcCgUGAAGgGcaucaccggGGAAccggugau.. 124 :::CCGUGA GG::: +:C:GGGGAACC:G:+ U 108 ugucgaccgguugccuuggcgacuUUUCCGUGA-GGAGG-GCCUGGGGAACCAGGC-Uca 164 ......<<<<<<<____________._______________........________>>> 125 ......cgguGucAUCAGAAAUccA.acgguugagcuggcu........AUGGGAAuggC 169 C::UGUCA++AGAAAUC+A CGGU+G +CUG + AUGGGAA GGC 165 uaugguCAUUGUCACAAGAAAUCAAcUCGGUAGUCCUGUACuaucgaggAUGGGAA-GGC 223 >>>>...))))..),,...................,,,,,,,,,,,,,,,,,]]]]<<<< 170 accg...Ggcc..uUu...................CUGUUGAGUGCAAUgGuuGagcuga 205 A::G G::C UUU UGUUGAGUGCAAU+GU:G::C:G: 224 AAUGgacGUUCcgUUUaacuugaucucaucaagguUUGUUGAGUGCAAUCGUAGGACGGU 283 <______>>>>.>::::::::::: 206 guuaggCcuca.gAACCCAAUcag 228 :UUA ::C: GAA 284 CUUA---GACCuGAA--------- 295 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #16118,sp|AF186230.1|AF186230 Wickerhamia fluorescens RNase P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: AACUUUCCUUGAAAGUUUCGGCUUAUGAGUUACAAACUGCUCUUGAGAGCGUCCUUAGCGUGCAAACGCUGGGCGGUGCUAUCAGAAAUUUACCAGUCCUUACUUCGUAUUGGGACUGGAUGGGAAUGGCACUGCGGAUGGUUGGCCCUCUGAAUGAGAGAGAGGGCUUUUGAGUGCAAUAUGCGAACUUGGAUAUUCCAAGAA hit 16 : 29 232 (fwd) 51.40 bits :::::::::::[[[[,,,,,<<<<---------<<<<<_____>>>>>--------->>> 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagugcUugucacuCaacuaacauacg 60 A::UU+ C +G+A A:: 29 --------------------AACUUUCCUUGAA------------------------AGU 44 >,,,,,,,,,,,,.,,,,,,(((((,,,,,,<<<<<_____>>>>>...<<<<<<<____ 61 ugGGGAAGGUCUG.AGAaACaggcCAauuauugCcCgUGAAGgGca...ucaccggGGAA 116 U UC+G +A :: :A+ +A+:GC:C+UGA G:GC: :A:CG:G AA 45 U--------UCGGc--UUAUGAGUUACAAACUGCUCUUGA-GAGCGuccUUAGCGUGCAA 93 >>>>>>>,<<<<<<<____________.............____________________ 117 ccggugaucgguGucAUCAGAAAUccA.............acgguugagcuggcuAUGGG 163 :CG:U: +C:GUG::AUCAGAAAU+ A + UUG+G +G+ AUGGG 94 ACGCUGGGCGGUGCUAUCAGAAAUUUAccaguccuuacuuCGUAUUGGGACUGG-AUGGG 152 ___>>>>>>>.))))),,........................,,,,,,,,,,,,,,,,,] 164 AAuggCaccg.GgccuUu........................CUGUUGAGUGCAAUgGuu 198 AAU::CAC:G : ::+U CU+UUGAGUGCAAU + + 153 AAUGGCACUGcGGAUGGUuggcccucugaaugagagagagggCUUUUGAGUGCAAUAUGC 212 ]]]<<<<<..______>>>>>::::::::::: 199 Gagcugag..uuaggCcucagAACCCAAUcag 228 GA+CU::G +U+ C::AGAA 213 GAACUUGGauAUU---CCAAGAA--------- 232 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #16119,sp|AF186231.1|AF186231 Zygosaccharomyces bailii RNase P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: GAACACUGUGGGACACUAUGCCGACCCGCUGACUUUCUCGGUCAACGGGCCGUUUCCGUGAGGAAAGUCUGGGGAACUAGGCUUGCAGCUGCUGUCACAAGAAAUCAACGCUCACAGUAGCGGAUGGGAAGACAGCAGAGUUCCAUUUAGCUUGAACACAACGUUGAUUGUUUAAGGCUUGUUGAGUGCAAUCGUAGGACAAGAA hit 17 : 1 205 (fwd) 32.68 bits :::::::::::[[[[,,,,,<<<<---------<<<<<_____>>>>>--------->>> 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagugcUugucacuCaacuaacauacg 60 - ------------------------------------------------------------ - >,,,,,,,,,,,,,,,,,,(.....((((,,,,,,......................... 61 ugGGGAAGGUCUGAGAaACa.....ggcCAauuau......................... 90 +AACA G :CA+U+ 1 ---------------GAACAcugugGGACACUAUGccgacccgcugacuuucucggucaa 45 .......<<<<<_____>>>>><<<<<<<____>>>>>>>,......<<<<<<<______ 91 .......ugCcCgUGAAGgGcaucaccggGGAAccggugau......cgguGucAUCAGA 137 U::CCGUGA GG::A + C: GGGAAC :G + U :G:UG:CA++AGA 46 cgggccgUUUCCGUGA-GGAAA-GUCUGGGGAACUAGGC-UugcagcUGCUGUCACAAGA 102 ______._______________________>>>>>>>..))))..),,............ 138 AAUccA.acgguugagcuggcuAUGGGAAuggCaccg..Ggcc..uUu............ 180 AAUC+A C +++ + G+ AUGGGAA G:CA:C: G: C UUU 103 AAUCAAcGCUCACAGUAGCGG-AUGGGAA-GACAGCAgaGUUCcaUUUagcuugaacaca 160 .................,.,,,,,,,,,,,,,,,,]]]]<<<<<______>>>>>::::: 181 .................C.UGUUGAGUGCAAUgGuuGagcugaguuaggCcucagAACCC 222 C UGUUGAGUGCAAU+GU+G++C ++ GAA 161 acguugauuguuuaaggCuUGUUGAGUGCAAUCGUAGGAC----AA--------GAA--- 205 :::::: 223 AAUcag 228 - ------ - ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #16120,sp|AF186232.1|AF186232 Zygosaccharomyces florentinus RNase P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: GCCUCUGCAGCGUAAGCUACAUUGGGGACUUUUCCGUGAGGAGGGAUCUUGGGGAACCAAGACCAUAUGGUUGUUGUCAUCAGAAAUCAACCAGGUUACGUAAGUUACCUGGUAUGGGAAGGCAACUGUAAGUUCCGUUUGACUUGUGCUAAUUAGUAUAAGGUCUGUUGAGUGCAAUCGAAGGACAAGUCUUAUAGAUUUGAA hit 18 : 59 262 (fwd) 51.62 bits :::::::::::[[[[,,,,,<<<<---------<<<<<_____>>>>>--------->>> 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagugcUugucacuCaacuaacauacg 60 :C:+UG A: 59 -----------GCCUCUGCAG--------------------------------------- 68 >,,,,,,,,,,,,,,,,,,(((((,,,,,,....<<<<<_____>>>>>.<<<<<<<___ 61 ugGGGAAGGUCUGAGAaACaggcCAauuau....ugCcCgUGAAGgGca.ucaccggGGA 115 : ++A+: ::CA+U + :::CCGUGA GG::: ::::GGGGA 69 C--------------GUAAGCUACAUUGGGgacuUUUCCGUGA-GGAGGgAUCUUGGGGA 113 _>>>>>>>,.......<<<<<<<____________.........________________ 116 Accggugau.......cgguGucAUCAGAAAUccA.........acgguugagcuggcuA 159 ACC:::: :G:UGUCAUCAGAAAUC+A +U A+CUGG A 114 ACCAAGACCauaugguUGUUGUCAUCAGAAAUCAAccagguuacGUAAGUUACCUGGU-A 172 _______>>>>>>>))))),,..............................,,,,,,,,, 160 UGGGAAuggCaccgGgccuUu..............................CUGUUGAGU 189 UGGGAA GGCA:C:G:: :UU CUGUUGAGU 173 UGGGAA-GGCAACUGUAAGUUccguuugacuugugcuaauuaguauaagguCUGUUGAGU 231 ,,,,,,,,]]]]<<<<<.______>>>>>::::::::::: 190 GCAAUgGuuGagcugag.uuaggCcucagAACCCAAUcag 228 GCAAU+G :G: C:: : UUA+ : ::GAA 232 GCAAUCGAAGGACAAGUcUUAUAGAUUUGAA--------- 262 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #16121,sp|AF186233.1|AF186233 Zygosaccharomyces rouxii RNase P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: UCCUACGCAAUUUUACCUGCCUUCAUAAGGAACUCAAAGGGUUCAGUUAGUACUUAACUUACUAUAUAAGCAGGUGGGAAAUUCGGUGGAACUCUAAGAGACAAUCAGCCGGAUCUUUAGCUUAAUUGUUAAAGAACUGUUUCCGUGAGGAAAGUCUGGGGAACUGGACUUGCAGCUGCUGUCACAAGAAAUCAACGCCCUUUGUUGGUGGAUGGGAAGGCAGUAGAGGUCUCUUUUGGCUUGGAUGCAAAUUUGGACGUCCAAGGCUUGCUGAGUGCAAUCGUGGGACAAAGAA hit 19 : 1 295 (fwd) 69.25 bits :::::::::::[[[[.....,,,,,<<<<.---------.<<<<<......._____... 1 GCGGAaGGAAGcuCa.....uUgUAacgu.ucAccagca.Gagug.......cUugu... 43 ::C +U+U+AC:U +C+ CA +A A::: +U+ 1 -----------UCCUacgcaAUUUUACCUgCCUUCAUAAgGAACUcaaagggUUCAGuua 49 .......>>>>>---------.>>>>,,,,,,,,,,,,,,,,,,(.....((((,,,,,, 44 .......cacuCaacuaacau.acgugGGGAAGGUCUGAGAaACa.....ggcCAauuau 90 :::U ++UA +A A:GU GGGAA++UC+G+G+AAC: :G:CAAU A 50 guacuuaACUUACUAUAUAAGcAGGU-GGGAAAUUCGGUGGAACUcuaagAGACAAUCAG 108 ...............................<<<<<_____>>>>><<<<<<<____>>> 91 ...............................ugCcCgUGAAGgGcaucaccggGGAAccg 119 U::CCGUGA GG::A +:C: GGGAAC : 109 ccggaucuuuagcuuaauuguuaaagaacugUUUCCGUGA-GGAAA-GUCUGGGGAACUG 166 >>>>,......<<<<<<<____________.._______________________>>>>> 120 gugau......cgguGucAUCAGAAAUccA..acgguugagcuggcuAUGGGAAuggCac 171 G:+ U :::UGUCA++AGAAAUC+A +C +UUG ++++G+ AUGGGAA GGCA: 167 GAC-UugcagcUGCUGUCACAAGAAAUCAAcgCCCUUUGUUGGUGG-AUGGGAA-GGCAG 223 >>...)))).),,..............................,.,,,,,,,,,,,,,,, 172 cg...Ggcc.uUu..............................C.UGUUGAGUGCAAUgG 196 :: G:C: :UU C UG UGAGUGCAAU+G 224 UAgagGUCUcUUUuggcuuggaugcaaauuuggacguccaaggCuUGCUGAGUGCAAUCG 283 ,]]]]<<<<<______>>>>>::::::::::: 197 uuGagcugaguuaggCcucagAACCCAAUcag 228 U G::C ++A GAA 284 UGGGAC----AAA-------GAA--------- 295 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #68282,sp|L12745.1|SBRPR1B Saccharomyces bayanus RNase P RNA (RPR1) gene. ----isReversed: 0 ----hitSequence: ACAGUGGUAAUUCCUACGAUUAAGAAACCUGUUUACAGAAGGAUCCCCACCUAUGGGCGGGUUAUCAGAUAUUAUCAGGUGGGAAAUUCGGUGGAACACAGUGGAGCCUUGUCCUCCGGGUUAAUGUCGCUUUUGGCAUUGACCCCUGCUCCUGAGAGAAGAAAUAUACUGGGGAACCAGUCUUUACCGACCGUUGUUAUCAGAAAUUCACGGAGUUCGGCCUAGGUCGGACUCCGAUGGGAACGGCAACGGUUGUUCCGUUUGACUUGUCGCCCGCUACGGCGUGAGCGUCAAGGUCUGUUGAGUGCAAUCGUAGGACGUCAUUUGUGGCGAACCCGAUACC hit 20 : 413 755 (fwd) 111.69 bits :::::::::::[[[[...,,,,,...<<<<.---------.<<<<<..._____...... 1 GCGGAaGGAAGcuCa...uUgUA...acgu.ucAccagca.Gagug...cUugu...... 43 +C+G++G AA ::C: +U+ A AC:U U+++CAG+A GA: C+U U 413 ACAGUGGUAAUUCCUacgAUUAAgaaACCUgUUUACAGAAgGAUCCccaCCUAUgggcgg 472 .>>>>>---------.>>>>,,,,,,,,,,,,,,,,,,(.....((((,,,,,,...... 44 .cacuCaacuaacau.acgugGGGAAGGUCUGAGAaACa.....ggcCAauuau...... 90 :UCA +UA AU A:GU GGGAA++UC+G+G+AACA G::C +U + 473 gUUAUCAGAUAUUAUcAGGU-GGGAAAUUCGGUGGAACAcagugGAGCCUUGUCcuccgg 531 ...........................<<<<<_____>>>>>.....<<<<<<<____>> 91 ...........................ugCcCgUGAAGgGca.....ucaccggGGAAcc 118 U C:C UGA G:G A ::AC:GGGGAACC 532 guuaaugucgcuuuuggcauugaccccUGCUCCUGA-GAGAAgaaauAUACUGGGGAACC 590 >>>>>,.......<<<<<<<____________.._______________.........__ 119 ggugau.......cgguGucAUCAGAAAUccA..acgguugagcuggcu.........AU 160 :GU::U CG:UGU:AUCAGAAAU+CA +G+U G++CU G+U AU 591 AGUCUUuaccgacCGUUGUUAUCAGAAAUUCAcgGAGUUCGGCCUAGGUcggacuccgAU 650 ______>>>>>>>...))))..),,.................................., 161 GGGAAuggCaccg...Ggcc..uUu..................................C 181 GGGAA+:GCA:CG G::C UUU C 651 GGGAACGGCAACGguuGUUCcgUUUgacuugucgcccgcuacggcgugagcgucaagguC 710 ,,,,,,,,,,,,,,,,]]]]<<<<<______>>>>>::::::::::: 182 UGUUGAGUGCAAUgGuuGagcugaguuaggCcucagAACCCAAUcag 228 UGUUGAGUGCAAU+GU:G::C: ::UU+G :: :GAACCC+AU+++ 711 UGUUGAGUGCAAUCGUAGGACGUCAUUUG--UGGCGAACCCGAUACC 755 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #68877,sp|U18530.1|SC9871 Saccharomyces cerevisiae chromosome V cosmids 9871, 8199, 9867, 9495 and lambda clones 6693 and 5898. ----isReversed: 1 ----hitSequence: ACAGUGGUAAUUCCUACGAUUAAGAAACCUGUUUACAGAAGGAUCCCCACCUAUGGGCGGGUUAUCAGAUAUUAUCAGGUGGGAAAUUCGGUGGAACACAGUGGAGCCUUGUCCUCCGGGUUAAUGUCGCUUUUGGCAUUGGCCCCUGCUCCUGAGAGAAGAAAUAUACUGGGGAACCAGUCUUUACCGACCGUUGUUAUCAGAAAUUCACGGAGUUCGGCCUAGGUCGGACUCCGAUGGGAACGGCAACGGUUGUUCCGUUUGACUUGUCGCCCGCUACGGCGUGAGCGUCAAGGUCUGUUGAGUGCAAUCGUAGGACGUCAUUAGUGGCGAACCCGAUACC hit 21 : 28436 28094 (rev) 111.87 bits :::::::::::[[[[...,,,,,...<<<<.---------.<<<<<..._____...... 1 GCGGAaGGAAGcuCa...uUgUA...acgu.ucAccagca.Gagug...cUugu...... 43 +C+G++G AA ::C: +U+ A AC:U U+++CAG+A GA: C+U U 34208 ACAGUGGUAAUUCCUacgAUUAAgaaACCUgUUUACAGAAgGAUCCccaCCUAUgggcgg 34267 .>>>>>---------.>>>>,,,,,,,,,,,,,,,,,,(.....((((,,,,,,...... 44 .cacuCaacuaacau.acgugGGGAAGGUCUGAGAaACa.....ggcCAauuau...... 90 :UCA +UA AU A:GU GGGAA++UC+G+G+AACA G::C +U + 34268 gUUAUCAGAUAUUAUcAGGU-GGGAAAUUCGGUGGAACAcagugGAGCCUUGUCcuccgg 34326 ...........................<<<<<_____>>>>>.....<<<<<<<____>> 91 ...........................ugCcCgUGAAGgGca.....ucaccggGGAAcc 118 U C:C UGA G:G A ::AC:GGGGAACC 34327 guuaaugucgcuuuuggcauuggccccUGCUCCUGA-GAGAAgaaauAUACUGGGGAACC 34385 >>>>>,.......<<<<<<<____________.._______________.........__ 119 ggugau.......cgguGucAUCAGAAAUccA..acgguugagcuggcu.........AU 160 :GU::U CG:UGU:AUCAGAAAU+CA +G+U G++CU G+U AU 34386 AGUCUUuaccgacCGUUGUUAUCAGAAAUUCAcgGAGUUCGGCCUAGGUcggacuccgAU 34445 ______>>>>>>>...))))..),,.................................., 161 GGGAAuggCaccg...Ggcc..uUu..................................C 181 GGGAA+:GCA:CG G::C UUU C 34446 GGGAACGGCAACGguuGUUCcgUUUgacuugucgcccgcuacggcgugagcgucaagguC 34505 ,,,,,,,,,,,,,,,,]]]]<<<<<______>>>>>::::::::::: 182 UGUUGAGUGCAAUgGuuGagcugaguuaggCcucagAACCCAAUcag 228 UGUUGAGUGCAAU+GU:G::C: ::UUAG :: :GAACCC+AU+++ 34506 UGUUGAGUGCAAUCGUAGGACGUCAUUAG--UGGCGAACCCGAUACC 34550 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #71382,sp|M27035.1|SCRPR1A Saccharomyces cerevisiae RNase P RNA (RPR1) gene. ----isReversed: 0 ----hitSequence: ACAGUGGUAAUUCCUACGAUUAAGAAACCUGUUUACAGAAGGAUCCCCACCUAUGGGCGGGUUAUCAGUAAUUAUCAGGUGGGAAAUUCGGUGGAACACAGUGGAGCCUUGUCCUCCGGGUUAAUGUCGCUUUUGGCAUUGGCCCCUGCUCCUGAGAGAAGAAAUAUACUGGGGAACCAGUCUUUACCGACCGUUGUUAUCAGAAAUUCACGGAGUUCGGCCUAGGUCGGACUCCGAUGGGAACGGCAACGGUUGUUCCGUUUGACUUGUCGCCCGCUACGGCGUGAGCGUCAAGGUCUGUUGAGUGCAAUCGUAGGACGUCAUUAGUGGCGAACCCGAUACC hit 22 : 413 755 (fwd) 111.16 bits :::::::::::[[[[...,,,,,...<<<<.---------.<<<<<..._____...... 1 GCGGAaGGAAGcuCa...uUgUA...acgu.ucAccagca.Gagug...cUugu...... 43 +C+G++G AA ::C: +U+ A AC:U U+++CAG+A GA: C+U U 413 ACAGUGGUAAUUCCUacgAUUAAgaaACCUgUUUACAGAAgGAUCCccaCCUAUgggcgg 472 .>>>>>---------.>>>>,,,,,,,,,,,,,,,,,,(.....((((,,,,,,...... 44 .cacuCaacuaacau.acgugGGGAAGGUCUGAGAaACa.....ggcCAauuau...... 90 :UCA + A AU A:GU GGGAA++UC+G+G+AACA G::C +U + 473 gUUAUCAGUAAUUAUcAGGU-GGGAAAUUCGGUGGAACAcagugGAGCCUUGUCcuccgg 531 ...........................<<<<<_____>>>>>.....<<<<<<<____>> 91 ...........................ugCcCgUGAAGgGca.....ucaccggGGAAcc 118 U C:C UGA G:G A ::AC:GGGGAACC 532 guuaaugucgcuuuuggcauuggccccUGCUCCUGA-GAGAAgaaauAUACUGGGGAACC 590 >>>>>,.......<<<<<<<____________.._______________.........__ 119 ggugau.......cgguGucAUCAGAAAUccA..acgguugagcuggcu.........AU 160 :GU::U CG:UGU:AUCAGAAAU+CA +G+U G++CU G+U AU 591 AGUCUUuaccgacCGUUGUUAUCAGAAAUUCAcgGAGUUCGGCCUAGGUcggacuccgAU 650 ______>>>>>>>...))))..),,.................................., 161 GGGAAuggCaccg...Ggcc..uUu..................................C 181 GGGAA+:GCA:CG G::C UUU C 651 GGGAACGGCAACGguuGUUCcgUUUgacuugucgcccgcuacggcgugagcgucaagguC 710 ,,,,,,,,,,,,,,,,]]]]<<<<<______>>>>>::::::::::: 182 UGUUGAGUGCAAUgGuuGagcugaguuaggCcucagAACCCAAUcag 228 UGUUGAGUGCAAU+GU:G::C: ::UUAG :: :GAACCC+AU+++ 711 UGUUGAGUGCAAUCGUAGGACGUCAUUAG--UGGCGAACCCGAUACC 755 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #71383,sp|L12746.1|SCRPR1C Saccharomyces carlsbergensis RNase P RNA (RPR1) gene. ----isReversed: 0 ----hitSequence: ACAGUGGUGAUUCCUACGAUUAAGAAACCUGUUUGCAAAAGGGCCUGCCCACGCGGGUCAUCUUAUUUAUCAGGUGGGAAAUUCGGUGGAACACAGUGGAGCCUUGCCUUCCGGGCCAUUGUCUCUGGCAGUGGCCCCUGCUCGUGAGAGAAGAAACUUGCUGGGGAACCAGUCUUUACCGACCGUUGCUAUCAGAAAUUGAACGGGGCCCGGUCCCGCCGGGCCUCGAUGGGAACGGCAACGGUUGUUCCGUUUGACUUGUCGCCCGCCACGGCGCGCUGCAAGGUCUGUUGAGUGCAAUCGUAGGACGCCAUUCGUGGCGAACCCGAUACC hit 23 : 291 623 (fwd) 104.15 bits :::::::::::[[[[...,,,,,...<<<<.---------.<<<<<._____..>>>>>- 1 GCGGAaGGAAGcuCa...uUgUA...acgu.ucAccagca.Gagug.cUugu..cacuCa 49 +C+G++G A ::C: +U+ A AC:U U++ CA++A G:+: C++ :+:CA 291 ACAGUGGUGAUUCCUacgAUUAAgaaACCUgUUUGCAAAAgGGCCUgCCCACgcGGGUCA 350 --------...>>>>,,,,,,,,,,,,,,,,,,(.....((((,,,,,,........... 50 acuaacau...acgugGGGAAGGUCUGAGAaACa.....ggcCAauuau........... 90 +CU+A +U A:GU GGGAA++UC+G+G+AACA G::C +U + 351 UCUUAUUUaucAGGU-GGGAAAUUCGGUGGAACAcagugGAGCCUUGCCuuccgggccau 409 ...................<<<<<_____>>>>>.....<<<<<<<____>>>>>>>,.. 91 ...................ugCcCgUGAAGgGca.....ucaccggGGAAccggugau.. 124 U C:CGUGA G:G A :::C:GGGGAACC:G:::U 410 ugucucuggcaguggccccUGCUCGUGA-GAGAAgaaacUUGCUGGGGAACCAGUCUUua 468 .....<<<<<<<____________......._______________....________>> 125 .....cgguGucAUCAGAAAUccA.......acgguugagcuggcu....AUGGGAAugg 168 CG:UG::AUCAGAAAU+ A +CGGU GC GG++ AUGGGAA+:: 469 ccgacCGUUGCUAUCAGAAAUUGAacggggcCCGGUCCCGCCGGGCcucgAUGGGAACGG 528 >>>>>...))))..),,................................,,,,,,,,,,, 169 Caccg...Ggcc..uUu................................CUGUUGAGUGC 191 CA:CG G::C UUU CUGUUGAGUGC 529 CAACGguuGUUCcgUUUgacuugucgcccgccacggcgcgcugcaagguCUGUUGAGUGC 588 ,,,,,,]]]]<<<<<______>>>>>::::::::::: 192 AAUgGuuGagcugaguuaggCcucagAACCCAAUcag 228 AAU+GU:G::C::::UU G ::::GAACCC+AU+++ 589 AAUCGUAGGACGCCAUUCG--UGGCGAACCCGAUACC 623 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #75632,sp|L12747.1|SDRPR1D Saccharomyces diastaticus RNase P RNA (RPR1) gene. ----isReversed: 0 ----hitSequence: ACAGUGGUAAUUCCUACGAUUAAGAAACCUGUUUACAGAAGGAUCCCCACCUAUGGGCGGGUUAUCAGAUAUUAUCAGGUGGGAAAUUCGGUGGAACACAGUGGAGCCUUGUCCUCCGGGUUAAUGUCGCUUUUGGCAUUGGCCCCUGCUCCUGAGAGAAGAAAUAUACUGGGGAACCAGUCUUUACCGACCGUUGUUAUCAGAAAUUCACGGAGUUCGGCCUAGGUCGGACUCCGAUGGGAACGGCAACGGUUGUUCCGUUUGACUUGUCGCCCGCUACGGCGUGAGCGUCAAGGUCUGUUGAGUGCAAUCGUAGGACGUCAUUUGUGGCGAACCCGAUACC hit 24 : 413 755 (fwd) 111.69 bits :::::::::::[[[[...,,,,,...<<<<.---------.<<<<<..._____...... 1 GCGGAaGGAAGcuCa...uUgUA...acgu.ucAccagca.Gagug...cUugu...... 43 +C+G++G AA ::C: +U+ A AC:U U+++CAG+A GA: C+U U 413 ACAGUGGUAAUUCCUacgAUUAAgaaACCUgUUUACAGAAgGAUCCccaCCUAUgggcgg 472 .>>>>>---------.>>>>,,,,,,,,,,,,,,,,,,(.....((((,,,,,,...... 44 .cacuCaacuaacau.acgugGGGAAGGUCUGAGAaACa.....ggcCAauuau...... 90 :UCA +UA AU A:GU GGGAA++UC+G+G+AACA G::C +U + 473 gUUAUCAGAUAUUAUcAGGU-GGGAAAUUCGGUGGAACAcagugGAGCCUUGUCcuccgg 531 ...........................<<<<<_____>>>>>.....<<<<<<<____>> 91 ...........................ugCcCgUGAAGgGca.....ucaccggGGAAcc 118 U C:C UGA G:G A ::AC:GGGGAACC 532 guuaaugucgcuuuuggcauuggccccUGCUCCUGA-GAGAAgaaauAUACUGGGGAACC 590 >>>>>,.......<<<<<<<____________.._______________.........__ 119 ggugau.......cgguGucAUCAGAAAUccA..acgguugagcuggcu.........AU 160 :GU::U CG:UGU:AUCAGAAAU+CA +G+U G++CU G+U AU 591 AGUCUUuaccgacCGUUGUUAUCAGAAAUUCAcgGAGUUCGGCCUAGGUcggacuccgAU 650 ______>>>>>>>...))))..),,.................................., 161 GGGAAuggCaccg...Ggcc..uUu..................................C 181 GGGAA+:GCA:CG G::C UUU C 651 GGGAACGGCAACGguuGUUCcgUUUgacuugucgcccgcuacggcgugagcgucaagguC 710 ,,,,,,,,,,,,,,,,]]]]<<<<<______>>>>>::::::::::: 182 UGUUGAGUGCAAUgGuuGagcugaguuaggCcucagAACCCAAUcag 228 UGUUGAGUGCAAU+GU:G::C: ::UU+G :: :GAACCC+AU+++ 711 UGUUGAGUGCAAUCGUAGGACGUCAUUUG--UGGCGAACCCGAUACC 755 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #75751,sp|L12748.1|SGRPR1E Saccharomyces globosus RNase P RNA (RPR1) gene. ----isReversed: 0 ----hitSequence: GCAGUAGCAACUCCUACGAUUUUAACCUGCUUACGAACUAUUAGUCUGAUCUAAUAAUACAUGCAGGUGGGAAAUUCGGUGAAACACAACAAAUGAGGUUUCAGUUAUUUGGGCUCGUGAGAGCAGCCUGGGGAACCUGGUUAUAAUAGCGGCGCUAUCAGAAAUUCAACGCUAUCAAAUUUUGAUGGUGAUGGGAACGGCGCUAGCAACAAACAUAUUUUAUGUACCUCACGUGUUUGACUUAAUCAUUUACUGGUUAAAGUCUGUUCAGUGCAAUCGUAGGACUUCUAAGCAAUUAGUUGCACCCGAUACC hit 25 : 280 592 (fwd) 92.21 bits :::::::::::[[[[....,,,,,<<<<.---------<<<<<._____..>>>>>---- 1 GCGGAaGGAAGcuCa....uUgUAacgu.ucAccagcaGagug.cUugu..cacuCaacu 52 GC+G+AG AA ::C: UU+UAAC:U ++++C ++ :A:U: ++UG :A:U:A+++ 280 GCAGUAGCAACUCCUacgaUUUUAACCUgCUUACGAACUAUUAgUCUGAucUAAUAAUAC 339 -----.>>>>,,,,,,,,,,,,,,,,,,(............((((,,,,,,...<<<<<_ 53 aacau.acgugGGGAAGGUCUGAGAaACa............ggcCAauuau...ugCcCg 96 A A:GU GGGAA++UC+G+GAAACA :: CA UUAU GC:CG 340 AUG--cAGGU-GGGAAAUUCGGUGAAACAcaacaaaugaggUUUCAGUUAUuugGGCUCG 396 ____>>>>><<<<<<<____>>>>>>>,.......<<<<<<<____________...... 97 UGAAGgGcaucaccggGGAAccggugau.......cgguGucAUCAGAAAUccA...... 143 UGA G:GC ::C GGGGAACC G:: U :G:G::AUCAGAAAU+CA 397 UGA-GAGCA-GCCUGGGGAACCUGGU-UauaauagCGGCGCUAUCAGAAAUUCAacgcua 453 .._______________________>>>>>>>))))........),,............. 144 ..acgguugagcuggcuAUGGGAAuggCaccgGgcc........uUu............. 180 A+ +UU + +G + AUGGGAA+::C:C: G :: UUU 454 ucAAAUUUUGAUGGUG-AUGGGAACGGCGCUAGCAAcaaacauaUUUuauguaccucacg 512 ..............................,,,,,,,,,,,,,,,,,]]]]<<<<<.... 181 ..............................CUGUUGAGUGCAAUgGuuGagcugag.... 206 CUGUU AGUGCAAU+GU:G::C ::: 513 uguuugacuuaaucauuuacugguuaaaguCUGUUCAGUGCAAUCGUAGGACUUCUaagc 572 .______>>>>>::::::::::: 207 .uuaggCcucagAACCCAAUcag 228 +U+ ::: G ACCC+AU+++ 573 aAUU---AGUUGCACCCGAUACC 592 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #75844,sp|L12750.1|SKRPR1G Saccharomyces kluyveri RNasr P RNA (RPR1) gene. ----isReversed: 0 ----hitSequence: ACAGUGGCAUUCCUACUACAAACCUGUUUGCACAAGGAGCGGUCGGCGUCAGUCGCACCCUGCUCAGAAAUACAGGUGGGAAAUUCGGUGAAACGCGGCGGAGCAACUAUUUCCGAGGGCCGUUCUCGGUCCUGAUUUCCGUGAGGAAAGCGUUUGGAAUUUAAACGCUUGGACGUUGUCAUCAGAAAUACACCAGUCUCUUGGCUGGAUGGGAAGGCAGCGGAUGCUCCGUUUGACUGUGUUUAGCUUCGGCGACACAGGUCUGUUGAGUGCAAUCGUAGGACACUUCUUAUGAGGUGAACCCGAUACC hit 26 : 273 582 (fwd) 94.38 bits :::::::::::[[[[.,,,,,.<<<<.---------.<<<<<_____...........>> 1 GCGGAaGGAAGcuCa.uUgUA.acgu.ucAccagca.GagugcUugu...........ca 45 +C+G++G A ::C: +U A AC:U U++ CA +A AG:G U+G C: 273 ACAGUGGC-AUUCCUaCUACAaACCUgUUUGCACAAgGAGCGGUCGGcgucagucgcaCC 331 >>>---------..>>>>,,,,,,,,,,,,,,,,,,(.....((((,,,,,,........ 46 cuCaacuaacau..acgugGGGAAGGUCUGAGAaACa.....ggcCAauuau........ 90 CU +C A+AU A:GU GGGAA++UC+G+GAAAC: G: CAA UAU 332 CUGCUCAGAAAUacAGGU-GGGAAAUUCGGUGAAACGcggcgGAGCAACUAUuuccgagg 390 .................<<<<<_____>>>>><<<<<<<____...>>>>>>>,....<< 91 .................ugCcCgUGAAGgGcaucaccggGGAA...ccggugau....cg 126 U::CCGUGA GG::A +:::::GGAA :::::+ U CG 391 gccguucucgguccugaUUUCCGUGA-GGAAA-GCGUUUGGAAuuuAAACGC-UuggaCG 447 <<<<<____________._______________________>>>>>>>...)))).),,. 127 guGucAUCAGAAAUccA.acgguugagcuggcuAUGGGAAuggCaccg...Ggcc.uUu. 180 :UGUCAUCAGAAAU CA ++G+ U +++ + AUGGGAA GGCA:CG G :C :UU 448 UUGUCAUCAGAAAUACAcCAGUCUCUUGGCUGGAUGGGAA-GGCAGCGgauGCUCcGUUu 506 ............................,,,,,,,,,,,,,,,,,]]]]<<<<<..____ 181 ............................CUGUUGAGUGCAAUgGuuGagcugag..uuag 210 CUGUUGAGUGCAAU+GU:G::C:: : U++G 507 gacuguguuuagcuucggcgacacagguCUGUUGAGUGCAAUCGUAGGACACUUcuUAUG 566 __>>>>>::::::::::: 211 gCcucagAACCCAAUcag 228 : ::GAACCC+AU+++ 567 --AGGUGAACCCGAUACC 582 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #76059,sp|X52531.1|SORRK1 S.octosporus rrk1 gene for K-RNA (component of RNase P) ----isReversed: 0 ----hitSequence: AACGCCGCACUUCCUCAAAUUCAGACGCACUUUUACAAGUGUUACGCGCAUUGAGGGGGUAAGGUCGGAGGAACUUCUUCGUUGCAUGCUCGUGAGGAGCGGAGGACGAAAGUCCUGCCGGGUGUACCAGAAAUUCGAUCUCUUGGUUCGUCCUUUGAGAUCUUGAAACGCACCCGAGAAGAUGUCUUUUAGUGCAAUGUGCGGCACCUGUGAAAAGUCAGGCAACUCGAUUCCG hit 27 : 55 289 (fwd) 52.25 bits :::::::::::[[[[..,,,,,<<<<.---------.<<<<<_____.>>>>>------- 1 GCGGAaGGAAGcuCa..uUgUAacgu.ucAccagca.GagugcUugu.cacuCaacuaac 55 AA ::C: +U C:U A + A +::::+UU ::::++AC C 55 --------AACGCCGcaCU---UCCUcAAAUUCAGAcGCACUUUUACaAGUGUUACGCGC 103 --..>>>>,,,,,,,,,,,,,,,,,,(.((((,,,,,,<<<<<_____>>>>><<<<<<< 56 au..acgugGGGAAGGUCUGAGAaACa.ggcCAauuauugCcCgUGAAGgGcaucaccgg 112 AU A:G GG AAGGUC+GAG+AAC: :::C +U :GC:CGUGA G:GC: A:::: 104 AUugAGGG-GGUAAGGUCGGAGGAACUuCUUCGUUGCAUGCUCGUGAGGAGCG-GAGGAC 161 ____>>>>>>>,.<<<<<<<____________.._______________.......____ 113 GGAAccggugau.cgguGucAUCAGAAAUccA..acgguugagcuggcu.......AUGG 162 G AA::::U :GGUGU A+CAGAAAU+C+ + +U G +C++ CU U G 162 GAAAGUCCUG-CcGGGUGU-ACCAGAAAUUCGauCUCUUGGUUCGUCCUuugagauCUUG 219 ____>>>>>>>..)))).),,,,,,,,,,,,,,,,,,,]]]]<<<<<..______>>>>> 163 GAAuggCaccg..Ggcc.uUuCUGUUGAGUGCAAUgGuuGagcugag..uuaggCcucag 217 +AA +GCACC: G::: :+U +UU AGUGCAAUG+ :G::::::G ++A G C:::: 220 AAA-CGCACCCgaGAAGaUGU-CUUUUAGUGCAAUGUGCGGCACCUGugAAAAGUCAGGC 277 :::::::.:::: 218 AACCCAA.Ucag 228 AAC C+A UC+G 278 AACUCGAuUCCG 289 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #76825,sp|AL022598.2|SPCC1795 S.pombe chromosome III cosmid c1795. ----isReversed: 1 ----hitSequence: AACGCCGCACUUCCUCAAAUUCAAACGCGUUGAAAAGCGCACAGCUCGUUGAGGGGGUAAGGUCGGAGAAACAUCUUCGUUGCGUGCUCGUGAGGAGCGAAGAACGAACGUUCUGCCGAAUGUACCAGAAAUUCAAUCAGUAUGGCCUCGUUUGUCGUACCUGAUUUUGAAACGCAUUCGAGAAGAUUUAUUUUAGUGCAAUGUGUGGCACCUGUUUGUCAGGUAACUCGAUUCCG hit 28 : 27002 26767 (rev) 49.30 bits :::::::::::[[[[..,,,,,<<<<---------<<<<<_____...>>>>>------- 1 GCGGAaGGAAGcuCa..uUgUAacguucAccagcaGagugcUugu...cacuCaacuaac 55 AA ::C: +U C:U+ A+ + +A: G:G+U C:C :A CU 7563 --------AACGCCGcaCU---UCCUCAAAUUCAAACGCGUUGAAaagCGCACAGCUCGU 7611 -->>>>,,,,,,,,,,,,,,,,,,(.((((,,,,,,<<<<<_____>>>>>.<<<<<<<_ 56 auacgugGGGAAGGUCUGAGAaACa.ggcCAauuauugCcCgUGAAGgGca.ucaccggG 113 + A:G GG AAGGUC+GAGAAACA :::C +U :GC:CGUGA G:GC: :+A:CG 7612 UGAGGG-GGUAAGGUCGGAGAAACAuCUUCGUUGCGUGCUCGUGAGGAGCGaAGAACG-- 7668 ___>>>>>>>,.<<<<<<<____________.._______________............ 114 GAAccggugau.cgguGucAUCAGAAAUccA..acgguugagcuggcu............ 158 AA CG:U+:+ CG::: :A+CAGAAAU+CA ++G+ UG++CU G U 7669 -AA-CGUUCUGcCGAAUGUACCAGAAAUUCAauCAGUAUGGCCUCGUUugucguaccuga 7726 .________>>>>>>>.)))).),,,,,,,,,,,,,,,,,,,]]]]<<<<<______>>> 159 .AUGGGAAuggCaccg.Ggcc.uUuCUGUUGAGUGCAAUgGuuGagcugaguuaggCcuc 215 U G+AA+: :::CG G::: UUU +UU AGUGCAAUG+ :G::::::GUU+ G C:: 7727 uUUUGAAACGCAUUCGaGAAGaUUU-AUUUUAGUGCAAUGUGUGGCACCUGUUU-GUCAG 7784 >>:::::::.:::: 216 agAACCCAA.Ucag 228 ::AAC C+A UC+G 7785 GUAACUCGAuUCCG 7798 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #77308,sp|X04013.1|SPKRNAG Fission yeast K RNA gene K1- and K2-RNA co-purified with RNase P activity ----isReversed: 0 ----hitSequence: AACGCCGCACUUCCUCAAAUUCAAACGCGUUGAAAAGCGCACAGCUCGUUGAGGGGGUAAGGUCGGAGAAACAUCUUCGUUGCGUGCUCGUGAGGAGCGAAGAACGAACGUUCUGCCGAAUGUACCAGAAAUUCAAUCAGUAUGGCCUCGUUUGUCGUACCUGAUUUUGAAACGCAUUCGAGAAGAUUUAUUUUAGUGCAAUGUGUGGCACCUGUUUGUCAGGUAACUCGAUUCCG hit 29 : 212 447 (fwd) 49.30 bits :::::::::::[[[[..,,,,,<<<<---------<<<<<_____...>>>>>------- 1 GCGGAaGGAAGcuCa..uUgUAacguucAccagcaGagugcUugu...cacuCaacuaac 55 AA ::C: +U C:U+ A+ + +A: G:G+U C:C :A CU 212 --------AACGCCGcaCU---UCCUCAAAUUCAAACGCGUUGAAaagCGCACAGCUCGU 260 -->>>>,,,,,,,,,,,,,,,,,,(.((((,,,,,,<<<<<_____>>>>>.<<<<<<<_ 56 auacgugGGGAAGGUCUGAGAaACa.ggcCAauuauugCcCgUGAAGgGca.ucaccggG 113 + A:G GG AAGGUC+GAGAAACA :::C +U :GC:CGUGA G:GC: :+A:CG 261 UGAGGG-GGUAAGGUCGGAGAAACAuCUUCGUUGCGUGCUCGUGAGGAGCGaAGAACG-- 317 ___>>>>>>>,.<<<<<<<____________.._______________............ 114 GAAccggugau.cgguGucAUCAGAAAUccA..acgguugagcuggcu............ 158 AA CG:U+:+ CG::: :A+CAGAAAU+CA ++G+ UG++CU G U 318 -AA-CGUUCUGcCGAAUGUACCAGAAAUUCAauCAGUAUGGCCUCGUUugucguaccuga 375 .________>>>>>>>.)))).),,,,,,,,,,,,,,,,,,,]]]]<<<<<______>>> 159 .AUGGGAAuggCaccg.Ggcc.uUuCUGUUGAGUGCAAUgGuuGagcugaguuaggCcuc 215 U G+AA+: :::CG G::: UUU +UU AGUGCAAUG+ :G::::::GUU+ G C:: 376 uUUUGAAACGCAUUCGaGAAGaUUU-AUUUUAGUGCAAUGUGUGGCACCUGUUU-GUCAG 433 >>:::::::.:::: 216 agAACCCAA.Ucag 228 ::AAC C+A UC+G 434 GUAACUCGAuUCCG 447 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #77580,sp|X52530.1|SPRRK1 S.pombe rrk1 gene for K-RNA (component of RNase P) ----isReversed: 0 ----hitSequence: AACGCCGCACUUCCUCAAAUUCAAACGCGUUGAAAAGCGCACAGCUCGUUGAGGGGGUAAGGUCGGAGAAACAUCUUCGUUGCGUGCUCGUGAGGAGCGAAGAACGAACGUUCUGCCGAAUGUACCAGAAAUUCAAUCAGUAUGGCCUCGUUUGUCGUACCUGAUUUUGAAACGCAUUCGAGAAGAUUUAUUUUAGUGCAAUGUGUGGCACCUGUUUGUCAGGUAACUCGAUUCCG hit 30 : 557 792 (fwd) 49.30 bits :::::::::::[[[[..,,,,,<<<<---------<<<<<_____...>>>>>------- 1 GCGGAaGGAAGcuCa..uUgUAacguucAccagcaGagugcUugu...cacuCaacuaac 55 AA ::C: +U C:U+ A+ + +A: G:G+U C:C :A CU 557 --------AACGCCGcaCU---UCCUCAAAUUCAAACGCGUUGAAaagCGCACAGCUCGU 605 -->>>>,,,,,,,,,,,,,,,,,,(.((((,,,,,,<<<<<_____>>>>>.<<<<<<<_ 56 auacgugGGGAAGGUCUGAGAaACa.ggcCAauuauugCcCgUGAAGgGca.ucaccggG 113 + A:G GG AAGGUC+GAGAAACA :::C +U :GC:CGUGA G:GC: :+A:CG 606 UGAGGG-GGUAAGGUCGGAGAAACAuCUUCGUUGCGUGCUCGUGAGGAGCGaAGAACG-- 662 ___>>>>>>>,.<<<<<<<____________.._______________............ 114 GAAccggugau.cgguGucAUCAGAAAUccA..acgguugagcuggcu............ 158 AA CG:U+:+ CG::: :A+CAGAAAU+CA ++G+ UG++CU G U 663 -AA-CGUUCUGcCGAAUGUACCAGAAAUUCAauCAGUAUGGCCUCGUUugucguaccuga 720 .________>>>>>>>.)))).),,,,,,,,,,,,,,,,,,,]]]]<<<<<______>>> 159 .AUGGGAAuggCaccg.Ggcc.uUuCUGUUGAGUGCAAUgGuuGagcugaguuaggCcuc 215 U G+AA+: :::CG G::: UUU +UU AGUGCAAUG+ :G::::::GUU+ G C:: 721 uUUUGAAACGCAUUCGaGAAGaUUU-AUUUUAGUGCAAUGUGUGGCACCUGUUU-GUCAG 778 >>:::::::.:::: 216 agAACCCAA.Ucag 228 ::AAC C+A UC+G 779 GUAACUCGAuUCCG 792 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/fun.dat.fasta.gz ----sequence: #78027,sp|L12749.1|SURPR1F Saccharomyces uvarum RNase P RNA (RPR1) gene. ----isReversed: 0 ----hitSequence: ACAGUGGUAAUUCCUACGAUUAAGAAACCUGUUUACAGAAGGAUCCCCACCUAUGGGCGGGUUAUCAGAUAUUAUCAGGUGGGAAAUUCGGUGGAACACAGUGGAGCCUUGUCCUCCGGGUUAAUGUCGCUUUUGGCAUUGACCCCUGCUCCUGAGAGAAGAAAUAUACUGGGGAACCAGUCUUUACCGACCGUUGUUAUCAGAAAUUCACGGAGUUCGGCCUAGGUCGGACUCCGAUGGGAACGGCAACGGUUGUUCCGUUUGACUUGUCGCCCGCUACGGCGUGAGCGUCAAGGUCUGUUGAGUGCAAUCGUAGGACGUCAUUUGUGGCGAACCCGAUACC hit 31 : 756 1098 (fwd) 111.69 bits :::::::::::[[[[...,,,,,...<<<<.---------.<<<<<..._____...... 1 GCGGAaGGAAGcuCa...uUgUA...acgu.ucAccagca.Gagug...cUugu...... 43 +C+G++G AA ::C: +U+ A AC:U U+++CAG+A GA: C+U U 756 ACAGUGGUAAUUCCUacgAUUAAgaaACCUgUUUACAGAAgGAUCCccaCCUAUgggcgg 815 .>>>>>---------.>>>>,,,,,,,,,,,,,,,,,,(.....((((,,,,,,...... 44 .cacuCaacuaacau.acgugGGGAAGGUCUGAGAaACa.....ggcCAauuau...... 90 :UCA +UA AU A:GU GGGAA++UC+G+G+AACA G::C +U + 816 gUUAUCAGAUAUUAUcAGGU-GGGAAAUUCGGUGGAACAcagugGAGCCUUGUCcuccgg 874 ...........................<<<<<_____>>>>>.....<<<<<<<____>> 91 ...........................ugCcCgUGAAGgGca.....ucaccggGGAAcc 118 U C:C UGA G:G A ::AC:GGGGAACC 875 guuaaugucgcuuuuggcauugaccccUGCUCCUGA-GAGAAgaaauAUACUGGGGAACC 933 >>>>>,.......<<<<<<<____________.._______________.........__ 119 ggugau.......cgguGucAUCAGAAAUccA..acgguugagcuggcu.........AU 160 :GU::U CG:UGU:AUCAGAAAU+CA +G+U G++CU G+U AU 934 AGUCUUuaccgacCGUUGUUAUCAGAAAUUCAcgGAGUUCGGCCUAGGUcggacuccgAU 993 ______>>>>>>>...))))..),,.................................., 161 GGGAAuggCaccg...Ggcc..uUu..................................C 181 GGGAA+:GCA:CG G::C UUU C 994 GGGAACGGCAACGguuGUUCcgUUUgacuugucgcccgcuacggcgugagcgucaagguC 1053 ,,,,,,,,,,,,,,,,]]]]<<<<<______>>>>>::::::::::: 182 UGUUGAGUGCAAUgGuuGagcugaguuaggCcucagAACCCAAUcag 228 UGUUGAGUGCAAU+GU:G::C: ::UU+G :: :GAACCC+AU+++ 1054 UGUUGAGUGCAAUCGUAGGACGUCAUUUG--UGGCGAACCCGAUACC 1098 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #5595,sp|AC008221.4|AC008221 Drosophila melanogaster, chromosome 3R, region 100B-100C, BAC clone BACR30B13, complete sequence. ----isReversed: 1 ----hitSequence: CAGUUGCAAACUAGCAUCUGGGGCCCACACAACGAGUAUCUGAUUACUCCACAAACCAUUGCCCCGGGAAGGUCUGAGAAUCGGCCGAGCCAGCUGUUUGUUGCGGCUUCAUUUCCCAGCAGGAAACCUGUGUGAUUGCAGGGCGAAAGUACCAGAAAUCCUGCUACCAGGUGUUGCCGUUGCCCCCGGUGACCGCCGCCUGGUUGGCAUUGAAACCUUUCGUGGCCAGCGUUUUUAGUGCGAUGUGCUUGCUGCCUCUAAGGCAGAACUCAAUUCAG hit 32 : 55055 54778 (rev) 51.88 bits :::::::::::[[[[,,,,,<<<<.---------<<<<<_____.>>>>>---------. 1 GCGGAaGGAAGcuCauUgUAacgu.ucAccagcaGagugcUugu.cacuCaacuaacau. 57 C+G+ G AA C ::+ + +: G: +CAC ++ GAGU:++UG :ACUC AC AAC + 129224 -CAGUUGCAAACUAGCAUCUGGGGcCCACACAACGAGUAUCUGAuUACUCCACAAACCAu 129282 ..>>>>,,,,,,,,,,,,,,,,,,(((((,,,,,,..................<<<<<__ 58 ..acgugGGGAAGGUCUGAGAaACaggcCAauuau..................ugCcCgU 97 :C : GGGAAGGUCUGAGAA+C:G C A A U::CC 129283 ugCCCC-GGGAAGGUCUGAGAAUCGGCCGAGCCAGcuguuuguugcggcuucaUUUCCCA 129341 ___>>>>><<<<<<<____>>>>>>>,<<<<<<<____________......________ 98 GAAGgGcaucaccggGGAAccggugaucgguGucAUCAGAAAUccA......acgguuga 151 G+AGG::A C::::: GA :::::G +CG::: A+CAGAAAUCC A G++U + 129342 GCAGGAAA-CCUGUGUGAUUGCAGG-GCGAAAGUACCAGAAAUCCUgcuaccAGGUGUUG 129399 _______.........................________>>>>>>>.))))),,,.,,, 152 gcuggcu.........................AUGGGAAuggCaccg.GgccuUuC.UGU 184 +C++ ++ AU G+AA :::CG G C:++ U+U 129400 CCGUUGCccccggugaccgccgccugguuggcAUUGAAA-CCUUUCGuGGCCAGC-gUUU 129457 ,,,,,,,,,,,,,]]]]<<<<<..______>>>>>:::::::.:::: 185 UGAGUGCAAUgGuuGagcugag..uuaggCcucagAACCCAA.Ucag 228 U AGUGC AUG+ :: GCUG:: U+A ::CAGAAC CAA UCAG 129458 UUAGUGCGAUGUGCUUGCUGCCucUAA---GGCAGAACUCAAuUCAG 129501 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #7793,sp|AE003777.2|AE003777 Drosophila melanogaster chromosome 3R, section 115 of 118 of the complete sequence. ----isReversed: 1 ----hitSequence: CAGUUGCAAACUAGCAUCUGGGGCCCACACAACGAGUAUCUGAUUACUCCACAAACCAUUGCCCCGGGAAGGUCUGAGAAUCGGCCGAGCCAGCUGUUUGUUGCGGCUUCAUUUCCCAGCAGGAAACCUGUGUGAUUGCAGGGCGAAAGUACCAGAAAUCCUGCUACCAGGUGUUGCCGUUGCCCCCGGUGACCGCCGCCUGGUUGGCAUUGAAACCUUUCGUGGCCAGCGUUUUUAGUGCGAUGUGCUUGCUGCCUCUAAGGCAGAACUCAAUUCAG hit 33 : 85280 85003 (rev) 51.88 bits :::::::::::[[[[,,,,,<<<<.---------<<<<<_____.>>>>>---------. 1 GCGGAaGGAAGcuCauUgUAacgu.ucAccagcaGagugcUugu.cacuCaacuaacau. 57 C+G+ G AA C ::+ + +: G: +CAC ++ GAGU:++UG :ACUC AC AAC + 147011 -CAGUUGCAAACUAGCAUCUGGGGcCCACACAACGAGUAUCUGAuUACUCCACAAACCAu 147069 ..>>>>,,,,,,,,,,,,,,,,,,(((((,,,,,,..................<<<<<__ 58 ..acgugGGGAAGGUCUGAGAaACaggcCAauuau..................ugCcCgU 97 :C : GGGAAGGUCUGAGAA+C:G C A A U::CC 147070 ugCCCC-GGGAAGGUCUGAGAAUCGGCCGAGCCAGcuguuuguugcggcuucaUUUCCCA 147128 ___>>>>><<<<<<<____>>>>>>>,<<<<<<<____________......________ 98 GAAGgGcaucaccggGGAAccggugaucgguGucAUCAGAAAUccA......acgguuga 151 G+AGG::A C::::: GA :::::G +CG::: A+CAGAAAUCC A G++U + 147129 GCAGGAAA-CCUGUGUGAUUGCAGG-GCGAAAGUACCAGAAAUCCUgcuaccAGGUGUUG 147186 _______.........................________>>>>>>>.))))),,,.,,, 152 gcuggcu.........................AUGGGAAuggCaccg.GgccuUuC.UGU 184 +C++ ++ AU G+AA :::CG G C:++ U+U 147187 CCGUUGCccccggugaccgccgccugguuggcAUUGAAA-CCUUUCGuGGCCAGC-gUUU 147244 ,,,,,,,,,,,,,]]]]<<<<<..______>>>>>:::::::.:::: 185 UGAGUGCAAUgGuuGagcugag..uuaggCcucagAACCCAA.Ucag 228 U AGUGC AUG+ :: GCUG:: U+A ::CAGAAC CAA UCAG 147245 UUAGUGCGAUGUGCUUGCUGCCucUAA---GGCAGAACUCAAuUCAG 147288 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz ----sequence: #45922,sp|AF434763.1|AF434763 Drosophila melanogaster ribonuclease P RNA subunit gene, partial sequence. ----isReversed: 0 ----hitSequence: CAGUUGCAAACUAGCAUCUGGGGCCCACACAACGAGUAUCUGAUUACUCCACAAACCAUUGCCCCGGGAAGGUCUGAGAAUCGGCCGAGCCAGCUGUUUGUUGCGGCUUCAUUUCCCAGCAGGAAACCUGUGUGAUUGCAGGGCGAAAGUACCAGAAAUCCUGCUACCAGGUGUUGCCGUUGCCCCCGGUGACCGCCGCCUGGUUGGCAUUGAAACCUUUCGUGGCCAGCGUUUUUAGUGCGAUGUGCUUGCUGCCUCUAAGGCAGAACUCAAUUCAG hit 34 : 4 281 (fwd) 51.88 bits :::::::::::[[[[,,,,,<<<<.---------<<<<<_____.>>>>>---------. 1 GCGGAaGGAAGcuCauUgUAacgu.ucAccagcaGagugcUugu.cacuCaacuaacau. 57 C+G+ G AA C ::+ + +: G: +CAC ++ GAGU:++UG :ACUC AC AAC + 4 -CAGUUGCAAACUAGCAUCUGGGGcCCACACAACGAGUAUCUGAuUACUCCACAAACCAu 62 ..>>>>,,,,,,,,,,,,,,,,,,(((((,,,,,,..................<<<<<__ 58 ..acgugGGGAAGGUCUGAGAaACaggcCAauuau..................ugCcCgU 97 :C : GGGAAGGUCUGAGAA+C:G C A A U::CC 63 ugCCCC-GGGAAGGUCUGAGAAUCGGCCGAGCCAGcuguuuguugcggcuucaUUUCCCA 121 ___>>>>><<<<<<<____>>>>>>>,<<<<<<<____________......________ 98 GAAGgGcaucaccggGGAAccggugaucgguGucAUCAGAAAUccA......acgguuga 151 G+AGG::A C::::: GA :::::G +CG::: A+CAGAAAUCC A G++U + 122 GCAGGAAA-CCUGUGUGAUUGCAGG-GCGAAAGUACCAGAAAUCCUgcuaccAGGUGUUG 179 _______.........................________>>>>>>>.))))),,,.,,, 152 gcuggcu.........................AUGGGAAuggCaccg.GgccuUuC.UGU 184 +C++ ++ AU G+AA :::CG G C:++ U+U 180 CCGUUGCccccggugaccgccgccugguuggcAUUGAAA-CCUUUCGuGGCCAGC-gUUU 237 ,,,,,,,,,,,,,]]]]<<<<<..______>>>>>:::::::.:::: 185 UGAGUGCAAUgGuuGagcugag..uuaggCcucagAACCCAA.Ucag 228 U AGUGC AUG+ :: GCUG:: U+A ::CAGAAC CAA UCAG 238 UUAGUGCGAUGUGCUUGCUGCCucUAA---GGCAGAACUCAAuUCAG 281 ----endhit ----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: #41075,sp|L08685.1|GGRNASEP Gorilla RNase P RNA subunit. ----isReversed: 0 ----hitSequence: GCGGAGGGAAGCUCAUCAGUGGGGCCACGAGCUGAGUGCGUCCUGUCACUCCACUCCCAUGUCCCUUGGGAAGGUCUGAGACUAGGGCCAGAAGCGGCCCUAACAGGGCUCUCCCUGAGCUUCGGGGAGGUGAGUUCCCAGAGAACGGGGCUCCGCGCGAGGUCAGACUGGGCAGGAGAUGCCGUGGACCCCGCCCUUCGGGGAGGGGCCCGGCGGAUGCCUCCUUUGCCGGAGCUUGGAACAGACUCACGGCCAGCGAAGUGAGUUCAAUGGCUGAGGUGAGGUACCCCGUAGGGGACCUCAUAACCCAAUUCAN hit 35 : 6 321 (fwd) 110.38 bits :::::::::::[[[[,,,,,<<<<---------<<<<<._____..>>>>>--------- 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagug.cUugu..cacuCaacuaacau 57 GCGGA+GGAAGCUCAU +: G:+CAC AGC+GAGUG U+ U CACUC ACU +CAU 6 GCGGAGGGAAGCUCAUCAGUGGGGCCACGAGCUGAGUGcGUCCUguCACUCCACUCCCAU 65 ..>>>>,,,,,,,,,,,,,,,,,,(((((,,,,,,<<<<<_____>>>>><<<<<<<___ 58 ..acgugGGGAAGGUCUGAGAaACaggcCAauuauugCcCgUGAAGgGcaucaccggGGA 115 :C :+GGGAAGGUCUGAGA+++:GGCCA +++:GCCC+ +AGGGC::::CC:G+G 66 guCCCUUGGGAAGGUCUGAGACUAGGGCCAGAAGCGGCCCUAACAGGGCUCUCCCUGAGC 125 _.>>>>>>>,<<<<<<<____________.........._______________...... 116 A.ccggugaucgguGucAUCAGAAAUccA..........acgguugagcuggcu...... 158 C:GG::: ::G:G::++CAGA A C + +GGU ++ CUGG++ 126 UuCGGGGAG-GUGAGUUCCCAGAGAACGGggcuccgcgcGAGGUCAGACUGGGCaggaga 184 ........................................................____ 159 ........................................................AUGG 162 UGG 185 ugccguggaccccgcccuucggggaggggcccggcggaugccuccuuugccggagcUUGG 244 ____>>>>>>>))))),,,.,,,,,,,,,,,,,,,,]]]]<<<<<.......____..._ 163 GAAuggCaccgGgccuUuC.UGUUGAGUGCAAUgGuuGagcugag.......uuag...g 211 +A ::C:C::GGCC:++ UGAGU CAAUGG UGAG:UGAG UAG 245 AACAGACUCACGGCCAGC-gAAGUGAGUUCAAUGGCUGAGGUGAGguaccccGUAGgggA 303 _>>>>>:::::::.:::: 212 CcucagAACCCAA.Ucag 228 CCUCA:AACCCAA UCA 304 CCUCAUAACCCAAuUCAN 321 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mam.dat.fasta.gz ----sequence: #42624,sp|L08687.1|MMRNASEP1 Rhesus monkey RNase P RNA subunit. ----isReversed: 0 ----hitSequence: GCGGAGGGAAGCUCAUCAGUGGGGCCACGAGCUGAGUGCGUCCUGUCACUCCACUCCCAUGUCCCUUGGGAAGGUCUGAGACUAGGGCCAGAGGCGGCCCUAACAGGGCUCUCCCUGAUCUUCGGGGAGGUGAGUUCCCAGAGAAUGGGGCUCCGCGCGAGGUCAGACUGGGCAGGAGAUGCCGUGGACCCCGCCCUUCGGGGAGGGGCCCGNCGGAUGCCUCCUUUGCCGGAGCUUGGAACAGACUCACGGCCAGCGAAGUGAGUUCAAUGGCUGAGGUGAGGUACCCCGGAGGGGACCUCAUAACCCAAUUCAN hit 36 : 6 321 (fwd) 105.26 bits :::::::::::[[[[,,,,,<<<<---------<<<<<._____..>>>>>--------- 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagug.cUugu..cacuCaacuaacau 57 GCGGA+GGAAGCUCAU +: G:+CAC AGC+GAGUG U+ U CACUC ACU +CAU 6 GCGGAGGGAAGCUCAUCAGUGGGGCCACGAGCUGAGUGcGUCCUguCACUCCACUCCCAU 65 ..>>>>,,,,,,,,,,,,,,,,,,(((((,,,,,,<<<<<_____>>>>><<<<<<<___ 58 ..acgugGGGAAGGUCUGAGAaACaggcCAauuauugCcCgUGAAGgGcaucaccggGGA 115 :C :+GGGAAGGUCUGAGA+++:GGCCA ++:GCCC+ +AGGGC::::CC:G+ 66 guCCCUUGGGAAGGUCUGAGACUAGGGCCAGAGGCGGCCCUAACAGGGCUCUCCCUGAUC 125 _.>>>>>>>,<<<<<<<____________.........._______________...... 116 A.ccggugaucgguGucAUCAGAAAUccA..........acgguugagcuggcu...... 158 C:GG::: ::G:G::++CAGA A + + +GGU ++ CUGG++ 126 UuCGGGGAG-GUGAGUUCCCAGAGAAUGGggcuccgcgcGAGGUCAGACUGGGCaggaga 184 ........................................................____ 159 ........................................................AUGG 162 UGG 185 ugccguggaccccgcccuucggggaggggcccgncggaugccuccuuugccggagcUUGG 244 ____>>>>>>>))))),,,.,,,,,,,,,,,,,,,,]]]]<<<<<....____......_ 163 GAAuggCaccgGgccuUuC.UGUUGAGUGCAAUgGuuGagcugag....uuag......g 211 +A ::C:C::GGCC:++ UGAGU CAAUGG UGAG:UGAG + G 245 AACAGACUCACGGCCAGC-gAAGUGAGUUCAAUGGCUGAGGUGAGguacCCCGgaggggA 303 _>>>>>:::::::.:::: 212 CcucagAACCCAA.Ucag 228 CCUCA:AACCCAA UCA 304 CCUCAUAACCCAAuUCAN 321 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mam.dat.fasta.gz ----sequence: #46572,sp|L08688.1|PPRNASEP Orangutan RNase P RNA subunit. ----isReversed: 0 ----hitSequence: GCGGAGGGAAGCUCAUCAGUGGGGCCACGUGCUGAGUGCGUCCUGUCACUCCACUCCCAUGUCCCUUGGGAAGGUCUGAGACUAGGGCCAGAGGCGGCCCUAACAGGGCUCUCCCUGAGCUUCGGGGAGGUGAGUUCCCAGAGAACGGGGCUCCGCGCGAGGUCAGACUGGGCAGGAGAUGCCGUGGACCCCGCCCUUCGGGGAGGGGCCCGGCGGAUGCCUCCUUUGCCGGAGCUUGGAACAGACUCACGGCCAGCGAAGUGAGUUCAAUGGCUGAGGUGAGGUACCCCGCAGGGGACCUCAUAACCCAAUUCAN hit 37 : 6 321 (fwd) 108.34 bits :::::::::::[[[[,,,,,<<<<---------<<<<<._____..>>>>>--------- 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagug.cUugu..cacuCaacuaacau 57 GCGGA+GGAAGCUCAU +: G:+CAC +GC+GAGUG U+ U CACUC ACU +CAU 6 GCGGAGGGAAGCUCAUCAGUGGGGCCACGUGCUGAGUGcGUCCUguCACUCCACUCCCAU 65 ..>>>>,,,,,,,,,,,,,,,,,,(((((,,,,,,<<<<<_____>>>>><<<<<<<___ 58 ..acgugGGGAAGGUCUGAGAaACaggcCAauuauugCcCgUGAAGgGcaucaccggGGA 115 :C :+GGGAAGGUCUGAGA+++:GGCCA ++:GCCC+ +AGGGC::::CC:G+G 66 guCCCUUGGGAAGGUCUGAGACUAGGGCCAGAGGCGGCCCUAACAGGGCUCUCCCUGAGC 125 _.>>>>>>>,<<<<<<<____________.........._______________...... 116 A.ccggugaucgguGucAUCAGAAAUccA..........acgguugagcuggcu...... 158 C:GG::: ::G:G::++CAGA A C + +GGU ++ CUGG++ 126 UuCGGGGAG-GUGAGUUCCCAGAGAACGGggcuccgcgcGAGGUCAGACUGGGCaggaga 184 ........................................................____ 159 ........................................................AUGG 162 UGG 185 ugccguggaccccgcccuucggggaggggcccggcggaugccuccuuugccggagcUUGG 244 ____>>>>>>>))))),,,.,,,,,,,,,,,,,,,,]]]]<<<<<.......____..._ 163 GAAuggCaccgGgccuUuC.UGUUGAGUGCAAUgGuuGagcugag.......uuag...g 211 +A ::C:C::GGCC:++ UGAGU CAAUGG UGAG:UGAG +AG 245 AACAGACUCACGGCCAGC-gAAGUGAGUUCAAUGGCUGAGGUGAGguaccccGCAGgggA 303 _>>>>>:::::::.:::: 212 CcucagAACCCAA.Ucag 228 CCUCA:AACCCAA UCA 304 CCUCAUAACCCAAuUCAN 321 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mam.dat.fasta.gz ----sequence: #47216,sp|L08686.1|PTRNASEP Chimpanzee RNase P RNA subunit. ----isReversed: 0 ----hitSequence: GCGGAGGGAAGCUCAUCAGUGGGGCCACGAGCUGAGUGCGUCCUGUCACUCCACUCCCAUGUCCCUUGGGAAGGUCUGAGACUAGGGCCAAAGGCGGCCCUAACAGGGCUCUCCCUGAGCUUCGGGGAGGUGAGUUCCCAGAGAACGGGGCUCCACGCGAGGUCAGACUGGGCAGGAGAUGCCGUGGACCCCGCCCUUCGGGGAGGGGCCCGGCGGAUGCCUCCUUUGCCGGAGCUUGGAACAGACUCACGGCCAGCGAAGUGAGUUCAAUGGCUGAGGUGAGGUACCCCGCAGGGGACCUCAUAACCCAAUUCAN hit 38 : 6 321 (fwd) 109.53 bits :::::::::::[[[[,,,,,<<<<---------<<<<<._____..>>>>>--------- 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagug.cUugu..cacuCaacuaacau 57 GCGGA+GGAAGCUCAU +: G:+CAC AGC+GAGUG U+ U CACUC ACU +CAU 6 GCGGAGGGAAGCUCAUCAGUGGGGCCACGAGCUGAGUGcGUCCUguCACUCCACUCCCAU 65 ..>>>>,,,,,,,,,,,,,,,,,,(((((,,,,,,<<<<<_____>>>>><<<<<<<___ 58 ..acgugGGGAAGGUCUGAGAaACaggcCAauuauugCcCgUGAAGgGcaucaccggGGA 115 :C :+GGGAAGGUCUGAGA+++:GGCCAA ++:GCCC+ +AGGGC::::CC:G+G 66 guCCCUUGGGAAGGUCUGAGACUAGGGCCAAAGGCGGCCCUAACAGGGCUCUCCCUGAGC 125 _.>>>>>>>,<<<<<<<____________.........._______________...... 116 A.ccggugaucgguGucAUCAGAAAUccA..........acgguugagcuggcu...... 158 C:GG::: ::G:G::++CAGA A C + +GGU ++ CUGG++ 126 UuCGGGGAG-GUGAGUUCCCAGAGAACGGggcuccacgcGAGGUCAGACUGGGCaggaga 184 ........................................................____ 159 ........................................................AUGG 162 UGG 185 ugccguggaccccgcccuucggggaggggcccggcggaugccuccuuugccggagcUUGG 244 ____>>>>>>>))))),,,.,,,,,,,,,,,,,,,,]]]]<<<<<.......____..._ 163 GAAuggCaccgGgccuUuC.UGUUGAGUGCAAUgGuuGagcugag.......uuag...g 211 +A ::C:C::GGCC:++ UGAGU CAAUGG UGAG:UGAG +AG 245 AACAGACUCACGGCCAGC-gAAGUGAGUUCAAUGGCUGAGGUGAGguaccccGCAGgggA 303 _>>>>>:::::::.:::: 212 CcucagAACCCAA.Ucag 228 CCUCA:AACCCAA UCA 304 CCUCAUAACCCAAuUCAN 321 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mam.dat.fasta.gz ----sequence: #50448,sp|L08801.1|TSRNASEP Tarsius syrichta RNase P RNA subunit gene sequence. ----isReversed: 0 ----hitSequence: NNNNNCCACAAGCUGCAUGCCACAUGUCAUCCCACCCCCAUGUCCCUUGGGAAGGUCUGAGUCAAGGGCCAGAGCACCCUAACAGGACUUUCCCUGAGUUUUGGGGAGGUGAAUUCCCAGAGAACUCAGCUCCCUGCGAGGUCAGACUGGGCUGGACAUGCCACGGACCCACCCUUCUGGGAAGGGCCAGGUGGAUGCCUCCUCAGCCAGAACUUGGAACAGACUCAUGGCCAACCAAGUGAGUUCAAUGAGGUGAGGCACCCCACCCAAGGGGCCUCAUAACCCAAUUCAN hit 39 : 25 316 (fwd) 37.77 bits :::::::::::[[[[,,,,,<<<<.---------<<<<<._____..>>>>>-------- 1 GCGGAaGGAAGcuCauUgUAacgu.ucAccagcaGagug.cUugu..cacuCaacuaaca 56 + +CAC AGC+G::UG C + U CA::C AC+ +CA 25 --------------------NNNNnCCACAAGCUGCAUGcCACAUguCAUCCCACCCCCA 64 -..>>>>,,,,,,,,,,,,,,,,,,(((((,,,,,,<<<<<_____>>>>><<<<<<<__ 57 u..acgugGGGAAGGUCUGAGAaACaggcCAauuauugCcCgUGAAGgGcaucaccggGG 114 U ++GGGAAGGUCUGAG +A+:GGCCA :: CC+ +AGG ::U::CC :+G 65 UguCCCUUGGGAAGGUCUGAGUCAAGGGCCAGAG--CACCCUAACAGGACUUUCCCUGAG 122 __>>>>>>>,<<<<<<<____________.........._______________...... 115 AAccggugaucgguGucAUCAGAAAUccA..........acgguugagcuggcu...... 158 : GG::A++:G::::++CAGA A C +GGU ++ CUGG++ 123 UUUUGGGGAGGUGAAUUCCCAGAGAACUCagcucccugcGAGGUCAGACUGGGCuggaca 182 ......................................................._____ 159 .......................................................AUGGG 163 UGG+ 183 ugccacggacccacccuucugggaagggccagguggaugccuccucagccagaacUUGGA 242 ___>>>>>>>))))),,,,,,,,,,,,,,,,,,,]]]]<<<<<..........____.._ 164 AAuggCaccgGgccuUuCUGUUGAGUGCAAUgGuuGagcugag..........uuag..g 211 A ::::C:+GGCC: +C UGAGU CAAU GAG:UGAG +AG G 243 ACAGACUCAUGGCCAACCAAGUGAGUUCAAU----GAGGUGAGgcaccccaccCAAGggG 298 _>>>>>:::::::.:::: 212 CcucagAACCCAA.Ucag 228 CCUCA:AACCCAA UCA 299 CCUCAUAACCCAAuUCAN 316 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #4889,sp|AC087183.9|AC087183 Mus musculus Strain C57BL6/J Chromosome 8 RP23-316J6, complete sequence. ----isReversed: 1 ----hitSequence: GCGGAGGAAGCUAAUCAGCAGGGCCACGUGCUGAGUGCUCGUCACUCUUCGGCCCCUGAGAAGGUCUGAGACUGGGGCCUCCCGCGGCCCUAACCGGGCUCUCCCCAAGCGGGGAGGUGAGUUCCCAGAGAGCAGGGCUCUACGUGUGGGCAGGCUGGGCAGGAGAAGUCCCGAGUCGGGGCAGAUGCCUCCCUCGCCGGAGCUUGGAACAGACUCAUGGCCAGCAGAGCGAAUUUUAACCAUUUAUAUUUUUUAACAUGAA hit 40 : 147966 147705 (rev) 36.45 bits :::::::::::[[[[,,,,,<<<<---------<<<<<_____>>>>>--------->>> 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagugcUugucacuCaacuaacauacg 60 GCGGA+G AAG U:AU A G:+CAC +GC+GAGUGCU+GUCACUC++C + :C 39394 GCGGAGG-AAGCUAAUCAGCAGGGCCACGUGCUGAGUGCUCGUCACUCUUCGGC---CCC 39449 >,,,,,,,,,,,,,,,,,,(((((,,,,,,<<<<<_____>>>>><<<<<<<____>>>> 61 ugGGGAAGGUCUGAGAaACaggcCAauuauugCcCgUGAAGgGcaucaccggGGAAccgg 120 U G GAAGGUCUGAGA++ :GGCC + ++:GCCC+ + GGGC::::CC: +G :GG 39450 U-GAGAAGGUCUGAGACUGGGGCCUCCCGCGGCCCUAACCGGGCUCUCCCCAAG--CGGG 39506 >>>,<<<<<<<____________......_______________................ 121 ugaucgguGucAUCAGAAAUccA......acgguugagcuggcu................ 158 ::: +:G:G::++CAGA A C++ ACG++UG+GC GGCU 39507 GAG-GUGAGUUCCCAGAGAGCAGggcucuACGUGUGGGCAGGCUgggcaggagaaguccc 39565 ...............................________>>>>>>>))))),,,.,,,,, 159 ...............................AUGGGAAuggCaccgGgccuUuC.UGUUG 186 UGG+A ::C:C:+GGCC:++ G 39566 gagucggggcagaugccucccucgccggagcUUGGAACAGACUCAUGGCCAGC-a----G 39620 ,,,,,,,,,,,]]]]<<<<<.......______>>>>>::::::::::: 187 AGUGCAAUgGuuGagcugag.......uuaggCcucagAACCCAAUcag 228 AG G AAU +UU:A C:: : UUA : ::GAA 39621 AGCG-AAU-UUUAACCAUUUauauuuuUUA---ACAUGAA--------- 39655 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #14804,sp|AF191547.1|AF191547 Mus musculus poly (ADP-ribose) polymerase 2 (Parp2) gene, complete cds. ----isReversed: 1 ----hitSequence: GCGGAGGAAGCUCAUCAGCGGGGCCACGUGCUGAGUGCUCGUCACUCUUCGGCCCCUGGGAAGGUCUGAGACUGGGGCCUCCCGCGGCCCUAACCGGGCUCUCCCCGAGCGGGGAGGUGAGUUCCCAGAGAGCAGGGCUCUACGCUUGGGCAGACUGGGCAGGAGAAGCCCCGAGUCGGGGCGGAUGCCUCCCUCGCCGGAGCUUGGAACAGACUCACGGCCAGCAGUGCGAGUUCAAUGGCUGAGGUGAGGCACCUCCCGGGCCUCAUAACCCAAUUCAG hit 41 : 2289 2009 (rev) 100.25 bits :::::::::::[[[[,,,,,<<<<---------<<<<<_____>>>>>--------->>> 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagugcUugucacuCaacuaacauacg 60 GCGGA+G AAGCUCAU : G:+CAC +GC+GAGUGCU+GUCACUC++C :C 13485 GCGGAGG-AAGCUCAUCAGCGGGGCCACGUGCUGAGUGCUCGUCACUCUUCGG----CCC 13539 >,,,,,,,,,,,,,,,,,,(((((,,,,,,<<<<<_____>>>>><<<<<<<____>>>> 61 ugGGGAAGGUCUGAGAaACaggcCAauuauugCcCgUGAAGgGcaucaccggGGAAccgg 120 :+GGGAAGGUCUGAGA++ :GGCC + ++:GCCC+ + GGGC::::CC:G+G C:GG 13540 CUGGGAAGGUCUGAGACUGGGGCCUCCCGCGGCCCUAACCGGGCUCUCCCCGAG--CGGG 13597 >>>,<<<<<<<____________......_______________................ 121 ugaucgguGucAUCAGAAAUccA......acgguugagcuggcu................ 158 ::: ::G:G::++CAGA A C++ ACG UUG+GC G CU 13598 GAG-GUGAGUUCCCAGAGAGCAGggcucuACGCUUGGGCAGACUgggcaggagaagcccc 13656 ...............................________>>>>>>>))))),,,.,,,,, 159 ...............................AUGGGAAuggCaccgGgccuUuC.UGUUG 186 UGG+A ::C:C::GGCC:++ + G 13657 gagucggggcggaugccucccucgccggagcUUGGAACAGACUCACGGCCAGC-aGUGCG 13715 ,,,,,,,,,,,]]]]<<<<<......____.__>>>>>:::::::.:::: 187 AGUGCAAUgGuuGagcugag......uuag.gCcucagAACCCAA.Ucag 228 AGU CAAUGG UGAG:UGAG + G GCCUCA:AACCCAA UCAG 13716 AGUUCAAUGGCUGAGGUGAGgcaccuCCCGgGCCUCAUAACCCAAuUCAG 13765 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #53560,sp|U24680.1|MM24680 Mus musculus RNaseP RNA component, partial sequence. ----isReversed: 0 ----hitSequence: UGGGAAGGUCUGAGACUGGGGCCUCCCGCGGCCCUAACCGGGCUCUCCCCGAGCGGGGAGGUGAGUUCCCAGAGAGCAGGGCUCUACGCUUGGGCAGACUGGGCAGGAGAAGCCCCGAGUCGGGGCGGAUGCCUCCCUCGCCGGAGCUUGGAACAGACUCACGGCCAGCAGUGCGAGUUCAAUGGCUGAGGUGAGGCACCUCCCGGGCCUCAUAACCCAAUUCAG hit 42 : 1 225 (fwd) 59.33 bits :::::::::::[[[[,,,,,<<<<---------<<<<<_____>>>>>--------->>> 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagugcUugucacuCaacuaacauacg 60 - ------------------------------------------------------------ - >,,,,,,,,,,,,,,,,,,(((((,,,,,,<<<<<_____>>>>><<<<<<<____>>>> 61 ugGGGAAGGUCUGAGAaACaggcCAauuauugCcCgUGAAGgGcaucaccggGGAAccgg 120 +GGGAAGGUCUGAGA++ :GGCC + ++:GCCC+ + GGGC::::CC:G+G C:GG 1 -UGGGAAGGUCUGAGACUGGGGCCUCCCGCGGCCCUAACCGGGCUCUCCCCGAG--CGGG 57 >>>,<<<<<<<____________......_______________................ 121 ugaucgguGucAUCAGAAAUccA......acgguugagcuggcu................ 158 ::: ::G:G::++CAGA A C++ ACG UUG+GC G CU 58 GAG-GUGAGUUCCCAGAGAGCAGggcucuACGCUUGGGCAGACUgggcaggagaagcccc 116 ...............................________>>>>>>>))))),,,.,,,,, 159 ...............................AUGGGAAuggCaccgGgccuUuC.UGUUG 186 UGG+A ::C:C::GGCC:++ + G 117 gagucggggcggaugccucccucgccggagcUUGGAACAGACUCACGGCCAGC-aGUGCG 175 ,,,,,,,,,,,]]]]<<<<<......____.__>>>>>:::::::.:::: 187 AGUGCAAUgGuuGagcugag......uuag.gCcucagAACCCAA.Ucag 228 AGU CAAUGG UGAG:UGAG + G GCCUCA:AACCCAA UCAG 176 AGUUCAAUGGCUGAGGUGAGgcaccuCCCGgGCCUCAUAACCCAAuUCAG 225 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #54025,sp|U31003.1|MM31003 Mus musculus RNAase P RNA subunit (RPRH2) gene, complete sequence. ----isReversed: 0 ----hitSequence: GCGGAAGAAGUUUAUCAGUGGGGCCACGUGCUGAGUGAUCGUCACUCUUCGGUCCCUGGCAAGGUCUGAGACUGGGGCCUCCCGCAGCCCUAACCGGGCUCUCCCCGAGCGAGGAGAUGAGUUCCCAGAGAGCAGGGCUCUACGAGUGGGCAGACUGGGCAGGAGAAGCCCUGAGUCUGGGCAAGAUGCCUCCCUCGCCAGAGCUUGGAACAGACUCACAGCCAGCAGAGCGAGUUUUAACCAUUUAUUUUUUUUAACAUGAA hit 43 : 349 611 (fwd) 29.38 bits :::::::::::[[[[,,,,,<<<<---------<<<<<_____>>>>>---------.>> 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagugcUugucacuCaacuaacau.ac 59 GCGGAAG AAG U:AU +: G:+CAC +GC+GAGUG U+GUCACUC++C :C 349 GCGGAAG-AAGUUUAUCAGUGGGGCCACGUGCUGAGUGAUCGUCACUCUUCGG----uCC 403 >>,,,,,,,,,,,,,,,,,,(((((,,,,,,<<<<<_____>>>>><<<<<<<____>>> 60 gugGGGAAGGUCUGAGAaACaggcCAauuauugCcCgUGAAGgGcaucaccggGGAAccg 119 : GG AAGGUCUGAGA++ :GGC + ++ GCCC+ + GGGC :::C :G+G C: 404 CU-GGCAAGGUCUGAGACUGGGGCCUCCCGCAGCCCUAACCGGGCUCUCCCCGAG--CGA 460 >>>>,<<<<<<<____________.........._______________........... 120 gugaucgguGucAUCAGAAAUccA..........acgguugagcuggcu........... 158 G::: :G:G::++CAGA A C++ GG+ ++ CUGG++ 461 GGAG-AUGAGUUCCCAGAGAGCAGggcucuacgaGUGGGCAGACUGGGCaggagaagccc 519 .................................________>>>>>>>))))),,,.,,, 159 .................................AUGGGAAuggCaccgGgccuUuC.UGU 184 UGG+A ::C:C: GCC:++ 520 ugagucugggcaagaugccucccucgccagagcUUGGAACAGACUCACAGCCAGC-aGAG 578 ,,,,,,,,,,,,,]]]]<<<<<.......______>>>>>::::::::::: 185 UGAGUGCAAUgGuuGagcugag.......uuaggCcucagAACCCAAUcag 228 GAGU +UU:A C:: : UUA : ::GAA 579 CGAGU------UUUAACCAUUUauuuuuuUUA---ACAUGAA--------- 611 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #54027,sp|U31227.1|MM31227 Mus musculus RNAase P RNA subunit (RPRH3) gene, complete sequence. ----isReversed: 0 ----hitSequence: GCGGAGGAAGCUCAUCAGUGGGGCCACGUGCUGAGUGCUGGUCACUCUUCGGCCCCUGGGCAGGUCUGAGACUGGGGCCUCCCACGGCCCUAACCGGGCUCUCCCUGAGUGGGGAGGUGAGUUCCCAGAGAGCAGGGCUCUAUGCAUGGGCAGACUGGGCAGUAGAAGCCCCAAGUCGGGGUGGAUGCCUCCCUUGCCGGAGCUUGGAACAGACUCACGGCCAGCAGAGCAAGUUUUAACCAUUUAUAUUUUUUAACAUGAA hit 44 : 436 697 (fwd) 47.54 bits :::::::::::[[[[,,,,,<<<<---------<<<<<_____>>>>>--------->>> 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagugcUugucacuCaacuaacauacg 60 GCGGA+G AAG U AU +: G:+CAC +GC+GAGUGCU GUCACUC++C :C 436 GCGGAGG-AAGCUCAUCAGUGGGGCCACGUGCUGAGUGCUGGUCACUCUUCGG----CCC 490 >,,,,,,,,,,,,,,,,,,(((((,,,,,,<<<<<_____>>>>><<<<<<<____>>>> 61 ugGGGAAGGUCUGAGAaACaggcCAauuauugCcCgUGAAGgGcaucaccggGGAAccgg 120 :+GGG AGGUCUGAGA++ :GGCC + A+:GCCC+ + GGGC::::CC::+G ::GG 491 CUGGGCAGGUCUGAGACUGGGGCCUCCCACGGCCCUAACCGGGCUCUCCCUGAG--UGGG 548 >>>,<<<<<<<____________.........._______________............ 121 ugaucgguGucAUCAGAAAUccA..........acgguugagcuggcu............ 158 ::: ::G:G::++CAGA A C++ A GG+ ++ CUGG++ 549 GAG-GUGAGUUCCCAGAGAGCAGggcucuaugcAUGGGCAGACUGGGCaguagaagcccc 607 ...............................________>>>>>>>))))),,,,,,,,, 159 ...............................AUGGGAAuggCaccgGgccuUuCUGUUGA 187 UGG+A ::C:C::GGCC:++ A 608 aagucgggguggaugccucccuugccggagcUUGGAACAGACUCACGGCCAGC------A 661 ,,,,,,,,,,]]]]<<<<<.......______>>>>>::::::::::: 188 GUGCAAUgGuuGagcugag.......uuaggCcucagAACCCAAUcag 228 G GCAA +UU A C:: : UUA : ::GAA 662 GAGCAAGUUUUAACCAUUUauauuuuUUA---ACAUGAA--------- 697 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #54028,sp|U31228.1|MM31228 Mus musculus RNAase P RNA subunit (RPRH4) gene, complete sequence. ----isReversed: 0 ----hitSequence: GCGGAGGAAGCUCAUCAGCAGGGCCACGUGCUGAGUGCUCGUCACUCUUCGGCCCCUGAGAAGGUCUGAGACUGGGGCCUCCCGCGGCCCUAACCGGGCUCUCCCCAAGUGGGGAGGUGAAUUCCCAGAGAGCAGGGCUCUACACGUGGGCAGACUGGGCAGGAGGAAGUCCCGAGUCGGGGGGGAUGCCUCCCUCGCCGGAGCUUGGAACAGACUCACGGCCAGCAGAGCGAAUUUUAACCAUUUAUAUUUUUUAACAUGAA hit 45 : 338 600 (fwd) 33.91 bits :::::::::::[[[[,,,,,<<<<---------<<<<<_____>>>>>--------->>> 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagugcUugucacuCaacuaacauacg 60 GCGGA+G AAG U AU A G:+CAC +GC+GAGUGCU+GUCACUC++C + :C 338 GCGGAGG-AAGCUCAUCAGCAGGGCCACGUGCUGAGUGCUCGUCACUCUUCGGC---CCC 393 >,,,,,,,,,,,,,,,,,,(((((,,,,,,<<<<<_____>>>>><<<<<<<____>>>> 61 ugGGGAAGGUCUGAGAaACaggcCAauuauugCcCgUGAAGgGcaucaccggGGAAccgg 120 U G GAAGGUCUGAGA++ :GGCC + ++:GCCC+ + GGGC::::CC::+G ::GG 394 U-GAGAAGGUCUGAGACUGGGGCCUCCCGCGGCCCUAACCGGGCUCUCCCCAAG--UGGG 450 >>>,<<<<<<<____________.........._______________............ 121 ugaucgguGucAUCAGAAAUccA..........acgguugagcuggcu............ 158 ::: ::G::::++CAGA A C++ GG+ ++ CUGG++ 451 GAG-GUGAAUUCCCAGAGAGCAGggcucuacacGUGGGCAGACUGGGCaggaggaagucc 509 ................................________>>>>>>>))))),,,.,,,, 159 ................................AUGGGAAuggCaccgGgccuUuC.UGUU 185 UGG+A ::::C::GGCC:++ 510 cgagucgggggggaugccucccucgccggagcUUGGAACAGACUCACGGCCAGC-a---- 564 ,,,,,,,,,,,,]]]]<<<<<.......______>>>>>::::::::::: 186 GAGUGCAAUgGuuGagcugag.......uuaggCcucagAACCCAAUcag 228 GAG G AAU +UU A C:: : UUA : ::GAA 565 GAGCG-AAU-UUUAACCAUUUauauuuuUUA---ACAUGAA--------- 600 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/mus.dat.fasta.gz ----sequence: #68848,sp|L08802.1|MMRNASEP Mouse RNase P RNA subunit gene sequnce. ----isReversed: 0 ----hitSequence: GCGGAGGAAGCUCAUCAGCGGGGCCACGUGCUGAGUGCUCGUCACUCUUCGGCCCCUGGGAAGGUCUGAGACUNGGGCCUCCCGCGGCCCUAACCGGGCUCUCCCCGAGCGGGGAGGUGAGUUCCCAGAGAGCAGGGCUCUACGCUUGGGCAGACUGGGCAGGAGAAAAGGCCCCGAGUUCGGGGCGGAUGCCUCCCUCGCCGGAGCUUGGAACAGACUCACGGCCAGCAGUGCGAGUUCAAUGGCUGAGGUGAGGCACCUCCCGGGCCUCAUAACCCAAUUCAN hit 46 : 6 290 (fwd) 98.78 bits :::::::::::[[[[,,,,,<<<<---------<<<<<_____>>>>>--------->>> 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagugcUugucacuCaacuaacauacg 60 GCGGA+G AAGCUCAU : G:+CAC +GC+GAGUGCU+GUCACUC++C :C 6 GCGGAGG-AAGCUCAUCAGCGGGGCCACGUGCUGAGUGCUCGUCACUCUUCGG----CCC 60 >,,,,,,,,,,,,,,,,,,(((((,,,,,,<<<<<_____>>>>><<<<<<<____>>>> 61 ugGGGAAGGUCUGAGAaACaggcCAauuauugCcCgUGAAGgGcaucaccggGGAAccgg 120 :+GGGAAGGUCUGAGA++ :GGCC + ++:GCCC+ + GGGC::::CC:G+G C:GG 61 CUGGGAAGGUCUGAGACUNGGGCCUCCCGCGGCCCUAACCGGGCUCUCCCCGAG--CGGG 118 >>>,<<<<<<<____________......_______________................ 121 ugaucgguGucAUCAGAAAUccA......acgguugagcuggcu................ 158 ::: ::G:G::++CAGA A C++ ACG UUG+GC G CU 119 GAG-GUGAGUUCCCAGAGAGCAGggcucuACGCUUGGGCAGACUgggcaggagaaaaggc 177 ...................................________>>>>>>>))))),,,., 159 ...................................AUGGGAAuggCaccgGgccuUuC.U 182 UGG+A ::C:C::GGCC:++ 178 cccgaguucggggcggaugccucccucgccggagcUUGGAACAGACUCACGGCCAGC-aG 236 ,,,,,,,,,,,,,,,]]]]<<<<<......____.__>>>>>:::::::.:::: 183 GUUGAGUGCAAUgGuuGagcugag......uuag.gCcucagAACCCAA.Ucag 228 + GAGU CAAUGG UGAG:UGAG + G GCCUCA:AACCCAA UCA 237 UGCGAGUUCAAUGGCUGAGGUGAGgcaccuCCCGgGCCUCAUAACCCAAuUCAN 290 ----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: #19730,sp|L08800.1|RNRNASEP Rat RNase P RNA subunit gene sequence. ----isReversed: 0 ----hitSequence: NNNNCCACGCGCUGAGUGCUCGUCACUCUCUCGGCCCCUGGGAAGGUCUGAGACUGGGGCCUCCCGCCGCCCUAACCGGGCUCUCCCCGAGUGGGGAGGUGAGUUCCCAGAGAGCAGGGCUCCACGCGUGGGCAGACUGGGCAGGAGAAGCCCCCGGGUGGGCGGAUGCCUCCCUCGCCGGGGCUUGGAACAGACUCACGGCCAGCAAUUCGAGUUCAAUGGCUGAGGUGAGGCACCUCGCGGGCCUCAUAACCCAAUUCAN hit 47 : 25 286 (fwd) 77.16 bits :::::::::::[[[[,,,,,<<<<---------<<<<<_____>>>>>--------->>> 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagugcUugucacuCaacuaacauacg 60 + +CAC GC+GAGUGCU+GUCACUC+ ++ C 25 --------------------NNNNCCACGCGCUGAGUGCUCGUCACUCUCUCGGC--CCC 62 >,,,,,,,,,,,,,,,,,,(((((,,,,,,<<<<<_____>>>>><<<<<<<____>>>> 61 ugGGGAAGGUCUGAGAaACaggcCAauuauugCcCgUGAAGgGcaucaccggGGAAccgg 120 + GGGAAGGUCUGAGA++ :GGCC + ++:GCCC+ + GGGC::::CC::+G ::GG 63 U-GGGAAGGUCUGAGACUGGGGCCUCCCGCCGCCCUAACCGGGCUCUCCCCGAG--UGGG 119 >>>,<<<<<<<____________.........._______________............ 121 ugaucgguGucAUCAGAAAUccA..........acgguugagcuggcu............ 158 ::: ::G:G::++CAGA A C++ GG+ ++ CUGG++ 120 GAG-GUGAGUUCCCAGAGAGCAGggcuccacgcGUGGGCAGACUGGGCaggagaagcccc 178 ..............................________>>>>>>>))))),,,.,,,,,, 159 ..............................AUGGGAAuggCaccgGgccuUuC.UGUUGA 187 UGG+A ::C:C::GGCC:++ +U GA 179 cgggugggcggaugccucccucgccggggcUUGGAACAGACUCACGGCCAGC-aAUUCGA 237 ,,,,,,,,,,]]]]<<<<<....____...__>>>>>:::::::.:::: 188 GUGCAAUgGuuGagcugag....uuag...gCcucagAACCCAA.Ucag 228 GU CAAUGG UGAG:UGAG U G GCCUCA:AACCCAA UCA 238 GUUCAAUGGCUGAGGUGAGgcacCUCGcggGCCUCAUAACCCAAuUCAN 286 ----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: #5139,sp|AF004371.1|AF004371 Pelobates cultripes RNase P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: GUGGAGGGAAGCUCAGUGCUGAGGCUACAACCUGAGUGCAUUUGUCACUCUCAUACAUUCCUCAGGGAAGGUCUGAGAUUAGAGCCAUCUAUUGUCUUAACAAGGCAUUGCUUGGUUUGAGCAAAUGAGUUACCAUCAAACCUUGUUCUGUUGUCGCUAGACUGCACAAGUAAUAGAAGUGGUUUUCCUCUAUGGAUGCUGAGGCAACUGAUUUGGAAAGUGACUCAUGACUAGCAAAUUCAAGUUCAAUUGCUGAGAGGAAGUCAUUACUUCCUAACCCAAUUCAG hit 48 : 5 291 (fwd) 93.18 bits :::::::::::[[[[,,,,,<<<<---------<<<<<._____.>>>>>---------> 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagug.cUugu.cacuCaacuaacaua 58 G GGA+GGAAGCUCA UG +::G:++AC A C+GAGUG UU CACUC+ +UA+++U: 5 GUGGAGGGAAGCUCAGUGCUGAGGCUACAACCUGAGUGcAUUUGuCACUCUCAUACAUUC 64 >>>,,,,,,,,,,,,,,,,,,(((((,,,,,,<<<<<_____>>>>><<<<<<<____>> 59 cgugGGGAAGGUCUGAGAaACaggcCAauuauugCcCgUGAAGgGcaucaccggGGAAcc 118 C:: GGGAAGGUCUGAGA+++::G CA+ UAUUG:C:+ +A:G:CAU::C:::G :: 65 CUCAGGGAAGGUCUGAGAUUAGAGCCAUCUAUUGUCUUAACAAGGCAUUGCUUGGUU-UG 123 >>>>>,<<<<<<<____________...._______________................ 119 ggugaucgguGucAUCAGAAAUccA....acgguugagcuggcu................ 158 :G::A ::G:G::A+CA AA CC + G+U GCU G + 124 AGCAA-AUGAGUUACCAUCAAACCUuguuCUGUUGUCGCUAGACugcacaaguaauagaa 182 .................................._______._>>>>>>>))))),,,., 159 ..................................AUGGGAA.uggCaccgGgccuUuC.U 182 UGG+AA U::C:C::G C::++ 183 gugguuuuccucuauggaugcugaggcaacugauUUGGAAAgUGACUCAUGACUAGCAaA 242 ,,,,,,,,,,,,,,,]]]]<<<<<.____.__>>>>>:::::::.:::: 183 GUUGAGUGCAAUgGuuGagcugag.uuag.gCcucagAACCCAA.Ucag 228 +U AGU CAAU G UGAG::GA: U+A+ C:UC::AACCCAA UCAG 243 UUCAAGUUCAAUUGCUGAGAGGAAgUCAUuACUUCCUAACCCAAuUCAG 291 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----sequence: #5140,sp|AF004372.1|AF004372 Discoglossus jeanneae RNase P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: GCGGAAGGAAGCUCACUGUAGAGGUUACAUACUGAGUGCGUCAAUUCUGUGAUGUCACUUCAUUAUUCCCUCCGGGAAGGUCUGAGACAAGAGCCAAUAGCCGCCCUUACAGGGCGUCACUUGAGCGGGUGAGUGAGUCCCCAGCAACCCCACGGUGGAGUGGACCGGCCCGCUGUGUGGAGGAGGCUCUGCAGGAGAGGCGGGGUGGGCUUGUGGUGAGAGGGAGUGGUCGCAGAUUGAGGCUGCUCCCACCUUACACACGGCUCCACCCGGCUGAUGCUGCCUCCUCCCCGGGCCUUGGAAGUGGCUCUCGGCUGGCUGUAUGAGUCCAAUGGCUGAGGUGGGGCAGCUGCACGGGAUGUGUGCGCGCCCCAUAACCCAAUUCAG hit 49 : 1 387 (fwd) 109.47 bits :::::::::::[[[[,,,,,<<<<---------<<<<<......._____.....>>>>> 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagug.......cUugu.....cacuC 48 GCGGAAGGAAGCUCA+UGUA::G:U+AC ++C++AGUG ++UGU CACU+ 1 GCGGAAGGAAGCUCACUGUAGAGGUUACAUACUGAGUGcgucaauUCUGUgauguCACUU 60 --------->>>>,,,,,,,,,,,,,,,,,,(((((,,,,,,<<<<<_____>>>>><<< 49 aacuaacauacgugGGGAAGGUCUGAGAaACaggcCAauuauugCcCgUGAAGgGcauca 108 A+UA :C:: GGGAAGGUCUGAGA+A+::GCCAAU+++:GCCC+U +AGGGC:UCA 61 CAUUAUUC-CCUCCGGGAAGGUCUGAGACAAGAGCCAAUAGCCGCCCUUACAGGGCGUCA 119 <<<<____>>>>>>>,<<<<<<<____________....._______________..... 109 ccggGGAAccggugaucgguGucAUCAGAAAUccA.....acgguugagcuggcu..... 158 C::G+G C::GUGA : G:GUC++CAG AA CC GU GA+C GGC+ 120 CUUGAG--CGGGUGA-GUGAGUCCCCAGCAACCCCacgguGGAGUGGACC-GGCCcgcug 175 ............................................................ - ............................................................ - 176 uguggaggaggcucugcaggagaggcggggugggcuuguggugagagggaguggucgcag 235 ............................................................ - ............................................................ - 236 auugaggcugcucccaccuuacacacggcuccacccggcugaugcugccuccuccccggg 295 ..________>>>>>>>))))),,,.,,,,,,,,,,,,,,,,]]]]<<<<<......... 159 ..AUGGGAAuggCaccgGgccuUuC.UGUUGAGUGCAAUgGuuGagcugag......... 206 UGG+A UGGC:C :GGC::++ + UGAGU CAAUGG UGAG:UG:G 296 ccUUGGAAGUGGCUCUCGGCUGGC-uGUAUGAGUCCAAUGGCUGAGGUGGGgcagcugca 354 ...____.......__>>>>>:::::::.:::: 207 ...uuag.......gCcucagAACCCAA.Ucag 228 ++G GCC:CA:AACCCAA UCAG 355 cggGAUGugugcgcGCCCCAUAACCCAAuUCAG 387 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----sequence: #5141,sp|AF004373.1|AF004373 Ascaphus truei RNase P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: GCGGAAGGAAGCUCACUGUAGAGGCUACUUGCUGGGUGCUGUUGUUACUCUAUCAACCAGCCUUGGGGAAGGUCUGAGAUAAGAGCCACUUGUUGCCUUCACAAGGCAUUGCUUGGUGUAAGCAAGUGAGUUCCCAUCAAAGAUGGCUCAGUUGCAAGCUUAAUGCAAGAGACAUAGCAAAGAAGCCCAAUAUACUUCUGAUAUGGAUGCAAUGCCCAACAGACUGGAAAUGACUCACGGCUGGCAUGUUCAAGCUCAAUGACUGAGGGGAAGCAAGUGAUGGCUUCCUAACCCAAUUCAG hit 50 : 1 301 (fwd) 104.77 bits :::::::::::[[[[,,,,,<<<<---------<<<<<_____..>>>>>---------. 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagugcUugu..cacuCaacuaacau. 57 GCGGAAGGAAGCUCA+UGUA::G:++AC +GC+G:GU+CU U +AC:C+A++AAC + 1 GCGGAAGGAAGCUCACUGUAGAGGCUACUUGCUGGGUGCUGUUguUACUCUAUCAACCAg 60 >>>>,,,,,,,,,,,,,,,,,,(((((,,,,,,<<<<<_____>>>>><<<<<<<____> 58 acgugGGGAAGGUCUGAGAaACaggcCAauuauugCcCgUGAAGgGcaucaccggGGAAc 117 :C::GGGGAAGGUCUGAGA+A+::GCCA+UU+UUGCC:+ +A:GGCAU::C:::G : 61 CCUUGGGGAAGGUCUGAGAUAAGAGCCACUUGUUGCCUUCACAAGGCAUUGCUUGGUG-U 119 >>>>>>,<<<<<<<____________....._______________.............. 118 cggugaucgguGucAUCAGAAAUccA.....acgguugagcuggcu.............. 158 ::G::A ::G:G::++CA AA + A ++ +AGCU+ U 120 AAGCAA-GUGAGUUCCCAUCAAAGAUggcucAGUUGCAAGCUUAAUgcaagagacauagc 178 .............................................________>>>>>>> 159 .............................................AUGGGAAuggCaccg 173 UGG+AAU::C:C:: 179 aaagaagcccaauauacuucugauauggaugcaaugcccaacagaCUGGAAAUGACUCAC 238 ))))),,,.,,,,.,,,,,,,,,,,,]]]]<<<<<......______>>>>>:::::::. 174 GgccuUuC.UGUU.GAGUGCAAUgGuuGagcugag......uuaggCcucagAACCCAA. 224 GGC::++ UGUU AG CAAUG UGAG::GA: ++GGC:UC::AACCCAA 239 GGCUGGC-aUGUUcAAGCUCAAUGACUGAGGGGAAgcaaguGAUGGCUUCCUAACCCAAu 297 :::: 225 Ucag 228 UCAG 298 UCAG 301 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----sequence: #5142,sp|AF004374.1|AF004374 Alytes obstetricans RNase P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: CGGAAGGAAGCUCACUGUAGAGGUCAUGUACGGAGUGCGUCACAACUGUGAUGUCACUCCAUUAAUUCCUCCGGGAAGGUCUGAGACAGGAGCCAUUAGCUGCCCUCACAGGGCGUCACCUGAGUGGGUGAGUGAGUCCCCAGCAACCCCACGCUGGAGUGGACCGGCUCGACACGUGGAGUGGGCUCUGCAGGAGAGGCGGGGUGGACUGCAGUGAGAGGGUGGAGUUACAGAUUGACACUCCCACCCAACUCAGUGAGGCUCCGCCCAGCUGAUGCCGCCCCCUCCCCGGGCCUUGGAAGUGGCUCACGGCUGGCUGUGUUAGUCCAAUGGCUGAGGUGGAGCAGCUGCACGGGAUGUGUGCGCGCCCCAUAACCCAAUUCAG hit 51 : 1 385 (fwd) 100.77 bits :::::::::::[[[[,,,,,<<<<---------<<<<<......._____.....>>>>> 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagug.......cUugu.....cacuC 48 CGGAAGGAAGCUCA+UGUA::G:UCA ++C GAGUG +UGU CACUC 1 -CGGAAGGAAGCUCACUGUAGAGGUCAUGUACGGAGUGcgucacaACUGUgauguCACUC 59 --------->>>>,,,,,,,,,,,,,,,,,,(((((,,,,,,<<<<<_____>>>>><<< 49 aacuaacauacgugGGGAAGGUCUGAGAaACaggcCAauuauugCcCgUGAAGgGcauca 108 A+UAA + :C:: GGGAAGGUCUGAGA+A ::GCCA+U+++:GCCC+ +AGGGC:UCA 60 CAUUAAUU-CCUCCGGGAAGGUCUGAGACAGGAGCCAUUAGCUGCCCUCACAGGGCGUCA 118 <<<<____>>>>>>>,<<<<<<<____________....._______________..... 109 ccggGGAAccggugaucgguGucAUCAGAAAUccA.....acgguugagcuggcu..... 158 CC::+G ::GGUGA ::G:GUC++CAG AA CC GU GA+C GGCU 119 CCUGAG--UGGGUGA-GUGAGUCCCCAGCAACCCCacgcuGGAGUGGACC-GGCUcgaca 174 ............................................................ - ............................................................ - 175 cguggagugggcucugcaggagaggcgggguggacugcagugagaggguggaguuacaga 234 ............................................................ - ............................................................ - 235 uugacacucccacccaacucagugaggcuccgcccagcugaugccgcccccuccccgggc 294 .________>>>>>>>))))),,,.,,,,,,,,,,,,,,,,]]]]<<<<<.......... 159 .AUGGGAAuggCaccgGgccuUuC.UGUUGAGUGCAAUgGuuGagcugag.......... 206 UGG+A UGGC:C::GGC::++ + U AGU CAAUGG UGAG:UG: 295 cUUGGAAGUGGCUCACGGCUGGC-uGUGUUAGUCCAAUGGCUGAGGUGGAgcagcugcac 353 ..____.......__>>>>>:::::::.:::: 207 ..uuag.......gCcucagAACCCAA.Ucag 228 ++G GC :CA:AACCCAA UCAG 354 ggGAUGugugcgcGCCCCAUAACCCAAuUCAG 385 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----sequence: #5143,sp|AF004375.1|AF004375 Euproctus asper RNase P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: GCGGAAGGAAGCUCACUGUAGAGGCUACAUGCAGAGUGCAUAUGUCACUCAAGUACCUUGGGGAAGGUCUGAGACAGGAGCCGGUAAUUGCCCCAGCAGGGCAUCCCCUGAAAAGGGGAGCGAGCUCCCAGAGACCCGGGGCCCAAAGGGGGUGGCAUGAGACGCGUGACCGUGUAUCUGGUACUCGCUGAUGCUUACUCCUUCCGGGCAUUGGAAGUGGCUCGCGGCUGGCACUCCCCUGAGUGCAAUGGCUGAGGUGAGGUAAUGGCGCCUCAUAACCCAAUUCAG hit 52 : 1 288 (fwd) 132.35 bits :::::::::::[[[[,,,,,<<<<---------<<<<<._____.>>>>>---------> 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagug.cUugu.cacuCaacuaacaua 58 GCGGAAGGAAGCUCA+UGUA::G:++AC +GCAGAGUG U CACUCAA UA : 1 GCGGAAGGAAGCUCACUGUAGAGGCUACAUGCAGAGUGcAUAUGuCACUCAAGUA----C 56 >>>,,,,,,,,,,,,,,,,,,(((((,,,,,,<<<<<_____>>>>><<<<<<<____>> 59 cgugGGGAAGGUCUGAGAaACaggcCAauuauugCcCgUGAAGgGcaucaccggGGAAcc 118 C::GGGGAAGGUCUGAGA+A ::GCC U+AUUGCCC G+AGGGCA ::CC::G AA:: 57 CUUGGGGAAGGUCUGAGACAGGAGCCGGUAAUUGCCCCAGCAGGGCA-UCCCCUGAAAAG 115 >>>>>,<<<<<<<____________.........________________.......... 119 ggugaucgguGucAUCAGAAAUccA.........acgguugagcuggcuA.......... 159 GG:: ::G:G::++CAGA A CC+ GG+UG++ UG + A 116 GGGA--GCGAGCUCCCAGAGACCCGgggcccaaaGGGGGUGGCAUGAG-Acgcgugaccg 172 ......................................._______>>>>>>>))))),, 160 .......................................UGGGAAuggCaccgGgccuUu 180 UGG+A U::C:C::GGC::++ 173 uguaucugguacucgcugaugcuuacuccuuccgggcauUGGAAGUGGCUCGCGGCUGGC 232 ...,,,,,,,,,,,,,,,,,]]]]<<<<<..____..__>>>>>:::::::.:::: 181 ...CUGUUGAGUGCAAUgGuuGagcugag..uuag..gCcucagAACCCAA.Ucag 228 C UGAGUGCAAUGG UGAG:UGAG +++G GCCUCA:AACCCAA UCAG 233 acuCCCCUGAGUGCAAUGGCUGAGGUGAGguAAUGgcGCCUCAUAACCCAAuUCAG 288 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----sequence: #5144,sp|AF004376.1|AF004376 Lachesis muta RNase P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: GCGGAAGGAAGCUCACUGUAGAGGCCACUAGCUUGGGUGUCUAUCACCCUACUUCCGCCUCUGGGAAGGUCUGAGGGAAGGGCCAAAUUGCCGCCCUAGCAGGGUGCCACCUUCUGAAGGUGGGGUGAGUUCCCACCAAUGUGGGUCUCCGAUGAAGCCCUAGAAUUGAGGCAGGAGAAGUGGAGAGGGGUCGUAGGCUCCUCCCCGCGGAUGCCUCUGUGGCUCCGUUCGGGAUUUGGGAAUGACUCACGGCUGGCAGCUUUGAGUACAAUGGGAAGAGGUGAAGCCCGCCAGCUUCAUAACCCAAUUCAG hit 53 : 1 312 (fwd) 107.90 bits :::::::::::[[[[,,,,,<<<<---------.<<<<<_____>>>>>--------->> 1 GCGGAaGGAAGcuCauUgUAacguucAccagca.GagugcUugucacuCaacuaacauac 59 GCGGAAGGAAGCUC++UGUA::G:+CAC AGC+ G:GUG++U UCAC:C+ACU++C :C 1 GCGGAAGGAAGCUCACUGUAGAGGCCACUAGCUuGGGUGUCUAUCACCCUACUUCCG-CC 59 >>,,,,,,,,,,,,,,,,,,(((((,,.,,,,<<<<<_____>>>>><<<<<<<____>> 60 gugGGGAAGGUCUGAGAaACaggcCAa.uuauugCcCgUGAAGgGcaucaccggGGAAcc 118 ::+GGGAAGGUCUGAG+ A+: GCCAA UU++: CCC+ G+AGGG ::CACC:: :: 60 UCUGGGAAGGUCUGAGGGAAGGGCCAAaUUGCCGCCCUAGCAGGGUGCCACCUUCUG-AA 118 >>>>>,<<<<<<<____________.................................__ 119 ggugaucgguGucAUCAGAAAUccA.................................ac 145 GGUG:+::G:G::++CA AAU + + 119 GGUGGGGUGAGUUCCCACCAAUGUGggucuccgaugaagcccuagaauugaggcaggaGA 178 _____________............................................___ 146 gguugagcuggcu............................................AUG 161 GU GAG +GG+U UG 179 AGUGGAGAGGGGUcguaggcuccuccccgcggaugccucuguggcuccguucgggauUUG 238 _____>>>>>>>))))),,,.,,,,,,,,,,,,,.,,,]]]]<<<<<.____...__>>> 162 GGAAuggCaccgGgccuUuC.UGUUGAGUGCAAU.gGuuGagcugag.uuag...gCcuc 215 GGAAU::C:C::GGC :++ +UUGAGU CAAU GG +GAG:UGA: + G GC:UC 239 GGAAUGACUCACGGCUGGCAgCUUUGAGUACAAUgGGAAGAGGUGAAgCCCGccaGCUUC 298 >>:::::::.:::: 216 agAACCCAA.Ucag 228 A:AACCCAA UCAG 299 AUAACCCAAuUCAG 312 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----sequence: #5145,sp|AF004377.1|AF004377 Oncorhynchus sp. RNase P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: GCGGAGGGAAGCUCAUCAGUGGGGUCACAUGUAGGGUGCUUGUCACUCAACCAAUCACCUUGGGGAAGGUCUGAGACAAGAGCCAAUCACUUCCCUAGCAGGGUAUCACCUGAUCUGGGUGAGUGAGUGCACAGAGAAUAUGAGCCAUUGUGAGUUGUCUUUACGGAAGAAACCAGCCAGUACAGCUCUCCAGCACUACUGGUGGAUGUGACCUCACUGGCUUGGAAACACUCAUGGCUGGCAUAUGAGUUUAAUGUGUGAGUUGGAGUACACCUCCAGAACCCAAUUCAG hit 54 : 3 293 (fwd) 111.89 bits :::::::::::[[[[,,,,,<<<<---------<<<<<_____>>>>>--------->>> 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagugcUugucacuCaacuaacauacg 60 GCGGA+GGAAGCUCAU +: G:UCAC +G AG:GUGCUUGUCAC:CAAC+AA +:C 3 GCGGAGGGAAGCUCAUCAGUGGGGUCACAUGUAGGGUGCUUGUCACUCAACCAAUCACCU 62 >,,,,,,,,,,,,,,,,,,(((((,,,,,,<<<<<_____>>>>><<<<<<<____>>>> 61 ugGGGAAGGUCUGAGAaACaggcCAauuauugCcCgUGAAGgGcaucaccggGGAAccgg 120 :GGGGAAGGUCUGAGA+A+::GCCAAU A+U:CCC+ G+AGGG:AUCACC::+ ::GG 63 UGGGGAAGGUCUGAGACAAGAGCCAAUCACUUCCCUAGCAGGGUAUCACCUGAUC-UGGG 121 >>>,<<<<<<<____________...._______________.................. 121 ugaucgguGucAUCAGAAAUccA....acgguugagcuggcu.................. 158 UGA +:G:G: + CAGA A ++ ++ ++UGAG UG CU 122 UGA-GUGAGUGCACAGAGAAUAUgagcCAUUGUGAGUUGUCUuuacggaagaaaccagcc 180 ...........................................________>>>>>>>)) 159 ...........................................AUGGGAAuggCaccgGg 175 UGG+AA :C:C:+GG 181 aguacagcucuccagcacuacugguggaugugaccucacuggcUUGGAAA-CACUCAUGG 239 ))),,,,,,,,,,,,,,,,,,,]]]]<<<<<..______>>>>>:::::::.:::: 176 ccuUuCUGUUGAGUGCAAUgGuuGagcugag..uuaggCcucagAACCCAA.Ucag 228 C::++ + UGAGU AAUG+ UGAG:UG:: ++A C::CA:AACCCAA UCAG 240 CUGGC-AUAUGAGUUUAAUGUGUGAGUUGGAguACA-CCUCCAGAACCCAAuUCAG 293 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----sequence: #6238,sp|AF044325.1|AF044325 Uta stansburiana ribonuclease P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: GCGGAAGGAAGCUCACUGUAGAGGUCACUCGCUGGGUGUCUUGAUCACCCCCGUUGCUACCUUGGGGAAGGUCUGAGAGAAGGGCCAAGUGUCGUCCUAGCAGGGCGCCAUCUUAGGAAGGUGGGUGAGUUCCCAGCAAUAUGGAUCUCCAGUAAAGCCCUACUUUGAGGCAGGAGAAGCAGGGCUGGGGGGGUUCCCUCCUCCCUGCGGAUGCCUCCGUGGCUUACUCGGGGUUUGGGAAUGACUCACGGCCGGCAACGUUGAGUACAAUGGGCAGAGGUGGAGCACCCGCUUCAUAACCCAAUUCAG hit 55 : 1 309 (fwd) 120.16 bits :::::::::::[[[[,,,,,<<<<---------<<<<<._____.>>>>>---------> 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagug.cUugu.cacuCaacuaacaua 58 GCGGAAGGAAGCUC++UGUA::G:UCAC GC+G:GUG CUUG CAC:C U+ C++: 1 GCGGAAGGAAGCUCACUGUAGAGGUCACUCGCUGGGUGuCUUGAuCACCCCCGUUGCUAC 60 >>>,,,,,,,,,,,,,,,,,,(((((,,,,,,<<<<<_____>>>>><<<<<<<____>> 59 cgugGGGAAGGUCUGAGAaACaggcCAauuauugCcCgUGAAGgGcaucaccggGGAAcc 118 C::GGGGAAGGUCUGAGA A+:GGCCAA U+U:G:CC+ G+AGG:C::CA:C::+G :: 61 CUUGGGGAAGGUCUGAGAGAAGGGCCAAGUGUCGUCCUAGCAGGGCGCCAUCUUAGG-AA 119 >>>>>,<<<<<<<____________....._______________............... 119 ggugaucgguGucAUCAGAAAUccA.....acgguugagcuggcu............... 158 G:UG: ::G:G::++CAG AAU + +C GU++AGC + 120 GGUGG-GUGAGUUCCCAGCAAUAUGgaucuCCAGUAAAGCCCUACuuugaggcaggagaa 178 ........................................................____ 159 ........................................................AUGG 162 UGG 179 gcagggcuggggggguucccuccucccugcggaugccuccguggcuuacucgggguUUGG 238 ____>>>>>>>))))),,,.,,,,,,,,,,,,,.,,,]]]]<<<<<..______>>>>>: 163 GAAuggCaccgGgccuUuC.UGUUGAGUGCAAU.gGuuGagcugag..uuaggCcucagA 218 GAAU::C:C::GGCC:++ GUUGAGU CAAU GG +GAG:UG : ++ GC: CA:A 239 GAAUGACUCACGGCCGGCAaCGUUGAGUACAAUgGGCAGAGGUGGAgcACCCGCUUCAUA 298 ::::::.:::: 219 ACCCAA.Ucag 228 ACCCAA UCAG 299 ACCCAAuUCAG 309 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----sequence: #6239,sp|AF044326.1|AF044326 Lachesis muta ribonuclease P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: GCGGAAGGAAGCUCACUGUAGAGGCCACUAGCUUGGGUGUCUAUCACCCUACUUCCGCCUGUGGGAAGGUCUGAGGGAAGGGCCAAAUUGCCGCCCUAGCAGGGUGCCACCUUCUGAAGGUGGAGUGAGUUCCCACCAAUGUGGGUCUCCGAUGAAGCCCUAGAAUUGAGGCAGGAGAAGCGGAGAGGGGUCGUGGGUCGUGGGUCGUAGGCAUCCUCCCCGCGGAUGCCUCUGUGGCUCCGUUCGGGAUUUGAGAAUGACUUACGGCUGACAGCUUUGAGUACAAUGGGAAGAGGUGAAGCACCGCCAGCUUCAUAUAACCCAAUUCAG hit 56 : 1 330 (fwd) 87.91 bits :::::::::::[[[[,,,,,<<<<---------.<<<<<_____>>>>>--------->> 1 GCGGAaGGAAGcuCauUgUAacguucAccagca.GagugcUugucacuCaacuaacauac 59 GCGGAAGGAAGCUC++UGUA+:G:+CAC AGC+ G:GUG++U UCAC:C+ACU++C :C 1 GCGGAAGGAAGCUCACUGUAGAGGCCACUAGCUuGGGUGUCUAUCACCCUACUUCCG-CC 59 >>,,,,,,,,,,,,,,,,,,(((((,,.,,,,<<<<<_____>>>>><<<<<<<____>> 60 gugGGGAAGGUCUGAGAaACaggcCAa.uuauugCcCgUGAAGgGcaucaccggGGAAcc 118 :++GGGAAGGUCUGAG+ A+: GCCAA UU++: CCC+ G+AGGG ::CACC:: :: 60 UGUGGGAAGGUCUGAGGGAAGGGCCAAaUUGCCGCCCUAGCAGGGUGCCACCUUCUG-AA 118 >>>>>,<<<<<<<____________......________________............. 119 ggugaucgguGucAUCAGAAAUccA......acgguugagcuggcuA............. 159 GGUG: :: :G::++CA AAU + + ++++++C + + A 119 GGUGGAGUGAGUUCCCACCAAUGUGggucucCGAUGAAGCCCUAG-Aauugaggcaggag 177 ............................................................ - ............................................................ - 178 aagcggagaggggucgugggucgugggucguaggcauccuccccgcggaugccucugugg 237 .............._______>>>>>>>))))),,,.,,,,,,,,,,,,,.,,,]]]]<< 160 ..............UGGGAAuggCaccgGgccuUuC.UGUUGAGUGCAAU.gGuuGagcu 203 UG GAAU::C: ::GGC : + +UUGAGU CAAU GG +GAG:U 238 cuccguucgggauuUGAGAAUGACUUACGGCUGACAgCUUUGAGUACAAUgGGAAGAGGU 297 <<<..____...__>>>>>..:::::::.:::: 204 gag..uuag...gCcucag..AACCCAA.Ucag 228 GA: ++ G GC:UCA: AACCCAA UCAG 298 GAAgcACCGccaGCUUCAUauAACCCAAuUCAG 330 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----sequence: #6240,sp|AF044327.1|AF044327 Phrynosoma douglassii ribonuclease P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: GCGGAAGGAAGCUCACUGUAGAGGUCACGCGCUGGGUGUAUCGAUCACCCUCCUUGCUACCUUUGGGAAGGUCUGAGAGAAGGGCCAAGUGUCGCCUUAGCAGGGCGCCAUCUUAGGAAGGUGGGUGAGUUCCCAGCAAUAGGGGUCUCCUGUAAUGCCCCAGUUUGAGGCAGGAGAAGCGGGGCUGGAGGGGCUACUCCCUCCUUCCUGCGGAUGCCUCCGUGGCUUACGCGGGGCUUGGGAAUGACUCACGGCCGGCAACGUUGAGUACAAUGGGCAGAGGUGAAGCGGCCGCUUCAUAACCCAAUUCAG hit 57 : 1 312 (fwd) 120.22 bits :::::::::::[[[[,,,,,<<<<---------<<<<<._____.>>>>>---------> 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagug.cUugu.cacuCaacuaacaua 58 GCGGAAGGAAGCUC++UGUA::G:UCAC GC+G:GUG U+G CAC:C+ CU+ C++: 1 GCGGAAGGAAGCUCACUGUAGAGGUCACGCGCUGGGUGuAUCGAuCACCCUCCUUGCUAC 60 >>>,,,,,,,,,,,,,,,,,,(((((,,,,,,<<<<<_____>>>>><<<<<<<____>> 59 cgugGGGAAGGUCUGAGAaACaggcCAauuauugCcCgUGAAGgGcaucaccggGGAAcc 118 C::+GGGAAGGUCUGAGA A+:GGCCAA U+U:GCC:+ G+A:GGC::CA:C::+G :: 61 CUUUGGGAAGGUCUGAGAGAAGGGCCAAGUGUCGCCUUAGCAGGGCGCCAUCUUAGG-AA 119 >>>>>,<<<<<<<____________............................_______ 119 ggugaucgguGucAUCAGAAAUccA............................acgguug 150 G:UG: ::G:G::++CAG AAU + A G +++ 120 GGUGG-GUGAGUUCCCAGCAAUAGGggucuccuguaaugccccaguuugaggcAGGAGAA 178 ________..................................................._ 151 agcuggcu...................................................A 159 ++++GGCU 179 GCGGGGCUggaggggcuacucccuccuuccugcggaugccuccguggcuuacgcggggcU 238 _______>>>>>>>))))),,,.,,,,,,,,,,,,,.,,,]]]]<<<<<...______>> 160 UGGGAAuggCaccgGgccuUuC.UGUUGAGUGCAAU.gGuuGagcugag...uuaggCcu 214 UGGGAAU::C:C::GGCC:++ GUUGAGU CAAU GG +GAG:UGA: + GC:U 239 UGGGAAUGACUCACGGCCGGCAaCGUUGAGUACAAUgGGCAGAGGUGAAgcgGCC-GCUU 297 >>>:::::::.:::: 215 cagAACCCAA.Ucag 228 CA:AACCCAA UCAG 298 CAUAACCCAAuUCAG 312 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz ----sequence: #6241,sp|AF044328.1|AF044328 Ensatina eschscholtzii ribonuclease P RNA gene, partial sequence. ----isReversed: 0 ----hitSequence: GCGGAAGGAAGCUCACUGUAGAGGUCAUGUGCCGAGUACAUUUGUUACUCUCUCACCUUGGGGAAGGUCUGAGACAAGAGCCGUUUCUGUCCUUGCAGGACAUCUUCCGAGCCGGGAGAGCGAGCUCCCAGACACUCGGUGCAUGGAGGGGUUUGCACAAGAUGCUAGUUAGUAGUUGGUGGCUUGAUACUGCCUUCCCUGGACUAGUUGAUGCCUAUUCAUCUGGGCAUUGGAAGUGGCUUGUGGCUAGCAUGGCACUGAGUCCAAUGGAUGAGGUGAGGCAACUGUGCCUCAUAACCCAAUUCAG hit 58 : 1 307 (fwd) 107.70 bits :::::::::::[[[[,,,,,<<<<---------<<<<<._____.>>>>>---------> 1 GCGGAaGGAAGcuCauUgUAacguucAccagcaGagug.cUugu.cacuCaacuaacaua 58 GCGGAAGGAAGCUCA+UGUA::G:UCA +GC GAGU: UU :ACUC+ ++A : 1 GCGGAAGGAAGCUCACUGUAGAGGUCAUGUGCCGAGUAcAUUUGuUACUCUCUCA----C 56 >>>,,,,,,,,,,,,,,,,,,(((((,,,,,,<<<<<_____>>>>><<<<<<<____>> 59 cgugGGGAAGGUCUGAGAaACaggcCAauuauugCcCgUGAAGgGcaucaccggGGAAcc 118 C::GGGGAAGGUCUGAGA+A+::GCC +UU UG:CC+UG+AGG:CAUC::C:G+G C: 57 CUUGGGGAAGGUCUGAGACAAGAGCCGUUUC-UGUCCUUGCAGGACAUCUUCCGAGC-CG 114 >>>>>,<<<<<<<____________....________________............... 119 ggugaucgguGucAUCAGAAAUccA....acgguugagcuggcuA............... 159 G::GA +: :G::++CAGA A +C+ A GG G+G U+GC A 115 GGAGA-GCGAGCUCCCAGACACUCGgugcAUGGAGGGGUUUGC-Acaagaugcuaguuag 172 ..........................................................__ 160 ..........................................................UG 161 UG 173 uaguugguggcuugauacugccuucccuggacuaguugaugccuauucaucugggcauUG 232 _____>>>>>>>))))),,...,,,,,,,,,,,,,,,,,]]]]<<<<<...____.__>> 162 GGAAuggCaccgG