Params: release/cmzasha --no-stderr --local --filter 500 20 /home/kasiaw/Rfam_7.0/CM/RF00028.cm /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta 1 specfile /home/kasiaw/results/Tetrahymena_thermophila.fasta/RF00028_Intron_gpI/RF00028_500_0.01.filterspec Build: release Host: node017 pid: 20217 ---time: Mon Jul 4 05:27:08 2005 ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----specfile: heur-hmm /home/kasiaw/Rfam_7.0_filters/RF00028_heur.hmm 2.90669751 ----hmm-from-cmFileName: /home/kasiaw/Rfam_7.0/CM/RF00028.cm ----hmm-build-info: ;(default construction of HMM) Params: release/cmzasha --no-stderr --local --create-heuristic-hmm 500 /home/kasiaw/Rfam_7.0/CM/RF00028.cm 0.01 data/default.heurcreationspec /home/kasiaw/Rfam_7.0_filters Build: release Host: node020 pid: 22453 ;Params: release/cmzasha --no-stderr --local --create-heuristic-hmm 500 /home/kasiaw/Rfam_7.0/CM/RF00028.cm 0.01 data/default.heurcreationspec /home/kasiaw/Rfam_7.0_filters Build: release Host: node020 pid: 22453 ;Params: release/cmzasha --no-stderr --local --create-heuristic-hmm 500 /home/kasiaw/Rfam_7.0/CM/RF00028.cm 0.01 data/default.heurcreationspec /home/kasiaw/Rfam_7.0_filters Build: release Host: node020 pid: 22453 ----2struct-info: only-hmm ----cmFile: /home/kasiaw/Rfam_7.0/CM/RF00028.cm (local) ----CM-scanning-logic: Infernal-0.55 ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #301,emb|8254415| 71046 bp 1 contigs ----isReversed: 1 ----hitSequence: UUAUCUGUAAAAUUAUUCUAUUUAUUUUUUGUAAUAAAAUUCACAAAAAAUAAUUAAUUCUUAAUUAAAUGAACAUUUAUAAAUGCAAAAAUCUUUGAACUGAAUUAAGUAACAAAUAAUUUAAAAAUGGUAAUCUAUUUUAUAGAUAUAAAUAAAUACUUUUUAAAUUCUAUUUGAGUUAAAUAUUGAGAGUUUUUUGUUUUCAAAUUAAAAACUGCUCAUCAAUACCUGCUUUAGUGCUGAUAUUAGAUUAUCCUCUUUCUUGUCUGAUAUACUUAAAGAUAUAGUCUAGACCAUAAGUAACUAUUA ----ssRNAplot: ....(((((((((..........))))))))).....(((((.((...????????????????????????????????????????????????????????????????????????????...)).))))).(((((((((...........???????????????????????????????????????????????????????????????????????????????????????????????????????????????)))))))))...................((((....)))).. ----hitGC: 0.194175 ----pairStats: 32,3,3,8 hit 0 : 21181 20873 (rev) 20.71 bits ::::<<<<<<<<<__..._____>>>>>>>>>,,,<<_>>,,,(((((-((,,,~~~~~~ 1 cuucgaaccuaaaaa...auUauauugggcucaUaguuuguAAaacuguCaAAU*[85]* 51 +U++:+::::AA:+A ++U U:UU::::+:A++ AAAA:U C:AA 49866 UUAUCUGUAAAAUUAuucUAUUUAUUUUUUGUAAU------AAAAUUCACAAAA*[76]* 49913 ,,,))-))))),<<<<<<<<<___________~~~~~~~>>>>>>>>>,,,,,,,,,,,, 137 AaAcGgcagucaucuuaauaaauauaaauAua*[ 2]*uaucuaagaUgAAGAUAUAGU 190 AAA:GG A:UC : U ::++:AUAUAAAUA+A :++:: A :U AAGAUAUAGU 49990 AAAUGGUAAUCUAUUUUAUAGAUAUAAAUAAA*[111]*UGAUAUACUUAAAGAUAUAGU 50153 ,,,,,,,,<<<<<____>>>>>:: 191 CcAAauccuuauuGAAAaauaaga 214 C+A+A CC:U : G+AA : A:+A 50154 CUAGA-CCAU-AAGUAACU-AUUA 50174 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #482,emb|8254464| 405752 bp 2 contigs ----isReversed: 0 ----hitSequence: AUUAGAAAUUAAUUAUUUAAUAAUUCAAUUUUAGUUACCUGUUAUUAAAAUUAAAUUUAUUAAGCAUCAUUAAAAAUUUAAAUAAUAUUUUCCUUUAUUUCUAAAUGAAUGAUAUACUAUCAAUCCUCACUAAUUAAAUAAGGAAGUAAGUAAGUAAGUAACCAAUCAACCACCCCUACCUACUUUUCUCCUUCCAAAAUGUAUCAUAUAUAAAAAUCUUUAUUUGAGGUUUUAAAUUAAGAUAUAGUCUUAUUUCAAAAAAAAUUAUCUUA ----ssRNAplot: .....((((((((.........))))))))...((................)).(((((.((.????)).))))).(((((((((......????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????)))))))))....................(((((....))))).. ----hitGC: 0.198529 ----pairStats: 32,1,0,11 hit 1 : 141176 141447 (fwd) 20.37 bits ::::<<<<<<<<<__.._____>>>>>>>>>,,,<<..............._>>,,,((( 1 cuucgaaccuaaaaa..auUauauugggcucaUagu...............uuguAAaac 43 UU GA::::AA:+A +++ +:UU::::U +UA:U UU: A+:: 141176 AUUAGAAAUUAAUUAuuUAAUAAUUCAAUU-UUAGUuaccuguuauuaaaaUUA--AAUU 141232 ((-((,~~~~~~))-))))),<<<<<<<<<______~~~~~~~>>>>>>>>>,,,,,,,, 44 uguCaA*[91]*cGgcagucaucuuaauaaauauaa*[ 7]*uaucuaagaUgAAGAUA 186 U:U:AA C: :A::+AU:U:A:U+++ +U++ ++U:U:A:AU+AAGAUA 141233 UAUUAA*[ 4]*CAUUAAAAAUUUAAAUAAUAUUUU*[136]*GGUUUUAAAUUAAGAUA 141419 ,,,,,,,,,,,,<<<<<____>>>>>:: 187 UAGUCcAAauccuuauuGAAAaauaaga 214 UAGUC+ A+U+C::A : AA : U::+A 141420 UAGUCUUAUUUCAAAAAAAAUUAUCUUA 141447 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #496,emb|8254610| 665075 bp 6 contigs ----isReversed: 0 ----hitSequence: UUUUAUUCUUAUUUACACUCUCAAUUAAAUCAGAAGAAAACUGAUAUAAUUGAGAGAACAUAGAAAUUUAAUAAGGAAUAAUUAUUGUUGAGAGGAAAAACCAUCAAUUAUUGAUCUUUCUUAAAAGUUUGAAUAAAUUUUUAGAAGAAUCAGAAAAUGUAACAAUUUUGCAAAAUAAAAUUAAAAAAUCUUUAUACUAUUUUAAUUACAAAAAUAUAUUUUUGAGGUAGAAAUCAAAUUUUUAAUUUUAAAACAAUCAAUCUUUUAUUGAAAUUAAAGAUAAAUAAUAGAGAGGAGAAAUCAUCAUUUAAUAGGUCUUUUUUUAAAUUUGAGAAGUUUUUUAAAAAAAAGAUAUAACUCUAUAACUUUUAGAAAUAAAAUU ----ssRNAplot: ....(((((((((..............)))))))))...((....)).(((((.((...???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????...)).))))).(((((((((..................................................................)))))))))....................(((((....))))).. ----hitGC: 0.180628 ----pairStats: 32,0,1,6 hit 2 : 47855 48236 (fwd) 20.30 bits ::::<<<<<<<<<__......._____>>>>>>>>>,,,<<..._>>,,,(((((-((,, 1 cuucgaaccuaaaaa.......auUauauugggcucaUagu...uuguAAaacuguCaAA 50 +UU+::+C::A+:+A A+U +:+U::G+::A+A:: U:: A:::::+::AA 47855 UUUUAUUCUUAUUUAcacucucAAUUAAAUCAGAAGAAAACugaUAU--AAUUGAGAGAA 47912 ,~~~~~~~,,,))-))))),<<<<<<<<<___________.................... 51 U*[ 85]*AaAcGgcagucaucuuaauaaauauaaauAua.................... 168 AAA:: ::::: U:UUA:U AA +UAAA+AUA 47913 C*[191]*AAACAAUCAAUCUUUUAUUGAAAUUAAAGAUAaauaauagagaggagaaauc 48156 .................................._>>>>>>>>>,,,,,,,,,.,,,,,, 169 ..................................uuaucuaagaUgAAGAUAU.AGUCcA 193 UU U:UAA:A AAGAUAU A UC+ 48157 aucauuuaauaggucuuuuuuuaaauuugagaagUUUUUUAAAAAAAAGAUAUaACUCU- 48215 ,,,,,<<<<<____>>>>>:: 194 AauccuuauuGAAAaauaaga 214 A+ CUU:U:GAAA:A:AA+ 48216 AUAACUUUUAGAAAUAAAAUU 48236 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #596,emb|8254630| 260511 bp 2 contigs ----isReversed: 1 ----hitSequence: AUUUAUUGUUAUACUUAAAAUUAUUAUUUUAUCUAUUCCUAGAUUUUUACAGUUCAUUUUAACAUUUUUAAUAGCUUUUAUUUAAAUAUUGUAAUAACCAAUCGUAUAUUUUUAUAUCGACCGAAUUGUGCUUUUAUCUUGAUUAUCACAUCAACUAAAAAUUAGUUUAGAGGAAGUAAGAAAGAUAUUUUAUAUUUAAUAAAUAAAAACAAUUAAUGCUAACAAAAAUAAUUAGCAUAAUAGUUUAAAUUUAACUUUAAUUUAUAUUUAUAAUUUUAUUUAUAUUGUUUUAAAAAAGGUGUAUUUAUUUUGUAAUUUAAGUAAUAUAAUUGUAAAUAAAGAACUAAAAUAUAAACAAUAUCUAUGUUCUCAUCAAAAUAAAUUUAAGAUAGAGUCUAAAUAAUUUGAAUAAAAUUA ----ssRNAplot: ....(((((((((.....)))))))))...((..........................)).(((((.((...????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????)).))))).(((((((((...........?????????????????????????????????????????????????????????????????????????????)))))))))..................(((((....))))).. ----hitGC: 0.158273 ----pairStats: 32,0,1,8 hit 3 : 255974 255558 (rev) 20.39 bits ::::<<<<<<<<<_______>>>>>>>>>,,,<<........................._ 1 cuucgaaccuaaaaaauUauauugggcucaUagu.........................u 35 UU+::++:+A+A UUA+A+U+:++::+U+:U U 4538 AUUUAUUGUUAUA--CUUAAAAUUAUUAUUUUAUcuauuccuagauuuuuacaguucauU 4595 >>,,,(((((-((,,,~~~~~~~))-))))),<<<<<<<<<___________~~~~~~>> 36 uguAAaacuguCaAAU*[ 88]*cGgcagucaucuuaauaaauauaaauAua*[ 2]*ua 171 U: A: :U:U: AAU : :A: : ::UUA: :+ U+U+AA A+A +: 4596 UU--AACAUUUUUAAU*[196]*UAUAAUUUUAUUUAUAUUGUUUUAAAAAA*[77]*AA 4913 >>>>>>>,,,,,,,,,,,,,,,,,,,,<<<<<____>>>>>:: 172 ucuaagaUgAAGAUAUAGUCcAAauccuuauuGAAAaauaaga 214 :UAA::U+AAGAUA AGUC+ AA +: :UUGAA AA: :+A 4914 AAUAAAUUUAAGAUAGAGUCU-AA-AUAAUUUGAAUAAAAUUA 4954 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #659,emb|8254645| 1076301 bp 3 contigs ----isReversed: 1 ----hitSequence: UUAUAGAAAUUAAAAUUUACCAGAUUUAAUUUUCGAAAUAUUAGUAACUAGGAUAAAUGAGUUUACAGAUAAUAUAAAUUCUUUUUAAGUCUGGCAAUCAAACAUUAAUAUCAAACAAAUAAAUGAUACACUCAAAAUUAUUUAAUAACAAAAAAUUUAAGGUUAUUAUGAAUUCUUUAAAUGUUAAAAAUAGAGUAAUUUACUAAAUUCUUUUUAAAUCUGACAUUUAAAUAUUUAAAUAAAUGAUAUACUCAAAAUUAUUUAAAAAUUAAAAA ----ssRNAplot: ....(((((((((...)))))))))...(((((.((...???????????????????????????????????????????????????????????????????????????????????????....)).))))).(((((((((???????????????????????????????????????????????????????????????????????????????????)))))))))...................(((((....))))).. ----hitGC: 0.16 ----pairStats: 32,2,1,10 hit 4 : 802293 802019 (rev) 20.47 bits ::::<<<<<<<<<_______>>>>>>>>>,,,<<_>>,,,(((((-((,,,~~~~~~,,, 1 cuucgaaccuaaaaaauUauauugggcucaUaguuuguAAaacuguCaAAU*[84]*UAa 138 +U++:: :::+A+ +AU+U+::: ::+U A:::U: AAAU UA 274009 UUAUAGAAAUUAA----AAUUUACCAGAUUU--------AAUUUUCGAAAU*[87]*UAC 274137 ,))-))))),<<<<<<<<<~~~~~~>>>>>>>>>,,,,,,,,,,,,,,,,,,,,<<<<<_ 139 AcGgcagucaucuuaauaa*[13]*uaucuaagaUgAAGAUAUAGUCcAAauccuuauuG 204 AC +:A::: ::UUA:UAA UAU:UAA:: A GAUAUA UC AAA ++ U: : 274138 ACUCAAAAUUAUUUAAUAA*[83]*UAUUUAAAUAAAUGAUAUACUCAAAA-UUAUUUAA 274273 ___>>>>>:: 205 AAAaauaaga 214 AAA: :A +A 274274 AAAUUAAAAA 274283 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #680,emb|8254652| 611172 bp 7 contigs ----isReversed: 1 ----hitSequence: UUACAUGAUUAUUACAAUAGUUAAUAGUUCAAAUCCUUAAAAUAAAAUUCCUAGAUUUAAAUUAUGACAGAAGAAAACUAAAUUGAAGAAAGAAAGAAAAUUAUAAAAGAUGCAACAUACUCUGGUGCAAUCACUUUACUGACCAAAAUUUUUGGUAGAGGUAUAGAUUUCUAAGUUAAUGAUACUAUUAUAUUUUAAAAUUAUGGAGUUCAUGUUAUUCAAACUUUCUUUUCUGAAGAUAAGUCUGAAGAGACCUAGAUAAAAGGAA ----ssRNAplot: ....(((((((((.....))))))))).....(((((.((...?????????????????????????????????......)).))))).(((((((((.......?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????)))))))))...................(((((....))))).. ----hitGC: 0.25 ----pairStats: 32,2,3,9 hit 5 : 14879 14612 (rev) 20.08 bits ::::<<<<<<<<<_______>>>>>>>>>,,,<<_>>,,,(((((-((,,,~~~~~~,,, 1 cuucgaaccuaaaaaauUauauugggcucaUaguuuguAAaacuguCaAAU*[82]*ACU 136 +U+C:::::+A+: A +AU:+U+:::::+U AA+:C :U::AAU ACU 596294 UUACAUGAUUAUU--ACAAUAGUUAAUAGUUC------AAAUCCUUAAAAU*[33]*ACU 596372 ,,,))-))))),<<<<<<<<<_______~~~~~~~>>>>>>>>>,,,,,,,,,,,,,,,, 137 AaAcGgcagucaucuuaauaaauauaaa*[ 6]*uaucuaagaUgAAGAUAUAGUCcAA 194 AAA::G: G:+A:::::A:+A+UAUAAA U+:C:::::UGAAGAUA AGUC++A 596373 AAAUUGAAGAAAGAAAGAAAAUUAUAAA*[117]*UUUCUUUUCUGAAGAUA-AGUCUGA 596541 ,,,,<<<<<____>>>>>:: 195 auccuuauuGAAAaauaaga 214 A ::U+GA A+A:: +A 596542 AGAGACCUAGAUAAAAGGAA 596561 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #840,emb|8253883| 2060 bp 1 contigs ----isReversed: 1 ----hitSequence: UAAAAAGGGUGAUACAAAAAUUUUUUACAGUAUAUUCAUUUUUUAAAAAUAAAAAAAAGUGUUUAAAAUAACCAAAAUAUUUAAUUCAAAUUUUCAGCACUAAAAAUACACCAUAAAACCUCGCAUAAAUUAAUGACUUUUAAUUUUCUUAAGACAUAAUCUAAAUUUUUUUAAAAAAAAAGA ----ssRNAplot: ....(((((((((....................)))))))))...((......))..(((((.((...()((...((((.....))))...))...........)).))))).(((((((((.................)))))))))...................(((((....))))).. ----hitGC: 0.174863 ----pairStats: 39,0,3,15 hit 6 : 960 778 (rev) 25.82 bits ::::<<<<<<<<<__............._____>>>>>>>>>,,,<<....._>>,,,(( 1 cuucgaaccuaaaaa.............auUauauugggcucaUagu.....uuguAAaa 42 + + :A:+ ::A:A A UAU:U:: +:U:+UA:: :: AAA: 1101 UAAAAAGGGUGAUACaaaaauuuuuuacAGUAUAUUCAUUUUUUAAAaauaaAAA-AAAG 1159 (((-((,,,<~~~~~~><<---<<<<----~~~~~~->>>>--->>,,,,,,,,,,,,)) 43 cuguCaAAUU*[32]*AgccAAgucaauag*[19]*auguaAAaguuCAgAGACUAaAcG 141 :::U: AA U A: CAA: :A+U++ AU: :AA :UCAG+ ACUAAA : 1160 UGUUUAAAAU*[ 0]*AACCAAAAUAUUUA*[ 0]*AUUCAAAUUUUCAGC-ACUAAAAA 1206 -))))),<<<<<<<<<___________....._>>>>>>>>>,,,,,,,,,,,,,,,,,, 142 gcagucaucuuaauaaauauaaauAua.....uuaucuaagaUgAAGAUAUAGUCcAAau 196 ::::CA :::A ::: AUAAAU +A U::: U::: U+AAGA AUA UC+AAA 1207 UACACCAUAAAACCUCGCAUAAAUUAAugacuUUUAAUUUUCUUAAGACAUAAUCUAAA- 1265 ,,<<<<<____>>>>>:: 197 ccuuauuGAAAaauaaga 214 ++UU:UU AAAAA:AAGA 1266 UUUUUUUAAAAAAAAAGA 1283 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #895,emb|8254697| 1227316 bp 10 contigs ----isReversed: 0 ----hitSequence: GUAUCUAUUUAAAAAUAUCAAUUUCAUAAAUAUUAUUUGAAUGAAUUAUUUACUUAUUUAAAAUGAAUUCAAGUUAGCAAAUCAAUUUGUUAGCUGACUGAAAUCAAUCAAUCAUUCAUUCAUUCAAUCAAUCAAUCAAUCACAAAUGCAUGAGCAGUUAUAAAAUAUAUAAUUUUUUGAUUAUGUAUUUGAAAGGGCAUAAAUAAUAUAACAAUAAUAAUUAAAAGUUAUUGGAUAGUUACCAAAUUCAAAGCGAGAAUAUCAAUACAAAAUUUAAAGUAGUAAAUAAUAUUUUCAAAGAAGAUGGGUGAUAUUGUAAAUAAAUUAAUUAUAAAAAAUAUAAAAUGAAGAUAUAGUAAUUUGGAUUAAAAAUAAUUUU ----ssRNAplot: ....(((((((((......................)))))))))...(()).(((((.((...(((?????????????????????????????????????)))((...((((....(((?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????)))...))))...))..........)).))))).(((((((((..............)))))))))..................(((((....))))).. ----hitGC: 0.189974 ----pairStats: 44,0,7,9 hit 7 : 1124478 1124856 (fwd) 21.62 bits ::::<<<<<<<<<__..............._____>>>>>>>>>,,,<<_>>,,,((((( 1 cuucgaaccuaaaaa...............auUauauugggcucaUaguuuguAAaacug 45 U++:+:::UAA+AA ++U ++UUG:::+:AU+:U U: A ::: 1124478 GUAUCUAUUUAAAAAuaucaauuucauaaaUAUUAUUUGAAUGAAUUAU-UU--ACUUAU 1124534 -((,,,<<<~~~~~~>>><<---<<<<----<<<~~~~~~~>>>--->>>>--->>,,,, 46 uCaAAUUgC*[28]*GcAgccAAgucaauaguau*[ 11]*aaaagauguaAAaguuCAg 131 U::AA UG: :CA::CAA:::++ A++:: ::+++A+::: A ::UCA+ 1124535 UUAAAAUGA*[37]*UCAAUCAAUCAUUCAUUCA*[157]*UAGUAAAUAAUAUUUUCAA 1124775 ,,,,,,,,))-))))),<<<<<<<<<___________.._>>>>>>>>>,,,,,,,,,,, 132 AGACUAaAcGgcagucaucuuaauaaauauaaauAua..uuaucuaagaUgAAGAUAUAG 189 AGA A A::G ::: AU: UA :: A +UAA UAUA + :: UA :AUGAAGAUAUAG 1124776 AGA--AGAUGGGUGAUAUUGUAAAUAAAUUAAUUAUAaaAAAUAUAAAAUGAAGAUAUAG 1124833 ,,,,,,,,,<<<<<____>>>>>:: 190 UCcAAauccuuauuGAAAaauaaga 214 U AA+U+ :::U: AAA:A:::+ 1124834 U--AAUUUGGAUUAAAAAUAAUUUU 1124856 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #1015,emb|8255697| 1084 bp 1 contigs ----isReversed: 0 ----hitSequence: UUACAUGAUUAUUACAAUAGUUAAUAGUUCAAAUCCUUAAAAUAAAAUUCCUAGAUUUAAAUUAUGACAGAAGAAAACUAAAUUGAAGAAAGAAAGAAAAUUAUAAAAGAUGCAACAUACUCUGGUGCAAUCACUUUACUGACCAAAAUUUUUGGUAGAGGUAUAGAUUUCUAAGUUAAUGAUACUAUUAUAUUUUAAAAUUAUGGAGUUCAUGUUAUUCAAACUUUCUUUUCUGAAGAUAAGUCUGAAGAGACCUAGAUAAAAGGAA ----ssRNAplot: ....(((((((((.....))))))))).....(((((.((...?????????????????????????????????......)).))))).(((((((((.......?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????)))))))))...................(((((....))))).. ----hitGC: 0.25 ----pairStats: 32,2,3,9 hit 8 : 539 806 (fwd) 20.08 bits ::::<<<<<<<<<_______>>>>>>>>>,,,<<_>>,,,(((((-((,,,~~~~~~,,, 1 cuucgaaccuaaaaaauUauauugggcucaUaguuuguAAaacuguCaAAU*[82]*ACU 136 +U+C:::::+A+: A +AU:+U+:::::+U AA+:C :U::AAU ACU 539 UUACAUGAUUAUU--ACAAUAGUUAAUAGUUC------AAAUCCUUAAAAU*[33]*ACU 617 ,,,))-))))),<<<<<<<<<_______~~~~~~~>>>>>>>>>,,,,,,,,,,,,,,,, 137 AaAcGgcagucaucuuaauaaauauaaa*[ 6]*uaucuaagaUgAAGAUAUAGUCcAA 194 AAA::G: G:+A:::::A:+A+UAUAAA U+:C:::::UGAAGAUA AGUC++A 618 AAAUUGAAGAAAGAAAGAAAAUUAUAAA*[117]*UUUCUUUUCUGAAGAUA-AGUCUGA 786 ,,,,<<<<<____>>>>>:: 195 auccuuauuGAAAaauaaga 214 A ::U+GA A+A:: +A 787 AGAGACCUAGAUAAAAGGAA 806 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #1416,emb|8254545| 1045189 bp 3 contigs ----isReversed: 1 ----hitSequence: UUUUCAAAUUUAUAUAGAUAGUACUUAUAAAAAUAAAGUUAAUCAAUUUUUAAGAUGUAAAAUAUCUAUCUAUCUUAUCUUUUGCGUUUCACACUUGCUAGUUUUUUGAAAUGCUUUAAAAAUCUAGAAGUUUUUGUUUUAAUUUCUAAAAAAUAAAUGCUAUAAUAAAUAUUUAAUCUAUUUUAGCUAAAAAAAUCUAAUUGUAAAAUGAAAAUUAUUUUGAAAAAACAUUUUAAUUUUUAAUUCAAUCAAAUUUAUUUUUAAGAUAUAUUGCAAAAUUUUGUGAAAAUAAAAU ----ssRNAplot: ....(((((((((....)))))))))...((...)).(((((.((...?????????????????????????????????????????????????????????????????????????????????????????????????????????....)).))))).(((((((((........????????????????????????????????????????????????????????????????????)))))))))...................(((((....))))).. ----hitGC: 0.155932 ----pairStats: 32,0,2,12 hit 9 : 208601 208307 (rev) 20.52 bits ::::<<<<<<<<<_______>>>>>>>>>,,,<<.._>>,,,(((((-((,,,~~~~~~~ 1 cuucgaaccuaaaaaauUauauugggcucaUagu..uuguAAaacuguCaAAU*[ 84]* 51 +UU+:AA: U+A:A UA :U+G :CU:AUA:: U:: A:: :UC:A U 836589 UUUUCAAAUUUAUA---UAGAUAGUACUUAUAAAaaUAA--AGUUAAUCAAUU*[105]* 836636 ,,,,))-))))),<<<<<<<<<________~~~~~~>>>>>>>>>,,,,,,,,,,,,,,, 136 UAaAcGgcagucaucuuaauaaauauaaau*[ 5]*uaucuaagaUgAAGAUAUAGUCcA 193 UAAA:G+: :: :::UA:U: AU UA+ U :U:UA:::U+AAGAUAUA U CA 836742 UAAAUGCUAUAAUAAAUAUUUAAUCUAUUU*[68]*AAUUUAUUUUUAAGAUAUAUUGCA 836863 ,,,,,<<<<<____>>>>>:: 194 AauccuuauuGAAAaauaaga 214 AA +UU: UGAAAA :AA+ 836864 AA-AUUUUGUGAAAAUAAAAU 836883 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #1483,emb|8254564| 889818 bp 4 contigs ----isReversed: 0 ----hitSequence: AAUUUUUAUUAAAUAAAUUUCCAUAAAAAAUAAAUCACAUUUAAUAUAAUGAAGCUUAACUGUAUUAUGAUUAGUAUUUUUCUUUUUUCUUUGGCUAUAUCUUUUUAUAAUUUGAAGACUAAAGAUAUUUUAUUUUUAUUUCAUUAACUCGUCACUUAAUUGAAAUUUGUGUCUAUAAUCAAAAGAUACAUUGUUAACAUAUCUUUUUUCCCUUACUCCUAAUUAUUAAGUUAAAAAUAUUAAUCAAUUUUUUACCUCUAAAUGCUCUAACUUUUGCCAAAUAAAAGCAAUAAAAAAUUAUUAUUUAGAAUGCUUAUAUCAGUAAUUCUAUUUAGAAUAUCAUUUAUUUUAUUAAUGGAGAUUAUUAUUUUAAUUGCGAAAUAGUAUGUGUUUCUUAUUCAGUAAUAAAUUUCAAAUAGAGUGAAUAUGAUAAAUUAUAAAAAUAAAAAUUUAGUCCAUUAUUUUAGAAAUAGAAAA ----ssRNAplot: ....(((((((((....)))))))))....(((((.((...?????????????????????????????????????????????????????????????????????????.........)).))))).(((((((((?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????)))))))))..................(((((....))))).. ----hitGC: 0.18239 ----pairStats: 32,2,1,8 hit 10 : 54318 54794 (fwd) 20.01 bits ::::<<<<<<<<<_______>>>>>>>>>,,,<<_>>,,,(((((-((,,,~~~~~~,,, 1 cuucgaaccuaaaaaauUauauugggcucaUaguuuguAAaacuguCaAAU*[79]*gAG 133 U+ :+:::AA+ U+A++UU:::+: A+ AA:A::: : A U +AG 54318 AAUUUUUAUUAAA---UAAAUUUCCAUAAAA-------AAUAAAUCACAUU*[73]*AAG 54434 ,,,,,,))-))))),<<<<<<<<<~~~~~~~>>>>>>>>>,,,,,,,,,,,,,,,,,,,, 134 ACUAaAcGgcagucaucuuaauaa*[ 13]*uaucuaagaUgAAGAUAUAGUCcAAaucc 198 ACUAAA : :::U:AU:UU::+:: ::+::AA:AU AA AU UAGUCC A+ + 54435 ACUAAAGAUAUUUUAUUUUUAUUU*[293]*UUAUAAAAAUAAAAAUUUAGUCC-AU-UA 54778 <<<<<____>>>>>:: 199 uuauuGAAAaauaaga 214 UU U:GAAA:A AA+A 54779 UUUUAGAAAUAGAAAA 54794 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #1608,emb|8254734| 33779 bp 1 contigs ----isReversed: 1 ----hitSequence: AUUUAAUCAUUUUAAUAUUAGGUGAUUUUGGAUUAUCUACUUAACUUGAAAAAAAUUGUGAAUAAAUUGAAAUUUUAGAUGUAAGUCAUUUUAGUUAAUAUACAAUUAUCAAGAAGUUUUAAUAUAUUUUUAGAUGGUAGGAAAUUGGGCGUACAUGGCACCUGAAAUUUUAACUAAAAAUAAUGAUUAAAAUAAGAUAUACUCUAAAAAAGUAAUUAUUAUUAUAA ----ssRNAplot: ....(((((((((.....)))))))))...((................))..(((((.((...????????????....)).))))).(((((((((.....?????????????????????????????????????????????????????????????????????????????????)))))))))...................(((((....))))).. ----hitGC: 0.198238 ----pairStats: 32,0,7,5 hit 11 : 12369 12143 (rev) 21.41 bits ::::<<<<<<<<<_______>>>>>>>>>,,,<<..............._>>,,,((((( 1 cuucgaaccuaaaaaauUauauugggcucaUagu...............uuguAAaacug 45 UU+:A+C:U++ A+UAU ++G:G+U:+U :: :: AAAA U: 21411 AUUUAAUCAUUUU--AAUAUUAGGUGAUUUUGGAuuaucuacuuaacuuGAA-AAAAAUU 21467 -((,,,~~~~~~,,,,))-))))),<<<<<<<<<_____~~~~~~>>>>>>>>>,,,,,, 46 uCaAAU*[84]*UAaAcGgcagucaucuuaauaaauaua*[ 8]*uaucuaagaUgAAGA 184 +::AAU UA A:: :A UCAU:UUA +:AAUAUA U:+ UAA:AU AAGA 21468 GUGAAU*[12]*UAGAUGUAAGUCAUUUUAGUUAAUAUA*[81]*UGAUUAAAAU-AAGA 21607 ,,,,,,,,,,,,,,<<<<<____>>>>>:: 185 UAUAGUCcAAauccuuauuGAAAaauaaga 214 UAUA UC+AAA :UA:U A A:UA:+A 21608 UAUACUCUAAAAAAGUAAUUAUUAUUAUAA 21637 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #1641,emb|8254598| 267927 bp 4 contigs ----isReversed: 0 ----hitSequence: AUUCAUUGUUUUAAUAUUAUUCAUAGAGAUAUUAAACCUGACAAUUUUUUGGUUUGUUUGGAUGGCAAUCAACUUGAAAUCAAACUAUGUAAUUUAUCCUGAUAUUUUUUAAUUUUUAAAAACAAUUUAAUCAUUUUAAUAUUAGGCGAUUUUGGAUUAUCAGCUUAACUUGAAUAAAAUUGUGAAUAAAUUGAAACUUUAGAUGUAAGUCAUUUUAGUUAAUAUACAAUUAAUUAUCAAGAAAUUUUAAUAUAUUUUUAGAUGGUAGGAAAUUGGGCGUACAUGGCACCUGAAAUUUUAGCUAAAAAUGAUGAUUAAAAUAAGAUAUACUCUAAAAAAGUAACUAUUGUUAUAA ----ssRNAplot: ....(((((((((...........)))))))))..(((((.((...?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????....)).))))).(((((((((.....?????????????????????????????????????????????????????????????????????????????????????)))))))))...................(((((....))))).. ----hitGC: 0.219718 ----pairStats: 32,2,6,5 hit 12 : 16472 16826 (fwd) 20.10 bits ::::<<<<<<<<<__...._____>>>>>>>>>,,,<<_>>,,,(((((-((,,,~~~~~ 1 cuucgaaccuaaaaa....auUauauugggcucaUaguuuguAAaacuguCaAAU*[ 84 51 UUC: ++:U++AA+ +U AUA++G:++ : AAA CU C:A U 16472 AUUCAUUGUUUUAAUauuaUUCAUAGAGAUAUU---------AAACCUGACAAUU*[153 16517 ~~,,,,))-))))),<<<<<<<<<_____~~~~~~>>>>>>>>>,,,,,,,,,,,,,,,, 136 ]*UAaAcGgcagucaucuuaauaaauaua*[ 8]*uaucuaagaUgAAGAUAUAGUCcAA 194 UA A:G AG CAU:UUA +:AAUAUA U:+ UAA:AU AAGAUAUA UC+AA 16671 ]*UAGAUGUAAGUCAUUUUAGUUAAUAUA*[85]*UGAUUAAAAU-AAGAUAUACUCUAA 16806 ,,,,<<<<<____>>>>>:: 195 auccuuauuGAAAaauaaga 214 A :UA:: A ::UA:+A 16807 AAAAGUAACUAUUGUUAUAA 16826 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #1743,emb|8254766| 42306 bp 2 contigs ----isReversed: 1 ----hitSequence: AUUUAAUCAUUUUAAUAUUAGGUGAUUUUGGAUUAUCUACUUAACUUGAAAAAAAUUGUGAAUAAAUUGAAAUUUUAGAUGUAAGUCAUUUUAGUUAAUAUACAAUUAUCAAGAAGUUUUAAUAUAUUUUUAGAUGGUAGGAAAUUGGGCGUACAUGGCACCUGAAAUUUUAACUAAAAAUAAUGAUUAAAAUAAGAUAUACUCUAAAAAAGUAAUUAUUAUUAUAA ----ssRNAplot: ....(((((((((.....)))))))))...((................))..(((((.((...????????????....)).))))).(((((((((.....?????????????????????????????????????????????????????????????????????????????????)))))))))...................(((((....))))).. ----hitGC: 0.198238 ----pairStats: 32,0,7,5 hit 13 : 3553 3327 (rev) 21.41 bits ::::<<<<<<<<<_______>>>>>>>>>,,,<<..............._>>,,,((((( 1 cuucgaaccuaaaaaauUauauugggcucaUagu...............uuguAAaacug 45 UU+:A+C:U++ A+UAU ++G:G+U:+U :: :: AAAA U: 38754 AUUUAAUCAUUUU--AAUAUUAGGUGAUUUUGGAuuaucuacuuaacuuGAA-AAAAAUU 38810 -((,,,~~~~~~,,,,))-))))),<<<<<<<<<_____~~~~~~>>>>>>>>>,,,,,, 46 uCaAAU*[84]*UAaAcGgcagucaucuuaauaaauaua*[ 8]*uaucuaagaUgAAGA 184 +::AAU UA A:: :A UCAU:UUA +:AAUAUA U:+ UAA:AU AAGA 38811 GUGAAU*[12]*UAGAUGUAAGUCAUUUUAGUUAAUAUA*[81]*UGAUUAAAAU-AAGA 38950 ,,,,,,,,,,,,,,<<<<<____>>>>>:: 185 UAUAGUCcAAauccuuauuGAAAaauaaga 214 UAUA UC+AAA :UA:U A A:UA:+A 38951 UAUACUCUAAAAAAGUAAUUAUUAUUAUAA 38980 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #1972,emb|rRNA-8234198| 9027 bp 1 contigs ----isReversed: 0 ----hitSequence: CUUUAAACCAAUAGAUUGCAUCGGUUUAAAAGGCAAGACCGUCAAAUUGCGGGAAAGGGGUCAACAGCCGUUCAGUACCAAGUCUCAGGGGAAACUUUGAGAUGGCCUUGCAAAGGGUAUGGUAAUAAGCUGACGGACAUGGUCCUAACCACGCAGCCAAGUCCUAAGUCAACAGAUCUUCUGUUGAUAUGGAUGCAGUUCACAGACUAAAUGUCGGUCGGGGAAGAUGUAUUCUUCUCAUAAGAUAUAGUCGGACCUCUCCUUAAUGGGAGCU ----ssRNAplot: ....(((((((((.....)))))))))...((.)).(((((.((...((((((...((((??????????????????????????????????????????????????????????????????????????????????))))..)).))))((...((((....(((((.........)))))...))))...))............)).))))).(((((((((.)))))))))...................(((((....))))).. ----hitGC: 0.456204 ----pairStats: 53,0,6,5 hit 14 : 5708 5981 (fwd) 53.75 bits ::::<<<<<<<<<_______>>>>>>>>>,,,<<_>>,,,(((((-((,,,<<<<<<--- 1 cuucgaaccuaaaaaauUauauugggcucaUaguuuguAAaacuguCaAAUUgCgggAAA 60 CUU+:A:CC:A+ +U +U:GG:U:A+A:: :: A:AC:GUC:AAUUGCGG:AAA 5708 CUUUAAACCAAUA--GAUUGCAUCGGUUUAAAAGGCA--AGACCGUCAAAUUGCGGGAAA 5763 <<<<~~~~~~>>>>-->>.>>>><<---<<<<----<<<<<_______..>>>>>--->> 61 ccCc*[ 9]*gGgcAAuc.cGcAgccAAgucaauaguauuaaAaAcag..gaaaaagaug 120 ::+: :+::AA:C CGCAGCCAA++C:++AGU::+:A A C :+::A+++:G 5764 GGGG*[82]*UCCUAACCaCGCAGCCAAGUCCUAAGUCAACAGAUCUUcuGUUGAUAUGG 5899 >>--->>,,,,,,,,,,,,))-))))),<<<<<<<<<____________>>>>>>>>>,, 121 uaAAaguuCAgAGACUAaAcGgcagucaucuuaauaaauauaaauAuauuaucuaagaUg 180 ++ AGUUCA AGACUAAA:G C:GU:+: ::A::::+ ::::U:: : + 5900 AUGCAGUUCACAGACUAAAUGUCGGUCGGGGAAGAUGU-----------AUUCUUCUCAU 5948 ,,,,,,,,,,,,,,,,,,<<<<<____>>>>>:: 181 AAGAUAUAGUCcAAauccuuauuGAAAaauaaga 214 AAGAUAUAGUC +A+C+:U:: AA ::A: 5949 AAGAUAUAGUCG-GACCUCUCCUUAAUGGGAGCU 5981 ----endhit Found 15 hits. done 2.08166e+08 nucs (frac lets thru so far=0.0100032903, 2d-fracLetsThru=0.0051464). Filter report: done 2.08166e+08 nucs (frac lets thru so far=0.0100032903, 2d-fracLetsThru=0.0051464). FULL: done 2.08166e+08 nucs (frac lets thru so far=0.0100032903, 2d-fracLetsThru=0.0051464). CPU time: 65742.25u 58.75s 18:16:41.00 Elapsed: 18:16:49 DONEdoneDONEdone