Params: release/cmzasha --no-stderr --filter 220 20 /home/kasiaw/Rfam_7.0/CM/RF00004.cm /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta 1 specfile /home/kasiaw/results/Tetrahymena_thermophila.fasta/RF00004_U2/RF00004_at20.filterspec Build: release Host: node007 pid: 26882 ---time: Mon Jul 4 05:26:56 2005 ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----specfile: hmm /home/kasiaw/Rfam_7.0_filters/RF00004_Saureus_expanded.hmm 2struct-str /home/kasiaw/Rfam_7.0_filters/RF00004_Saureus_expanded.hmm 1/remember-nuc,26,r-CU-A-G-_,25,r-ACGU-_,60,r-AGU-C-_,59,r-ACG_-U,78,l-AGU-C-_,77,r-CGU-A-_,130,l-ACGU-_,129,r-ACGU-_,128,l-ACGU-_,152,r-ACGU-_,151,r-ACU-G_ 2struct-str /home/kasiaw/Rfam_7.0_filters/RF00004_Saureus_expanded.hmm 1/sub,24,42/sub,75,48 ----hmm-from-cmFileName: /home/kasiaw/Rfam_7.0/CM/RF00004.cm ----hmm-build-info: ;(default construction of HMM) Params: release/cmzasha --create-rigorous-filter 220 20 /home/kasiaw/Rfam_7.0/CM/RF00004.cm /home/kasiaw/Rfam_7.0_filters data/default.filtercreationspec Build: release Host: cs002 pid: 20539 ;Params: release/cmzasha --create-rigorous-filter 220 20 /home/kasiaw/Rfam_7.0/CM/RF00004.cm /home/kasiaw/Rfam_7.0_filters data/default.filtercreationspec Build: release Host: cs002 pid: 20539 ----2struct-info: only-hmm Exploded HMM has 1675 states ----hmm-from-cmFileName: /home/kasiaw/Rfam_7.0/CM/RF00004.cm ----hmm-build-info: ;(default construction of HMM) Params: release/cmzasha --create-rigorous-filter 220 20 /home/kasiaw/Rfam_7.0/CM/RF00004.cm /home/kasiaw/Rfam_7.0_filters data/default.filtercreationspec Build: release Host: cs002 pid: 20539 ;Params: release/cmzasha --create-rigorous-filter 220 20 /home/kasiaw/Rfam_7.0/CM/RF00004.cm /home/kasiaw/Rfam_7.0_filters data/default.filtercreationspec Build: release Host: cs002 pid: 20539 ----2struct-info: 1/remember-nuc,26,r-CU-A-G-_/remember-nuc,25,r-ACGU-_/remember-nuc,60,r-AGU-C-_/remember-nuc,59,r-ACG_-U/remember-nuc,78,l-AGU-C-_/remember-nuc,77,r-CGU-A-_/remember-nuc,130,l-ACGU-_/remember-nuc,129,r-ACGU-_/remember-nuc,128,l-ACGU-_/remember-nuc,152,r-ACGU-_/remember-nuc,151,r-ACU-G_ ----hmm-from-cmFileName: /home/kasiaw/Rfam_7.0/CM/RF00004.cm ----hmm-build-info: ;(default construction of HMM) Params: release/cmzasha --create-rigorous-filter 220 20 /home/kasiaw/Rfam_7.0/CM/RF00004.cm /home/kasiaw/Rfam_7.0_filters data/default.filtercreationspec Build: release Host: cs002 pid: 20539 ;Params: release/cmzasha --create-rigorous-filter 220 20 /home/kasiaw/Rfam_7.0/CM/RF00004.cm /home/kasiaw/Rfam_7.0_filters data/default.filtercreationspec Build: release Host: cs002 pid: 20539 ----2struct-info: 1/sub,24,42/sub,75,48 ----cmFile: /home/kasiaw/Rfam_7.0/CM/RF00004.cm (global) ----CM-scanning-logic: Infernal-0.55 ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #815,emb|8254824| 137162 bp 2 contigs ----isReversed: 1 ----hitSequence: AUACCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGUGUGAAAACUGAUACUGUCCCUACUGGGACAUGUGGUUUCACAUUAAUUUUUCAAGGGGUCGGAUAUAUUAGUGGCUUGCCACUGGUCCCGACGCGGUUGCCCUUAGCAUGCACGUAACUAAGGAGUGGCUAACCCUA ----ssRNAplot: ......(((.((((....)))).)))....................((((((........)))))).(((((((..)))))))...........................((((((((.....(((((..)))))..))))))))..((((((((((((...........)))))).))))))....... ----hitGC: 0.457895 ----pairStats: 45,0,5,4 hit 0 : 48695 48506 (rev) 174.56 bits ::::::<<<-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,<<<<<<________ 1 AUACCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGUUUAAUAU 60 AUACCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGU+U A A 88468 AUACCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGUGUGAAAA 88527 >>>>>>,<<<<<<<___>>>>>>>,,.,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<< 61 CUGAUAUgugcccCAUuGgggcacAa.GAuAUUAAaUUuAUUUUUgAAggGgGggggggc 119 CUGAUA+:::CCC:A :GGG:::+ G+U U A AUU+AUUUUU AAGGG G::GG::: 88528 CUGAUACUGUCCCUAC-UGGGACAUGuGGUUUCACAUUAAUUUUUCAAGGG-GUCGGAUA 88585 ----.<<<<<__>>>>>-.>>>>>>>>,,<<<<<<-<<<<<<__________.>>>>>>- 120 Auca.guaGCUUGCuacu.gccccccCACGggUcgcCcuGgggUUGCACUAC.ucCagGG 176 + ++ GU:GCUUGC:ACU :::CC::C+C G:U : CCU::+ UGCAC + +::AGG 88586 UAUUaGUGGCUUGCCACUgGUCCCGACGCGGUUGC-CCUUAGCAUGCACGUAaCUAAGG- 88643 -->>>>>>::::::: 177 CcugGccCACCCCuc 191 : G:C A CCCU 88644 -AGUGGCUAACCCUA 88657 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #815,emb|8254824| 137162 bp 2 contigs ----isReversed: 1 ----hitSequence: AUACCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGUGUGAAAACUGAUACUGUCCCUACUGGGACAUGUGGUUUCACAUUAAUUUUUCAAGGGGUCGGACAAACUAGUGGCUUGCCACUGGUCCCGACGCUGUUGCCCUUAGCAUGCACGUAACUAAGGAGUGGCUAACCCUA ----ssRNAplot: ......(((.((((....)))).)))....................((((((........)))))).(((((((..)))))))...........................((((((((.....(((((..))))).)).))))))..((((((((((((...........)))))).))))))....... ----hitGC: 0.463158 ----pairStats: 45,0,4,4 hit 1 : 48092 47903 (rev) 173.96 bits ::::::<<<-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,<<<<<<________ 1 AUACCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGUUUAAUAU 60 AUACCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGU+U A A 89071 AUACCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGUGUGAAAA 89130 >>>>>>,<<<<<<<___>>>>>>>,,.,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<< 61 CUGAUAUgugcccCAUuGgggcacAa.GAuAUUAAaUUuAUUUUUgAAggGgGggggggc 119 CUGAUA+:::CCC:A :GGG:::+ G+U U A AUU+AUUUUU AAGGG G::GG::: 89131 CUGAUACUGUCCCUAC-UGGGACAUGuGGUUUCACAUUAAUUUUUCAAGGG-GUCGGACA 89188 ----.<<<<<__>>>>>->>.>>>>>>,,<<<<<<-<<<<<<__________.>>>>>>- 120 Auca.guaGCUUGCuacugc.cccccCACGggUcgcCcuGgggUUGCACUAC.ucCagGG 176 A C+ GU:GCUUGC:ACU:: :CC::C+C:G:U : CCU::+ UGCAC + +::AGG 89189 AACUaGUGGCUUGCCACUGGuCCCGACGCUGUUGC-CCUUAGCAUGCACGUAaCUAAGG- 89246 -->>>>>>::::::: 177 CcugGccCACCCCuc 191 : G:C:A CCCU 89247 -AGUGGCUAACCCUA 89260 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #1320,emb|8254377| 298147 bp 1 contigs ----isReversed: 0 ----hitSequence: AUACCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGUGUGAAAACUGAUACUGUCCCUACUAGGGACAUGUGGUUUCACAUUAAUUUUUCACAGGGGUCGGAUUUACUAGUGGCUUGCCCUAGUCCCGACGCGGUUGCCCUUGGCAUGCACGCUACUAAGGAGCGGCUACCCCUG ----ssRNAplot: ......(((.((((....)))).)))....................((((((........)))))).(((((((...)))))))............................((((((((.....(((((..))))).))))))))..((((((((((((...........)))))).))))))....... ----hitGC: 0.486911 ----pairStats: 45,0,7,3 hit 2 : 199075 199265 (fwd) 165.63 bits ::::::<<<-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,<<<<<<________ 1 AUACCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGUUUAAUAU 60 AUACCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGU+U A A 199075 AUACCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGUGUGAAAA 199134 >>>>>>,<<<<<<<___>>>>>>>,,.,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<< 61 CUGAUAUgugcccCAUuGgggcacAa.GAuAUUAAaUUuAUUUUUgAAggGgGggggggc 119 CUGAUA+:::CCC A U GGG:::+ G+U U A AUU+AUUUUU A GGGG::GG::: 199135 CUGAUACUGUCCCUACUAGGGACAUGuGGUUUCACAUUAAUUUUUCACAGGGGUCGGAUU 199194 ----.<<<<<__>>>>>->>>>>>>>,,<<<<<<-<<<<<<__________.>>>>>>-- 120 Auca.guaGCUUGCuacugccccccCACGggUcgcCcuGgggUUGCACUAC.ucCagGGC 177 + C+ : :GCUUGC: : :::CC::C+C G:U+: CCU:++ UGCAC ++:AGG 199195 UACUaGUGGCUUGCCCUAGUCCCGACGCGGUUGC-CCUUGGCAUGCACGCUaCUAAGG-- 199251 ->>>>>>::::::: 178 cugGccCACCCCuc 191 :+G:C ACCCCU 199252 AGCGGCUACCCCUG 199265 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #1320,emb|8254377| 298147 bp 1 contigs ----isReversed: 0 ----hitSequence: AUACCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGUGUGAAAACUGAUACUGUCCCUACUAGGGACAUGUGGUUUCACAUUAAUUUUUCACAGGGGUCGGAUUUACUAGUGGCUUGCCCUAGUCCCGACGCGGUUGCCCUUGGCCUGCACGCUACUAAGGAGCGGCUACCCCUG ----ssRNAplot: ......(((.((((....)))).)))....................((((((........)))))).(((((((...)))))))............................((((((((.....(((((..))))).))))))))..((((((((((((...........)))))).))))))....... ----hitGC: 0.492147 ----pairStats: 45,0,7,3 hit 3 : 200019 200209 (fwd) 165.16 bits ::::::<<<-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,<<<<<<________ 1 AUACCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGUUUAAUAU 60 AUACCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGU+U A A 200019 AUACCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGUGUGAAAA 200078 >>>>>>,<<<<<<<___>>>>>>>,,.,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<< 61 CUGAUAUgugcccCAUuGgggcacAa.GAuAUUAAaUUuAUUUUUgAAggGgGggggggc 119 CUGAUA+:::CCC A U GGG:::+ G+U U A AUU+AUUUUU A GGGG::GG::: 200079 CUGAUACUGUCCCUACUAGGGACAUGuGGUUUCACAUUAAUUUUUCACAGGGGUCGGAUU 200138 ----.<<<<<__>>>>>->>>>>>>>,,<<<<<<-<<<<<<__________.>>>>>>-- 120 Auca.guaGCUUGCuacugccccccCACGggUcgcCcuGgggUUGCACUAC.ucCagGGC 177 + C+ : :GCUUGC: : :::CC::C+C G:U+: CCU:++ UGCAC ++:AGG 200139 UACUaGUGGCUUGCCCUAGUCCCGACGCGGUUGC-CCUUGGCCUGCACGCUaCUAAGG-- 200195 ->>>>>>::::::: 178 cugGccCACCCCuc 191 :+G:C ACCCCU 200196 AGCGGCUACCCCUG 200209 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #1320,emb|8254377| 298147 bp 1 contigs ----isReversed: 0 ----hitSequence: GUCCUUCUCGGCGUAAAAGCUGAGAUCGAUUGUAGUAUCUGUUCUUAUCAGUGUGAAAACUGAUAGUGUCUCAUCCACAAGAGACAUUUUCACAUUAAUUUCUCUGUGGGGUUGGAUAAACUAGUGGCUAGCCCUAGUCCCAACAAAGUUGUGUUUGGUUUGCACUCUACCAAAAUUCAACUAUCCCAU ----ssRNAplot: .....(((.((((....)))).)))....................((((((........)))))).((((((........))))))........................((((((((.....(((((..))))).))))))))..((((((.((((((.........))))))..))))))....... ----hitGC: 0.407407 ----pairStats: 45,1,2,6 hit 4 : 204406 204594 (fwd) 71.62 bits ::::::<<<-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,<<<<<<________ 1 AUACCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGUUUAAUAU 60 U+ CUUCUCGGC U GCU AGAUC A UGUAGUAUCUGUUCUUAUCAGU+U A A 204406 GUC-CUUCUCGGCGUAAAAGCUGAGAUCGAUUGUAGUAUCUGUUCUUAUCAGUGUGAAAA 204464 >>>>>>,<<<<<<<___....>>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<< 61 CUGAUAUgugcccCAUu....GgggcacAaGAuAUUAAaUUuAUUUUUgAAggGgGgggg 116 CUGAUA :::C:C AU+ G:G:::+ U U A AUU+AUUU U GGGG: GG 204465 CUGAUAGUGUCUC-AUCcacaAGAGACAU---UUUCACAUUAAUUUCUCUGUGGGGUUGG 204520 <<<----.<<<<<__>>>>>->>>>>>>>,,<<<<<<-<<<<<<__________>>>>>> 117 ggcAuca.guaGCUUGCuacugccccccCACGggUcgcCcuGgggUUGCACUACucCagG 175 :::A C+ : :GCU GC: : :::CC :CA :G :+ ::UGG UUGCACU CCA:: 204521 AUAAACUaGUGGCUAGCCCUAGUCCCAACAAAGUUGUGUUUGGU-UUGCACUCUACCAAA 204579 --->>>>>>::::::: 176 GCcugGccCACCCCuc 191 + +: C:A CCC++ 204580 -AUUCAACUAUCCCAU 204594 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #1320,emb|8254377| 298147 bp 1 contigs ----isReversed: 0 ----hitSequence: GUCCUUCUCGGCGUAAAAGCUGAGAUCGAUUGUAGUAUCUGUUCUUAUCAGUGUGAAAACUGAUAGUGUCUCAUCCACAAGAGACAUUUUCACAUUAAUUUCUCUAUGGGGUUGGAUAAACUAGUGGCUAGCCCUAGUCCCAACAAAGUUGUGUUUGGUUUGCACUCUACCAAAAUUCAGCUAUCCCAU ----ssRNAplot: .....(((.((((....)))).)))....................((((((........)))))).((((((........))))))........................((((((((.....(((((..))))).))))))))..((((((.((((((.........))))))..))))))....... ----hitGC: 0.407407 ----pairStats: 45,1,3,6 hit 5 : 205383 205571 (fwd) 78.61 bits ::::::<<<-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,<<<<<<________ 1 AUACCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGUUUAAUAU 60 U+ CUUCUCGGC U GCU AGAUC A UGUAGUAUCUGUUCUUAUCAGU+U A A 205383 GUC-CUUCUCGGCGUAAAAGCUGAGAUCGAUUGUAGUAUCUGUUCUUAUCAGUGUGAAAA 205441 >>>>>>,<<<<<<<___....>>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<< 61 CUGAUAUgugcccCAUu....GgggcacAaGAuAUUAAaUUuAUUUUUgAAggGgGgggg 116 CUGAUA :::C:C AU+ G:G:::+ U U A AUU+AUUU U A GGGG: GG 205442 CUGAUAGUGUCUC-AUCcacaAGAGACAU---UUUCACAUUAAUUUCUCUAUGGGGUUGG 205497 <<<----.<<<<<__>>>>>->>>>>>>>,,<<<<<<-<<<<<<__________>>>>>> 117 ggcAuca.guaGCUUGCuacugccccccCACGggUcgcCcuGgggUUGCACUACucCagG 175 :::A C+ : :GCU GC: : :::CC :CA :G::+ ::UGG UUGCACU CCA:: 205498 AUAAACUaGUGGCUAGCCCUAGUCCCAACAAAGUUGUGUUUGGU-UUGCACUCUACCAAA 205556 --->>>>>>::::::: 176 GCcugGccCACCCCuc 191 + +::C:A CCC++ 205557 -AUUCAGCUAUCCCAU 205571 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #1320,emb|8254377| 298147 bp 1 contigs ----isReversed: 0 ----hitSequence: GUCCUUCUCGGCGUAAAAGCUGAGAUCGAUUGUAGUAUCUGUUCUUAUCAGUGUGAAAACUGAUAGUGUCUCAUCCACAAGAGACAUUUUCACAUUAAUUUCUCUGUGGGGUUGGAUAAACUAGUGGCUAGCCCUAGUCCCAACAAAGUUGUGUUUGGUUUGCACUCUACCAAAAUUCAGCUAUCCCAU ----ssRNAplot: .....(((.((((....)))).)))....................((((((........)))))).((((((........))))))........................((((((((.....(((((..))))).))))))))..((((((.((((((.........))))))..))))))....... ----hitGC: 0.412698 ----pairStats: 45,1,3,6 hit 6 : 206412 206600 (fwd) 76.20 bits ::::::<<<-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,<<<<<<________ 1 AUACCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGUUUAAUAU 60 U+ CUUCUCGGC U GCU AGAUC A UGUAGUAUCUGUUCUUAUCAGU+U A A 206412 GUC-CUUCUCGGCGUAAAAGCUGAGAUCGAUUGUAGUAUCUGUUCUUAUCAGUGUGAAAA 206470 >>>>>>,<<<<<<<___....>>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<< 61 CUGAUAUgugcccCAUu....GgggcacAaGAuAUUAAaUUuAUUUUUgAAggGgGgggg 116 CUGAUA :::C:C AU+ G:G:::+ U U A AUU+AUUU U GGGG: GG 206471 CUGAUAGUGUCUC-AUCcacaAGAGACAU---UUUCACAUUAAUUUCUCUGUGGGGUUGG 206526 <<<----.<<<<<__>>>>>->>>>>>>>,,<<<<<<-<<<<<<__________>>>>>> 117 ggcAuca.guaGCUUGCuacugccccccCACGggUcgcCcuGgggUUGCACUACucCagG 175 :::A C+ : :GCU GC: : :::CC :CA :G::+ ::UGG UUGCACU CCA:: 206527 AUAAACUaGUGGCUAGCCCUAGUCCCAACAAAGUUGUGUUUGGU-UUGCACUCUACCAAA 206585 --->>>>>>::::::: 176 GCcugGccCACCCCuc 191 + +::C:A CCC++ 206586 -AUUCAGCUAUCCCAU 206600 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #1320,emb|8254377| 298147 bp 1 contigs ----isReversed: 0 ----hitSequence: GUCCUUCUCGGCGUAAAAGCUGAGAUCGAUUGUAGUAUCUGUUCUUAUCAGUGUGAAAACUGAUAGUGUCUCAUCCACAAGAGACAUUUUCACAUUAAUUUCUCUGUGGGGUUGGAUAAACUAGUGGCUAGCCCUAGUCCCAACAAAGUUGUGUUUGGUUUGCACUCUACCAAAAUUCAGCUAUCCCAU ----ssRNAplot: .....(((.((((....)))).)))....................((((((........)))))).((((((........))))))........................((((((((.....(((((..))))).))))))))..((((((.((((((.........))))))..))))))....... ----hitGC: 0.412698 ----pairStats: 45,1,3,6 hit 7 : 207338 207526 (fwd) 76.20 bits ::::::<<<-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,<<<<<<________ 1 AUACCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGUUUAAUAU 60 U+ CUUCUCGGC U GCU AGAUC A UGUAGUAUCUGUUCUUAUCAGU+U A A 207338 GUC-CUUCUCGGCGUAAAAGCUGAGAUCGAUUGUAGUAUCUGUUCUUAUCAGUGUGAAAA 207396 >>>>>>,<<<<<<<___....>>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<< 61 CUGAUAUgugcccCAUu....GgggcacAaGAuAUUAAaUUuAUUUUUgAAggGgGgggg 116 CUGAUA :::C:C AU+ G:G:::+ U U A AUU+AUUU U GGGG: GG 207397 CUGAUAGUGUCUC-AUCcacaAGAGACAU---UUUCACAUUAAUUUCUCUGUGGGGUUGG 207452 <<<----.<<<<<__>>>>>->>>>>>>>,,<<<<<<-<<<<<<__________>>>>>> 117 ggcAuca.guaGCUUGCuacugccccccCACGggUcgcCcuGgggUUGCACUACucCagG 175 :::A C+ : :GCU GC: : :::CC :CA :G::+ ::UGG UUGCACU CCA:: 207453 AUAAACUaGUGGCUAGCCCUAGUCCCAACAAAGUUGUGUUUGGU-UUGCACUCUACCAAA 207511 --->>>>>>::::::: 176 GCcugGccCACCCCuc 191 + +::C:A CCC++ 207512 -AUUCAGCUAUCCCAU 207526 ----endhit ----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #1320,emb|8254377| 298147 bp 1 contigs ----isReversed: 0 ----hitSequence: GUCCUUCUCGGCGUAAAAGCUGAGAUCGAUUGUAGUAUCUGUUCUUAUCAGUGUGAAAACUGAUAGUGUCUCAUCCACAAGAGACAUUUUCACAUUAAUUUCUCUGUGGGGUUGGAUAAACUAGUGGCUAGCCCUAGUCCCAACAAAGUUGUGUUUGGUUUGCACUCUACCAAAAUUCAGCCAUCCCAC ----ssRNAplot: .....(((.((((....)))).)))....................((((((........)))))).((((((........))))))........................((((((((.....(((((..))))).))))))))..((((((.((((((.........))))))..))))))....... ----hitGC: 0.42328 ----pairStats: 45,1,3,7 hit 8 : 208157 208345 (fwd) 75.69 bits ::::::<<<-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,<<<<<<________ 1 AUACCUUCUCGGCCUUUUGGCUAAGAUCAAGUGUAGUAUCUGUUCUUAUCAGUUUAAUAU 60 U+ CUUCUCGGC U GCU AGAUC A UGUAGUAUCUGUUCUUAUCAGU+U A A 208157 GUC-CUUCUCGGCGUAAAAGCUGAGAUCGAUUGUAGUAUCUGUUCUUAUCAGUGUGAAAA 208215 >>>>>>,<<<<<<<___....>>>>>>>,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<< 61 CUGAUAUgugcccCAUu....GgggcacAaGAuAUUAAaUUuAUUUUUgAAggGgGgggg 116 CUGAUA :::C:C AU+ G:G:::+ U U A AUU+AUUU U GGGG: GG 208216 CUGAUAGUGUCUC-AUCcacaAGAGACAU---UUUCACAUUAAUUUCUCUGUGGGGUUGG 208271 <<<----.<<<<<__>>>>>->>>>>>>>,,<<<<<<-<<<<<<__________>>>>>> 117 ggcAuca.guaGCUUGCuacugccccccCACGggUcgcCcuGgggUUGCACUACucCagG 175 :::A C+ : :GCU GC: : :::CC :CA :G::+ ::UGG UUGCACU CCA:: 208272 AUAAACUaGUGGCUAGCCCUAGUCCCAACAAAGUUGUGUUUGGU-UUGCACUCUACCAAA 208330 --->>>>>>::::::: 176 GCcugGccCACCCCuc 191 + +::C:A CCC+C 208331 -AUUCAGCCAUCCCAC 208345 ----endhit Found 9 hits. done 2.08166e+08 nucs (frac lets thru so far=0.00171567151, 2d-fracLetsThru=0.000896447). Filter report: done 2.08166e+08 nucs (frac lets thru so far=0.0293935898, 2d-fracLetsThru=0.0157802). Filter report: done 6.11876e+06 nucs (frac lets thru so far=0.164747567, 2d-fracLetsThru=0.160669). Filter report: done 1.00805e+06 nucs (frac lets thru so far=0.354292942, 2d-fracLetsThru=0.353575). FULL: done 2.08166e+08 nucs (frac lets thru so far=0.00171567151, 2d-fracLetsThru=0.000896447). CPU time: 14485.60u 8.87s 04:01:34.47 Elapsed: 04:02:19 DONEdoneDONEdone