Params: release/cmzasha --no-stderr --filter 350 37 /projects/null/bio3/kasiaw/bio/temp_U3_redo/U3_results/results/RF00012_1U3.cm ../Tetrahymena_thermophila/Tetrahymena_thermophila.fasta 1 specfile /projects/null/bio3/kasiaw/bio/temp_U3_redo/U3_results/RF00012_1U3_at37.filterspec Build: release Host: gattaca.cs.washington.edu pid: 27164 ---time: Mon Jan 9 12:08:08 2006 ----fastaFile: ../Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----specfile: hmm /projects/null/bio3/kasiaw/bio/temp_U3_redo/U3_results/RF00012_1U3_Saureus_compact.hmm hmm /projects/null/bio3/kasiaw/bio/temp_U3_redo/U3_results/RF00012_1U3_Saureus_expanded.hmm ----hmm-from-cmFileName: /projects/null/bio3/kasiaw/bio/temp_U3_redo/RF00012_1U3.cm ----hmm-build-info: ;(default construction of HMM) Params: release/cmzasha --create-rigorous-filter 350 37 /projects/null/bio3/kasiaw/bio/temp_U3_redo/RF00012_1U3.cm /projects/null/bio3/kasiaw/bio/temp_U3_redo/U3_results data/default.filtercreationspec Build: release Host: gattaca.cs.washington.edu pid: 23723 ;Params: release/cmzasha --create-rigorous-filter 350 37 /projects/null/bio3/kasiaw/bio/temp_U3_redo/RF00012_1U3.cm /projects/null/bio3/kasiaw/bio/temp_U3_redo/U3_results data/default.filtercreationspec Build: release Host: gattaca.cs.washington.edu pid: 23723 ----2struct-info: only-hmm ----hmm-from-cmFileName: /projects/null/bio3/kasiaw/bio/temp_U3_redo/RF00012_1U3.cm ----hmm-build-info: ;(default construction of HMM) Params: release/cmzasha --create-rigorous-filter 350 37 /projects/null/bio3/kasiaw/bio/temp_U3_redo/RF00012_1U3.cm /projects/null/bio3/kasiaw/bio/temp_U3_redo/U3_results data/default.filtercreationspec Build: release Host: gattaca.cs.washington.edu pid: 23723 ;Params: release/cmzasha --create-rigorous-filter 350 37 /projects/null/bio3/kasiaw/bio/temp_U3_redo/RF00012_1U3.cm /projects/null/bio3/kasiaw/bio/temp_U3_redo/U3_results data/default.filtercreationspec Build: release Host: gattaca.cs.washington.edu pid: 23723 ----2struct-info: only-hmm ----cmFile: /projects/null/bio3/kasiaw/bio/temp_U3_redo/U3_results/results/RF00012_1U3.cm (global) ----CM-scanning-logic: Infernal-0.55 ----fastaFile: ../Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #542,emb|8254479| 384242 bp 2 contigs ----isReversed: 1 ----hitSequence: AAGACUGUACUUAUACAGGAUCUUUCUUAUAGUAAUUACUUACUGUAAGUUUCUUCAUUUGAAGACAACAACUCAAACUAGGAUGAUUAAAAGGACACUCUCAUCCGUAAAUGGGAUACAGAAACCAUUAGUAUUUUACUCUCUUCGGAGAGUAGGUAUUUUUGCGUUUCACGAUGAUCAUCCACCGCUGUGUUUGACCGAUCGUCUAUACGAGAAGUCACCAGUGGUUGGAGGGUGUGAGUGCUUCUGACUAG ----ssRNAplot: .......((((((((.(((..((((((..((((......))))..))))))..))))))))))).............((((..............(((((((((((................((...(((((.(((((.......))))).)))))..)).........................................(((..(.((((..........)))))..)))))))))))))).......)))) ----hitGC: 0.393701 ----pairStats: 59,3,16,18 hit 0 : 40042 39789 (rev) 86.77 bits ::::::.<<<<<<<<-<<<--<<<<<<--<<<<_____.>>>>-->>>>>>-->>>>>>> 1 aagaCU.aucuuucacaggAUcauuucUAuaggAUgcg.ucccUcuuagucUcuuaaaaa 58 AAGACU ::C::::AC+GGAU+:UU:+UAU::+A+++ +::CU +:AG:+UCUU+A::: 344201 AAGACUgUACUUAUACAGGAUCUUUCUUAUAGUAAUUAcUUACUGUAAGUUUCUUCAUUU 344260 >>>>-------------((((-----------.--((((((((((((,.,,,,,,,,,,, 59 uagucaaaCAacucAAaccagGAUGAUGAgac.uAgcccucgcacccg.GAGCGUGAugC 116 :A::+ AACAACUCAAAC:AGGAUGAU A A A C:CUC:CA:CCG A G GAU+C 344261 GAAGACAACAACUCAAACUAGGAUGAUUAAAAgGA-CACUCUCAUCCGuAAAUGGGAUAC 344319 ,<----<<---<<<<<-<<<<<____.__>>>>>->>>>>-->>>,,,.........,,, 117 cgCGGcgagcauuagguguugguUuu.uUccgacuucaguUgucuUUU.........GAU 166 +G :A CA+UA::+:UU:: U+U UU::GA:+::AG+U U: UUU GAU 344320 AG---AAACCAUUAGUAUUUUACUCUcUUCGGAGAGUAGGUAUU-UUUgcguuucacGAU 344375 ,,,,,,....................<<<--<<<<<<____._____>>>>>>-->>>,) 167 GAUCGU....................ucuUcucuccuUcuu.UUuGuagggaaUaaggUg 205 GAUC U :C:UC:+U:C: + + U +++:G:G :U+:G: G 344376 GAUCAUccaccgcuguguuugaccgaUCGUCUAUACGAGAAgUCACCAGUG-GUUGGA-G 344433 )))))))))).)-------)))) 206 ggugcgaggg.ccGUCUGAcugg 227 G:UG:GAG:G + UCUGACU:G 344434 GGUGUGAGUGcU--UCUGACUAG 344454 ----endhit ----fastaFile: ../Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #582,emb|8254484| 94841 bp 4 contigs ----isReversed: 1 ----hitSequence: AAGACUGUACUUAUACAGGAUCUUUCUUAUAGUAAUUACUUACUGUAAGUUUCUUCAUUUGAAGACAACAACUCAAUCUAGGAUGAUUAAAAGGACACUCUCAUCCGUAAAUGGGAUACAGAAACCAUUAGUAUUUUAUUCUCUUCGGAGAAUAGGUAUUUUUGCGUUUCACGAUGAUCAUCCAUCGCUGUGUUUGACCGAUCGUCUAUACGAAAAGUCACCAGCGGUUGGAGGGUGUGAGUGCUUCUGACUAG ----ssRNAplot: .......((((((((.(((..((((((..((((......))))..))))))..))))))))))).............((((..............(((((((((((................((...(((((.(((((.......))))).)))))..)).........................................(((..(.((((..........)))))..)))))))))))))).......)))) ----hitGC: 0.38189 ----pairStats: 59,3,15,19 hit 1 : 82748 82495 (rev) 81.71 bits ::::::.<<<<<<<<-<<<--<<<<<<--<<<<_____.>>>>-->>>>>>-->>>>>>> 1 aagaCU.aucuuucacaggAUcauuucUAuaggAUgcg.ucccUcuuagucUcuuaaaaa 58 AAGACU ::C::::AC+GGAU+:UU:+UAU::+A+++ +::CU +:AG:+UCUU+A::: 12094 AAGACUgUACUUAUACAGGAUCUUUCUUAUAGUAAUUAcUUACUGUAAGUUUCUUCAUUU 12153 >>>>-------------((((-----------.--((((((((((((,.,,,,,,,,,,, 59 uagucaaaCAacucAAaccagGAUGAUGAgac.uAgcccucgcacccg.GAGCGUGAugC 116 :A::+ AACAACUCAA C:AGGAUGAU A A A C:CUC:CA:CCG A G GAU+C 12154 GAAGACAACAACUCAAUCUAGGAUGAUUAAAAgGA-CACUCUCAUCCGuAAAUGGGAUAC 12212 ,<----<<---<<<<<-<<<<<____.__>>>>>->>>>>-->>>,,,.........,,, 117 cgCGGcgagcauuagguguugguUuu.uUccgacuucaguUgucuUUU.........GAU 166 +G :A CA+UA::+:UU::UU+U UU::GA:+::AG+U U: UUU GAU 12213 AG---AAACCAUUAGUAUUUUAUUCUcUUCGGAGAAUAGGUAUU-UUUgcguuucacGAU 12268 ,,,,,,....................<<<--<<<<<<____._____>>>>>>-->>>,) 167 GAUCGU....................ucuUcucuccuUcuu.UUuGuagggaaUaaggUg 205 GAUC U :C:UC:+U C: + U +++:G G :U+:G: G 12269 GAUCAUccaucgcuguguuugaccgaUCGUCUAUACGAAAAgUCACCAGCG-GUUGGA-G 12326 )))))))))).)-------)))) 206 ggugcgaggg.ccGUCUGAcugg 227 G:UG:GAG:G + UCUGACU:G 12327 GGUGUGAGUGcU--UCUGACUAG 12347 ----endhit ----fastaFile: ../Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #792,emb|8254676| 73992 bp 5 contigs ----isReversed: 1 ----hitSequence: AAGACUGUACUUAUACAGGAUCUUUCUUAUAGUAAUUACUUACUGUAAGUUUCUUCAUUUGAAGACAACAACUCAAUCUAGGAUGAUUAAAAGGACACUCUCAUCCGUAAAUGGGAUACAGAAACCAUUAGUAUUUUAUUCUCUUCGGAGAAUAGGUAUUUUUGCGUUUCACGAUGAUCAUCCAUCGCUGUGUUUGACCGAUCGUCUAUACGAAAAGUCACCAGUGGUUGGAGGGUGUGAGUGCUUCUGACUAG ----ssRNAplot: .......((((((((.(((..((((((..((((......))))..))))))..))))))))))).............((((..............(((((((((((................((...(((((.(((((.......))))).)))))..)).........................................(((..(.((((..........)))))..)))))))))))))).......)))) ----hitGC: 0.377953 ----pairStats: 59,3,15,18 hit 2 : 70077 69824 (rev) 83.22 bits ::::::.<<<<<<<<-<<<--<<<<<<--<<<<_____.>>>>-->>>>>>-->>>>>>> 1 aagaCU.aucuuucacaggAUcauuucUAuaggAUgcg.ucccUcuuagucUcuuaaaaa 58 AAGACU ::C::::AC+GGAU+:UU:+UAU::+A+++ +::CU +:AG:+UCUU+A::: 3916 AAGACUgUACUUAUACAGGAUCUUUCUUAUAGUAAUUAcUUACUGUAAGUUUCUUCAUUU 3975 >>>>-------------((((-----------.--((((((((((((,.,,,,,,,,,,, 59 uagucaaaCAacucAAaccagGAUGAUGAgac.uAgcccucgcacccg.GAGCGUGAugC 116 :A::+ AACAACUCAA C:AGGAUGAU A A A C:CUC:CA:CCG A G GAU+C 3976 GAAGACAACAACUCAAUCUAGGAUGAUUAAAAgGA-CACUCUCAUCCGuAAAUGGGAUAC 4034 ,<----<<---<<<<<-<<<<<____.__>>>>>->>>>>-->>>,,,.........,,, 117 cgCGGcgagcauuagguguugguUuu.uUccgacuucaguUgucuUUU.........GAU 166 +G :A CA+UA::+:UU::UU+U UU::GA:+::AG+U U: UUU GAU 4035 AG---AAACCAUUAGUAUUUUAUUCUcUUCGGAGAAUAGGUAUU-UUUgcguuucacGAU 4090 ,,,,,,....................<<<--<<<<<<____._____>>>>>>-->>>,) 167 GAUCGU....................ucuUcucuccuUcuu.UUuGuagggaaUaaggUg 205 GAUC U :C:UC:+U:C: + U +++:G:G :U+:G: G 4091 GAUCAUccaucgcuguguuugaccgaUCGUCUAUACGAAAAgUCACCAGUG-GUUGGA-G 4148 )))))))))).)-------)))) 206 ggugcgaggg.ccGUCUGAcugg 227 G:UG:GAG:G + UCUGACU:G 4149 GGUGUGAGUGcU--UCUGACUAG 4169 ----endhit ----fastaFile: ../Tetrahymena_thermophila/Tetrahymena_thermophila.fasta ----sequence: #1699,emb|8253957| 118128 bp 6 contigs ----isReversed: 1 ----hitSequence: AAGACUGUACUUAUACAGGAUCUUUCUUAUAGUAAUUACUUACUGUAAGUUUCUUCAUUUGAAGACAACAACUCAAUCUAGGAUGAUUAAAAGGACACUCUCAUCCGUAAAUGGGAUACAGAAACCAUUAGUAUUUUAUUCUCUUCGGAGAAUAGGUAUUUUUGCGUUUCACGAUGAUCAUCCAUCGCUGUGUUUGACCGAUCGUCUAUACGAGAAGUCACCAGUGGUUGGAGGGUGUGAGUGCUUCUGACUAG ----ssRNAplot: .......((((((((.(((..((((((..((((......))))..))))))..))))))))))).............((((..............(((((((((((................((...(((((.(((((.......))))).)))))..)).........................................(((..(.((((..........)))))..)))))))))))))).......)))) ----hitGC: 0.38189 ----pairStats: 59,3,15,18 hit 3 : 67983 67730 (rev) 86.11 bits ::::::.<<<<<<<<-<<<--<<<<<<--<<<<_____.>>>>-->>>>>>-->>>>>>> 1 aagaCU.aucuuucacaggAUcauuucUAuaggAUgcg.ucccUcuuagucUcuuaaaaa 58 AAGACU ::C::::AC+GGAU+:UU:+UAU::+A+++ +::CU +:AG:+UCUU+A::: 50146 AAGACUgUACUUAUACAGGAUCUUUCUUAUAGUAAUUAcUUACUGUAAGUUUCUUCAUUU 50205 >>>>-------------((((-----------.--((((((((((((,.,,,,,,,,,,, 59 uagucaaaCAacucAAaccagGAUGAUGAgac.uAgcccucgcacccg.GAGCGUGAugC 116 :A::+ AACAACUCAA C:AGGAUGAU A A A C:CUC:CA:CCG A G GAU+C 50206 GAAGACAACAACUCAAUCUAGGAUGAUUAAAAgGA-CACUCUCAUCCGuAAAUGGGAUAC 50264 ,<----<<---<<<<<-<<<<<____.__>>>>>->>>>>-->>>,,,.........,,, 117 cgCGGcgagcauuagguguugguUuu.uUccgacuucaguUgucuUUU.........GAU 166 +G :A CA+UA::+:UU::UU+U UU::GA:+::AG+U U: UUU GAU 50265 AG---AAACCAUUAGUAUUUUAUUCUcUUCGGAGAAUAGGUAUU-UUUgcguuucacGAU 50320 ,,,,,,....................<<<--<<<<<<____._____>>>>>>-->>>,) 167 GAUCGU....................ucuUcucuccuUcuu.UUuGuagggaaUaaggUg 205 GAUC U :C:UC:+U:C: + + U +++:G:G :U+:G: G 50321 GAUCAUccaucgcuguguuugaccgaUCGUCUAUACGAGAAgUCACCAGUG-GUUGGA-G 50378 )))))))))).)-------)))) 206 ggugcgaggg.ccGUCUGAcugg 227 G:UG:GAG:G + UCUGACU:G 50379 GGUGUGAGUGcU--UCUGACUAG 50399 ----endhit Found 4 hits. done 2.08166e+08 nucs (frac lets thru so far=1.23410942e-05, 2d-fracLetsThru=9.01782e-06). Filter report: done 2.08166e+08 nucs (frac lets thru so far=2.6603729e-05, 2d-fracLetsThru=1.82814e-05). Filter report: done 5538 nucs (frac lets thru so far=0.463885879, 2d-fracLetsThru=0.493277). FULL: done 2.08166e+08 nucs (frac lets thru so far=1.23410942e-05, 2d-fracLetsThru=9.01782e-06). CPU time: 8966.45u 0.87s 02:29:27.32 Elapsed: 02:29:31 DONEdoneDONEdone