Params: release/cmzasha --no-stderr --local --filter 180 20 /home/kasiaw/Rfam_7.0/CM/RF00002.cm /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta 1 specfile /home/kasiaw/results/Tetrahymena_thermophila.fasta/RF00002_5_8S_rRNA/RF00002_180_0.01.filterspec 
Build: release
Host: node022
pid: 713
---time: Mon Jul  4 05:26:55 2005

----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta
----specfile: heur-hmm /home/kasiaw/Rfam_7.0_filters/RF00002_heur.hmm 4.94879246
----hmm-from-cmFileName: /home/kasiaw/Rfam_7.0/CM/RF00002.cm
----hmm-build-info: ;(default construction of HMM) Params: release/cmzasha --no-stderr --local --create-heuristic-hmm 180 /home/kasiaw/Rfam_7.0/CM/RF00002.cm 0.01 data/default.heurcreationspec /home/kasiaw/Rfam_7.0_filters 	Build: release	Host: cs005	pid: 652	;Params: release/cmzasha --no-stderr --local --create-heuristic-hmm 180 /home/kasiaw/Rfam_7.0/CM/RF00002.cm 0.01 data/default.heurcreationspec /home/kasiaw/Rfam_7.0_filters 	Build: release	Host: cs005	pid: 652	;Params: release/cmzasha --no-stderr --local --create-heuristic-hmm 180 /home/kasiaw/Rfam_7.0/CM/RF00002.cm 0.01 data/default.heurcreationspec /home/kasiaw/Rfam_7.0_filters 	Build: release	Host: cs005	pid: 652	
----2struct-info: only-hmm
----cmFile: /home/kasiaw/Rfam_7.0/CM/RF00002.cm (local)
----CM-scanning-logic: Infernal-0.55

----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta
----sequence: #896,emb|8253895| 1007 bp 1 contigs
----isReversed: 1
----hitSequence: GAUUUUCAACGGUGGAUAUCUAGGUUCCCGUGACGAUGAAGAACGCAGCGAAAUGCGAUACGCAAUGCGAAUUGCAGAACCGCGAGUCAUCAGAUCUUUGAACGCAAGUGGUGGAGGUGUAAAAACCUUCAUGUUUGUUUCAGUGUGG
----ssRNAplot:   ................................((.((......(((((....))))).((((((...(...........)..)).))))))))...................(((((((....)))))))..................
----hitGC: 0.466216
----pairStats: 26,3,1,11
hit 0   :    998    851 (rev)   147.62 bits
           ::::::::::::::::::::::::::::::::((-((,,,,,,<<<<<____>>>>>,<<
         1 AACUUUcAGCGAUGGAUgUCUUGGCUCccGCAuCGAUGAAGAACGCAgCgAAaUGCGAuA 60      
            A UUUCA+CG+UGGAU UCU GG UCCCG+ +:GAUGAAGAACGCAGCGAAAUGCGAUA
        10 GAUUUUCAACGGUGGAUAUCUAGGUUCCCGUGACGAUGAAGAACGCAGCGAAAUGCGAUA 69      

           <<<<---<<__________>->-->>->>>>))))-------------------<<<<<<
        61 cGuaAUGugAAUUGCAGAAuUcCGugAAuCaUCGaAUCUUUGAACGCAaAUUGCgCccac 120     
           C:::AUG+GAAUUGCAGAA  +CG::A:UCAUC:+AUCUUUGAACGCAA U+G G ::::
        70 CGCAAUGCGAAUUGCAGAA--CCGCGAGUCAUCAGAUCUUUGAACGCAAGUGGUGGAGGU 127     

           <<<____>>>>>>>>>::::::::::::::::::
       121 gggUacucccguggGcAUGCCUGuuUgAGUGUCu 154     
           :  UA+   ::::: CAUG+ UGUUU+AGUGU +
       128 G--UAAA--AACCUUCAUGUUUGUUUCAGUGUGG 157     

----endhit

----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta
----sequence: #1483,emb|8254564| 889818 bp 4 contigs
----isReversed: 0
----hitSequence: UUGAUUAAGAAAGAAAUGAUAUUUCUACAUUAUAAAAUAAAAGAACUAAUAAUGAUGUUUCAAUACUAAAUGAGAACUAGUAAGACUAAACAAAUGCUUUCAUAAAUUAACAAAAUUUUGAAAAUGCUUAUU
----ssRNAplot:   ((.((......((((???????????????????????????????????????????)))).((((((...((....???????????????????).)..)).)))))))).........?.........
----hitGC: 0.19697
----pairStats: 16,0,1,4
hit 1   : 600743 600874 (fwd)    20.44 bits
           ((-((,,,,,,<<<<~~~~~~>>>>,<<<<<<---<<____~~~~~~>->-->>->>>>)
        33 uCGAUGAAGAACGCA*[ 6]*UGCGAuAcGuaAUGugAAUU*[ 7]*uUcCGugAAuCaU 92      
           U:GA  AAGAA:G:A      U:C:AU+C::AAUG:GAA U      UU:C U:A:U+A 
    600743 UUGAUUAAGAAAGAA*[43]*UUCAAUACUAAAUGAGAACU*[19]*UUUCAUAAAUUAA 600852  

           )))---------~~~~~~:::::::::
        93 CGaAUCUUUGAA*[33]*AUGCCUGuu 145     
           C:AA++UUUGAA      AUGC U UU
    600853 CAAAAUUUUGAA*[ 1]*AUGCUUAUU 600874  

----endhit

----fastaFile: /home/kasiaw/Tetrahymena_thermophila/Tetrahymena_thermophila.fasta
----sequence: #1972,emb|rRNA-8234198| 9027 bp 1 contigs
----isReversed: 0
----hitSequence: AAUUUUCAACGGUGGAUAUCUAGGUUCCCGUGACGAUGAAGAACGCAGCGAAAUGCGAUACGCAAUGCGAAUUGCAGAACCGCGAGUCAUCAGAUCUUUGAACGCAAGUGGUGGAGGUGUAAAAACCUUCAUGUUUGUUUCAGUGUGG
----ssRNAplot:   ................................((.((......(((((....))))).((((((...(...........)..)).))))))))...................(((((((....)))))))..................
----hitGC: 0.459459
----pairStats: 26,3,1,11
hit 2   :   3060   3207 (fwd)   149.69 bits
           ::::::::::::::::::::::::::::::::((-((,,,,,,<<<<<____>>>>>,<<
         1 AACUUUcAGCGAUGGAUgUCUUGGCUCccGCAuCGAUGAAGAACGCAgCgAAaUGCGAuA 60      
           AA UUUCA+CG+UGGAU UCU GG UCCCG+ +:GAUGAAGAACGCAGCGAAAUGCGAUA
      3060 AAUUUUCAACGGUGGAUAUCUAGGUUCCCGUGACGAUGAAGAACGCAGCGAAAUGCGAUA 3119    

           <<<<---<<__________>->-->>->>>>))))-------------------<<<<<<
        61 cGuaAUGugAAUUGCAGAAuUcCGugAAuCaUCGaAUCUUUGAACGCAaAUUGCgCccac 120     
           C:::AUG+GAAUUGCAGAA  +CG::A:UCAUC:+AUCUUUGAACGCAA U+G G ::::
      3120 CGCAAUGCGAAUUGCAGAA--CCGCGAGUCAUCAGAUCUUUGAACGCAAGUGGUGGAGGU 3177    

           <<<____>>>>>>>>>::::::::::::::::::
       121 gggUacucccguggGcAUGCCUGuuUgAGUGUCu 154     
           :  UA+   ::::: CAUG+ UGUUU+AGUGU +
      3178 G--UAAA--AACCUUCAUGUUUGUUUCAGUGUGG 3207    

----endhit

Found 3 hits.

done 2.08166e+08 nucs (frac lets thru so far=0.0100009701, 2d-fracLetsThru=0.00599732).
Filter report: done 2.08166e+08 nucs (frac lets thru so far=0.0100009701, 2d-fracLetsThru=0.00599732).

FULL: done 2.08166e+08 nucs (frac lets thru so far=0.0100009701, 2d-fracLetsThru=0.00599732).

CPU time: 25236.12u 12.41s 07:00:48.52 Elapsed: 07:01:12
DONEdoneDONEdone