params (warning: commas chnged to semicolons),CM file,fastaFile,sequence #,EMBL accession,is in RFAMSEQ,sequence description (warning: commas chnged to semicolons),is reversed?,hit #,start nuc,end nuc,score (bits),hit sequence,hit Id(s) in Rfam with same seq,hit ranges within the same EMBL id,new hitness (0=in Rfam; 1=overlaps hit in Rfam;2=entirely new),amount of overlap with Rfam,this hit in Rfam format ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/fun.dat.fasta.gz,50488,X96517.1,1,sp|X96517.1|CAEF1BGEN C.albicans EF-1B gene,0,0,284,381,38.46,UUAAAAUGAUGAUCUCAAUCUUUGGUCCGUGUUUAUGAGGUGGCCUCAAGACCCACCGCAUGAGUGACAAAGAAGAUUUAAAUCUUAUAUCUGACAAU,X96517.1/284-381,284-381,0,97,X96517.1/284-381 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/fun.dat.fasta.gz,68394,U12981.1,1,sp|U12981.1|SC12981 Saccharomyces cerevisiae U18 snRNA; complete sequence.,0,1,1,88,38.62,GUGAAUGAUGAAUUUAAUUCUUUGGUCCGUGUUUAUGAUGGGAAGUAAGACCCCCGAUAUGAGUGACAAAAGAGAUGUGGUUGACUAU,U12981.1/1-88,1-88,0,87,U12981.1/1-88 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/fun.dat.fasta.gz,69350,L22015.1,1,sp|L22015.1|SCCHROMI Saccharomyces cerevisiae chromosome I centromere and right arm sequence.,0,2,8813,8901,41.95,UGUGAAUGAUGAAUUUAAUUCUUUGGUCCGUGUUUAUGAUGGGAAGUAAGACCCCCGAUAUGAGUGACAAAAGAGAUGUGGUUGACUAU,D14080.1/373-461 L22015.1/8813-8901,8813-8901,0,88,L22015.1/8813-8901 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/fun.dat.fasta.gz,69779,D14080.1,1,sp|D14080.1|SCEFB1DNA Yeast DNA for elongation factor-1 beta; complete cds.,0,3,373,461,41.95,UGUGAAUGAUGAAUUUAAUUCUUUGGUCCGUGUUUAUGAUGGGAAGUAAGACCCCCGAUAUGAGUGACAAAAGAGAUGUGGUUGACUAU,D14080.1/373-461 L22015.1/8813-8901,373-461,0,88,D14080.1/373-461 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/fun.dat.fasta.gz,76728,AL031534.1,1,sp|AL031534.1|SPBC4F6 S.pombe chromosome II cosmid c4F6.,1,4,35527,35439,31.97,AAGCUAUGAUGACCAAAAUUGGUCCGUGUUACUGAGCGGGAUUAAGACCCCAGCAAACGAAGAGAAACCCAAUUUUUAAUUCUGAUUUU,AL031534.1/35527-35439,35527-35439,0,88,AL031534.1/35527-35439 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/fun.dat.fasta.gz,77650,X61926.1,1,sp|X61926.1|SPSWI10 S.pombe swi10 gene,0,5,688,775,32.28,AAGCUAUGAUGACCAAAAUUGGUCCGUGUUACUGAGCGGAUUAAGACCCCAGCAAACGAAGAGAAACCCAAUUUUUAAUUCUGAUUUU,X61926.1/688-775,688-775,0,87,X61926.1/688-775 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,6735,AC093546.2,1,sp|AC093546.2|AC093546 Drosophila melanogaster 3L BAC RP98-8G7 (Roswell Park Cancer Institute Drosophila BAC Library) complete sequence.,0,6,122417,122488,23.16,UGACUGUGAUGAAAUUAAUUGGUCCGUGUUUAUGAAUUUAUAUUGAUUAAAAACCUUCCAAUUACUGAGCAA,AE003539.3/150351-150422 AC093546.2/122417-122488,122417-122488,0,71,AC093546.2/122417-122488 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,7555,AE003539.3,1,sp|AE003539.3|AE003539 Drosophila melanogaster chromosome 3L; section 46 of 83 of the complete sequence.,0,7,150351,150422,23.16,UGACUGUGAUGAAAUUAAUUGGUCCGUGUUUAUGAAUUUAUAUUGAUUAAAAACCUUCCAAUUACUGAGCAA,AE003539.3/150351-150422 AC093546.2/122417-122488,150351-150422,0,71,AE003539.3/150351-150422 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz,43313,U28944.1,1,sp|U28944.1|CEC18A3 Caenorhabditis elegans cosmid C18A3; complete sequence.,0,8,237,301,26.24,UGGCAGUGAUGAUCACAAAUCCGUGUUUCUGACAAGCGAUUGACGAUAGAAAACCGGCUGAGCCA,Z75111.1/1-65 U28944.1/237-301,237-301,0,64,U28944.1/237-301 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/inv02.dat.fasta.gz,45375,Z75111.1,1,sp|Z75111.1|CEU18SNOR C.elegans U18 small nucleolar RNA gene.,0,9,1,65,26.24,UGGCAGUGAUGAUCACAAAUCCGUGUUUCUGACAAGCGAUUGACGAUAGAAAACCGGCUGAGCCA,Z75111.1/1-65 U28944.1/237-301,1-65,0,64,Z75111.1/1-65 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,9000,AC010676.6,1,sp|AC010676.6|AC010676 Arabidopsis thaliana chromosome III BAC T22N4 genomic sequence; complete sequence.,0,10,33901,33978,24.83,GAGAUAUGAUGAUCAACAAAUUGGUCCGUGUUUCAGAUUAACCGUGACCGAAAAAAUUCUUAACCAAACUCUGAUCUC,AC010870.6/7752-7675 AC010676.6/33901-33978 AF317985.1/3-80,33901-33978,0,77,AC010676.6/33901-33978 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,9008,AC010870.6,1,sp|AC010870.6|AC010870 Arabidopsis thaliana chromosome III BAC T13O15 genomic sequence; complete sequence.,1,11,7752,7675,24.83,GAGAUAUGAUGAUCAACAAAUUGGUCCGUGUUUCAGAUUAACCGUGACCGAAAAAAUUCUUAACCAAACUCUGAUCUC,AC010870.6/7752-7675 AC010676.6/33901-33978 AF317985.1/3-80,7752-7675,0,77,AC010870.6/7752-7675 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,9407,AC084320.10,1,sp|AC084320.10|AC084320 Oryza sativa chromosome 3 BAC OSJNBa0091J19 genomic sequence; complete sequence.,1,12,96112,96031,38.24,GGAACAUGAUGAAGAACCAUUGGUCCGUGUUUCUGAUCAUCUCGUGAUGAAACUACAAUGAAGCACUCAUACUUCUGAUUCC,AJ309198.1/115-34 AY103182.1/2-83 AJ307927.1/2-83 AC084320.10/96112-96031,96112-96031,0,81,AC084320.10/96112-96031 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,9850,AC135320.6,1,sp|AC135320.6|AC135320 Medicago truncatula clone mth2-28e9; complete sequence.,1,13,55300,55226,26.50,GAGAAAUGACGAGCUUUACAUUGGUCCGUGUUUCUGAAUCACCGUGACCGACAAAUCUUACCAAUUUCUGAUCUC,AC135320.6/55300-55226,55300-55226,0,74,AC135320.6/55300-55226 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,39810,AF317985.1,1,sp|AF317985.1|AF317985 Arabidopsis thaliana clone 1 small nucleolar RNA R63; complete sequence.,0,14,3,80,24.83,GAGAUAUGAUGAUCAACAAAUUGGUCCGUGUUUCAGAUUAACCGUGACCGAAAAAAUUCUUAACCAAACUCUGAUCUC,AC010870.6/7752-7675 AC010676.6/33901-33978 AF317985.1/3-80,3-80,0,77,AF317985.1/3-80 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,39811,AF317986.1,1,sp|AF317986.1|AF317986 Arabidopsis thaliana clone 2 small nucleolar RNA R63; complete sequence.,0,15,1,77,25.26,GAGAUGUGAUGAGUAACAAAUUGGUCCGUGUUUCUGAUUAACCGUGACUGAGAAUUUAUUAACCAAACUCUGAUCUC,AF317986.1/1-77 AL391146.1/51211-51287,1-77,0,76,AF317986.1/1-77 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,102281,AL391146.1,1,sp|AL391146.1|ATF2G14 Arabidopsis thaliana DNA chromosome 5; BAC clone F2G14 (ESSA project),0,16,51211,51287,25.26,GAGAUGUGAUGAGUAACAAAUUGGUCCGUGUUUCUGAUUAACCGUGACUGAGAAUUUAUUAACCAAACUCUGAUCUC,AF317986.1/1-77 AL391146.1/51211-51287,51211-51287,0,76,AL391146.1/51211-51287 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,149183,AY103182.1,1,sp|AY103182.1|AY103182 Oryza sativa (indica cultivar-group) snoRNA J7 gene; complete sequence.,0,17,2,83,38.24,GGAACAUGAUGAAGAACCAUUGGUCCGUGUUUCUGAUCAUCUCGUGAUGAAACUACAAUGAAGCACUCAUACUUCUGAUUCC,AJ309198.1/115-34 AY103182.1/2-83 AJ307927.1/2-83 AC084320.10/96112-96031,2-83,0,81,AY103182.1/2-83 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,164079,AY220636.1,1,sp|AY220636.1|AY220636 Oryza sativa box C/D snoRNA J7.3; complete sequence.,0,18,3,69,29.86,UGGAAAUGAUGAAGAAAACAUUGGUCCGUGUUUCUGAUAACCCGUGACUGAUAGCCAUGUUUUCUAA,AY220636.1/3-69 AJ490457.1/2-68,3-69,0,66,AY220636.1/3-69 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,197670,AJ307927.1,1,sp|AJ307927.1|OSA307927 Oryza sativa Z106 snoRNA gene,0,19,2,83,38.24,GGAACAUGAUGAAGAACCAUUGGUCCGUGUUUCUGAUCAUCUCGUGAUGAAACUACAAUGAAGCACUCAUACUUCUGAUUCC,AJ309198.1/115-34 AY103182.1/2-83 AJ307927.1/2-83 AC084320.10/96112-96031,2-83,0,81,AJ307927.1/2-83 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,197681,AJ309198.1,1,sp|AJ309198.1|OSA309198 Oryza sativa snoRNA gene cluster V (Z104a; Z104b; Z105; Z106),1,20,115,34,38.24,GGAACAUGAUGAAGAACCAUUGGUCCGUGUUUCUGAUCAUCUCGUGAUGAAACUACAAUGAAGCACUCAUACUUCUGAUUCC,AJ309198.1/115-34 AY103182.1/2-83 AJ307927.1/2-83 AC084320.10/96112-96031,115-34,0,81,AJ309198.1/115-34 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,197751,AJ489951.1,1,sp|AJ489951.1|OSA489951 Oryza sativa z106b snoRNA gene,0,21,5,85,34.11,GGAACAUGAUGAAGAACCAUGGUCCGUGUUUCUGAUCAUCUCGUGAUGAAACUACAAUGAAGCACUCAUACUUCUGAUUCC,AJ489951.1/5-85,5-85,0,80,AJ489951.1/5-85 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/pln.dat.fasta.gz,197899,AJ490457.1,1,sp|AJ490457.1|OSA490457 Oryza sativa z106c snoRNA gene,0,22,2,68,29.86,UGGAAAUGAUGAAGAAAACAUUGGUCCGUGUUUCUGAUAACCCGUGACUGAUAGCCAUGUUUUCUAA,AY220636.1/3-69 AJ490457.1/2-68,2-68,0,66,AJ490457.1/2-68 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz,51475,X75488.1,1,sp|X75488.1|XLIX1L1B X.laevis intron for XlL1b gene.,0,23,49,119,62.92,UGGAUAUGAUGAGCUCCACUUCAUGGUCCGUGUUUCUGAACCGAAGUGAUAUCAAUGGAAGUUCUGAUUAC,X75488.1/49-119,49-119,0,70,X75488.1/49-119 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz,51866,X06552.1,1,sp|X06552.1|XLRPL1AG X.laevis gene for ribosomal protein L1a,0,24,2182,2251,66.18,UCGAUAUGAUGAGUUCCACUUCAUGGUCCGUGUUUCUGAACCUAGUGAUAUUAAUGGAAGUUCUGAUUUC,X06552.1/2182-2251,4707-4777 5485-5556 2182-2251 2863-2934,0,69,X06552.1/2182-2251 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz,51866,X06552.1,1,sp|X06552.1|XLRPL1AG X.laevis gene for ribosomal protein L1a,0,25,2863,2934,58.25,GCUUUAUGAUGAGCUCCACUUCUAUGGUCCGUGUUUCUGAUGCAUCAUGAUCUCUGUGGAAGUUCUGAUCAG,X06552.1/2863-2934,4707-4777 5485-5556 2182-2251 2863-2934,0,71,X06552.1/2863-2934 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz,51866,X06552.1,1,sp|X06552.1|XLRPL1AG X.laevis gene for ribosomal protein L1a,0,26,4707,4777,68.09,UAUACAUGAUGAUUUCCACUUCUAUGGUCCGUGUUUCUGAAACUCAUGAUAUUUGUGGAAGUUCUGAUUUA,X06552.1/4707-4777,4707-4777 5485-5556 2182-2251 2863-2934,0,70,X06552.1/4707-4777 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz,51866,X06552.1,1,sp|X06552.1|XLRPL1AG X.laevis gene for ribosomal protein L1a,0,27,5485,5556,62.35,UGUUAAUGAUGAGUUCCACUUCAUUGGUCCGUGUUUCUGAAACCUUAUGAUCUAAGUGGAAGUUCUGACUGA,X06552.1/5485-5556,4707-4777 5485-5556 2182-2251 2863-2934,0,71,X06552.1/5485-5556 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz,52529,X75486.1,1,sp|X75486.1|XTIXTL1 X.tropicalis intron for XtL1 gene.,0,28,57,126,66.07,UGAAUAUGAUGAGUUCCACUUCAUGGUCCGUGUUUCUGAACCCAGUGAUAAUAAUGGAAGUUCUGAUUUA,X75486.1/57-126,57-126,0,69,X75486.1/57-126 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz,52539,M15678.1,1,sp|M15678.1|XTRPL1 Xenopus tropicalis ribosomal protein L1 gene; partial cds.,0,29,705,773,67.03,UAUACAUGAUGAUCUCCACUUCUGGUCCGUGUUUCUGAAACUCAUGAUCUUUGUGGAAGUUCUGACUUA,M15678.1/705-773,1373-1441 705-773,0,68,M15678.1/705-773 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz,52539,M15678.1,1,sp|M15678.1|XTRPL1 Xenopus tropicalis ribosomal protein L1 gene; partial cds.,0,30,1373,1441,63.22,UGUUAAUGAUGAGCUCCACUUCAUGGUCCGUGUUUCUGACCUUAUGAUCUGAGUGGAAGUUCUGAUAUA,M15678.1/1373-1441,1373-1441 705-773,0,68,M15678.1/1373-1441 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/hum01.dat.fasta.gz,5753,AB061820.1,1,sp|AB061820.1|AB061820 Homo sapiens RPL4; U18 genes for ribosomal protein L4 and U18 snoRNA; complete cds and sequence.,0,31,2178,2249,52.54,CAGUAGUGAUGAAAUUCCACUUCAUUGGUCCGUGUUUCUGAACCACAUGAUUUUCUCGGAUGUUCUGAUGCU,AC116913.6/73982-73911 AB061820.1/2178-2249 X75487.1/44-115,2178-2249 3401-3472 4174-4242,0,71,AB061820.1/2178-2249 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/hum01.dat.fasta.gz,5753,AB061820.1,1,sp|AB061820.1|AB061820 Homo sapiens RPL4; U18 genes for ribosomal protein L4 and U18 snoRNA; complete cds and sequence.,0,32,3401,3472,62.10,UCAAAAUGAUGAGAUUCCACUUAAUUGGUCCGUGUUUCUGAAACACAUGAUAUUUGUGGAAAUUCUGACUUG,AC116913.6/72759-72688 AB061820.1/3401-3472,2178-2249 3401-3472 4174-4242,0,71,AB061820.1/3401-3472 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/hum01.dat.fasta.gz,5753,AB061820.1,1,sp|AB061820.1|AB061820 Homo sapiens RPL4; U18 genes for ribosomal protein L4 and U18 snoRNA; complete cds and sequence.,0,33,4174,4242,58.21,UUGUUAUGAUGAGAUUCCACUUAAGGUCCGUGUUUCUGAAACAAAUGAUUUUGUGGAAGUUCUGAUUUA,AC116913.6/71986-71918 AB061820.1/4174-4242,2178-2249 3401-3472 4174-4242,0,68,AB061820.1/4174-4242 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz,928,AC005800.1,1,sp|AC005800.1|AC005800 Homo sapiens Chromosome 15q26.1 PAC clone pDJ427d15; complete sequence.,0,34,98098,98167,41.21,CUAUUAUGAUGAGAUUACGCUCUGUGGUCCGUGUUUCUGAAACACAGGAUUUUGUGGAAGUUCUCAUUUG,AC005800.1/98098-98167 AC021422.25/127025-126956 AC002312.1/76920-76989 AC000379.1/36566-36635,98098-98167,0,69,AC005800.1/98098-98167 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz,4344,AC013471.7,1,sp|AC013471.7|AC013471 Homo sapiens BAC clone RP11-489A14 from 2; complete sequence.,1,35,130038,129969,50.13,UGUGUAUGAUGAGAUUUCACUUCAUGGUCUGUGUUUCUGAAACACAUGAUGUUGUGGAAGUUCUGAUUUG,AC013471.7/130038-129969,130038-129969,0,69,AC013471.7/130038-129969 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz,5535,AC021422.25,1,sp|AC021422.25|AC021422 Homo sapiens chromosome 15; clone RP11-387D10; complete sequence.,1,36,127025,126956,41.21,CUAUUAUGAUGAGAUUACGCUCUGUGGUCCGUGUUUCUGAAACACAGGAUUUUGUGGAAGUUCUCAUUUG,AC005800.1/98098-98167 AC021422.25/127025-126956 AC002312.1/76920-76989 AC000379.1/36566-36635,127025-126956,0,69,AC021422.25/127025-126956 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz,5150,AC116913.6,1,sp|AC116913.6|AC116913 Homo sapiens chromosome 15; clone CTD-3185P2; complete sequence.,1,37,73982,73911,52.54,CAGUAGUGAUGAAAUUCCACUUCAUUGGUCCGUGUUUCUGAACCACAUGAUUUUCUCGGAUGUUCUGAUGCU,AC116913.6/73982-73911 AB061820.1/2178-2249 X75487.1/44-115,73982-73911 71986-71918 72759-72688,0,71,AC116913.6/73982-73911 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz,5150,AC116913.6,1,sp|AC116913.6|AC116913 Homo sapiens chromosome 15; clone CTD-3185P2; complete sequence.,1,38,72759,72688,62.10,UCAAAAUGAUGAGAUUCCACUUAAUUGGUCCGUGUUUCUGAAACACAUGAUAUUUGUGGAAAUUCUGACUUG,AC116913.6/72759-72688 AB061820.1/3401-3472,73982-73911 71986-71918 72759-72688,0,71,AC116913.6/72759-72688 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz,5150,AC116913.6,1,sp|AC116913.6|AC116913 Homo sapiens chromosome 15; clone CTD-3185P2; complete sequence.,1,39,71986,71918,58.21,UUGUUAUGAUGAGAUUCCACUUAAGGUCCGUGUUUCUGAAACAAAUGAUUUUGUGGAAGUUCUGAUUUA,AC116913.6/71986-71918 AB061820.1/4174-4242,73982-73911 71986-71918 72759-72688,0,68,AC116913.6/71986-71918 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/hum20.dat.fasta.gz,3850,AC002312.1,1,sp|AC002312.1|HSAC2312 Human Chromosome 15 pac pDJ138o23; complete sequence.,0,40,76920,76989,41.21,CUAUUAUGAUGAGAUUACGCUCUGUGGUCCGUGUUUCUGAAACACAGGAUUUUGUGGAAGUUCUCAUUUG,AC005800.1/98098-98167 AC021422.25/127025-126956 AC002312.1/76920-76989 AC000379.1/36566-36635,76920-76989,0,69,AC002312.1/76920-76989 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/hum20.dat.fasta.gz,3920,AC000379.1,1,sp|AC000379.1|HSAC379 Human Chromosome 15 pac pDJ24m8; complete sequence.,0,41,36566,36635,41.21,CUAUUAUGAUGAGAUUACGCUCUGUGGUCCGUGUUUCUGAAACACAGGAUUUUGUGGAAGUUCUCAUUUG,AC005800.1/98098-98167 AC021422.25/127025-126956 AC002312.1/76920-76989 AC000379.1/36566-36635,36566-36635,0,69,AC000379.1/36566-36635 ./cmzasha --no-stderr --filter 150 23 Rfam/cm/RF00093.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00093_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00093.cm (global),/projects/bio/zasha/seqs/embl/hum22.dat.fasta.gz,2950,X75487.1,1,sp|X75487.1|HSIL41 H.sapiens intron for L4 gene.,0,42,44,115,52.54,CAGUAGUGAUGAAAUUCCACUUCAUUGGUCCGUGUUUCUGAACCACAUGAUUUUCUCGGAUGUUCUGAUGCU,AC116913.6/73982-73911 AB061820.1/2178-2249 X75487.1/44-115,44-115,0,71,X75487.1/44-115 THINGS IN Rfam THAT WEREN'T FOUND: # hits found that weren't in Rfam: 0 (totally new = 0, overlaps hit in Rfam = 0, overlap hits with more than 10 nucs = 0, total # hits with 0 overlap with Rfam (ignoring sequence matching) = 0) # Rfam hits not found: 0 (no overlap of >= 10 nucs: 0) # Rfam seqs not found: 0 (no overlap of >= 10 nucs: too tricky to calculate)