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 100 30 Rfam/cm/RF00053.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00053_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00053.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,5507,AC007837.4,1,sp|AC007837.4|AC007837 Drosophila melanogaster; chromosome 2R; region 57B2-B3; BAC clone BACR04I07; complete sequence.,0,0,16002,16089,34.57,GAGUGCAUUCCGUAUGGAAGACUAGUGAUUUUGUUGUUUGGUCUUUGGUAAUAACAAUAAAUCCCUUGUCUUCUUACGGCGUGCAUUU,AC007837.4/16002-16089 AE003791.4/91950-92037 AC009218.7/49108-49195,16002-16089,0,87,AC007837.4/16002-16089
./cmzasha --no-stderr --filter 100 30 Rfam/cm/RF00053.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00053_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00053.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,5702,AC009218.7,1,sp|AC009218.7|AC009218 Drosophila melanogaster; chromosome 2R; region 57B-57B; BAC clone BACR33D17; complete sequence.,0,1,49108,49195,34.57,GAGUGCAUUCCGUAUGGAAGACUAGUGAUUUUGUUGUUUGGUCUUUGGUAAUAACAAUAAAUCCCUUGUCUUCUUACGGCGUGCAUUU,AC007837.4/16002-16089 AE003791.4/91950-92037 AC009218.7/49108-49195,49108-49195,0,87,AC009218.7/49108-49195
./cmzasha --no-stderr --filter 100 30 Rfam/cm/RF00053.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00053_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00053.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,7807,AE003791.4,1,sp|AE003791.4|AE003791 Drosophila melanogaster chromosome 2R; section 59 of 74 of the complete sequence.,0,2,91950,92037,34.57,GAGUGCAUUCCGUAUGGAAGACUAGUGAUUUUGUUGUUUGGUCUUUGGUAAUAACAAUAAAUCCCUUGUCUUCUUACGGCGUGCAUUU,AC007837.4/16002-16089 AE003791.4/91950-92037 AC009218.7/49108-49195,91950-92037,0,87,AE003791.4/91950-92037
./cmzasha --no-stderr --filter 100 30 Rfam/cm/RF00053.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00053_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00053.cm (global),/projects/bio/zasha/seqs/embl/mus.dat.fasta.gz,4664,AC026385.19,1,sp|AC026385.19|AC026385 Mus musculus 17 BAC RP23-413K14 complete sequence.,0,3,122238,122323,35.90,GAGCCAGUGCUAUGUGGAAGACUUGUGAUUUUGUUGUUCUGAUAUGAUAUGACAACAAGUCACAGCCAGCCUCAUAGCGUGGACUC,AC026385.19/122238-122323,122238-122323,0,85,AC026385.19/122238-122323
./cmzasha --no-stderr --filter 100 30 Rfam/cm/RF00053.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00053_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00053.cm (global),/projects/bio/zasha/seqs/embl/vrt.dat.fasta.gz,24261,AL929155.4,1,sp|AL929155.4|AL929155 Zebrafish DNA sequence from clone DKEY-265M8,0,4,163041,163131,37.29,UAUUUUGGGCAUUAUGGAAGACUAGUGAUUUUGUUGUUGUGACGUCAUCAGUACUGACAACAAGUCACAGUCUGCCUCAGUGACCAGAAUC,AL929155.4/163041-163131,163041-163131,0,90,AL929155.4/163041-163131
./cmzasha --no-stderr --filter 100 30 Rfam/cm/RF00053.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00053_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00053.cm (global),/projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz,734,AC005523.1,1,sp|AC005523.1|AC005523 Homo sapiens chromosome 19; cosmid R28154; complete sequence.,0,5,3567,3652,37.65,GGUCUAGUGCUGUGUGGAAGACUAGUGAUUUUGUUGUUCUGAUGUACUACGACAACAAGUCACAGCCGGCCUCAUAGCGCAGACUC,AC006537.1/35676-35761 AC005523.1/3567-3652,3567-3652,0,85,AC005523.1/3567-3652
./cmzasha --no-stderr --filter 100 30 Rfam/cm/RF00053.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00053_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00053.cm (global),/projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz,1382,AC006537.1,1,sp|AC006537.1|AC006537 Homo sapiens chromosome 19; cosmid R30140; complete sequence.,0,6,35676,35761,37.65,GGUCUAGUGCUGUGUGGAAGACUAGUGAUUUUGUUGUUCUGAUGUACUACGACAACAAGUCACAGCCGGCCUCAUAGCGCAGACUC,AC006537.1/35676-35761 AC005523.1/3567-3652,35676-35761,0,85,AC006537.1/35676-35761
./cmzasha --no-stderr --filter 100 30 Rfam/cm/RF00053.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00053_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00053.cm (global),/projects/bio/zasha/seqs/embl/hum02.dat.fasta.gz,4356,AC013489.17,1,sp|AC013489.17|AC013489 Homo sapiens chromosome 15; clone RP11-97O12; complete sequence.,1,7,21820,21733,37.45,CGGCUGGCCCCAUCUGGAAGACUAGUGAUUUUGUUGUUGUCUUACUGCGCUCAACAACAAAUCCCAGUCUACCUAAUGGUGCCAGCCA,AC104259.14/97327-97240 AC013489.17/21820-21733,21820-21733,0,87,AC013489.17/21820-21733
./cmzasha --no-stderr --filter 100 30 Rfam/cm/RF00053.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00053_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00053.cm (global),/projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz,2806,AC104259.14,1,sp|AC104259.14|AC104259 Homo sapiens chromosome 15; clone CTD-2525I4; complete sequence.,1,8,97327,97240,37.45,CGGCUGGCCCCAUCUGGAAGACUAGUGAUUUUGUUGUUGUCUUACUGCGCUCAACAACAAAUCCCAGUCUACCUAAUGGUGCCAGCCA,AC104259.14/97327-97240 AC013489.17/21820-21733,97327-97240,0,87,AC104259.14/97327-97240
./cmzasha --no-stderr --filter 100 30 Rfam/cm/RF00053.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00053_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00053.cm (global),/projects/bio/zasha/seqs/embl/hum10.dat.fasta.gz,1519,AL354733.15,1,sp|AL354733.15|AL354733 Human DNA sequence from clone RP11-575L7 on chromosome 9,1,9,170740,170651,36.31,GGCCUAGUUCUGUGUGGAAGACUAGUGAUUUUGUUGUUUUUAGAUAACUAAAUCGACAACAAAUCACAGUCUGCCAUAUGGCACAGGCCA,AL354733.15/170740-170651,170740-170651,0,89,AL354733.15/170740-170651



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)