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
./cmzasha --no-stderr --filter 75 5 Rfam/cm/RF00151.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00151_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00151.cm (global),/projects/bio/zasha/seqs/embl/hum01.dat.fasta.gz,5757,AB061824.1,1,sp|AB061824.1|AB061824 Homo sapiens RPL17; U58a; U58b genes for ribosomal protein L17; U58a and U58b snoRNA; complete cds and sequence.,0,0,2018,2083,5.90,CUGCGAUGAUGGCAUUUCUUAGGACACCUUUGGAUUAAUAAUGAAAACAACUACUCUCUGAGCAGC,BC000502.1/125-190 AC100778.5/8118-8183 X96658.1/1-66 AC091170.15/127951-128016 AB061824.1/2018-2083,,0,66
./cmzasha --no-stderr --filter 75 5 Rfam/cm/RF00151.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00151_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00151.cm (global),/projects/bio/zasha/seqs/embl/hum01.dat.fasta.gz,5757,AB061824.1,1,sp|AB061824.1|AB061824 Homo sapiens RPL17; U58a; U58b genes for ribosomal protein L17; U58a and U58b snoRNA; complete cds and sequence.,0,1,2400,2464,26.23,CUGCAGUGAUGACUUUCUUGGGACACCUUUGGAUUUACCGUGAAAAUUAAUAAAUUCUGAGCAGC,AB061824.1/2400-2464,,0,65
./cmzasha --no-stderr --filter 75 5 Rfam/cm/RF00151.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00151_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00151.cm (global),/projects/bio/zasha/seqs/embl/hum01.dat.fasta.gz,5757,AB061824.1,1,sp|AB061824.1|AB061824 Homo sapiens RPL17; U58a; U58b genes for ribosomal protein L17; U58a and U58b snoRNA; complete cds and sequence.,0,2,4441,4504,25.36,UUGCUGUGAUGACUAUCUUAGGACACCUUUGGAAUAACUAUGAAAGAAAACUAUUCUGAGCAAC,AC100778.5/10539-10602 AC091170.15/130374-130437 AB061824.1/4441-4504,,0,64
./cmzasha --no-stderr --filter 75 5 Rfam/cm/RF00151.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00151_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00151.cm (global),/projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz,89,AC091170.15,1,sp|AC091170.15|AC091170 Homo sapiens chromosome 18; clone RP11-879D5; complete sequence.,0,3,127951,128016,5.90,CUGCGAUGAUGGCAUUUCUUAGGACACCUUUGGAUUAAUAAUGAAAACAACUACUCUCUGAGCAGC,BC000502.1/125-190 AC100778.5/8118-8183 X96658.1/1-66 AC091170.15/127951-128016 AB061824.1/2018-2083,,0,66
./cmzasha --no-stderr --filter 75 5 Rfam/cm/RF00151.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00151_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00151.cm (global),/projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz,89,AC091170.15,1,sp|AC091170.15|AC091170 Homo sapiens chromosome 18; clone RP11-879D5; complete sequence.,0,4,128333,128397,27.09,CUGCAGUGAUGACUUUCUUAGGACACCUUUGGAUUUACCGUGAAAAUUAAUAAAUUCUGAGCAGC,AC091170.15/128333-128397 AC100778.5/8500-8564 X96657.1/1-65,,0,65
./cmzasha --no-stderr --filter 75 5 Rfam/cm/RF00151.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00151_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00151.cm (global),/projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz,89,AC091170.15,1,sp|AC091170.15|AC091170 Homo sapiens chromosome 18; clone RP11-879D5; complete sequence.,0,5,130374,130437,25.36,UUGCUGUGAUGACUAUCUUAGGACACCUUUGGAAUAACUAUGAAAGAAAACUAUUCUGAGCAAC,AC100778.5/10539-10602 AC091170.15/130374-130437 AB061824.1/4441-4504,,0,64
./cmzasha --no-stderr --filter 75 5 Rfam/cm/RF00151.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00151_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00151.cm (global),/projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz,2436,AC100778.5,1,sp|AC100778.5|AC100778 Homo sapiens chromosome 18; clone RP11-110H1; complete sequence.,0,6,8118,8183,5.90,CUGCGAUGAUGGCAUUUCUUAGGACACCUUUGGAUUAAUAAUGAAAACAACUACUCUCUGAGCAGC,BC000502.1/125-190 AC100778.5/8118-8183 X96658.1/1-66 AC091170.15/127951-128016 AB061824.1/2018-2083,,0,66
./cmzasha --no-stderr --filter 75 5 Rfam/cm/RF00151.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00151_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00151.cm (global),/projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz,2436,AC100778.5,1,sp|AC100778.5|AC100778 Homo sapiens chromosome 18; clone RP11-110H1; complete sequence.,0,7,8500,8564,27.09,CUGCAGUGAUGACUUUCUUAGGACACCUUUGGAUUUACCGUGAAAAUUAAUAAAUUCUGAGCAGC,AC091170.15/128333-128397 AC100778.5/8500-8564 X96657.1/1-65,,0,65
./cmzasha --no-stderr --filter 75 5 Rfam/cm/RF00151.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00151_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00151.cm (global),/projects/bio/zasha/seqs/embl/hum03.dat.fasta.gz,2436,AC100778.5,1,sp|AC100778.5|AC100778 Homo sapiens chromosome 18; clone RP11-110H1; complete sequence.,0,8,10539,10602,25.36,UUGCUGUGAUGACUAUCUUAGGACACCUUUGGAAUAACUAUGAAAGAAAACUAUUCUGAGCAAC,AC100778.5/10539-10602 AC091170.15/130374-130437 AB061824.1/4441-4504,,0,64
./cmzasha --no-stderr --filter 75 5 Rfam/cm/RF00151.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00151_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00151.cm (global),/projects/bio/zasha/seqs/embl/hum11.dat.fasta.gz,8551,BC000502.1,1,sp|BC000502.1|BC000502 Homo sapiens; ribosomal protein L17; clone MGC:8457 IMAGE:2821464; mRNA; complete cds.,0,9,125,190,5.90,CUGCGAUGAUGGCAUUUCUUAGGACACCUUUGGAUUAAUAAUGAAAACAACUACUCUCUGAGCAGC,BC000502.1/125-190 AC100778.5/8118-8183 X96658.1/1-66 AC091170.15/127951-128016 AB061824.1/2018-2083,,0,66
./cmzasha --no-stderr --filter 75 5 Rfam/cm/RF00151.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00151_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00151.cm (global),/projects/bio/zasha/seqs/embl/hum16.dat.fasta.gz,7421,X96657.1,1,sp|X96657.1|HSA18ASN H.sapiens mRNA for U58a small nuclear RNA,0,10,1,65,27.09,CUGCAGUGAUGACUUUCUUAGGACACCUUUGGAUUUACCGUGAAAAUUAAUAAAUUCUGAGCAGC,AC091170.15/128333-128397 AC100778.5/8500-8564 X96657.1/1-65,,0,65
./cmzasha --no-stderr --filter 75 5 Rfam/cm/RF00151.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00151_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00151.cm (global),/projects/bio/zasha/seqs/embl/hum16.dat.fasta.gz,7422,X96658.1,1,sp|X96658.1|HSA18BSN Homo sapiens U58b snoRNA gene,0,11,1,66,5.90,CUGCGAUGAUGGCAUUUCUUAGGACACCUUUGGAUUAAUAAUGAAAACAACUACUCUCUGAGCAGC,BC000502.1/125-190 AC100778.5/8118-8183 X96658.1/1-66 AC091170.15/127951-128016 AB061824.1/2018-2083,,0,66



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)
# 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)