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 12 Rfam/cm/RF00173.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00173_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00173.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,137680,D00721.1,1,sp|D00721.1|CHYSATS1 Chicory yellow mottle virus satellite RNA; complete cds.,1,0,306,255,16.32,CAACAGCGAAGCGCGCCAGGGAAACACACCAUGUGUGGUAUAUUAUCUGGCA,D00685.1/306-255 D00721.1/306-255,306-255,0,51,D00721.1/306-255
./cmzasha --no-stderr --filter 100 12 Rfam/cm/RF00173.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00173_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00173.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,189565,M21212.1,1,sp|M21212.1|SAM300CG Arabis mosaic virus small satellite RNA; complete genome.,1,1,157,106,16.32,CAACAGCGAAGCGGAACGGCGAAACACACCUUGUGUGGUAUAUUACCCGUUG,M21212.1/157-106,157-106,0,51,M21212.1/157-106
./cmzasha --no-stderr --filter 100 12 Rfam/cm/RF00173.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00173_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00173.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,193436,M14879.1,1,sp|M14879.1|TRSSATA Tobacco ringspot virus satellite RNA.,1,2,224,175,12.11,AAACAGAGAAGUCAACCAGAGAAACACACGUUGUGGUAUAUUACCUGGUA,M14879.1/224-175 M17439.1/226-177,224-175,0,49,M14879.1/224-175
./cmzasha --no-stderr --filter 100 12 Rfam/cm/RF00173.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00173_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00173.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,193437,M17439.1,1,sp|M17439.1|TRSSTO01 Tobacco ringspot virus (TobRV) mRNA.,1,3,226,177,12.11,AAACAGAGAAGUCAACCAGAGAAACACACGUUGUGGUAUAUUACCUGGUA,M14879.1/224-175 M17439.1/226-177,226-177,0,49,M17439.1/226-177
./cmzasha --no-stderr --filter 100 12 Rfam/cm/RF00173.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm/RF00173_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00173.cm (global),/projects/bio/zasha/seqs/embl/vrl.dat.fasta.gz,195785,D00685.1,1,sp|D00685.1|UTSSR Chicory yellow mottle virus small satellite RNA.,1,4,306,255,16.32,CAACAGCGAAGCGCGCCAGGGAAACACACCAUGUGUGGUAUAUUAUCUGGCA,D00685.1/306-255 D00721.1/306-255,306-255,0,51,D00685.1/306-255



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)