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 200 40 Rfam/cm/RF00025.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00025_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00025.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,43322,AF399707.1,1,sp|AF399707.1|AF399707 Tetrahymena thermophila telomerase RNA; complete sequence.,0,0,2183,2342,127.42,AUACCCGCUUAAUUCAUUCAGAUCUGUAAUAGAACUGUCAUUCAACCCCAAAAAUCUAGUGCUGAUAUAACCUUCACCAAUUAGGUUCAAAUAAGUGGUAAUGCGGGACAAAAGACUAUCGACAUUUGAUACACUAUUUAUCAAUGGAUGUCUUAUUUUU,AF399707.1/2183-2342,2183-2342,0,159,AF399707.1/2183-2342 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00025.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00025_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00025.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,44349,AF417609.1,1,sp|AF417609.1|AF417609 Colpidium campylum telomerase RNA gene; complete sequence.,0,1,194,352,102.30,AUCCCCGCAAAUUCAUUCUGUUUGCAUUCAAACAGUCAUUCAACCCCAAAAAUCUAGACCAAAUAUUGUCUUCCCUUCUUGGCACAAACAAAGAAGAGACGCGGGAUAAAGAUACUCCGACGAUUGAUACAAUAUUUAUCAACGGGAGGUCUUACUUUU,AF417609.1/194-352 AF417611.1/283-441,194-352,0,158,AF417609.1/194-352 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00025.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00025_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00025.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,44350,AF417610.1,1,sp|AF417610.1|AF417610 Colpidium colpoda telomerase RNA gene; complete sequence.,0,2,220,376,102.12,AUCCCCGCAACUCCAUUCAGUUCGAAAUUGAACUGUCAUUCAACCCCAAAAAUCUAGUAAAAAAUAUUGCCGAAACUUUCAGGCAUUAAGGAAAGUAAAGCGGGAUCAGAUACUCCGACUUGUGAUACACUAUUUAUCACAUGGGAGAUCUAUUUUU,AF417610.1/220-376,220-376,0,156,AF417610.1/220-376 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00025.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00025_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00025.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,44351,AF417611.1,1,sp|AF417611.1|AF417611 Colpidium striatum telomerase RNA gene; complete sequence.,0,3,283,441,102.30,AUCCCCGCAAAUUCAUUCUGUUUGCAUUCAAACAGUCAUUCAACCCCAAAAAUCUAGACCAAAUAUUGUCUUCCCUUCUUGGCACAAACAAAGAAGAGACGCGGGAUAAAGAUACUCCGACGAUUGAUACAAUAUUUAUCAACGGGAGGUCUUACUUUU,AF417609.1/194-352 AF417611.1/283-441,283-441,0,158,AF417611.1/283-441 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00025.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00025_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00025.cm (global),/projects/bio/zasha/seqs/embl/inv01.dat.fasta.gz,44352,AF417612.1,1,sp|AF417612.1|AF417612 Glaucoma sp. ME60q telomerase RNA gene; complete sequence.,0,4,231,392,92.43,UACCUCCUGUGGAUCCAUUCAGGAUUAAUGAAAUCCUGUCAUUCAACCCCAAAAAUCUUGUCAAAUUAUUGCCUCGUCUUUUGGGCACAAACAAAAGUCACGCAGGAGGUUCAGACAUUCGACAUAAGAUACACUAUUUAUCUUAUGGAAGGUCUAGUUUUU,AF417612.1/231-392,231-392,0,161,AF417612.1/231-392 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00025.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00025_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00025.cm (global),/projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz,6767,U10565.1,1,sp|U10565.1|EA10565 Euplotes aediculatus telomerase RNA gene; complete sequence.,0,5,50,238,49.90,AGUUUCUCGAUAAUUGAUCUGUAGAAUCUGUCAAGCAAAACCCCAAAACCUUACACUGAGAGCAUUUAGCCUGAUUACUCUUUAAAUCAAAUCAGGCAAUAGAGAGAAACUCGAGAGGUGAAAACCCCACAGCAUUCUGAAAUGUAUUUGGGAGUAAUCUCAUAUUAGUUUGCUGUCCUCUCAUCUUUU,U10565.1/50-238,50-238,0,188,U10565.1/50-238 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00025.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00025_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00025.cm (global),/projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz,7086,U10566.1,1,sp|U10566.1|EE10566 Euplotes eurystomus telomerase RNA gene; complete sequence.,0,6,72,260,46.65,AGUUUCUCGAUAAUUGAUCUGUAGAAUCUGUCAAGCAAAACCCCAAAACCUUACACUGAGAGCAUUUAGCUUGAUUACUCUUUAAAUUAAAUCAGGCAAUAGAGAGAAACUCGAGAGGUGAAAACCCCACAGCAUUCUGAAAUGUAUUUGGGAGUAAUCUCAUAUUGGUUUGCUGUCCUCUCAUCUUUU,U10566.1/72-260,72-260,0,188,U10566.1/72-260 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00025.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00025_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00025.cm (global),/projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz,13797,U10567.1,1,sp|U10567.1|ON10567 Oxytricha nova H10 telomerase RNA gene; complete sequence.,0,7,1,190,44.75,AGCUGGUGGAAGUGCGUCAGUCAUAGCACUGUCAACAAAACCCCAAAACCGUAAACUCAGAGCAAUUCGCCUGGUUCCUCUUUAAAGCAAAACCAGGAGGUUCCGCCAGCUACCAGAGGACGAAGUGGGCUAAGUGAAAUGAAAAUUUGAGAGUUUCUCUCCAUCACUUAGCCCCGCCUCUCAUUCUUUU,U10567.1/1-190,1-190,0,189,U10567.1/1-190 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00025.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00025_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00025.cm (global),/projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz,14042,U10568.1,1,sp|U10568.1|OT10568 Oxytricha trifallax telomerase RNA gene; complete sequence.,0,8,27,212,51.08,AGUCGGCGGAAAUCAGUCAGUCAUAGCGCUGUCAACAAAACCCCAAAACCGUAAAAUUAGAGCAAUUCGCCUGGUUCCUCUUUAAAGCAAAACCAGGAGGCUCCGCCGACUCAGAGGGCACUGUGGGCUGAGCAAAAUGAAAAUUUGAGAGUUUCUCUCCAUUGCUUAGCCCUACCUCUAUCUUUU,U10568.1/27-212,27-212,0,185,U10568.1/27-212 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00025.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00025_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00025.cm (global),/projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz,20611,U10569.1,1,sp|U10569.1|SL10569 Stylonychia lemnae telomerase RNA gene; complete sequence.,0,9,28,216,52.59,AGUUCGGCGGAAAUCCGUCAGCUAUAACGCUGUCAAGAAAACCCCAAAACCGUAAAAUGAGAGCAAUUCGCCUGGUUCCUCUUUAAAGUCAAACCAGGAGGCUCCGCCGGACUAGAGGUCGAAAAGGACUGAGUAAAAUACUGCAUUUGAGAGUUUCUCUCCAUUGCAAAGUCCUCCCUCUCUUCUUUU,U10569.1/28-216,28-216,0,188,U10569.1/28-216 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00025.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00025_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00025.cm (global),/projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz,20742,U10570.1,1,sp|U10570.1|SM10570 Stylonychia mytilis telomerase RNA gene; complete sequence.,0,10,71,259,49.41,AGUUCGGCGGAAAUCCGUCAGCUAUAACGCUGUCAAGAAAACCCCAAAACCGUAAAUUGAGAGCAAUUCGCCUGGUUCCUCUUUAAAGUUAAACCAGGAAGCUCCGCCGAACUAGAGGUCGAUAAGGGCUGAGUAAAAUACUGCAUUUGAGAGCUUCUCUCCAUUGCAAAGUCCUCCCUCUCUUCUUUU,U10570.1/71-259,71-259,0,188,U10570.1/71-259 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00025.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00025_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00025.cm (global),/projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz,21754,U22349.1,1,sp|U22349.1|TA22349 Tetrahymena australis telomerase RNA gene; complete sequence.,0,11,201,360,103.54,AUACCCGCAUAUCAUUCAGACCCUUUAUGGAACUGUCAUUCAACCCCAAAAAUCUAGUGCAAAUAUUGUCUUAAUUACUUAGGCUAAAAGAAAUAAGUAUUAAAGCGGGACAAGGCAUCGACAUUUGAUACAAAUAUUGAUCAAUGGAUGUCUUAUUUUU,U22349.1/201-360,201-360,0,159,U22349.1/201-360 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00025.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00025_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00025.cm (global),/projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz,21924,U22350.1,1,sp|U22350.1|TB22350 Tetrahymena borealis telomerase RNA gene; complete sequence.,0,12,54,211,126.79,AUACCCGCAAAUUCAUUCAGGUCUGUAAUAGAUCUGUCAUUCAACCCCAAAAAUCUAGUGCAAAUAUUACCUUCACCAAUUAGGUAUAAUCAAUGGUAUCGCGGGACAAAAGACUAUCGACAUUUGGUACACUAUUUAUCAAUGGAUGUCUUAUUUUU,U22350.1/54-211,54-211,0,157,U22350.1/54-211 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00025.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00025_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00025.cm (global),/projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz,22639,U22351.1,1,sp|U22351.1|TC22351 Tetrahymena capricornis telomerase RNA gene; complete sequence.,0,13,82,237,106.44,AUACCCGCAUUUUCAUUCAGAUCUUUAAUGGAGCUGUCAUUCAACCCCAAAAAUCUAGUGCAACUACUGCCUUAACUACUUAGGCAAAAUAAGUCGUAAAGCGGGACAAGGCAUCGACAUUUGAUACAAAUAUUGAUCAAUGGAUAUCUUAUUUUU,U22351.1/82-237,82-237,0,155,U22351.1/82-237 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00025.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00025_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00025.cm (global),/projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz,23997,U22352.1,1,sp|U22352.1|TP22352 Tetrahymena paravorax telomerase RNA gene; complete sequence.,0,14,510,657,64.78,AAUCCCGCUAUUGCAUUCCAUUUCGAGUCAUUCAACCCCAAAAUUCUAGUACACACUAAAGCUUGCCUUUGGGCAUAUCAGGGGCAGCGGGAGAAUUUAGAAUUUCGACAUGUGGUACACUAUUUAUCUCAUGGAGAUUCUAAUUUUU,U22352.1/510-657,510-657,0,147,U22352.1/510-657 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00025.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00025_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00025.cm (global),/projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz,24421,U22353.1,1,sp|U22353.1|TS22353 Tetrahymena silvana telomerase RNA gene; complete sequence.,0,15,55,206,108.30,AUACCCGCAAAUUCACUCAAAUCUGUAAUAGGUUUGUCAUUCAACCCCAAAAAUCUAGUGCAAAUAUUACUUUCGCCAAUUAGGUAUAAUAAUGGUAAGCGGGACAAGACUCGACAUUUGAUACACUAUUUAUCAAUGGAUGUCUUUUUUCU,U22353.1/55-206,55-206,0,151,U22353.1/55-206 ./cmzasha --no-stderr --filter 200 40 Rfam/cm/RF00025.cm @/projects/bio/zasha/seqs/embl_release76/full-embl.list 1 hmm data/TryAllCm_orig/RF00025_greedy_forwardinf_cfsqp_cycling_Ecoli_0MM.bin ,Rfam/cm/RF00025.cm (global),/projects/bio/zasha/seqs/embl/inv03.dat.fasta.gz,24971,U22354.1,1,sp|U22354.1|TV22354 Tetrahymena vorax telomerase RNA gene; complete sequence.,0,16,218,376,113.52,AUACCCGCACAUUCACUCAAAUCUGUAAUAGACUUGUCAUUCAACCCCAAAAAUCUAGUGCAAAUAUUACCUUCGCCAAUUAGGUACAAUUAAUGGUUCUCGCGGGACAAAAGACUAUCGACAUUUGAUACAUUAUUUAUCAAUGGAUGUCUUAUUUUU,U22354.1/218-376,218-376,0,158,U22354.1/218-376 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)