Params: ./cmzasha --no-stderr --filter 450 20 Rfam/cm/RF00174.cm /projects/bio/zasha/seqs/embl_release76/hum03.dat.fasta.gz 1 specfile data/RF00174.filterspec Build: release Host: xmen.cs.washington.edu pid: 1612 ----fastaFile: /projects/bio/zasha/seqs/embl_release76/hum03.dat.fasta.gz ----specfile: 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,41,r-CU_-AG,40,r-ACU-G_,79,l-ACU_-G,78,r-AGU_-C,93,l-ACU-G_,92,r-AGU_-C,91,l-ACG-U_,154,r-ACU-G-_,153,r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,41,l-AG-CU-_,40,r-ACU-G_,39,l-AGU-C_,79,l-ACU-G-_,78,r-AGU-C-_,76,r-ACU-G_,93,l-ACU-G_,92,r-AGU-C-_,91,l-AC-G-U-_,154,r-ACU-G-_,153,r-A-C-G-U-_,152,l-ACU-G_ 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,41,l-AG-CU-_,40,l-AGU-C-_,39,r-CU-A-G-_,79,l-ACU-G-_,78,r-AGU-C-_,77,l-AG_-CU,76,r-ACU-G_,75,r-CU_-AG,93,r-ACU-G-_,92,r-AGU-C-_,91,r-A-C-G-U-_,154,r-CU-A-G-_,153,l-AC-GU-_,152,r-AG-CU-_,150,r-ACU_-G 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,41,r-CU-A-G-_,40,l-AG-C-U-_,39,r-CU-A-G-_,79,l-ACU-G-_,78,r-AGU-C-_,77,r-AU-C_-G,76,r-AU-C_-G,75,r-CU_-AG,93,r-ACU-G-_,92,r-AG-C-U-_,91,r-A-C-G-U-_,154,r-ACU-G-_,153,r-A-C-G-U-_,152,r-AG-CU-_,150,r-ACU_-G,142,l-ACU-G-_ 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub,133,240/sub,91,40 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub,133,240/sub,75,430 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub,101,450 Exploded HMM has 1410 states ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,41,r-CU_-AG/remember-nuc,40,r-ACU-G_/remember-nuc,79,l-ACU_-G/remember-nuc,78,r-AGU_-C/remember-nuc,93,l-ACU-G_/remember-nuc,92,r-AGU_-C/remember-nuc,91,l-ACG-U_/remember-nuc,154,r-ACU-G-_/remember-nuc,153,r-AGU-C_ Exploded HMM has 3608 states ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,41,l-AG-CU-_/remember-nuc,40,r-ACU-G_/remember-nuc,39,l-AGU-C_/remember-nuc,79,l-ACU-G-_/remember-nuc,78,r-AGU-C-_/remember-nuc,76,r-ACU-G_/remember-nuc,93,l-ACU-G_/remember-nuc,92,r-AGU-C-_/remember-nuc,91,l-AC-G-U-_/remember-nuc,154,r-ACU-G-_/remember-nuc,153,r-A-C-G-U-_/remember-nuc,152,l-ACU-G_ Exploded HMM has 8989 states ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,41,l-AG-CU-_/remember-nuc,40,l-AGU-C-_/remember-nuc,39,r-CU-A-G-_/remember-nuc,79,l-ACU-G-_/remember-nuc,78,r-AGU-C-_/remember-nuc,77,l-AG_-CU/remember-nuc,76,r-ACU-G_/remember-nuc,75,r-CU_-AG/remember-nuc,93,r-ACU-G-_/remember-nuc,92,r-AGU-C-_/remember-nuc,91,r-A-C-G-U-_/remember-nuc,154,r-CU-A-G-_/remember-nuc,153,l-AC-GU-_/remember-nuc,152,r-AG-CU-_/remember-nuc,150,r-ACU_-G Exploded HMM has 20480 states ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,41,r-CU-A-G-_/remember-nuc,40,l-AG-C-U-_/remember-nuc,39,r-CU-A-G-_/remember-nuc,79,l-ACU-G-_/remember-nuc,78,r-AGU-C-_/remember-nuc,77,r-AU-C_-G/remember-nuc,76,r-AU-C_-G/remember-nuc,75,r-CU_-AG/remember-nuc,93,r-ACU-G-_/remember-nuc,92,r-AG-C-U-_/remember-nuc,91,r-A-C-G-U-_/remember-nuc,154,r-ACU-G-_/remember-nuc,153,r-A-C-G-U-_/remember-nuc,152,r-AG-CU-_/remember-nuc,150,r-ACU_-G/remember-nuc,142,l-ACU-G-_ ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/sub,133,240/sub,91,40 ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/sub,133,240/sub,75,430 ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/sub,101,450 ----cmFile: Rfam/cm/RF00174.cm (global) Found 0 hits. done 1.7382e+09 nucs (frac lets thru so far=2.59695e-06, 2d-fracLetsThru=1.30864e-06). Filter report: done 1.7382e+09 nucs (frac lets thru so far=0.169513, 2d-fracLetsThru=0.100691). Filter report: done 2.94646e+08 nucs (frac lets thru so far=0.311337, 2d-fracLetsThru=0.281394). Filter report: done 9.17344e+07 nucs (frac lets thru so far=0.244809, 2d-fracLetsThru=0.23567). Filter report: done 2.24574e+07 nucs (frac lets thru so far=0.3229, 2d-fracLetsThru=0.319355). Filter report: done 7.2515e+06 nucs (frac lets thru so far=0.082056, 2d-fracLetsThru=0.0813145). Filter report: done 595029 nucs (frac lets thru so far=0.15312, 2d-fracLetsThru=0.153031). Filter report: done 91111 nucs (frac lets thru so far=0.049544, 2d-fracLetsThru=0.0493159). FULL: done 1.7382e+09 nucs (frac lets thru so far=2.59695e-06, 2d-fracLetsThru=1.30864e-06). CPU time: 379767.82u 180.69s 105:32:28.51 Elapsed: 105:39:07 Params: ./cmzasha --no-stderr --filter 450 20 Rfam/cm/RF00174.cm /projects/bio/zasha/seqs/embl_release76/hum10.dat.fasta.gz 1 specfile data/RF00174.filterspec Build: release Host: xmen.cs.washington.edu pid: 1578 ----fastaFile: /projects/bio/zasha/seqs/embl_release76/hum10.dat.fasta.gz ----specfile: 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,41,r-CU_-AG,40,r-ACU-G_,79,l-ACU_-G,78,r-AGU_-C,93,l-ACU-G_,92,r-AGU_-C,91,l-ACG-U_,154,r-ACU-G-_,153,r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,41,l-AG-CU-_,40,r-ACU-G_,39,l-AGU-C_,79,l-ACU-G-_,78,r-AGU-C-_,76,r-ACU-G_,93,l-ACU-G_,92,r-AGU-C-_,91,l-AC-G-U-_,154,r-ACU-G-_,153,r-A-C-G-U-_,152,l-ACU-G_ 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,41,l-AG-CU-_,40,l-AGU-C-_,39,r-CU-A-G-_,79,l-ACU-G-_,78,r-AGU-C-_,77,l-AG_-CU,76,r-ACU-G_,75,r-CU_-AG,93,r-ACU-G-_,92,r-AGU-C-_,91,r-A-C-G-U-_,154,r-CU-A-G-_,153,l-AC-GU-_,152,r-AG-CU-_,150,r-ACU_-G 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,41,r-CU-A-G-_,40,l-AG-C-U-_,39,r-CU-A-G-_,79,l-ACU-G-_,78,r-AGU-C-_,77,r-AU-C_-G,76,r-AU-C_-G,75,r-CU_-AG,93,r-ACU-G-_,92,r-AG-C-U-_,91,r-A-C-G-U-_,154,r-ACU-G-_,153,r-A-C-G-U-_,152,r-AG-CU-_,150,r-ACU_-G,142,l-ACU-G-_ 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub,133,240/sub,91,40 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub,133,240/sub,75,430 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub,101,450 Exploded HMM has 1410 states ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,41,r-CU_-AG/remember-nuc,40,r-ACU-G_/remember-nuc,79,l-ACU_-G/remember-nuc,78,r-AGU_-C/remember-nuc,93,l-ACU-G_/remember-nuc,92,r-AGU_-C/remember-nuc,91,l-ACG-U_/remember-nuc,154,r-ACU-G-_/remember-nuc,153,r-AGU-C_ Exploded HMM has 3608 states ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,41,l-AG-CU-_/remember-nuc,40,r-ACU-G_/remember-nuc,39,l-AGU-C_/remember-nuc,79,l-ACU-G-_/remember-nuc,78,r-AGU-C-_/remember-nuc,76,r-ACU-G_/remember-nuc,93,l-ACU-G_/remember-nuc,92,r-AGU-C-_/remember-nuc,91,l-AC-G-U-_/remember-nuc,154,r-ACU-G-_/remember-nuc,153,r-A-C-G-U-_/remember-nuc,152,l-ACU-G_ Exploded HMM has 8989 states ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,41,l-AG-CU-_/remember-nuc,40,l-AGU-C-_/remember-nuc,39,r-CU-A-G-_/remember-nuc,79,l-ACU-G-_/remember-nuc,78,r-AGU-C-_/remember-nuc,77,l-AG_-CU/remember-nuc,76,r-ACU-G_/remember-nuc,75,r-CU_-AG/remember-nuc,93,r-ACU-G-_/remember-nuc,92,r-AGU-C-_/remember-nuc,91,r-A-C-G-U-_/remember-nuc,154,r-CU-A-G-_/remember-nuc,153,l-AC-GU-_/remember-nuc,152,r-AG-CU-_/remember-nuc,150,r-ACU_-G Exploded HMM has 20480 states ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,41,r-CU-A-G-_/remember-nuc,40,l-AG-C-U-_/remember-nuc,39,r-CU-A-G-_/remember-nuc,79,l-ACU-G-_/remember-nuc,78,r-AGU-C-_/remember-nuc,77,r-AU-C_-G/remember-nuc,76,r-AU-C_-G/remember-nuc,75,r-CU_-AG/remember-nuc,93,r-ACU-G-_/remember-nuc,92,r-AG-C-U-_/remember-nuc,91,r-A-C-G-U-_/remember-nuc,154,r-ACU-G-_/remember-nuc,153,r-A-C-G-U-_/remember-nuc,152,r-AG-CU-_/remember-nuc,150,r-ACU_-G/remember-nuc,142,l-ACU-G-_ ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/sub,133,240/sub,91,40 ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/sub,133,240/sub,75,430 ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/sub,101,450 ----cmFile: Rfam/cm/RF00174.cm (global) Found 0 hits. done 1.71341e+09 nucs (frac lets thru so far=4.49689e-06, 2d-fracLetsThru=2.27525e-06). Filter report: done 1.71341e+09 nucs (frac lets thru so far=0.175977, 2d-fracLetsThru=0.104578). Filter report: done 3.0152e+08 nucs (frac lets thru so far=0.312294, 2d-fracLetsThru=0.282085). Filter report: done 9.41629e+07 nucs (frac lets thru so far=0.244531, 2d-fracLetsThru=0.235554). Filter report: done 2.30258e+07 nucs (frac lets thru so far=0.320054, 2d-fracLetsThru=0.316255). Filter report: done 7.3695e+06 nucs (frac lets thru so far=0.0777177, 2d-fracLetsThru=0.0770081). Filter report: done 572741 nucs (frac lets thru so far=0.154674, 2d-fracLetsThru=0.154223). Filter report: done 88588 nucs (frac lets thru so far=0.0869757, 2d-fracLetsThru=0.0871757). FULL: done 1.71341e+09 nucs (frac lets thru so far=4.49689e-06, 2d-fracLetsThru=2.27525e-06). CPU time: 381004.16u 160.58s 105:52:44.73 Elapsed: 105:59:23 Params: ./cmzasha --no-stderr --filter 450 20 Rfam/cm/RF00174.cm @/projects/bio/zasha/seqs/embl_release76/hum.list 1 specfile data/RF00174.filterspec Build: release Host: xmen.cs.washington.edu pid: 3588 ----specfile: 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,41,r-CU_-AG,40,r-ACU-G_,79,l-ACU_-G,78,r-AGU_-C,93,l-ACU-G_,92,r-AGU_-C,91,l-ACG-U_,154,r-ACU-G-_,153,r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,41,l-AG-CU-_,40,r-ACU-G_,39,l-AGU-C_,79,l-ACU-G-_,78,r-AGU-C-_,76,r-ACU-G_,93,l-ACU-G_,92,r-AGU-C-_,91,l-AC-G-U-_,154,r-ACU-G-_,153,r-A-C-G-U-_,152,l-ACU-G_ 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,41,l-AG-CU-_,40,l-AGU-C-_,39,r-CU-A-G-_,79,l-ACU-G-_,78,r-AGU-C-_,77,l-AG_-CU,76,r-ACU-G_,75,r-CU_-AG,93,r-ACU-G-_,92,r-AGU-C-_,91,r-A-C-G-U-_,154,r-CU-A-G-_,153,l-AC-GU-_,152,r-AG-CU-_,150,r-ACU_-G 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,41,r-CU-A-G-_,40,l-AG-C-U-_,39,r-CU-A-G-_,79,l-ACU-G-_,78,r-AGU-C-_,77,r-AU-C_-G,76,r-AU-C_-G,75,r-CU_-AG,93,r-ACU-G-_,92,r-AG-C-U-_,91,r-A-C-G-U-_,154,r-ACU-G-_,153,r-A-C-G-U-_,152,r-AG-CU-_,150,r-ACU_-G,142,l-ACU-G-_ 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub,133,240/sub,91,40 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub,133,240/sub,75,430 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub,101,450 Exploded HMM has 1410 states ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,41,r-CU_-AG/remember-nuc,40,r-ACU-G_/remember-nuc,79,l-ACU_-G/remember-nuc,78,r-AGU_-C/remember-nuc,93,l-ACU-G_/remember-nuc,92,r-AGU_-C/remember-nuc,91,l-ACG-U_/remember-nuc,154,r-ACU-G-_/remember-nuc,153,r-AGU-C_ Exploded HMM has 3608 states ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,41,l-AG-CU-_/remember-nuc,40,r-ACU-G_/remember-nuc,39,l-AGU-C_/remember-nuc,79,l-ACU-G-_/remember-nuc,78,r-AGU-C-_/remember-nuc,76,r-ACU-G_/remember-nuc,93,l-ACU-G_/remember-nuc,92,r-AGU-C-_/remember-nuc,91,l-AC-G-U-_/remember-nuc,154,r-ACU-G-_/remember-nuc,153,r-A-C-G-U-_/remember-nuc,152,l-ACU-G_ Exploded HMM has 8989 states ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,41,l-AG-CU-_/remember-nuc,40,l-AGU-C-_/remember-nuc,39,r-CU-A-G-_/remember-nuc,79,l-ACU-G-_/remember-nuc,78,r-AGU-C-_/remember-nuc,77,l-AG_-CU/remember-nuc,76,r-ACU-G_/remember-nuc,75,r-CU_-AG/remember-nuc,93,r-ACU-G-_/remember-nuc,92,r-AGU-C-_/remember-nuc,91,r-A-C-G-U-_/remember-nuc,154,r-CU-A-G-_/remember-nuc,153,l-AC-GU-_/remember-nuc,152,r-AG-CU-_/remember-nuc,150,r-ACU_-G Exploded HMM has 20480 states ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,41,r-CU-A-G-_/remember-nuc,40,l-AG-C-U-_/remember-nuc,39,r-CU-A-G-_/remember-nuc,79,l-ACU-G-_/remember-nuc,78,r-AGU-C-_/remember-nuc,77,r-AU-C_-G/remember-nuc,76,r-AU-C_-G/remember-nuc,75,r-CU_-AG/remember-nuc,93,r-ACU-G-_/remember-nuc,92,r-AG-C-U-_/remember-nuc,91,r-A-C-G-U-_/remember-nuc,154,r-ACU-G-_/remember-nuc,153,r-A-C-G-U-_/remember-nuc,152,r-AG-CU-_/remember-nuc,150,r-ACU_-G/remember-nuc,142,l-ACU-G-_ ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/sub,133,240/sub,91,40 ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/sub,133,240/sub,75,430 ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/sub,101,450 ----cmFile: Rfam/cm/RF00174.cm (global) ----fastaFile: /projects/bio/zasha/seqs/embl_release76/hum01.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl_release76/hum02.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl_release76/hum03.dat.fasta.gz Params: ./cmzasha --no-stderr --filter 450 20 Rfam/cm/RF00174.cm @/projects/bio/zasha/seqs/embl_release76/hum-rev.list 1 specfile data/RF00174.filterspec Build: release Host: gattaca.cs.washington.edu pid: 10116 ----specfile: 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,41,r-CU_-AG,40,r-ACU-G_,79,l-ACU_-G,78,r-AGU_-C,93,l-ACU-G_,92,r-AGU_-C,91,l-ACG-U_,154,r-ACU-G-_,153,r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,41,l-AG-CU-_,40,r-ACU-G_,39,l-AGU-C_,79,l-ACU-G-_,78,r-AGU-C-_,76,r-ACU-G_,93,l-ACU-G_,92,r-AGU-C-_,91,l-AC-G-U-_,154,r-ACU-G-_,153,r-A-C-G-U-_,152,l-ACU-G_ 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,41,l-AG-CU-_,40,l-AGU-C-_,39,r-CU-A-G-_,79,l-ACU-G-_,78,r-AGU-C-_,77,l-AG_-CU,76,r-ACU-G_,75,r-CU_-AG,93,r-ACU-G-_,92,r-AGU-C-_,91,r-A-C-G-U-_,154,r-CU-A-G-_,153,l-AC-GU-_,152,r-AG-CU-_,150,r-ACU_-G 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,41,r-CU-A-G-_,40,l-AG-C-U-_,39,r-CU-A-G-_,79,l-ACU-G-_,78,r-AGU-C-_,77,r-AU-C_-G,76,r-AU-C_-G,75,r-CU_-AG,93,r-ACU-G-_,92,r-AG-C-U-_,91,r-A-C-G-U-_,154,r-ACU-G-_,153,r-A-C-G-U-_,152,r-AG-CU-_,150,r-ACU_-G,142,l-ACU-G-_ 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub,133,240/sub,91,40 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub,133,240/sub,75,430 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub,101,450 Exploded HMM has 1410 states ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,41,r-CU_-AG/remember-nuc,40,r-ACU-G_/remember-nuc,79,l-ACU_-G/remember-nuc,78,r-AGU_-C/remember-nuc,93,l-ACU-G_/remember-nuc,92,r-AGU_-C/remember-nuc,91,l-ACG-U_/remember-nuc,154,r-ACU-G-_/remember-nuc,153,r-AGU-C_ Exploded HMM has 3608 states ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,41,l-AG-CU-_/remember-nuc,40,r-ACU-G_/remember-nuc,39,l-AGU-C_/remember-nuc,79,l-ACU-G-_/remember-nuc,78,r-AGU-C-_/remember-nuc,76,r-ACU-G_/remember-nuc,93,l-ACU-G_/remember-nuc,92,r-AGU-C-_/remember-nuc,91,l-AC-G-U-_/remember-nuc,154,r-ACU-G-_/remember-nuc,153,r-A-C-G-U-_/remember-nuc,152,l-ACU-G_ Exploded HMM has 8989 states ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,41,l-AG-CU-_/remember-nuc,40,l-AGU-C-_/remember-nuc,39,r-CU-A-G-_/remember-nuc,79,l-ACU-G-_/remember-nuc,78,r-AGU-C-_/remember-nuc,77,l-AG_-CU/remember-nuc,76,r-ACU-G_/remember-nuc,75,r-CU_-AG/remember-nuc,93,r-ACU-G-_/remember-nuc,92,r-AGU-C-_/remember-nuc,91,r-A-C-G-U-_/remember-nuc,154,r-CU-A-G-_/remember-nuc,153,l-AC-GU-_/remember-nuc,152,r-AG-CU-_/remember-nuc,150,r-ACU_-G Exploded HMM has 20480 states ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,41,r-CU-A-G-_/remember-nuc,40,l-AG-C-U-_/remember-nuc,39,r-CU-A-G-_/remember-nuc,79,l-ACU-G-_/remember-nuc,78,r-AGU-C-_/remember-nuc,77,r-AU-C_-G/remember-nuc,76,r-AU-C_-G/remember-nuc,75,r-CU_-AG/remember-nuc,93,r-ACU-G-_/remember-nuc,92,r-AG-C-U-_/remember-nuc,91,r-A-C-G-U-_/remember-nuc,154,r-ACU-G-_/remember-nuc,153,r-A-C-G-U-_/remember-nuc,152,r-AG-CU-_/remember-nuc,150,r-ACU_-G/remember-nuc,142,l-ACU-G-_ ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/sub,133,240/sub,91,40 ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/sub,133,240/sub,75,430 ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/sub,101,450 ----cmFile: Rfam/cm/RF00174.cm (global) ----fastaFile: /projects/bio/zasha/seqs/embl_release76/hum26.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl_release76/hum25.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl_release76/hum24.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl_release76/hum23.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl_release76/hum22.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl_release76/hum21.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl_release76/hum20.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl_release76/hum19.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl_release76/hum18.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl_release76/hum17.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl_release76/hum16.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl_release76/hum15.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl_release76/hum14.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl_release76/hum13.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl_release76/hum12.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl_release76/hum11.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl_release76/hum10.dat.fasta.gz Params: ./cmzasha --no-stderr --filter 450 20 Rfam/cm/RF00174.cm @t.list 1 specfile data/RF00174.filterspec Build: release Host: xmen.cs.washington.edu pid: 1728 ----specfile: 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,41,r-CU_-AG,40,r-ACU-G_,79,l-ACU_-G,78,r-AGU_-C,93,l-ACU-G_,92,r-AGU_-C,91,l-ACG-U_,154,r-ACU-G-_,153,r-AGU-C_ 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,41,l-AG-CU-_,40,r-ACU-G_,39,l-AGU-C_,79,l-ACU-G-_,78,r-AGU-C-_,76,r-ACU-G_,93,l-ACU-G_,92,r-AGU-C-_,91,l-AC-G-U-_,154,r-ACU-G-_,153,r-A-C-G-U-_,152,l-ACU-G_ 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,41,l-AG-CU-_,40,l-AGU-C-_,39,r-CU-A-G-_,79,l-ACU-G-_,78,r-AGU-C-_,77,l-AG_-CU,76,r-ACU-G_,75,r-CU_-AG,93,r-ACU-G-_,92,r-AGU-C-_,91,r-A-C-G-U-_,154,r-CU-A-G-_,153,l-AC-GU-_,152,r-AG-CU-_,150,r-ACU_-G 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/remember-nuc,41,r-CU-A-G-_,40,l-AG-C-U-_,39,r-CU-A-G-_,79,l-ACU-G-_,78,r-AGU-C-_,77,r-AU-C_-G,76,r-AU-C_-G,75,r-CU_-AG,93,r-ACU-G-_,92,r-AG-C-U-_,91,r-A-C-G-U-_,154,r-ACU-G-_,153,r-A-C-G-U-_,152,r-AG-CU-_,150,r-ACU_-G,142,l-ACU-G-_ 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub,133,240/sub,91,40 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub,133,240/sub,75,430 2struct-str data/TryAllCm_5.0/RF00174_forwardinf_hmmtype1_Ecoli_0MM.bin 1/sub,101,450 Exploded HMM has 1410 states ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,41,r-CU_-AG/remember-nuc,40,r-ACU-G_/remember-nuc,79,l-ACU_-G/remember-nuc,78,r-AGU_-C/remember-nuc,93,l-ACU-G_/remember-nuc,92,r-AGU_-C/remember-nuc,91,l-ACG-U_/remember-nuc,154,r-ACU-G-_/remember-nuc,153,r-AGU-C_ Exploded HMM has 3608 states ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,41,l-AG-CU-_/remember-nuc,40,r-ACU-G_/remember-nuc,39,l-AGU-C_/remember-nuc,79,l-ACU-G-_/remember-nuc,78,r-AGU-C-_/remember-nuc,76,r-ACU-G_/remember-nuc,93,l-ACU-G_/remember-nuc,92,r-AGU-C-_/remember-nuc,91,l-AC-G-U-_/remember-nuc,154,r-ACU-G-_/remember-nuc,153,r-A-C-G-U-_/remember-nuc,152,l-ACU-G_ Exploded HMM has 8989 states ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,41,l-AG-CU-_/remember-nuc,40,l-AGU-C-_/remember-nuc,39,r-CU-A-G-_/remember-nuc,79,l-ACU-G-_/remember-nuc,78,r-AGU-C-_/remember-nuc,77,l-AG_-CU/remember-nuc,76,r-ACU-G_/remember-nuc,75,r-CU_-AG/remember-nuc,93,r-ACU-G-_/remember-nuc,92,r-AGU-C-_/remember-nuc,91,r-A-C-G-U-_/remember-nuc,154,r-CU-A-G-_/remember-nuc,153,l-AC-GU-_/remember-nuc,152,r-AG-CU-_/remember-nuc,150,r-ACU_-G Exploded HMM has 20480 states ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/remember-nuc,41,r-CU-A-G-_/remember-nuc,40,l-AG-C-U-_/remember-nuc,39,r-CU-A-G-_/remember-nuc,79,l-ACU-G-_/remember-nuc,78,r-AGU-C-_/remember-nuc,77,r-AU-C_-G/remember-nuc,76,r-AU-C_-G/remember-nuc,75,r-CU_-AG/remember-nuc,93,r-ACU-G-_/remember-nuc,92,r-AG-C-U-_/remember-nuc,91,r-A-C-G-U-_/remember-nuc,154,r-ACU-G-_/remember-nuc,153,r-A-C-G-U-_/remember-nuc,152,r-AG-CU-_/remember-nuc,150,r-ACU_-G/remember-nuc,142,l-ACU-G-_ ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/sub,133,240/sub,91,40 ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/sub,133,240/sub,75,430 ----hmm-from-cmFileName: Rfam/cm/RF00174.cm ----hmm-build-info: ;(default construction of HMM) Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ;Params: ./cmzasha --no-stderr --set-input-mm-file data/Ecoli_0mm.mm --cm2hmm-set-node-combiner-forward-inf Rfam/cm/RF00174.cm 1 1 100000 1 Build: release Host: gattaca.cs.washington.edu ----2struct-info: 1/sub,101,450 ----cmFile: Rfam/cm/RF00174.cm (global) ----fastaFile: /projects/bio/zasha/seqs/embl/174cont_mus.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/org.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/phg.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #16671,sp|M34485.1|ACTRPF Acinetobacter calcoaceticus 5'-phosphoribosyl anthranilate isomerase (trpF) gene, complete cds; and tryptophan synthase (trpB) gene, partial cds. ----isReversed: 1 ----hitSequence: UUUACACAAUUCGUAACAAGUUAAAAGCAUUCGCUUUAGGGAAACUGGUGCAAAUCCAGUGCUGCCCCCGCAACGGUAAAAAUGUAAACCAUAUUAAAAAAGUCAUUUAGACUUACGCCACUGCAUGCAUAGAUGUGGGAAGGUGAAUAUGCUUGUCUCUUUUUGAGAUGCCAUUUGAGUCCGGAGACCUGCUUGUUACAUCUAUCCACUC hit 0 : 360 150 (rev) 83.70 bits ::::::::::::::[[[[[[,.<<<________.____>>>,,,,,(((,,,<<<<<___ 1 uuauauuagccacgugaaGGU.ccccccagaau.gggggggUUAAaAGGGAAucCGGUGa 58 UU++ + A +++:::::GU ::: + + + G+::: AGGGAA:C:GGUG+ 1107 UUUACACAAUUCGUAACAAGUuAAA----AGCAuUCGCUUU-----AGGGAAACUGGUGC 1157 ____>>>>>,,<<<____>>>,<<<---<<<<------<<<<<<-----........... 59 AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccgccAaaau........... 107 AAAUCC:G:GCUGCCCCCGCAAC:GUAA::::G A +C:::::AAAA+ 1158 AAAUCCAGUGCUGCCCCCGCAACGGUAAAAAUGUAAACCAUAUUAAAAAagucauuuaga 1217 .....<<<-<<<<<<.____.>>>>>>--->>>.>>>>>>----------.......... 108 .....GCCACUgggc.ucaa.gcccGGGAAGGC.ggcgggaaggaggaaa.......... 149 CCACU:::: A ::::GGGAAGG :::::G+ G + 1218 cuuacGCCACUGCAUgCAUAgAUGUGGGAAGGUgAAUAUGCUUGUCUCUUuuugagaugc 1277 .>>>>---->>>,,,,)))]]]]]]::::::::::::::: 150 .cCgcgAGCCAGGAGACCUGCcgugaguguuaacaccccc 188 ::::GAG+C:GGAGACCUG:::::+++ U +A++C C+C 1278 cAUUUGAGUCCGGAGACCUGCUUGUUACAUCUAUCCACUC 1317 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #17825,sp|AE001694.1|AE001694 Thermotoga maritima section 6 of 136 of the complete genome. ----isReversed: 1 ----hitSequence: AAAGGGGAAGCCGGUGAAAAUCCGGCGCGGGGCCGCCACCGUGACCGGGGACGAAACCCGCAGAACGCCACUGGGGCGAUCACCCUGGGAAGGCGCGGGGAGUAGGAUGAUCCGGAAGCCGGGAAACCCGCCCGCGGUGAAGGGGAACC hit 1 : 12102 11954 (rev) 28.34 bits ::::::::::::::[[[[[[,<<<____________>>>,,,,,(((,,,<<<<<_____ 1 uuauauuagccacgugaaGGUccccccagaaugggggggUUAAaAGGGAAucCGGUGaAA 60 AAA:GGGAA:CCGGUGAAA 1 -----------------------------------------AAAGGGGAAGCCGGUGAAA 19 __>>>>>,,<<<____>>>,<<<---<<<<.------<<<<<<-----<<<-<<<<<<.. 61 AUCCGgaGCUGcCCCCgCAACUGUAAgcGg.gaaggacccgccAaaauGCCACUgggc.. 117 AUCCGG:GC:G CC C:AC:GU+A:CGG GA G A:CC::CA AA GCCACU:GG: 20 AUCCGGCGCGGG-GCCGCCACCGUGACCGGgGACGAAACCCGCAGAACGCCACUGGGGcg 78 ____>>>>>>--->>>>>>>>>----------.>>>>---->>>,,,,)))]]]]]]::: 118 ucaagcccGGGAAGGCggcgggaaggaggaaa.cCgcgAGCCAGGAGACCUGCcgugagu 176 ++ A:CC:GGGAAGGCG::GG:A+ +G +A CCG:+AGCC:GGA ACC: C G G+ 79 AUCACCCUGGGAAGGCGCGGGGAGUAGGAUGAuCCGGAAGCCGGGAAACCC-GCCCGCGG 137 :::::::::::: 177 guuaacaccccc 188 A+ +CC 138 UGAAGGGGAACC 149 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #18878,sp|AE004105.1|AE004105 Vibrio cholerae chromosome I, section 13 of 251 of the complete chromosome. ----isReversed: 0 ----hitSequence: UACUAUCAGCGCCAAGCUGGUGCUAUUUAGAUGCCUGGAUGGCUAAAAAUGGCUGAAAAGGGAAUCCGGUGUAACUCCGGAACUGACGCGCAGCGGUAAGAGAGAACGAACGCUCAAACGACACUGCUUUUCGAGUGGGAAGUCGAGCCAGUAGGCCAACAGUGCUCUCAAGUCCGAAGACCUGCCAGCAACUGAGUUAUGCAG hit 2 : 5235 5438 (fwd) 101.85 bits ::::::::::::::[[[[[[,<<<____.........____.....____>>>,,,,,(( 1 uuauauuagccacgugaaGGUcccccca.........gaau.....gggggggUUAAaAG 46 U UAU AGC++C ::::GGU:C: GA :G:U+AAAAG 5235 UACUAUCAGCGCCAAGCUGGUGCUAUUUagaugccugGAUGgcuaaAAAUGGCUGAAAAG 5294 (,,,<<<<<_______>>>>>,,<<<____>>>,<<<---<<<<------<<<<<<---- 47 GGAAucCGGUGaAAAUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccgccAaaa 106 GGAAUCCGGUG AA UCCGGA+CUG: C C:CA C:GUAAG:G:GAA+GA:::::CAAA 5295 GGAAUCCGGUGUAACUCCGGAACUGA-CGCGCAGCGGUAAGAGAGAACGAACGCUCAAAC 5353 -<<<-<<<<<<____>>>>>>--->>>>>>>>>----------.....>>>>---->>>, 107 uGCCACUgggcucaagcccGGGAAGGCggcgggaaggaggaaa.....cCgcgAGCCAGG 161 G:CACU:::: + +::::GGGAAG:CG:::::+ G+ AA+ :C:C+AG+C:G+ 5354 -GACACUGCUU-UUCGAGUGGGAAGUCGAGCCAGUAGGCCAACagugcUCUCAAGUCCGA 5411 ,,,)))]]]]]]::::::::::::::: 162 AGACCUGCcgugaguguuaacaccccc 188 AGACCUGC::::A++ +A+ C 5412 AGACCUGCCAGCAACUGAGUUAUGCAG 5438 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #19486,sp|AE004716.1|AE004716 Pseudomonas aeruginosa PAO1, section 277 of 529 of the complete genome. ----isReversed: 1 ----hitSequence: GGGCCGAAGAGGGAACACGGAGCCGCGGUCUUUUCGAAGCCCGGGCCUAGCCGUGGCUGCCCCCGCAACUGUAUGCAGCCUGUAUUCGCGCCAUUCGCCACUGGAUUACCGGGAAGGCGGCGCGAAGCGGAGGUUCCUCCCCCGGGUGGAACGCCGGGCUGCGAGCCAGGAGACCUGCCGCCGAAACCAGUCGCGAG hit 3 : 11608 11412 (rev) 49.44 bits ::::::::::::::[[[[[[,<<<____________>>>,,.,,,(((,,,<<<<<____ 1 uuauauuagccacgugaaGGUccccccagaaugggggggUU.AAaAGGGAAucCGGUGaA 59 + AG + + ::A+GG CC+C GG U : GAA C G G+ 3 GGGCCGAAGAGGGAACACGGAGCCGC----------GGUCUu---UUCGAAGCCCGGGCC 49 ___>>>>>,,<<<____>>>,<<<---<<<<..------<<<<<<-----<<<-<<<<<< 60 AAUCCGgaGCUGcCCCCgCAACUGUAAgcGg..gaaggacccgccAaaauGCCACUgggc 117 A C G GCUGCCCCCGCAACUGUA GC:G + C:CGCCA++ GCCACUGG 50 UAGCCGUGGCUGCCCCCGCAACUGUAUGCAGccUGUAUUCGCGCCAUUC-GCCACUGG-- 106 ____>>>>>>--->>>>>>>>>----------........................>>>> 118 ucaagcccGGGAAGGCggcgggaaggaggaaa........................cCgc 153 ++ A CCGGGAAGGCGGCG:GAAG +G ++ C:GC 107 AUUA--CCGGGAAGGCGGCGCGAAGCGGAGGUuccucccccggguggaacgccgggCUGC 164 ---->>>,,,,)))]]]]]]::::::::::::::: 154 gAGCCAGGAGACCUGCcgugaguguuaacaccccc 188 GAGCCAGGAGA : GC+G:: + A+++ C 165 GAGCCAGGAGACCUGCCGCCGAAACCAGUCGCGAG 199 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #19487,sp|AE004717.1|AE004717 Pseudomonas aeruginosa PAO1, section 278 of 529 of the complete genome. ----isReversed: 0 ----hitSequence: CCCAUCCGGCCCGUUCCAGGUGCCUCCUGCCGCCGCGCAGGAGGUGAAACGGGAAGCCGGUGCGUCACUUCGGUGAUCAGUCCGGCGCUGCCCCCGCAACGGUAAGCGAGCGAAAUCCUCUUCAGGCCACUGUGCUCCGGCAUGGGAAGGCGAGGAUUUCACGACCCUCGCAAGCCCGGAGACCGGCCUGCAACGCCCUGUUGGCA hit 4 : 4221 4426 (fwd) 123.07 bits ::::::::::::::[[[[[[,.<<<____..____..____>>>,,,,,(((,,,<<<<< 1 uuauauuagccacgugaaGGU.cccccca..gaau..gggggggUUAAaAGGGAAucCGG 55 ++ GCC+++:::AGGU CC:CC + G GG:GGU+AAA:GGGAA:CCGG 4221 CCCAUCCGGCCCGUUCCAGGUgCCUCCUGccGCCGcgCAGGAGGUGAAACGGGAAGCCGG 4280 ___..............____>>>>>,,<<<____>>>,<<<---<<<<------<<<<< 56 UGa..............AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccgc 101 UG+ A UCCGG:GCUGCCCCCGCAAC:GUAAGCG: + G A :C:: 4281 UGCgucacuucggugauCAGUCCGGCGCUGCCCCCGCAACGGUAAGCGA-GCGAAAUCCU 4339 <-----<<<-<<<<<<____>>>>>>--->>>>>>>>>---------->>>>---->>>, 102 cAaaauGCCACUgggcucaagcccGGGAAGGCggcgggaaggaggaaacCgcgAGCCAGG 161 C + A GCCACU::GCUC GC::GGGAAGGCG::G: + G +:CGC+AGCC:GG 4340 CUUCAGGCCACUGUGCUCCGGCAUGGGAAGGCGAGGAUUUCACGACCCUCGCAAGCCCGG 4399 ,,,)))]]]]]]::::::::::::::: 162 AGACCUGCcgugaguguuaacaccccc 188 AGACC:GCC:::A++G + C 4400 AGACCGGCCUGCAACGCCCUGUUGGCA 4426 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #19491,sp|AE004721.1|AE004721 Pseudomonas aeruginosa PAO1, section 282 of 529 of the complete genome. ----isReversed: 0 ----hitSequence: CCUAGGCGGGUUGUCCCAGGUGUCUCGUGCCGGCGCGCACGAGGUGAAACGGGAAGCCGGUGACGCUCUCCGAGCCAGUCCGGCGCUGCCCCCGCAACGGUAAGCGCAUCGCGCGCGAGCCCGGAGACCGGCCUGGAACCUUUCGUUUGAUUCACCCGCGGUGGGCGGGCGCAAGCGUGAAGCGGGCCGUCCGGGCCUGUUCCUCG hit 5 : 1492 1697 (fwd) 43.04 bits ::::::::::::::[[[[[[,.<<<____..____..____>>>,,,,,(((,,,<<<<< 1 uuauauuagccacgugaaGGU.cccccca..gaau..gggggggUUAAaAGGGAAucCGG 55 ++ + G+ ++:::AGGU C:C + G +G:G U+AAA: GGAA:CCGG 1492 CCUAGGCGGGUUGUCCCAGGUgUCUCGUGccGGCGcgCACGAGGUGAAACGGGAAGCCGG 1551 ___............____>>>>>,,<<<____>>>,<<<---<<<<------<<<<<<- 56 UGa............AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccgccA 103 UGA A UCCGG:GCUGCCCCCGCAAC UAAGCG:+ G+ C:CG : 1552 UGAcgcucuccgagcCAGUCCGGCGCUGCCCCCGCAACGGUAAGCGCAUCGCGCGCGAGC 1611 ----<<<-<<<<<<..____....>>>>>>--->>>.>>>>>>---------->>>>--- 104 aaauGCCACUgggc..ucaa....gcccGGGAAGGC.ggcgggaaggaggaaacCgcgAG 156 + G: AC:: : A+ : ::G A :C : CG:G+ GG+ G+ :CGC+AG 1612 CCG-GAGACCGGCCugGAACcuuuCGUUUG--AUUCaCCCGCGGUGGGCGG--GCGCAAG 1666 ->>>,,,,)))]]]]]]::::::::::::::: 157 CCAGGAGACCUGCcgugaguguuaacaccccc 188 C G+AG C :GCC::: G+G +++ CC C 1667 CGUGAAG-CGGGCCGUCCGGGCCUGUUCCUCG 1697 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #19491,sp|AE004721.1|AE004721 Pseudomonas aeruginosa PAO1, section 282 of 529 of the complete genome. ----isReversed: 1 ----hitSequence: GUAGCCUUGCCGGUUCGAGGUUCCUCGCCGGCGACGGCGGGGCUAAGAGGGAACGCGGUCGAUGCCGCGGCUGCCCCCGCAACUGUGAACGGCGAUCGUUCCCCAAUGCCACUGCGUGACGCGGGAAGGCGGGGAACCGGCGGAGACGCCAGACCGUGAGCCAGGAGACCUGCCUCGUCGAUCCCGUGGCGC hit 6 : 1433 1242 (rev) 127.11 bits ::::::::::::::[[[[[[,.<<<____.____.____>>>,,,,,(((,,,<<<<<__ 1 uuauauuagccacgugaaGGU.cccccca.gaau.gggggggUUAAaAGGGAAucCGGUG 57 UA U+GCC ++U::AGGU CC:C C+ G + GG+G:GG UAA+AGGGAA::CGGU 10954 GUAGCCUUGCCGGUUCGAGGUuCCUCGCCgGCGAcGGCGGGGCUAAGAGGGAACGCGGUC 11013 _____>>>>>,,<<<____>>>,<<<---<<<<------<<<<<<-----<<<-<<<<<< 58 aAAAUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccgccAaaauGCCACUgggc 117 +A CCG::GCUGCCCCCGCAACUGU+A:CGG +A + ::C:CCAA+ GCCACUG:G 11014 -GAUGCCGCGGCUGCCCCCGCAACUGUGAACGGCGAUCGUUCCCCAAU--GCCACUGCG- 11069 ____>>>>>>--->>>>>>>>>----------.......>>>>---->>>,,,,)))]]] 118 ucaagcccGGGAAGGCggcgggaaggaggaaa.......cCgcgAGCCAGGAGACCUGCc 170 + A C:CGGGAAGGCGG:G::+ GG GGA+A CCG:GAGCCAGGAGACCUGCC 11070 -UGA-CGCGGGAAGGCGGGGAACCGGCGGAGAcgccagaCCGUGAGCCAGGAGACCUGCC 11127 ]]]::::::::::::::: 171 gugaguguuaacaccccc 188 ::G+ + U C C 11128 UCGUCGAUCCCGUGGCGC 11145 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #20392,sp|AE005628.1|AE005628 Escherichia coli O157:H7 EDL933 genome, contig 3 of 3, section 247 of 290. ----isReversed: 0 ----hitSequence: CUGUAGCAUCCACUUGCCGGUCCUGUGAGUUAAUAGGGAAUCCAGUGCGAAUCUGGAGCUGACGCGCAGCGGUAAGGAAAGGUGCGAUGAUUGCGUUAUGCGGACACUGCCAUUCGGUGGGAAGUCAUCAUCUCUUAGUAUCUUAGAUACCCCUCCAAGCCCGAAGACCUGCCGGCCAACGUCGCAUCUGG hit 7 : 5121 5311 (fwd) 91.14 bits ::::::::::::::[[[[[[,.<<<____________>>>,,,,,(((,,,<<<<<____ 1 uuauauuagccacgugaaGGU.ccccccagaaugggggggUUAAaAGGGAAucCGGUGaA 59 U UA+ A+CCAC+:::+GGU C: G+ :GUUAA+AGGGAAUCC:GUG++ 5121 CUGUAGCAUCCACUUGCCGGUcCU-----GUG------AGUUAAUAGGGAAUCCAGUGCG 5169 ___>>>>>,,<<<____>>>,<<<---<<<<------<<<<<<-----......<<<-<< 60 AAUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccgccAaaau......GCCACU 113 AAUC:GGAGCUG: C C:CA C:GUAAG:: +++ G+:::G:: +U G:CACU 5170 AAUCUGGAGCUGA-CGCGCAGCGGUAAGGAAAGGUGCGAUGAUUGCGUuaugcgGACACU 5228 <<<<____>>>>>>--->>>>>>>>>----------..........>>>>---->>>,,, 114 gggcucaagcccGGGAAGGCggcgggaaggaggaaa..........cCgcgAGCCAGGAG 163 ::: ++ + :::GGGAAG:C::C::: AG+A + ::C+AGCC:G+AG 5229 GCC-AUUC-GGUGGGAAGUCAUCAUCUCUUAGUAUCuuagauacccCUCCAAGCCCGAAG 5286 ,)))]]]]]]::::::::::::::: 164 ACCUGCcgugaguguuaacaccccc 188 ACCUGC+::: + U +CA+C 5287 ACCUGCCGGCCAACGUCGCAUCUGG 5311 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #20482,sp|AE005721.1|AE005721 Caulobacter crescentus CB15 section 47 of 359 of the complete genome. ----isReversed: 0 ----hitSequence: GUCUGUUGCCGUUGUCGUGGUCUGCGGACGUUCGCGUCCGGAGCUAAGAGGGAAGUCGGUGAGGGCGUGAAACCCUGAAUCCGGCGCUGCCCCCGCAACUGUGAGCGGCGAGCCGCUGUCCGUUUCGUGUCACUGACGCGCCGAAGCUGGUUCGGGGAUGCGUCGGGAAGGCCAGGGCAGGGGUGACGACCCGUGAGCCAGGAGACCUGCCUCGACAGAUAACGUCCUC hit 8 : 1901 2129 (fwd) 106.92 bits ::::::::::::::[[[[[[,<<<____.____...____>>>,,,,,(((,,,<<<<<_ 1 uuauauuagccacgugaaGGUcccccca.gaau...gggggggUUAAaAGGGAAucCGGU 56 U U UU C+ GU:::GGUC: C +A G+ + +G :G UAA+AGGGAA: CGGU 1901 GUCUGUUGCCGUUGUCGUGGUCUGCGGAcGUUCgcgUCCGGAGCUAAGAGGGAAGUCGGU 1960 __..............____>>>>>,,<<<____>>>,<<<---<<<<.------<<<<< 57 Ga..............AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGg.gaaggacccgc 101 GA +AAUCCG :GCUGCCCCCGCAACUGU+A:CGG GA+++ C:::C 1961 GAgggcgugaaacccuGAAUCCGGCGCUGCCCCCGCAACUGUGAGCGGcGAGCCGCUGUC 2020 <-----..<<<-<<<<<<...____...............>>>>>>--->>>..>>>>>> 102 cAaaau..GCCACUgggc...ucaa...............gcccGGGAAGGC..ggcggg 139 C ++ G:CACUG::: AA :::CGGGAAG:C GG:::G 2021 CGUUUCguGUCACUGACGcgcCGAAgcugguucggggaugCGUCGGGAAGGCcaGGGCAG 2080 ---------->>>>---->>>,,,,)))]]]]]]::::::::::::::: 140 aaggaggaaacCgcgAGCCAGGAGACCUGCcgugaguguuaacaccccc 188 ++G ++ +A+CCG:GAGCCAGGAGACCUGC:::GA G+UAAC +CC+C 2081 GGGUGACGACCCGUGAGCCAGGAGACCUGCCUCGACAGAUAACGUCCUC 2129 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #20610,sp|AE005849.1|AE005849 Caulobacter crescentus CB15 section 175 of 359 of the complete genome. ----isReversed: 0 ----hitSequence: AGCUCUAGCUUCGCGUCAGGUUCCUCGAAAGAGGAUGAAAAGGGAACGAGGUUGAAGACCUCGGCUGCCCCCGCAACUGUAAGCGGCGAGCUUCGCGUCACAUGCCACUGGGCCCAAAAGGCCUGGGAAGGCGACGCCCAGAAGCAUUGACCCGUGAGCCAGGAGACCUGCCCGGCGCAGUCGUUCAUCG hit 9 : 870 1059 (fwd) 127.83 bits ::::::::::::::[[[[[[,<<<____________>>>,,,,,(((,,,<<<<<_____ 1 uuauauuagccacgugaaGGUccccccagaaugggggggUUAAaAGGGAAucCGGUGaAA 60 + U U ++ :::AGGU:CC C GAA+ G GG:U+AAAAGGGAA:::GGU AA 870 AGCUCUAGCUUCGCGUCAGGUUCCUC--GAAA--GAGGAUGAAAAGGGAACGAGGUUGAA 925 __>>>>>,,<<<____>>>,<<<---<<<<.------<<<<<<-----<<<-<<<<<<.. 61 AUCCGgaGCUGcCCCCgCAACUGUAAgcGg.gaaggacccgccAaaauGCCACUgggc.. 117 CC:::GCUGCCCCCGCAACUGUAA:CGG GA++ :CG:CA A GCCACU:GGC 926 GACCUCGGCUGCCCCCGCAACUGUAAGCGGcGAGCUUCGCGUCACAU-GCCACUGGGCcc 984 ____.>>>>>>--->>>>>>>>>----------...>>>>---->>>,,,,)))]]]]]] 118 ucaa.gcccGGGAAGGCggcgggaaggaggaaa...cCgcgAGCCAGGAGACCUGCcgug 173 + AA GCC:GGGAAGGCG:CG: +AG AG A CCG:GAGCCAGGAGACCUGCC::: 985 AAAAgGCCUGGGAAGGCGACGCCCAGAAGCAUUgacCCGUGAGCCAGGAGACCUGCCCGG 1044 ::::::::::::::: 174 aguguuaacaccccc 188 G+ U ++ C C 1045 CGCAGUCGUUCAUCG 1059 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #21682,sp|AE006935.1|AE006935 Mycobacterium tuberculosis CDC1551, section 21 of 280 of the complete genome. ----isReversed: 1 ----hitSequence: CCACGCUCUGCAUGCCAAUAUUCUUCCCGUCAGGCGAUGACGAUGCAGGAAGCCGGUGAGAAUCCGGCGCGGUCCCGCCACUGUCACCGGGGAGCGACCCUCGUAAGCCACGGCCACAGGCUGGAAGGCGAGGCAAGCAACGAUCCGGGAGCCAGGAGACUCGCGUCAUCGCGUCCUGCCACC hit 10 : 7139 6957 (rev) 88.25 bits ::::::::::::::[[[[[[,<<<________.____>>>,,,,,(((,,,<<<<<____ 1 uuauauuagccacgugaaGGUccccccagaau.gggggggUUAAaAGGGAAucCGGUGaA 59 A U+++CA G :: ::U:C CC+G+ + G G G: +A +::GGAA:CCGGUGA+ 11405 CCACGCUCUGCAUGCCAAUAUUCUUCCCGUCAgGCGAUGACGAUGCAGGAAGCCGGUGAG 11464 ___>>>>>,,<<<____>>>,<<<---<<<<------<<<<<<-----<<<-<<<<<<__ 60 AAUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccgccAaaauGCCACUgggcuc 119 AAUCCGG:GC:G: CCC:C:ACUGU A:CGGG+AG+ ::C::C +AA GCCAC G:: 11465 AAUCCGGCGCGGU-CCCGCCACUGUCACCGGGGAGCGACCCUCGUAA-GCCACGGCC--A 11520 __>>>>>>--->>>>>>>>>---------->>>>---->>>,,,,)))]]]]]]:::::: 120 aagcccGGGAAGGCggcgggaaggaggaaacCgcgAGCCAGGAGACCUGCcgugaguguu 179 A ::C GGAAGGCG::G::A++ A GA CCG:GAGCCAGGAGAC:::: :: + + U 11521 CA-GGCUGGAAGGCGAGGCAAGCAACGAU-CCGGGAGCCAGGAGACUCGCGUCAUCGCGU 11578 ::::::::: 180 aacaccccc 188 + CC+CC 11579 CCUGCCACC 11587 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #21742,sp|AE006995.1|AE006995 Mycobacterium tuberculosis CDC1551, section 81 of 280 of the complete genome. ----isReversed: 1 ----hitSequence: GGCAUCGAGCGGGGCAACGAUGCUUCGCGAGAGGGAACCUGGUGAGAAUCCGGGACUGUCCCGCAGCGGUAUGCAGGAACGACCGCCGUCUUGGAAGUAGACAAGCACUGGUCUCAACGACUGGGAAGCGACGGCCAGUAGGAGCACCCACCGGGUGCGAGCCUGCGAGUCCGAAGACCUGCCAGCCGUGCCGGACGCGCC hit 11 : 10153 9953 (rev) 84.20 bits ::::::::::::::[[[[[[,.<<<____________>>>,,,,,(((,,,<<<<<____ 1 uuauauuagccacgugaaGGU.ccccccagaaugggggggUUAAaAGGGAAucCGGUGaA 59 ++ AGC+ +G::++G:U C::C C ::G AGGGAA:C:GGUGA+ 5352 GGCAUCGAGCGGGGCAACGAUgCUUCGC---------GAG-----AGGGAACCUGGUGAG 5397 ___>>>>>,,<<<____>>>,<<<---<<<<..------<<<<<<-----.........< 60 AAUCCGgaGCUGcCCCCgCAACUGUAAgcGg..gaaggacccgccAaaau.........G 108 AAUCC:G:+CUG: CCC:CA C:GUA GC:G + + ++:CCG:C + ++ 5398 AAUCCGGGACUGU-CCCGCAGCGGUAUGCAGgaACGACCGCCGUCUUGGAaguagacaa- 5455 <<-<<<<<<____.>>>>>>--->>>>>>>>>----------.................> 109 CCACUgggcucaa.gcccGGGAAGGCggcgggaaggaggaaa.................c 150 CACU:G:CUCAA G:C:GGGAAG G:CGG:+AG AGGA++ C 5456 GCACUGGUCUCAAcGACUGGGAAGC-GACGGCCAGUAGGAGCacccaccgggugcgagcC 5514 >>>---->>>,,,,)))]]]]]]::::::::::::::: 151 CgcgAGCCAGGAGACCUGCcgugaguguuaacaccccc 188 :GCGAG+C:G+AGACCU:C++:: GUG + + C CC 5515 UGCGAGUCCGAAGACCUGCCAGCCGUGCCGGACGCGCC 5552 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #22392,sp|AE007648.1|AE007648 Clostridium acetobutylicum ATCC824 section 136 of 356 of the complete genome. ----isReversed: 0 ----hitSequence: UUGCUACUAAAAUUUGUAGGUUCAACUGAGGAGUCUUAGUUGAUUAAAAAGGAAUCAGGUGAAAAGCCUGAGCGGUCCCGCCACUGUAAUAAAGGAGUUUAAGUACAAUAUGUCACUGGGAAACUGGGAAGGCGUACUUAAGCAAUGAUUUUUGAGCCAGGAUACUUGCCAUAUUCUAGUAUGUUUUU hit 12 : 1506 1693 (fwd) 109.69 bits ::::::::::::::[[[[[[,<<<____..____..____>>>,,,,,(((,,,<<<<<_ 1 uuauauuagccacgugaaGGUcccccca..gaau..gggggggUUAAaAGGGAAucCGGU 56 UU ++ + A +:G+AGGU:C: C + GA U + G :G:UUAAAA:GGAAUC:GGU 1506 UUGCUACUAAAAUUUGUAGGUUCAACUGagGAGUcuUAGUUGAUUAAAAAGGAAUCAGGU 1565 ______>>>>>,,<<<____>>>,<<<---.<<<<------<<<<<<-----<<<-<<<< 57 GaAAAUCCGgaGCUGcCCCCgCAACUGUAA.gcGggaaggacccgccAaaauGCCACUgg 115 GAAAA CC:GAGC:G: CCC:C:ACUGUAA ::: GA+ ::::CAA+AUG:CACU:G 1566 GAAAAGCCUGAGCGGU-CCCGCCACUGUAAuAAAGGAGUUUAAGUACAAUAUGUCACUGG 1624 <<____>>>>>>--->>>>>>>>>---------->>>>---->>>,,,,)))]]]]]]:: 116 gcucaagcccGGGAAGGCggcgggaaggaggaaacCgcgAGCCAGGAGACCUGCcgugag 175 AA C:GGGAAG:CG:::: AAG A+++A :::GAGCCAGGA AC:UGCC+U:+ 1625 --GAAA--CUGGGAAGGCGUACUUAAGCAAUGAUUUUUGAGCCAGGAUACUUGCCAUAUU 1680 ::::::::::::: 176 uguuaacaccccc 188 + +++A+ + + 1681 CUAGUAUGUUUUU 1693 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #22488,sp|AE007744.1|AE007744 Clostridium acetobutylicum ATCC824 section 232 of 356 of the complete genome. ----isReversed: 0 ----hitSequence: AAAUAAUACCAUAUUUUAGGCACCUAAUCUUAGGUUUAAUAGGGAAAUUGGUGAAAAUCCAAUGCAACCCCCGUUACUGUAUACAGUUACAAAACCAAUGUCCACUGGAGUUUUCUCUGGGAAGGAUGGUUGAGGCUAAACUGUGAGCCAGGAGACCUACCUAAAAUAUUAUGGAACUU hit 13 : 3364 3542 (fwd) 101.05 bits ::::::::::::::[[[[[[,<<<____________>>>,,,,,(((,,,<<<<<_____ 1 uuauauuagccacgugaaGGUccccccagaaugggggggUUAAaAGGGAAucCGGUGaAA 60 + AUA+UA C +:+:AG :CC + + GG:UUAA+AGGGAA:::GGUGAAA 3364 AAAUAAUACCAUAUUUUAGGCACCUAAUCUUA----GGUUUAAUAGGGAAAUUGGUGAAA 3419 __>>>>>,,<<<____>>>,<<<---<<<<------<<<<<<-----<<<-<<<<<<___ 61 AUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccgccAaaauGCCACUgggcuca 120 AUCC:::GC::CCCCCG::ACUGUA :C:G +A::::C:A+ :CCACU:G::U+ 3420 AUCCAAUGCAACCCCCGUUACUGUAUACAG-UUACAAAACCAAUG--UCCACUGGAGUUU 3476 _>>>>>>--->>>>>>>>>---------->>>>---->>>,,,,)))]]]]]]::::::: 121 agcccGGGAAGGCggcgggaaggaggaaacCgcgAGCCAGGAGACCUGCcgugaguguua 180 ::C:GGGAAGG::G::::A+G + A C:G:GAGCCAGGAGACCU CC:+:A+U UUA 3477 UCUCUGGGAAGGAUGGUUGAGGCUAAA--CUGUGAGCCAGGAGACCUACCUAAAAUAUUA 3534 :::::::: 181 acaccccc 188 C+ 3535 UGGAACUU 3542 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #22689,sp|AE007949.1|AE007949 Agrobacterium tumefaciens str. C58 circular chromosome, section 7 of 254 of the complete sequence. ----isReversed: 0 ----hitSequence: ACUAUAUGUGGUGUUCAAGGUUCUUCCGAUUCGCUAGGGUUGGGAGCUAAGACGGGAAUUCGGUGCGUAACGCCAUCACGGCGGAGCAAGGCCGAAACUGCCCCCGCAACUGUGAGCGGCGAGCAUCGUUCCGAUUUGAGCCACUGGAGCCAAAAGCUCCGGGAAGGCUGGAAUAGAUGUUGUGACCCGCAAGUCAGGAGACCUGCCUUGAGCGCAAAUGUCCAC hit 14 : 2778 3002 (fwd) 121.64 bits ::::::::::::::[[[[[[,.<<<____...____...____>>>,,,,,(.((,,,<< 1 uuauauuagccacgugaaGGU.cccccca...gaau...gggggggUUAAaA.GGGAAuc 52 + ++++U +++ ++U::AGGU C::CC+A G + + GG::G UAA+A GGGAAU: 2778 ACUAUAUGUGGUGUUCAAGGUuCUUCCGAuucGCUAgggUUGGGAGCUAAGAcGGGAAUU 2837 <<<___.....................____>>>>>,,<<<____>>>,<<<---<<<<. 53 CGGUGa.....................AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGg. 90 CGGUG+ AA CCG:A+CUGCCCCCGCAACUGU+AGCGG 2838 CGGUGCguaacgccaucacggcggagcAAGGCCGAAACUGCCCCCGCAACUGUGAGCGGc 2897 ------<<<<<<-----..<<<-<<<<<<..____.>>>>>>--->>>.>>>>>>----- 91 gaaggacccgccAaaau..GCCACUgggc..ucaa.gcccGGGAAGGC.ggcgggaagga 144 GA++ :::CC A+ U GCCACUGG:: + AA ::CCGGGAAGGC GG::: +A G 2898 GAGCAUCGUUCCGAUUUgaGCCACUGGAGccAAAAgCUCCGGGAAGGCuGGAAUAGAUGU 2957 -----.>>>>---->>>,,,,)))]]]]]]::::::::::::::: 145 ggaaa.cCgcgAGCCAGGAGACCUGCcgugaguguuaacaccccc 188 G +A CCGC+AG+CAGGAGACCUGCC::GAG+G AA+ +CC C 2958 UGUGAcCCGCAAGUCAGGAGACCUGCCUUGAGCGCAAAUGUCCAC 3002 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #22760,sp|AE008020.1|AE008020 Agrobacterium tumefaciens str. C58 circular chromosome, section 78 of 254 of the complete sequence. ----isReversed: 0 ----hitSequence: GGAUAACAUGUCCGUGAUGGUUCCUUCCGGGCGUUCCGGAAGGUGAAAAGGGAACACGAUAGGGACAAAUCCUCAUUCGUGGCUGCCCCCGCAACUGUGAGCGGAGAGCCUGAAACGAAAUGCCACUGGCAAGCCAUCUCGCCUCCAUCAAGGGGGAAGGCAAUGCCGGGAAGGUGUUUCAGGUUUUGACCCGUAAGCCAGGAGACCUGCCAUCACGGAAAUAUCCAUG hit 15 : 1643 1871 (fwd) 113.22 bits ::::::::::::::[[[[[[,.<<<____.____..____>>>,,,,,(((,,,<<<<<_ 1 uuauauuagccacgugaaGGU.cccccca.gaau..gggggggUUAAaAGGGAAucCGGU 56 AUA+ A++ +CG:G+:GGU CC: CC+ G U GG :GGU+AAAAGGGAA::CG:U 1643 GGAUAACAUGUCCGUGAUGGUuCCUUCCGgGCGUucCGGAAGGUGAAAAGGGAACACGAU 1702 __..........____>>>>>,,<<<____>>>,<<<---<<<<------<<<<<<---- 57 Ga..........AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccgccAaaa 106 AU:CG::GCUGCCCCCGCAACUGU+A:CGG++AG++:::::C AAA 1703 AGggacaaauccUCAUUCGUGGCUGCCCCCGCAACUGUGAGCGGAGAGCCUGAAACGAAA 1762 -<<<-<<<<<<................____............>>>>>>--->>>>>>>> 107 uGCCACUgggc................ucaa............gcccGGGAAGGCggcgg 138 U CCACUGG:: UCAA ::CCGGGAAGG G:::: 1763 UGCCACUGGCAagccaucucgccuccaUCAAgggggaaggcaaUGCCGGGAAGGUGUUUC 1822 >---------->>>>---->>>,,,,)))]]]]]]::::::::::::::: 139 gaaggaggaaacCgcgAGCCAGGAGACCUGCcgugaguguuaacaccccc 188 :++ GA CCG:+AGCCAGGAGACCUGC:+U:A +G+ A CC++ 1823 AGGUUUUGAC-CCGUAAGCCAGGAGACCUGCCAUCACGGAAAUAUCCAUG 1871 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #22827,sp|AE008087.1|AE008087 Agrobacterium tumefaciens str. C58 circular chromosome, section 145 of 254 of the complete sequence. ----isReversed: 1 ----hitSequence: CCAUAGCUUCUCCGGUCAGGUGCCCGCCCUUGCGGCGGGAGAAUCGGGAAUCCGGUGAAAGACCGGAACGUGCCCAACGCUGUAAGGCGGAUGCUCUUUUUCUCAUGCCACUGAAGCAAUUCGGGAAGGCGAAAGGGGCGGAUGAAGCUUAGUCAGAAGACCGGCCUGGCAGGAUAGACCGAAC hit 16 : 6687 6504 (rev) 106.50 bits ::::::::::::::[[[[[[,.<<<________.____>>>,,,,,(((,,,<<<<<___ 1 uuauauuagccacgugaaGGU.ccccccagaau.gggggggUUAAaAGGGAAucCGGUGa 58 AUA+ ++C +CG:::AGGU CCC+C U GG+GGG +AA+:GGGAAUCCGGUGA 5831 CCAUAGCUUCUCCGGUCAGGUgCCCGC--CCUUgCGGCGGGAGAAUCGGGAAUCCGGUGA 5888 ____>>>>>,,<<<____>>>,<<<---<<<<------<<<<<<-----<<<-<<<<<<_ 59 AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccgccAaaauGCCACUgggcu 118 AA CCGGA+C:: CCC :: CUGUAA:: GA G+ C :::: + AUGCCACUG:: 5889 AAGACCGGAACGUG-CCCAACGCUGUAAGGCGGAUGCUCUUUUUCUCAUGCCACUGAA-G 5946 ___>>>>>>--->>>>>>>>>---------->>>>---->>>,,,,)))]]]]]]::::: 119 caagcccGGGAAGGCggcgggaaggaggaaacCgcgAGCCAGGAGACCUGCcgugagugu 178 CAA ::CGGGAAGGC:::: G+++G++++A :: AG+CAG+AGACC:GCC::: ++G+ 5947 CAA-UUCGGGAAGGCGAAAGGGGCGGAUGA-AGCUUAGUCAGAAGACCGGCCUGGCAGGA 6004 :::::::::: 179 uaacaccccc 188 UA+ +C + C 6005 UAGACCGAAC 6014 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #22933,sp|AE008193.1|AE008193 Agrobacterium tumefaciens str. C58 circular chromosome, section 251 of 254 of the complete sequence. ----isReversed: 1 ----hitSequence: UUCCGCCCCGAGAAAGGGUCAUUCCGUGGCUGCCCCCGCAACUGUAAGCGGUAAGCCCGCACCGUAAAGCCACUGAACCUUUAUGAUCGGUUCGGGAAGGCGGUGACAGGGUGUUGAUAGCCGCAAGCCAGGAGACCUGCCGUUUCAGGAAAAAGCGUC hit 17 : 9538 9380 (rev) 36.25 bits ::::::::::::::[[[[[[,<<<____________>>>,,,,,(((,,,<<<<<_____ 1 uuauauuagccacgugaaGGUccccccagaaugggggggUUAAaAGGGAAucCGGUGaAA 60 +U +GCC+CG:GAA AGGG : A 1 ----UUCCGCCCCGAGAA--------------------------AGGG--U-------CA 21 __>>>>>,,<<<____>>>,<<<---<<<<------<<<<<<-----<<<-<<<<<<.._ 61 AUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccgccAaaauGCCACUgggc..u 118 UCCG :GCUGCCCCCGCAACUGUAAGCGG AAG++ C:CC +AA+GCCACUG::C U 22 UUCCGUGGCUGCCCCCGCAACUGUAAGCGGUAAGCCCGCACCGUAAAGCCACUGAACcuU 81 ___.....>>>>>>--->>>>>>>>>----------...>>>>---->>>,,,,)))]]] 119 caa.....gcccGGGAAGGCggcgggaaggaggaaa...cCgcgAGCCAGGAGACCUGCc 170 +A G::CGGGAAGGCGG:G A+GG G+ +A CCGC+AGCCAGGAGACCUGCC 82 UAUgaucgGUUCGGGAAGGCGGUGACAGGGUGUUGAuagCCGCAAGCCAGGAGACCUGCC 141 ]]]::::::::::::::: 171 gugaguguuaacaccccc 188 GU:+ G AA A C +C 142 GUUUCAGGAAAAAGCGUC 159 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #23040,sp|AE008300.1|AE008300 Agrobacterium tumefaciens str. C58 linear chromosome, section 104 of 187 of the complete sequence. ----isReversed: 1 ----hitSequence: ACAUUGGUUAGCCAUCGUGGUUCUGCGGACGAAGGUCCGGAGCUAAGAGGGAAUUCGGUGAGGGCUUUAAUCACAGCCUGAAUCCGAAGCUGCCCCCGCAACUGUAAGCGACGAGCGAAAGUCCAUCAUGUCACUGAGGCCGGCCUCGGGAAGACGGACCAAAGCUAUGACCCGCAAGCCAGGAGACCUGCCGCGAUAGAUAACGUCCAC hit 18 : 11923 11714 (rev) 127.59 bits ::::::::::::::[[[[[[,.<<<____.____.____>>>,,,,,(((,,,<<<<<__ 1 uuauauuagccacgugaaGGU.cccccca.gaau.gggggggUUAAaAGGGAAucCGGUG 57 + AU++ ++ ++C U: :GGU C: C +A GAA + +G :G UAA+AGGGAAU:CGGUG 26 ACAUUGGUUAGCCAUCGUGGUuCUGCGGAcGAAGgUCCGGAGCUAAGAGGGAAUUCGGUG 85 _..................____>>>>>,,<<<____>>>,<<<---<<<<.------<< 58 a..................AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGg.gaaggacc 98 A +AAUCCG:AGCUGCCCCCGCAACUGUAAGCG GA++GA: 86 AgggcuuuaaucacagccuGAAUCCGAAGCUGCCCCCGCAACUGUAAGCGAcGAGCGAAA 145 <<<<-----<<<-<<<<<<____>>>>>>--->>>>>>>>>---------->>>>----> 99 cgccAaaauGCCACUgggcucaagcccGGGAAGGCggcgggaaggaggaaacCgcgAGCC 158 ::CCA+ AUG:CACUG:G: C :C:CGGGAAG:CGG:: :AAG +++A+ CGC+AGCC 146 GUCCAUCAUGUCACUGAGGCCGGCCUCGGGAAGACGGACCAAAGCUAUGACCCGCAAGCC 205 >>,,,,)))]]]]]]::::::::::::::: 159 AGGAGACCUGCcgugaguguuaacaccccc 188 AGGAGACCUGC: :GA G+UAAC +CC C 206 AGGAGACCUGCCGCGAUAGAUAACGUCCAC 235 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #23082,sp|AE008342.1|AE008342 Agrobacterium tumefaciens str. C58 linear chromosome, section 146 of 187 of the complete sequence. ----isReversed: 0 ----hitSequence: CUUAUGUGAGAAAGCGACGGUUCCUACAGCCGAAAGGCGAAGGGAUUAAUAGGGAACAUGGUGCGGGCGAUCUUUUUCGUCCAAUGCCUUGGCUGCCCCCGCAACUGUAAGCGGAUUGUUGUUCAUCCCAGUGACGCUUGAAGGCGUCAUGCCACUGUUUUUUUCGGAAUGCGGGAAGGCAGAUGAGGGACGCAAAUCCGUGAGCCAGGAGACCUGCCGUCAAAAUGGAAACCAUC hit 19 : 7843 8078 (fwd) 106.10 bits ::::::::::::::[[[[[[,<<<____...____...____>>>,,,,,(((,,,<<<< 1 uuauauuagccacgugaaGGUcccccca...gaau...gggggggUUAAaAGGGAAucCG 54 U++++U + A G:GA+GGU:CC CA GAA+ G GGG:UUAA+AGGGAA:: G 7843 CUUAUGUGAGAAAGCGACGGUUCCUACAgccGAAAggcGAAGGGAUUAAUAGGGAACAUG 7902 <___..................____>>>>>,,<<<____>>>,<<<---<<<<.----- 55 GUGa..................AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGg.gaagg 95 GUG+ AA CC ::GCUGCCCCCGCAACUGUAA:CGG + 7903 GUGCgggcgaucuuuuucguccAAUGCCUUGGCUGCCCCCGCAACUGUAAGCGGaUUGUU 7962 -<<<<<<-----..................<<<-<<<<<<.____...>>>>>>--->>> 96 acccgccAaaau..................GCCACUgggc.ucaa...gcccGGGAAGGC 133 ::C::C A+U GCCACUG : U+ + : CGGGAAGGC 7963 GUUCAUCCCAGUgacgcuugaaggcgucauGCCACUGUUUuUUUCggaAUGCGGGAAGGC 8022 .>>>>>>---------->>>>---->>>,,,,)))]]]]]]::::::::::::::: 134 .ggcgggaaggaggaaacCgcgAGCCAGGAGACCUGCcgugaguguuaacaccccc 188 G::G::++ + AA CCG:GAGCCAGGAGACCUGC+GU:A+ U+ A ACC++C 8023 aGAUGAGGGACGCAAAUCCGUGAGCCAGGAGACCUGCCGUCAAAAUGGAAACCAUC 8078 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #23514,sp|AE008789.1|AE008789 Salmonella typhimurium LT2, section 93 of 220 of the complete genome. ----isReversed: 1 ----hitSequence: CCAUAACGUAAACCAACAGGUUUGCCACAUUUGUGGUAGGGAAGGGGGUGAAAAUCCCCCGCAGCCCCCGCUGCUGUGAUGCUGACGACCCCGUAAAGACCACUGAUCGCAAGAUUGGGAAGGACGGGCGAGGAGGACGCUAAGCCAGAAGACCUGCCUGUCGGUGAUAACCAACA hit 20 : 23249 23074 (rev) 102.60 bits ::::::::::::::[[[[[[,..<<<____________>>>,,,,,(((,,,<<<<<___ 1 uuauauuagccacgugaaGGU..ccccccagaaugggggggUUAAaAGGGAAucCGGUGa 58 AUA+ + AC :::AGGU CC C ++ U G GG AGGGAA:::GGUGA 61 CCAUAACGUAAACCAACAGGUuuGCCAC--AUUU--GUGGU-----AGGGAAGGGGGUGA 111 ____>>>>>,,<<<____>>>,<<<---<<<<------<<<<<<-----<<<-<<<<<<_ 59 AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccgccAaaauGCCACUgggcu 118 AAAUCC:::GC:GCCCCCGC: CUGU+A : +A+GA CC:::AAA++ CCACU:::C 112 AAAUCCCCCGCAGCCCCCGCUGCUGUGAUGC-UGACGACCCCGUAAAGA-CCACUGAUCG 169 ___>>>>>>--->>>>>>>>>---------->>>>---->>>,,,,)))]]]]]]::::: 119 caagcccGGGAAGGCggcgggaaggaggaaacCgcgAGCCAGGAGACCUGCcgugagugu 178 CAAG:::GGGAAGG :::GG +AGGAGGA : +AGCCAG+AGACCUGCC::: G+ 170 CAAGAUUGGGAAGG-ACGGGCGAGGAGGAC--GCUAAGCCAGAAGACCUGCCUGUCGGUG 226 :::::::::: 179 uaacaccccc 188 +A +C +C 227 AUAACCAACA 236 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #23618,sp|AE008893.1|AE008893 Salmonella typhimurium LT2, section 197 of 220 of the complete genome. ----isReversed: 0 ----hitSequence: CGGUAGCAUCCGUGGGCCGGUCCUGUGAGUUAAUAGGGAAUCCAGUGAAAAUCUGGAGCUGACGCGCAGCGGUAAGGAAAGGUGAGAUGAGAGCGUAAGCAGACACUGCCUCCGGCGGGAAGUCAUCAUUUCUGCUAUCCAGCCAACGGAUAACCCUCCAAGCCCGAAGACCUGCCGGCUAACGUCGCAUCUGG hit 21 : 4980 5173 (fwd) 86.55 bits ::::::::::::::[[[[[[,.<<<____________>>>,,,,,(((,,,<<<<<____ 1 uuauauuagccacgugaaGGU.ccccccagaaugggggggUUAAaAGGGAAucCGGUGaA 59 UA+ A+CC G ::+GGU C: G+ :GUUAA+AGGGAAUCC:GUGAA 4980 CGGUAGCAUCCGUGGGCCGGUcCU-----GUG------AGUUAAUAGGGAAUCCAGUGAA 5028 ___>>>>>,,<<<____>>>,<<<---<<<<------<<<<<<-----......<<<-<< 60 AAUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccgccAaaau......GCCACU 113 AAUC:GGAGCUG: C C:CA C:GUAAG:: +A+G ::::: A G:CACU 5029 AAUCUGGAGCUGA-CGCGCAGCGGUAAGGA-AAGGUGAGAUGAGAGCGuaagcaGACACU 5086 <<<<____>>>>>>--->>>.>>>>>>----------...............>>>>---- 114 gggcucaagcccGGGAAGGC.ggcgggaaggaggaaa...............cCgcgAGC 157 G:: + + ::CGGGAAG:C ::::: + G ++ A ::C+AGC 5087 GCC--UCC-GGCGGGAAGUCaUCAUUUCUGCUAUCCAgccaacggauaaccc-UCCAAGC 5142 >>>,,,,)))]]]]]]::::::::::::::: 158 CAGGAGACCUGCcgugaguguuaacaccccc 188 C:G+AGACCUGC+:: ++ U +CA+C 5143 CCGAAGACCUGCCGGCUAACGUCGCAUCUGG 5173 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #23702,sp|AE008981.1|AE008981 Agrobacterium tumefaciens strain C58 circular chromosome, section 7 of 256 of the complete sequence. ----isReversed: 0 ----hitSequence: ACUAUAUGUGGUGUUCAAGGUUCUUCCGAUUCGCUAGGGUUGGGAGCUAAGACGGGAAUUCGGUGCGUAACGCCAUCACGGCGGAGCAAGGCCGAAACUGCCCCCGCAACUGUGAGCGGCGAGCAUCGUUCCGAUUUGAGCCACUGGAGCCAAAAGCUCCGGGAAGGCUGGAAUAGAUGUUGUGACCCGCAAGUCAGGAGACCUGCCUUGAGCGCAAAUGUCCAC hit 22 : 4074 4298 (fwd) 121.64 bits ::::::::::::::[[[[[[,.<<<____...____...____>>>,,,,,(.((,,,<< 1 uuauauuagccacgugaaGGU.cccccca...gaau...gggggggUUAAaA.GGGAAuc 52 + ++++U +++ ++U::AGGU C::CC+A G + + GG::G UAA+A GGGAAU: 4074 ACUAUAUGUGGUGUUCAAGGUuCUUCCGAuucGCUAgggUUGGGAGCUAAGAcGGGAAUU 4133 <<<___.....................____>>>>>,,<<<____>>>,<<<---<<<<. 53 CGGUGa.....................AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGg. 90 CGGUG+ AA CCG:A+CUGCCCCCGCAACUGU+AGCGG 4134 CGGUGCguaacgccaucacggcggagcAAGGCCGAAACUGCCCCCGCAACUGUGAGCGGc 4193 ------<<<<<<-----..<<<-<<<<<<..____.>>>>>>--->>>.>>>>>>----- 91 gaaggacccgccAaaau..GCCACUgggc..ucaa.gcccGGGAAGGC.ggcgggaagga 144 GA++ :::CC A+ U GCCACUGG:: + AA ::CCGGGAAGGC GG::: +A G 4194 GAGCAUCGUUCCGAUUUgaGCCACUGGAGccAAAAgCUCCGGGAAGGCuGGAAUAGAUGU 4253 -----.>>>>---->>>,,,,)))]]]]]]::::::::::::::: 145 ggaaa.cCgcgAGCCAGGAGACCUGCcgugaguguuaacaccccc 188 G +A CCGC+AG+CAGGAGACCUGCC::GAG+G AA+ +CC C 4254 UGUGAcCCGCAAGUCAGGAGACCUGCCUUGAGCGCAAAUGUCCAC 4298 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #23775,sp|AE009054.1|AE009054 Agrobacterium tumefaciens strain C58 circular chromosome, section 80 of 256 of the complete sequence. ----isReversed: 0 ----hitSequence: GGAUAACAUGUCCGUGAUGGUUCCUUCCGGGCGUUCCGGAAGGUGAAAAGGGAACACGAUAGGGACAAAUCCUCAUUCGUGGCUGCCCCCGCAACUGUGAGCGGAGAGCCUGAAACGAAAUGCCACUGGCAAGCCAUCUCGCCUCCAUCAAGGGGGAAGGCAAUGCCGGGAAGGUGUUUCAGGUUUUGACCCGUAAGCCAGGAGACCUGCCAUCACGGAAAUAUCCAUG hit 23 : 2448 2676 (fwd) 113.22 bits ::::::::::::::[[[[[[,.<<<____.____..____>>>,,,,,(((,,,<<<<<_ 1 uuauauuagccacgugaaGGU.cccccca.gaau..gggggggUUAAaAGGGAAucCGGU 56 AUA+ A++ +CG:G+:GGU CC: CC+ G U GG :GGU+AAAAGGGAA::CG:U 2448 GGAUAACAUGUCCGUGAUGGUuCCUUCCGgGCGUucCGGAAGGUGAAAAGGGAACACGAU 2507 __..........____>>>>>,,<<<____>>>,<<<---<<<<------<<<<<<---- 57 Ga..........AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccgccAaaa 106 AU:CG::GCUGCCCCCGCAACUGU+A:CGG++AG++:::::C AAA 2508 AGggacaaauccUCAUUCGUGGCUGCCCCCGCAACUGUGAGCGGAGAGCCUGAAACGAAA 2567 -<<<-<<<<<<................____............>>>>>>--->>>>>>>> 107 uGCCACUgggc................ucaa............gcccGGGAAGGCggcgg 138 U CCACUGG:: UCAA ::CCGGGAAGG G:::: 2568 UGCCACUGGCAagccaucucgccuccaUCAAgggggaaggcaaUGCCGGGAAGGUGUUUC 2627 >---------->>>>---->>>,,,,)))]]]]]]::::::::::::::: 139 gaaggaggaaacCgcgAGCCAGGAGACCUGCcgugaguguuaacaccccc 188 :++ GA CCG:+AGCCAGGAGACCUGC:+U:A +G+ A CC++ 2628 AGGUUUUGAC-CCGUAAGCCAGGAGACCUGCCAUCACGGAAAUAUCCAUG 2676 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #23843,sp|AE009122.1|AE009122 Agrobacterium tumefaciens strain C58 circular chromosome, section 148 of 256 of the complete sequence. ----isReversed: 1 ----hitSequence: CCAUAGCUUCUCCGGUCAGGUGCCCGCCCUUGCGGCGGGAGAAUCGGGAAUCCGGUGAAAGACCGGAACGUGCCCAACGCUGUAAGGCGGAUGCUCUUUUUCUCAUGCCACUGAAGCAAUUCGGGAAGGCGAAAGGGGCGGAUGAAGCUUAGUCAGAAGACCGGCCUGGCAGGAUAGACCGAAC hit 24 : 6687 6504 (rev) 106.50 bits ::::::::::::::[[[[[[,.<<<________.____>>>,,,,,(((,,,<<<<<___ 1 uuauauuagccacgugaaGGU.ccccccagaau.gggggggUUAAaAGGGAAucCGGUGa 58 AUA+ ++C +CG:::AGGU CCC+C U GG+GGG +AA+:GGGAAUCCGGUGA 5548 CCAUAGCUUCUCCGGUCAGGUgCCCGC--CCUUgCGGCGGGAGAAUCGGGAAUCCGGUGA 5605 ____>>>>>,,<<<____>>>,<<<---<<<<------<<<<<<-----<<<-<<<<<<_ 59 AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccgccAaaauGCCACUgggcu 118 AA CCGGA+C:: CCC :: CUGUAA:: GA G+ C :::: + AUGCCACUG:: 5606 AAGACCGGAACGUG-CCCAACGCUGUAAGGCGGAUGCUCUUUUUCUCAUGCCACUGAA-G 5663 ___>>>>>>--->>>>>>>>>---------->>>>---->>>,,,,)))]]]]]]::::: 119 caagcccGGGAAGGCggcgggaaggaggaaacCgcgAGCCAGGAGACCUGCcgugagugu 178 CAA ::CGGGAAGGC:::: G+++G++++A :: AG+CAG+AGACC:GCC::: ++G+ 5664 CAA-UUCGGGAAGGCGAAAGGGGCGGAUGA-AGCUUAGUCAGAAGACCGGCCUGGCAGGA 5721 :::::::::: 179 uaacaccccc 188 UA+ +C + C 5722 UAGACCGAAC 5731 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #23949,sp|AE009228.1|AE009228 Agrobacterium tumefaciens strain C58 circular chromosome, section 254 of 256 of the complete sequence. ----isReversed: 1 ----hitSequence: UAAGGGUAAGGGACUGACGGUCUUUUCCCGGCAACGGGAAAAGCUAAGAGGGAACACGGUUCCGCCCCGAGAAAGGGUCAUUCCGUGGCUGCCCCCGCAACUGUAAGCGGUAAGCCCGCACCGUAAAGCCACUGAACCUUUAUGAUCGGUUCGGGAAGGCGGUGACAGGGUGUUGAUAGCCGCAAGCCAGGAGACCUGCCGUUUCAGGAAAAAGCGUC hit 25 : 1838 1621 (rev) 127.18 bits ::::::::::::::[[[[[[,<<<____..____..____>>>,,,,,(((,,,<<<<<_ 1 uuauauuagccacgugaaGGUcccccca..gaau..gggggggUUAAaAGGGAAucCGGU 56 U A +UA ++ +GA+GGUC:: C+ G A+ GG ::G UAA+AGGGAA::CGGU 9910 UAAGGGUAAGGGACUGACGGUCUUUUCCcgGCAAcgGGAAAAGCUAAGAGGGAACACGGU 9969 __................____>>>>>,,<<<____>>>,<<<---<<<<------<<<< 57 Ga................AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccg 100 + A UCCG::GCUGCCCCCGCAACUGUAAGCGG AAG++ C: 9970 UCcgccccgagaaaggguCAUUCCGUGGCUGCCCCCGCAACUGUAAGCGGUAAGCCCGCA 10029 <<-----<<<-<<<<<<..____.....>>>>>>--->>>>>>>>>----------...> 101 ccAaaauGCCACUgggc..ucaa.....gcccGGGAAGGCggcgggaaggaggaaa...c 150 CC +AA+GCCACUG::C U+A G::CGGGAAGGCGG:G A+GG G+ +A C 10030 CCGUAAAGCCACUGAACcuUUAUgaucgGUUCGGGAAGGCGGUGACAGGGUGUUGAuagC 10089 >>>---->>>,,,,)))]]]]]]::::::::::::::: 151 CgcgAGCCAGGAGACCUGCcgugaguguuaacaccccc 188 CGC+AGCCAGGAGACCUGC+GU++ G AA A C +C 10090 CGCAAGCCAGGAGACCUGCCGUUUCAGGAAAAAGCGUC 10127 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #23991,sp|AE009270.1|AE009270 Agrobacterium tumefaciens str. C58 linear chromosome, section 40 of 187 of the complete sequence. ----isReversed: 1 ----hitSequence: CUUAUGUGAGAAAGCGACGGUUCCUACAGCCGAAAGGCGAAGGGAUUAAUAGGGAACAUGGUGCGGGCGAUCUUUUUCGUCCAAUGCCUUGGCUGCCCCCGCAACUGUAAGCGGAUUGUUGUUCAUCCCAGUGACGCUUGAAGGCGUCAUGCCACUGUUUUUUUCGGAAUGCGGGAAGGCAGAUGAGGGACGCAAAUCCGUGAGCCAGGAGACCUGCCGUCAAAAUGGAAACCAUC hit 26 : 3802 3567 (rev) 106.10 bits ::::::::::::::[[[[[[,<<<____...____...____>>>,,,,,(((,,,<<<< 1 uuauauuagccacgugaaGGUcccccca...gaau...gggggggUUAAaAGGGAAucCG 54 U++++U + A G:GA+GGU:CC CA GAA+ G GGG:UUAA+AGGGAA:: G 7843 CUUAUGUGAGAAAGCGACGGUUCCUACAgccGAAAggcGAAGGGAUUAAUAGGGAACAUG 7902 <___..................____>>>>>,,<<<____>>>,<<<---<<<<.----- 55 GUGa..................AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGg.gaagg 95 GUG+ AA CC ::GCUGCCCCCGCAACUGUAA:CGG + 7903 GUGCgggcgaucuuuuucguccAAUGCCUUGGCUGCCCCCGCAACUGUAAGCGGaUUGUU 7962 -<<<<<<-----..................<<<-<<<<<<.____...>>>>>>--->>> 96 acccgccAaaau..................GCCACUgggc.ucaa...gcccGGGAAGGC 133 ::C::C A+U GCCACUG : U+ + : CGGGAAGGC 7963 GUUCAUCCCAGUgacgcuugaaggcgucauGCCACUGUUUuUUUCggaAUGCGGGAAGGC 8022 .>>>>>>---------->>>>---->>>,,,,)))]]]]]]::::::::::::::: 134 .ggcgggaaggaggaaacCgcgAGCCAGGAGACCUGCcgugaguguuaacaccccc 188 G::G::++ + AA CCG:GAGCCAGGAGACCUGC+GU:A+ U+ A ACC++C 8023 aGAUGAGGGACGCAAAUCCGUGAGCCAGGAGACCUGCCGUCAAAAUGGAAACCAUC 8078 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #24035,sp|AE009314.1|AE009314 Agrobacterium tumefaciens str. C58 linear chromosome, section 84 of 187 of the complete sequence. ----isReversed: 0 ----hitSequence: ACAUUGGUUAGCCAUCGUGGUUCUGCGGACGAAGGUCCGGAGCUAAGAGGGAAUUCGGUGAGGGCUUUAAUCACAGCCUGAAUCCGAAGCUGCCCCCGCAACUGUAAGCGACGAGCGAAAGUCCAUCAUGUCACUGAGGCCGGCCUCGGGAAGACGGACCAAAGCUAUGACCCGCAAGCCAGGAGACCUGCCGCGAUAGAUAACGUCCAC hit 27 : 45 254 (fwd) 127.59 bits ::::::::::::::[[[[[[,.<<<____.____.____>>>,,,,,(((,,,<<<<<__ 1 uuauauuagccacgugaaGGU.cccccca.gaau.gggggggUUAAaAGGGAAucCGGUG 57 + AU++ ++ ++C U: :GGU C: C +A GAA + +G :G UAA+AGGGAAU:CGGUG 45 ACAUUGGUUAGCCAUCGUGGUuCUGCGGAcGAAGgUCCGGAGCUAAGAGGGAAUUCGGUG 104 _..................____>>>>>,,<<<____>>>,<<<---<<<<.------<< 58 a..................AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGg.gaaggacc 98 A +AAUCCG:AGCUGCCCCCGCAACUGUAAGCG GA++GA: 105 AgggcuuuaaucacagccuGAAUCCGAAGCUGCCCCCGCAACUGUAAGCGAcGAGCGAAA 164 <<<<-----<<<-<<<<<<____>>>>>>--->>>>>>>>>---------->>>>----> 99 cgccAaaauGCCACUgggcucaagcccGGGAAGGCggcgggaaggaggaaacCgcgAGCC 158 ::CCA+ AUG:CACUG:G: C :C:CGGGAAG:CGG:: :AAG +++A+ CGC+AGCC 165 GUCCAUCAUGUCACUGAGGCCGGCCUCGGGAAGACGGACCAAAGCUAUGACCCGCAAGCC 224 >>,,,,)))]]]]]]::::::::::::::: 159 AGGAGACCUGCcgugaguguuaacaccccc 188 AGGAGACCUGC: :GA G+UAAC +CC C 225 AGGAGACCUGCCGCGAUAGAUAACGUCCAC 254 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #24224,sp|AE009507.1|AE009507 Brucella melitensis 16M chromosome I, section 64 of 195 of the complete sequence. ----isReversed: 0 ----hitSequence: UCGCAAUUUUCAGGAGACGGUUCCGCCAUUGCGGCGGAUGAAAAGGGAACACGGUGAAGCCAUAGGGCUGAAACCGAGACUGCCCCCGCAACUGUAACCGGAGAGCUAUCCUCCACAGGCCGCGCAAGCGGCCAAAGCCACUGAAAGCAGCAAUAUGCUGCAAUCGGGAAGGCGGAGGCAAAGCGAAGACCCGGAAGUCAGGAGACCUGCCGUAUCCGGUCACCCAUGC hit 28 : 7696 7924 (fwd) 119.42 bits ::::::::::::::[[[[[[,<<<________.____>>>,,,,,(((,,,<<<<<___. 1 uuauauuagccacgugaaGGUccccccagaau.gggggggUUAAaAGGGAAucCGGUGa. 58 U A+U++ CA+G GA+GGU:CC+C A U GG+GG:U+AAAAGGGAA: CGGUGA 7696 UCGCAAUUUUCAGGAGACGGUUCCGC--CAUUgCGGCGGAUGAAAAGGGAACACGGUGAa 7753 ...........____>>>>>,,<<<____>>>,<<<---<<<<------<<<<<<----- 59 ...........AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccgccAaaau 107 +AA CCG :+CUGCCCCCGCAACUGUAA:CGG++AG+ : C::C A A 7754 gccauagggcuGAAACCGAGACUGCCCCCGCAACUGUAACCGGAGAGCUAUCCUCCACAG 7813 ..................<<<-<<<<<<...____........>>>>>>--->>>.>>>> 108 ..................GCCACUgggc...ucaa........gcccGGGAAGGC.ggcg 137 GCCACUG: CAA :CGGGAAGGC G::G 7814 gccgcgcaagcggccaaaGCCACUGAAAgcaGCAAuaugcugcAAUCGGGAAGGCgGAGG 7873 >>---------->>>>---->>>,,,,)))]]]]]]::::::::::::::: 138 ggaaggaggaaacCgcgAGCCAGGAGACCUGCcgugaguguuaacaccccc 188 :AAG ++ +A+CCG:+AG+CAGGAGACCUGC+GU + +G U AC+C C 7874 CAAAGCGAAGACCCGGAAGUCAGGAGACCUGCCGUAUCCGGUCACCCAUGC 7924 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #24406,sp|AE009689.1|AE009689 Brucella melitensis 16M chromosome II, section 51 of 107 of the complete sequence. ----isReversed: 0 ----hitSequence: CCGUAAUACCGUCAUGACGGUUCCCCGACCGAGAGCGAAGGGGAUUAAUAGGGAACACGGUGAGGACGACCCAUCAAGGGGCCGAGACCGUGGCUGCCCCCGCAACUGUAAGCGGAUUGCCGUUCAUCCUCGUGACGCCGAAAGCGUCAUGCCACUGUGCCCACGGCACGGGAAGGCAGAUGGACGGCGAUUAUCCGCAAGCCAGGAGACCUGCCGUCUUACGUAGUCCAUUG hit 29 : 4862 5094 (fwd) 125.17 bits ::::::::::::::[[[[[[,<<<____..____...____>>>,,,,,(((,,,<<<<< 1 uuauauuagccacgugaaGGUcccccca..gaau...gggggggUUAAaAGGGAAucCGG 55 UA+UA C+ C :GA+GGU:CCCC+A GA + GGGG:UUAA+AGGGAA::CGG 4862 CCGUAAUACCGUCAUGACGGUUCCCCGAccGAGAgcgAAGGGGAUUAAUAGGGAACACGG 4921 ___....................____>>>>>,,<<<____>>>,<<<---<<<<.---- 56 UGa....................AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGg.gaag 94 UGA +A CCG::GCUGCCCCCGCAACUGUAAGCGG ++ 4922 UGAggacgacccaucaaggggccGAGACCGUGGCUGCCCCCGCAACUGUAAGCGGaUUGC 4981 --<<<<<<-----.................<<<-<<<<<<____.>>>>>>--->>>.>> 95 gacccgccAaaau.................GCCACUgggcucaa.gcccGGGAAGGC.gg 135 + : C::C + +U GCCACUG:GC CA+ GC:CGGGAAGGC G: 4982 CGUUCAUCCUCGUgacgccgaaagcgucauGCCACUGUGCCCACgGCACGGGAAGGCaGA 5041 >>>>---------->>>>---->>>,,,,)))]]]]]]::::::::::::::: 136 cgggaaggaggaaacCgcgAGCCAGGAGACCUGCcgugaguguuaacaccccc 188 :G :++G +++ A CCGC+AGCCAGGAGACCUGC+GU:+ UA+++C + 5042 UGGACGGCGAUUAUCCGCAAGCCAGGAGACCUGCCGUCUUACGUAGUCCAUUG 5094 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #24443,sp|AE009726.1|AE009726 Brucella melitensis 16M chromosome II, section 88 of 107 of the complete sequence. ----isReversed: 1 ----hitSequence: ACCAUAUCUUGUGUUCGAGGUUCUUUCGAUUCGACGAGUCGGGAGCUAAGACGGGAAUCCGGUGCGCUUGCCCAUGGUGGGCGGGCAAUGCCGGAGCUGCCCCCGCAACUGUAAGCGGCGAGCUUUGCGCCCCAUGCCACUGGCGAAAGCCGGGAAGGCGGGUGGAAGCGUUGAGCCGUGAGCCAGGAGACCUGCCUUGAGCGUGAACGUCCAC hit 30 : 9564 9351 (rev) 121.75 bits ::::::::::::::[[[[[[,.<<<____...____..____>>>,,,,,(.((,,,<<< 1 uuauauuagccacgugaaGGU.cccccca...gaau..gggggggUUAAaA.GGGAAucC 53 + +++U++ + ++U::AGGU C:: C+A GA + GG::G UAA+A GGGAAUCC 1838 ACCAUAUCUUGUGUUCGAGGUuCUUUCGAuucGACGagUCGGGAGCUAAGAcGGGAAUCC 1897 <<___.....................____>>>>>,,<<<____>>>,<<<---<<<<.. 54 GGUGa.....................AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGg.. 90 GGUG+ AA CCGGAGCUGCCCCCGCAACUGUAA:CGG 1898 GGUGCgcuugcccauggugggcgggcAAUGCCGGAGCUGCCCCCGCAACUGUAAGCGGcg 1957 ------<<<<<<-----<<<-<<<<<<____>>>>>>--->>>>>>>>>----------> 91 gaaggacccgccAaaauGCCACUgggcucaagcccGGGAAGGCggcgggaaggaggaaac 150 ++ C :CC A+ GCCACUGG: AA :CCGGGAAGGCGG: G AAG + ++A C 1958 AGCUUUGCGCCCCAU--GCCACUGGC-GAAA-GCCGGGAAGGCGGGUGGAAGCGUUGAGC 2013 >>>---->>>,,,,)))]]]]]]::::::::::::::: 151 CgcgAGCCAGGAGACCUGCcgugaguguuaacaccccc 188 CG:GAGCCAGGAGACCUGCC::GAG+GU+AAC +CC C 2014 CGUGAGCCAGGAGACCUGCCUUGAGCGUGAACGUCCAC 2051 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #25207,sp|AE010499.1|AE010499 Fusobacterium nucleatum subsp. nucleatum ATCC 25586, section 41 of 197 of the complete genome. ----isReversed: 1 ----hitSequence: AAUGAUAAGAAACAAAUAGGUGCUUAUUGGCUUAAUAAAGGAAGUUGGGUGCGAAUCCCACACAGCAAUGCUACUGUAUUGUGGACGAAAUUACAAUAGCCACUGGGAAACUGGGAAGGUGUAAAAGUAGGUUGAAACUAAGUCAGGAGACUUACCAUUAUUUUAUAUUAAACU hit 31 : 5969 5796 (rev) 66.38 bits ::::::::::::::[[[[[[,<<<____________>>>,,,,,(.((,,,<.<<<<___ 1 uuauauuagccacgugaaGGUccccccagaaugggggggUUAAaA.GGGAAu.cCGGUGa 58 + + AU AG AC ::+AG U:C: A U :G:UUAA+A :GGAA: ::GGUG+ 4265 AAUGAUAAGAAACAAAUAGGUGCU----UAUU----GGCUUAAUAaAGGAAGuUGGGUGC 4316 ____>>>>>,,<<<____>>>,<<<---<<<<------<<<<<<-----<<<-<<<<<<_ 59 AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccgccAaaauGCCACUgggcu 118 +AAUCC:::+C:GC GC:ACUGUA :: G+A+GA:::::CAA+A CCACU:G 4317 GAAUCCCACACAGC-AAUGCUACUGUAUUGU-GGACGAAAUUACAAUA-GCCACUGG--G 4371 ___>>>>>>--->>>>>>>>>---------->>>>---->>>,,,,)))]]]]]]::::: 119 caagcccGGGAAGGCggcgggaaggaggaaacCgcgAGCCAGGAGACCUGCcgugagugu 178 AA C:GGGAAGG G:::::+ G+ ++AA :: +AG+CAGGAGAC:U CC+::A U U 4372 AAA--CUGGGAAGGUGUAAAAGUAGGUUGAA-ACUAAGUCAGGAGACUUACCAUUAUUUU 4428 :::::::::: 179 uaacaccccc 188 +A+ +C 4429 AUAUUAAACU 4438 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #25250,sp|AE010542.1|AE010542 Fusobacterium nucleatum subsp. nucleatum ATCC 25586, section 84 of 197 of the complete genome. ----isReversed: 0 ----hitSequence: UUAAUAUCAUGUCAAUUAUGUUCCUUAUUUUUUAAGGCUAAGAGGGAAUUUGGUGAGAUACCAAAACGAGCCCGUCGCUGUAAUUGAGUUUUUUCUUGUUUUAUACCACUGGAUUUUUAUUUGGGAAGGUAAAGAAAUAUAAAUCAUAAGUCAGAAGACCUGCAUAAUUGAAUUACUCUAUC hit 32 : 7559 7740 (fwd) 82.72 bits ::::::::::::::[[[[[[,.<<<____.________>>>,,,,,(((,,,<<<<<___ 1 uuauauuagccacgugaaGGU.cccccca.gaaugggggggUUAAaAGGGAAucCGGUGa 58 UUA+++U+ + C +:::GU CC: + + :GG UAA+AGGGAAU::GGUGA 7559 UUAAUAUCAUGUCAAUUAUGUuCCUUAUUuUUUA----AGGCUAAGAGGGAAUUUGGUGA 7614 ____>>>>>,,<<<____>>>,<<<---<<<<------<<<<<<-----..<<<-<<<<< 59 AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccgccAaaau..GCCACUggg 116 +A CC::A+C:: CCC :: CUGUAA :G: + :::::: ++ U :CCACU: : 7615 GAUACCAAAACGAG-CCCGUCGCUGUAAUUGA--GUUUUUUCUUGUUUUauACCACUGGA 7671 <____>>>>>>--->>>.>>>>>>---------->>>>---->>>,,,,)))]]]]]]:: 117 cucaagcccGGGAAGGC.ggcgggaaggaggaaacCgcgAGCCAGGAGACCUGCcgugag 175 :U+ :: :GGGAAGG: :::::: A A+ :C: +AG+CAG+AGACCUG:::+ + 7672 UUUUUAUUUGGGAAGGUaAAGAAAUAUAAA----UCAUAAGUCAGAAGACCUGCAUAAUU 7727 ::::::::::::: 176 uguuaacaccccc 188 + +U+AC C ++C 7728 GAAUUACUCUAUC 7740 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #25350,sp|AE010642.1|AE010642 Fusobacterium nucleatum subsp. nucleatum ATCC 25586, section 184 of 197 of the complete genome. ----isReversed: 1 ----hitSequence: AAUAAUUUAUAAUAUUAUUGUACACGGGUGCAUAUUGCUUAAUAGAGGAAGAAGAGUGAAAAUCUCUCACAGCGAAAGCUACUGUAAUGUGGAUGAAAUCAUAAUAAACCACUGGGCAACUGGGAAGGUAUGAAAGUAAGGUGAAGCAAAGUCAGGAGACUUACCAUUAUAUUAAUAUUUAUA hit 33 : 9064 8882 (rev) 61.32 bits ::::::::::::::[[[[[[,<<<____...________>>>,,,,,(.((,,,<.<<<< 1 uuauauuagccacgugaaGGUcccccca...gaaugggggggUUAAaA.GGGAAu.cCGG 55 + ++AUU+ A +++:: U C:C ++ ++AU :G UUAA+A :GGAA: :::G 5442 AAUAAUUUAUAAUAUUAUUGUACACGGGugcAUAU----UGCUUAAUAgAGGAAGaAGAG 5497 _______>>>>>,,<<<____>>>,<<<---<<<<------<<<<<<-----<<<-<<<< 56 UGaAAAUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccgccAaaauGCCACUgg 115 UGAAAAUC::::+C:GC GC:ACUGUAA::: G+A GA::::::AA+A+:CCACU:G 5498 UGAAAAUCUCUCACAGCGAAAGCUACUGUAAUGU-GGAUGAAAUCAUAAUAAACCACUGG 5556 <<____>>>>>>--->>>>>>>>>---------->>>>---->>>,,,,)))]]]]]]:: 116 gcucaagcccGGGAAGGCggcgggaaggaggaaacCgcgAGCCAGGAGACCUGCcgugag 175 CAA C:GGGAAGG:::::::+ +G++AA :::+AG+CAGGAGAC:U ::+++A 5557 --GCAA--CUGGGAAGGUAUGAAAGUAAGGUGAA-GCAAAGUCAGGAGACUUACCAUUAU 5611 ::::::::::::: 176 uguuaacaccccc 188 U A + ++ 5612 AUUAAUAUUUAUA 5624 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #26023,sp|AE011315.1|AE011315 Leptospira interrogans serovar lai str. 56601 chromosome I, section 124 of 397 of the complete sequence. ----isReversed: 0 ----hitSequence: UGGAACGGAAAACUUGUUUAUUCUCGUGAUGAGGAAGGGAAUCCGGUUCAAAUCCGGAGCUGAACCCGCAGCUGUAAUCGCCGAAUGAGAUUUCGCAAUCAUGCCACUGCGUUAAAUACGCGGGAAGGCUGCGAAAUCGGCGAAAGCCAGAAGACCUAACAAGUAAAAAAACAAACUA hit 34 : 3428 3605 (fwd) 94.60 bits ::::::::::::::[[[[[[,<<<____________>>>,,,,,(((,,,<<<<<_____ 1 uuauauuagccacgugaaGGUccccccagaaugggggggUUAAaAGGGAAucCGGUGaAA 60 U +A AC+U +:::U:C:C +++ + :G: AGGGAAUCCGGU +AA 3428 UGGAACGGAAAACUUGUUUAUUCUCGUGAUGA----GGA-----AGGGAAUCCGGUUCAA 3478 __>>>>>,,<<<____>>>,<<<---<<<<....------<<<<<<-----<<<-<<<<< 61 AUCCGgaGCUGcCCCCgCAACUGUAAgcGg....gaaggacccgccAaaauGCCACUggg 116 AUCCGGAGCUG: CCC:CA CUGUAA:CG: +AG ::CGC:A+ AUGCCACUG:G 3479 AUCCGGAGCUGAACCCGCAGCUGUAAUCGCcgaaUGAGAUUUCGCAAUCAUGCCACUGCG 3538 <____.>>>>>>--->>>>>>>>>---------->>>>---->>>,,,,)))]]]]]]:: 117 cucaa.gcccGGGAAGGCggcgggaaggaggaaacCgcgAGCCAGGAGACCUGCcgugag 175 :U AA :C:CGGGAAGGC:GCG::A +G :CG:+AGCCAG+AGACCU:::+ G++ 3539 UUAAAuACGCGGGAAGGCUGCGAAAUCG------GCGAAAGCCAGAAGACCUAACAAGUA 3592 ::::::::::::: 176 uguuaacaccccc 188 + AACA C+ 3593 AAAAAACAAACUA 3605 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #26312,sp|AE011604.1|AE011604 Leptospira interrogans serovar lai str. 56601 chromosome II, section 16 of 34 of the complete sequence. ----isReversed: 1 ----hitSequence: GCACAGUUUUUUCAUAGGGUUUAUCUAUGUUUCACAUAGAUAGGAAGACGGUUAAAAUCCGUCACGGUAUCCGCCGCUGUAAGAAGGACGAAAGACAUACUAAGCCACUGGGACAACCUGGGAAGGCGUGUCGAGUAGAAAGAUUUCAAGUCAGAAUACGACCUAUGAAAAUUCCUGAAAG hit 35 : 13614 13434 (rev) 71.10 bits ::::::::::::::[[[[[[,<<<________.____>>>,,,,,(((,,,<<<<<____ 1 uuauauuagccacgugaaGGUccccccagaau.gggggggUUAAaAGGGAAucCGGUGaA 59 A A+U++ C + ::G:U:::C ++ U + +::: A+ G GAA::CGGU AA 123 GCACAGUUUUUUCAUAGGGUUUAUCU--AUGUuUCACAUA--GAUAG-GAAGACGGUUAA 177 ___>>>>>,,<<<____>>>,<<<---<<<<------<<<<<<-----<<<-<<<<<<__ 60 AAUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccgccAaaauGCCACUgggcuc 119 AAUCCG::+C:G: CC:C: CUGUAAG:: GA G A::::::A +A+GCCACU:GG +C 178 AAUCCGUCACGGUAUCCGCCGCUGUAAGAAGGACGAAAGACAUACUAAGCCACUGGG-AC 236 __>>>>>>--->>>>>>>>>---------->>>>---->>>,,,,)))]]]]]]:::::: 120 aagcccGGGAAGGCggcgggaaggaggaaacCgcgAGCCAGGAGACCUGCcgugaguguu 179 AA CC:GGGAAGGC::::::A+ ++ A+A ::C+AG+CAG+A A C :C:: + + +U 237 AA-CCUGGGAAGGCGUGUCGAGUAGAAAGAUUUCAAGUCAGAAUA-CGACCUAUGAAAAU 294 ::::::::: 180 aacaccccc 188 + C + 295 UCCUGAAAG 303 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #26672,sp|AE011964.1|AE011964 Xanthomonas axonopodis pv. citri str. 306, section 342 of 469 of the complete genome. ----isReversed: 1 ----hitSequence: UCGCCUUGGCGAGCUGCAAUUCCGGAGCUGCCCCCGCAACGGUGGGCGAGGUCAGAUGCCGCACUACGCCACUGUGCAGUCGCAUGGGAAGGCGCGGCAUCGGAAGCGCCAGCUUCCACUCGCAAGCCCGGAGACCGGCCUGAGGGAUUGACCCGGCA hit 36 : 10940 10783 (rev) 30.43 bits ::::::::::::::[[[[[[,.<<<____________>>>,,,,,(((,,,<<<<<____ 1 uuauauuagccacgugaaGGU.ccccccagaaugggggggUUAAaAGGGAAucCGGUGaA 59 U UU GC+A+ :::A::U :GG A 3 UCGCCUUGGCGAGCUGCAAUUc-----------------------CGG--A--------- 28 ___>>>>>,,<<<____>>>,<<<---<<<<.------<<<<<<-----<<<-<<<<<<_ 60 AAUCCGgaGCUGcCCCCgCAACUGUAAgcGg.gaaggacccgccAaaauGCCACUgggcu 118 GCUGCCCCCGCAAC:GU+ GCG: G GA::C::CA +A GCCACU::GC+ 29 --------GCUGCCCCCGCAACGGUGGGCGAgGUCAGAUGCCGCACUACGCCACUGUGCA 80 ___>>>>>>--->>>>>>>>>----------..........>>>>---->>>,,,,)))] 119 caagcccGGGAAGGCggcgggaaggaggaaa..........cCgcgAGCCAGGAGACCUG 168 +GC::GGGAAGGCG::G:: GGA+G ++ :CGC+AGCC:GGAGACC:: 81 GUCGCAUGGGAAGGCGCGGCAUCGGAAGCGCcagcuuccacUCGCAAGCCCGGAGACCGG 140 ]]]]]::::::::::::::: 169 Ccgugaguguuaacaccccc 188 :C::: G+ UU AC+C C 141 CCUGAGGGAUUGACCCGGCA 160 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #27128,sp|AE012421.1|AE012421 Xanthomonas campestris pv. campestris str. ATCC 33913, section 329 of 460 of the complete genome. ----isReversed: 1 ----hitSequence: UACCAUGCGCGCCCCUGAGGUGACUGCCGGAAUUCCGGUGGUUUAAACGGGAAUCCGGUGCGCGCAUCGCCUUGGCGAGACGCAAGUCCGGAGCUGCCCCCGCAACGGUGGGCGAGGUCAGGUGCCGCAACAGGCCACUGUGCACACGCAUGGGAAGGCGCGGUACCGGAAGCGCAGGCUUCCACUCGCGAGCCCGGAGACCGGCCUGAGGGAUUGACCCGGCA hit 37 : 6485 6262 (rev) 128.60 bits ::::::::::::::[[[[[[,.<<<____.____.____>>>,,,,,(((,,,<<<<<__ 1 uuauauuagccacgugaaGGU.cccccca.gaau.gggggggUUAAaAGGGAAucCGGUG 57 U AU +GC++C ::AGGU :C:+CC+ +A U GG :G:UUAAA:GGGAAUCCGGUG 5742 UACCAUGCGCGCCCCUGAGGUgACUGCCGgAAUUcCGGUGGUUUAAACGGGAAUCCGGUG 5801 _......................____>>>>>,,<<<____>>>,<<<---<<<<.---- 58 a......................AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGg.gaag 94 + AA UCCGGAGCUGCCCCCGCAAC:GU+ GCG: G 5802 CgcgcaucgccuuggcgagacgcAAGUCCGGAGCUGCCCCCGCAACGGUGGGCGAgGUCA 5861 --<<<<<<-----<<<-<<<<<<____>>>>>>--->>>>>>>>>----------..... 95 gacccgccAaaauGCCACUgggcucaagcccGGGAAGGCggcgggaaggaggaaa..... 149 G ::C::CAA A GCCACU::GC+CA+GC::GGGAAGGCG::G::+ GGA+G ++ 5862 GGUGCCGCAACAGGCCACUGUGCACACGCAUGGGAAGGCGCGGUACCGGAAGCGCaggcu 5921 .....>>>>---->>>,,,,)))]]]]]]::::::::::::::: 150 .....cCgcgAGCCAGGAGACCUGCcgugaguguuaacaccccc 188 :CGCGAGCC:GGAGACC:GCC:: G+ UU AC+C C 5922 uccacUCGCGAGCCCGGAGACCGGCCUGAGGGAUUGACCCGGCA 5965 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #27306,sp|AE012817.1|AE012817 Chlorobium tepidum TLS section 38 of 194 of the complete genome. ----isReversed: 1 ----hitSequence: UACUUCAUCCGAUUAUGUGGUGCCCGCCAUGGAAACAUACGGGCUUAAAAGGGAAUCCGGUGAGAGUCCGGAACAGUACCCGCUGCUGUAAUUCCGCGCUGGCCGCAAGGCUGGCGACAAGGUUUGCCGACAAUGCCACUGUCCCGUUCAGGGAUGGGAAGGCCGGCAGAAUCCGGGAAAGUCAGAAGACCUGCCUCAUAUUUUUUGGCUUCG hit 38 : 569 357 (rev) 100.49 bits ::::::::::::::[[[[[[,<<<____...____..____>>>,,,,,(((,,,<<<<< 1 uuauauuagccacgugaaGGUcccccca...gaau..gggggggUUAAaAGGGAAucCGG 55 U U+ + C+A + ::GGU:CCC C+ GAA+ + +GGG:UUAAAAGGGAAUCCGG 10290 UACUUCAUCCGAUUAUGUGGUGCCCGCCaugGAAAcaUACGGGCUUAAAAGGGAAUCCGG 10349 _______>>>>>,,<<<____>>>,<<<---.<<<<.....................--- 56 UGaAAAUCCGgaGCUGcCCCCgCAACUGUAA.gcGg.....................gaa 93 UGA+A UCCGGA+C:G: CCC:C: CUGUAA :C AA 10350 UGAGAGUCCGGAACAGUACCCGCUGCUGUAAuUCCGcgcuggccgcaaggcuggcgaCAA 10409 ---<<<<<<-----<<<-<<<<<<..____.>>>>>>--->>>>>>>>>----------> 94 ggacccgccAaaauGCCACUgggc..ucaa.gcccGGGAAGGCggcgggaaggaggaaac 150 GG ::::C:A AAUGCCACU:::C U+ A G:::GGGAAGGC:G::::AA 10410 GGUUUGCCGACAAUGCCACUGUCCcgUUCAgGGAUGGGAAGGCCGGCAGAAUCC-----G 10464 >>>---->>>,,,,)))]]]]]]::::::::::::::: 151 CgcgAGCCAGGAGACCUGCcgugaguguuaacaccccc 188 G:+AG+CAG+AGACCUGC:: ++U UU+ C C 10465 GGAAAGUCAGAAGACCUGCCUCAUAUUUUUUGGCUUCG 10502 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #27307,sp|AE012818.1|AE012818 Chlorobium tepidum TLS section 39 of 194 of the complete genome. ----isReversed: 0 ----hitSequence: UUCUUUCUCGCCAUGACAGGUGCCGGUUUAAAAGCCGGAGAAUAGGGAAGUACGUGAGAUUCGUACACUGUACCCGCAACUGUACAACGGUUAACCGCCGGGCAAAUUCCGUGGCCACACGGAUGCGCAAGGCGGGCUUUCAGGUCACUGCCGGUUUUCCUCCACGGAAAACUGCGGGAAGGUUUGGAGGCGCUCGAUGCCGUGAAAGUCAGGAGACCUGCCAGUCAUGCAUUUGCACCA hit 39 : 1974 2213 (fwd) 69.55 bits ::::::::::::::[[[[[[,.<<<________..____>>>,,,,,(((,,,<<<<<__ 1 uuauauuagccacgugaaGGU.ccccccagaau..gggggggUUAAaAGGGAAucCGGUG 57 UU U+U + +C+ +:::AGGU CC: G+ U G+:GG +AA+AGGGAA::: GUG 1974 UUCUUUCUCGCCAUGACAGGUgCCG----GUUUaaAAGCCGGAGAAUAGGGAAGUACGUG 2029 _____>>>>>,,<<<____>>>,<<<---.<<<<.......................... 58 aAAAUCCGgaGCUGcCCCCgCAACUGUAA.gcGg.......................... 90 A+A UC :::+CUG: CCC:CAACUGUA :CGG 2030 AGAUUCGUACACUGUACCCGCAACUGUACaACGGuuaaccgccgggcaaauuccguggcc 2089 ...............------<<<<<<-----<<<-<<<<<<.......____....... 91 ...............gaaggacccgccAaaauGCCACUgggc.......ucaa....... 121 G +GG+:: :: :CACUG: : UC A 2090 acacggaugcgcaagGCGGGCUUUCAG-----GUCACUGCCGguuuuccUCCAcggaaaa 2144 >>>>>>--->>>>>>>>>---------->>>>..---->>>,,,,)))]]]]]]:::::: 122 gcccGGGAAGGCggcgggaaggaggaaacCgc..gAGCCAGGAGACCUGCcgugaguguu 179 : :CGGGAAG: :: ::+ G GA CCG: +AG+CAGGAGACCUGCC::: +UG 2145 CUGCGGGAAGGUUUGGAGGCGCUCGAUGCCGUgaAAGUCAGGAGACCUGCCAGUCAUGCA 2204 ::::::::: 180 aacaccccc 188 + + C CC 2205 UUUGCACCA 2213 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #27309,sp|AE012820.1|AE012820 Chlorobium tepidum TLS section 41 of 194 of the complete genome. ----isReversed: 0 ----hitSequence: AAUAAAUAAUUCAGUUACGGUUUCCGGUGCCCGGUGGGGCGCCGGAAUGAAAAGGGAACCCGGUGAAAAUCCGGGACAGUGCCCGCUGCUGUGAUCCUCCCGUCGGCCACAAUCGGGUCGGCGGACGAUCGCUUCCGAUGAGGCCACUGGUUCGCGCCCGCGAACCGGGAAGGCCGGAAGCGAGGGGAGAGUCAGAAGACCUGCCGUAAUGCAGUAAAUGCUC hit 40 : 3705 3927 (fwd) 103.76 bits ::::::::::::::[[[[[[,<<<____.....____...____>>>,,,,,(((,,,<< 1 uuauauuagccacgugaaGGUcccccca.....gaau...gggggggUUAAaAGGGAAuc 52 + ++A+UA + G:+A+GGU::CC + G+ G +GG::U+AAAAGGGAA:C 3705 AAUAAAUAAUUCAGUUACGGUUUCCGGUgcccgGUGGggcGCCGGAAUGAAAAGGGAACC 3764 <<<_______>>>>>,,<<<____>>>,<<<---<<<<...................... 53 CGGUGaAAAUCCGgaGCUGcCCCCgCAACUGUAAgcGg...................... 90 CGGUGAAAAUCCGG:+C:G: CCC:C: CUGU+A:C : 3765 CGGUGAAAAUCCGGGACAGUGCCCGCUGCUGUGAUCCUcccgucggccacaaucgggucg 3824 .....------<<<<<<-----<<<-<<<<<<.....____.>>>>>>--->>>>>>>>> 91 .....gaaggacccgccAaaauGCCACUgggc.....ucaa.gcccGGGAAGGCggcggg 139 +A + C:::C:A+ A GCCACUGG:: C + ::CCGGGAAGGC:G:::G 3825 gcggaCGAUCGCUUCCGAUGAGGCCACUGGUUcgcgcCCGCgAACCGGGAAGGCCGGAAG 3884 ---------->>>>---->>>,,,,)))]]]]]]::::::::::::::: 140 aaggaggaaacCgcgAGCCAGGAGACCUGCcgugaguguuaacaccccc 188 ++ G : G:GAG+CAG+AGACCUGC+G+:A + +++A A+ C+C 3885 CGAG------GGGAGAGUCAGAAGACCUGCCGUAAUGCAGUAAAUGCUC 3927 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #27321,sp|AE012832.1|AE012832 Chlorobium tepidum TLS section 53 of 194 of the complete genome. ----isReversed: 0 ----hitSequence: GAGUUCUUUCAGCAUUACGGUGCCGGAUGAAAGAUGCCGGAUAAUAGGGAAGUGCGUGUGAAUCGCACACUGUGCCCGCAACUGUAAGAUGGUAUGUCGCGCGACGACAGGAGCAGCUCUGCUUUUGUGGCCGUUGCGGAUCGGGUGUAUCCACUCCGCCAACCUCUGAUAACCACGGGGAAUGCGGGGGAAGGCUGCCCGGAGGAAAACGUCGAAGUAAUUUCGCAGCCAUCGAAGUCAGGAGACCUGCCGUAGUGGUUGGCGCCGAA hit 41 : 3064 3332 (fwd) 75.76 bits ::::::::::::::[[[[[[,.<<<________.____>>>,,,,,(((,,,<<<<<___ 1 uuauauuagccacgugaaGGU.ccccccagaau.gggggggUUAAaAGGGAAucCGGUGa 58 U+ U++C C :+A+GGU CC:+ GAA+ G+:GG UAA+AGGGAA::: GUG 3064 GAGUUCUUUCAGCAUUACGGUgCCGGAU-GAAAgAUGCCGGAUAAUAGGGAAGUGCGUGU 3122 ____>>>>>,,<<<____>>>,<<<---<<<<............................ 59 AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGg............................ 90 +AAUC :::+CUG: CCC:CAACUGUAAG::G 3123 GAAUCGCACACUGUGCCCGCAACUGUAAGAUGguaugucgcgcgacgacaggagcagcuc 3182 ................------<<<<<<-----<<<-<<<<<<.........____.... 91 ................gaaggacccgccAaaauGCCACUgggc.........ucaa.... 121 G +G C::G: A+ CCACU :GC ++AA 3183 ugcuuuuguggccguuGCGGAUCGGGUGUAU---CCACUCCGCcaaccucugAUAAccac 3239 .......>>>>>>--->>>.>>>>>>----------..................>>>>.- 122 .......gcccGGGAAGGC.ggcgggaaggaggaaa..................cCgc.g 154 GC: GGGAAGG :C::G+AGGA+ A C::C + 3240 ggggaauGCGGGGGAAGG-cUGCCCGGAGGAAAACGucgaaguaauuucgcagcCAUCgA 3298 --->>>,,,,)))]]]]]]::::::::::::::: 155 AGCCAGGAGACCUGCcgugaguguuaacaccccc 188 AG+CAGGAGACCUGC+G+: +GUU +C CC 3299 AGUCAGGAGACCUGCCGUAGUGGUUGGCGCCGAA 3332 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #27347,sp|AE012858.1|AE012858 Chlorobium tepidum TLS section 79 of 194 of the complete genome. ----isReversed: 0 ----hitSequence: UCUUUCACAUGAUUAGCUGGUGCCGGUUUUAAAGCCGGAGAAUAGGGAAGUACGUGAGAUUCGUACACUGUACCCGCAACUGUACAACGGAAAACUGCCGCUGGCAGGUAUGGCCACAUGCCUCAAAGCCGCAGCCGGUGCACGUCACUGCCAGGCUCCUCCACGGAGCGGGCGGGAAGGC hit 42 : 6757 6937 (fwd) 22.14 bits ::::::::::::::[[[[[[,.<<<________..____>>>,,,,,(((,,,<<<<<__ 1 uuauauuagccacgugaaGGU.ccccccagaau..gggggggUUAAaAGGGAAucCGGUG 57 U +U+ + +A + :: G U CC: G+ U G+:GG +AA+AGGGAA::: GUG 6757 UCUUUCACAUGAUUAGCUGGUgCCG----GUUUuaAAGCCGGAGAAUAGGGAAGUACGUG 6812 _____>>>>>,,<<<____>>>,<<<---.<<<<------<<<<<<-----<<<-<<<<< 58 aAAAUCCGgaGCUGcCCCCgCAACUGUAA.gcGggaaggacccgccAaaauGCCACUggg 116 A+A UC :::+CUG: CCC:CAACUGUA :CG GAA +::C :C +G :A: G : 6813 AGAUUCGUACACUGUACCCGCAACUGUACaACG-GAAAACUGCCGCUGGCAGGUAUGGCC 6871 <____>>>>>>--->>>>>>>>>---------->>>>--..-->>>,,,,)))]]]]]]: 117 cucaagcccGGGAAGGCggcgggaaggaggaaacCgcgA..GCCAGGAGACCUGCcguga 174 +CA : C : AA: CG: G::++ G + CG: A GCCAGG CCU C :: A 6872 -ACAU-GCCUCAAAGCCGCAGCCGGUGCA-----CGUCAcuGCCAGGCU-CCUCCACGGA 6923 :::::::::::::: 175 guguuaacaccccc 188 G+G + + C 6924 GCGGGCGGGAAGGC 6937 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #27499,sp|AE013010.1|AE013010 Thermoanaerobacter tengcongensis strain MB4T, section 37 of 244 of the complete genome. ----isReversed: 0 ----hitSequence: UGAAUAUUAAAGCCUUAUGGUCCCAUGAUGGGUUAAAAGGGAAGACGGGUGAGAAUCCCGCGCAGCCCCCGCUACUGUGAGGGAGGACGAAGCCCUAGUAAGCCACUGUCCGGCACUCAACUGAGCGCGUUAGUAAGGAGAAAAGAGGGAGAGAAAUUGCGUUCAGUUGAGUGCCGGGUGGGAAGGCAGGGUGGAGGAUGAGUCCCGAGCCAGGAGACCUGCCAUAAGGUUUUAGAAGUUC hit 43 : 3537 3777 (fwd) 112.96 bits ::::::::::::::[[[[[[,<<<________.____>>>,,,,,(((,,,<.<<<<___ 1 uuauauuagccacgugaaGGUccccccagaau.gggggggUUAAaAGGGAAu.cCGGUGa 58 U A+++U+ C :++:GGUCCC ++ + GGGUUAAAAGGGAA: C:GGUGA 3537 UGAAUAUUAAAGCCUUAUGGUCCC----AUGAu----GGGUUAAAAGGGAAGaCGGGUGA 3588 ____>>>>>,,<<<____>>>,<<<---<<<<------<<<<<<-----<<<-<<<<<<. 59 AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccgccAaaauGCCACUgggc. 117 +AAUCC:G:GC:GCCCCCGC:ACUGU+AG:G:G+A+GA::C:C:A +A+GCCACU: :C 3589 GAAUCCCGCGCAGCCCCCGCUACUGUGAGGGAGGACGAAGCCCUAGUAAGCCACUGUCCg 3648 ....____.................................................... 118 ....ucaa.................................................... 121 UCAA 3649 gcacUCAAcugagcgcguuaguaaggagaaaagagggagagaaauugcguucaguugagu 3708 ...>>>>>>--->>>>>>>>>---------->>>>---->>>,,,,)))]]]]]]::::: 122 ...gcccGGGAAGGCggcgggaaggaggaaacCgcgAGCCAGGAGACCUGCcgugagugu 178 G: :GGGAAGGC:G:G::+AGGA GA+ :C:CGAGCCAGGAGACCUGC:++:AG+ U 3709 gccGGGUGGGAAGGCAGGGUGGAGGAUGAG-UCCCGAGCCAGGAGACCUGCCAUAAGGUU 3767 :::::::::: 179 uaacaccccc 188 U+A A +C 3768 UUAGAAGUUC 3777 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #27500,sp|AE013011.1|AE013011 Thermoanaerobacter tengcongensis strain MB4T, section 38 of 244 of the complete genome. ----isReversed: 0 ----hitSequence: GAAUAUAAAAAGCCUUAUGGUCCCGUGAUGGGUUAAAAGGGAAGACGGGUGAGAAUCCCGCGCAGCCCCCGCUACUGUGAGGGAGGACGAAGCCCUAGUAAGCCACUGUCCGGCACUCAACUGAGCGCGUUAGUAAGGAGAAAAGAGGGAGAGAAAUUGCGUUCAGUUGAGUGCCGGAUGGGAAGGCAGGGUGGAGGAUGAGUCCCGAGCCAGGAGACCUGCCAUAAGGUUUUUAAAAGUU hit 44 : 30 270 (fwd) 115.38 bits ::::::::::::::[[[[[[,<<<________.____>>>,,,,,(((,,,<.<<<<___ 1 uuauauuagccacgugaaGGUccccccagaau.gggggggUUAAaAGGGAAu.cCGGUGa 58 AUAU A C :++:GGUCCC G+ + GGGUUAAAAGGGAA: C:GGUGA 30 GAAUAUAAAAAGCCUUAUGGUCCC----GUGAu----GGGUUAAAAGGGAAGaCGGGUGA 81 ____>>>>>,,<<<____>>>,<<<---<<<<------<<<<<<-----<<<-<<<<<<. 59 AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccgccAaaauGCCACUgggc. 117 +AAUCC:G:GC:GCCCCCGC:ACUGU+AG:G:G+A+GA::C:C:A +A+GCCACU:::C 82 GAAUCCCGCGCAGCCCCCGCUACUGUGAGGGAGGACGAAGCCCUAGUAAGCCACUGUCCg 141 ....____.................................................... 118 ....ucaa.................................................... 121 UCAA 142 gcacUCAAcugagcgcguuaguaaggagaaaagagggagagaaauugcguucaguugagu 201 ...>>>>>>--->>>>>>>>>---------->>>>---->>>,,,,)))]]]]]]::::: 122 ...gcccGGGAAGGCggcgggaaggaggaaacCgcgAGCCAGGAGACCUGCcgugagugu 178 G:::GGGAAGGC:G:G::+AGGA GA+ :C:CGAGCCAGGAGACCUGC:++:AG+ U 202 gccGGAUGGGAAGGCAGGGUGGAGGAUGAG-UCCCGAGCCAGGAGACCUGCCAUAAGGUU 260 :::::::::: 179 uaacaccccc 188 U+ A + 261 UUUAAAAGUU 270 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #28117,sp|AE013632.1|AE013632 Yersinia pestis KIM section 32 of 415 of the complete genome. ----isReversed: 0 ----hitSequence: UCGUAGCAUUGUGGUCCGGCCUCAUGCUGUUAUUUAAACACCUAAGAGUUAAAAGGGAAUCCGGUGUAAAUCCGGAGCUGACGCGCAGCGGUAAGGGGAAGUCACGGCGAUAGGUUUCUAACAGACACUGUCCGCAAGGAUGGGAAGUCAUCGCCUGCUCUAUUUCGCGCCAUUUAUUUAUCACAGUAUUUUUACUGUCAUAACCAUGGCCUGAUACCAGAGAUCCUAAGCCCGAAGACCUGCCGGUAUUACGUCGCAAUA hit 45 : 2530 2790 (fwd) 83.84 bits ::::::::::::::[[[[[[,<<<____.____.........____>>>,,,,,(((,,, 1 uuauauuagccacgugaaGGUcccccca.gaau.........gggggggUUAAaAGGGAA 50 U UA+ A+ + +GU :+GG C:C ++ G+ + G:GUUAAAAGGGAA 2530 UCGUAGCAUUGUGGU-CCGGCCUCAUGCuGUUAuuuaaacacCUAAGAGUUAAAAGGGAA 2588 <<<<<_______>>>>>,,<<<____>>>,<<<---<<<<.------<<<<<<-----.. 51 ucCGGUGaAAAUCCGgaGCUGcCCCCgCAACUGUAAgcGg.gaaggacccgccAaaau.. 107 UCCGGUG AAAUCCGGAGCUG: C C:CA C:GUAA::G ++ + +::CG::A U 2589 UCCGGUGUAAAUCCGGAGCUGA-CGCGCAGCGGUAAGGGGaAGUCACGGCGAUAGGUUuc 2647 .....<<<-<<<<<<____>>>>>>--->>>>>>>>>----------............. 108 .....GCCACUgggcucaagcccGGGAAGGCggcgggaaggaggaaa............. 149 G:CACU:::C CAAG:::GGGAAG:C::CG:: ++ 2648 uaacaGACACUGUCCGCAAGGAUGGGAAGUCAUCGCCUGCUCUAUUUcgcgccauuuauu 2707 .............................................>>>>---->>>,,,, 150 .............................................cCgcgAGCCAGGAGA 164 C::+AGCC:G+AGA 2708 uaucacaguauuuuuacugucauaaccauggccugauaccagagaUCCUAAGCCCGAAGA 2767 )))]]]]]]::::::::::::::: 165 CCUGCcgugaguguuaacaccccc 188 CCUGC+: G++U + C C ++ 2768 CCUGCCG-GUAUUACGUCGCAAUA 2790 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #28811,sp|AE014429.1|AE014429 Brucella suis 1330 chromosome I section 115 of 190 of the complete genome. ----isReversed: 1 ----hitSequence: GUGUCAAACCAUGUGACAGGUUUUGCCGGAACGAAUCCCCGGCAAUACCAAAAGGGAAUGCGACGGACGGACCCACGCCGGGCGUCUUUAUCGCAGCCGACCCCGCGACUGUAGAGCGGAGAGGGAAGAGGCAAGCCGGGCAACCGGCAGCCACUGGAAAUCAGAUAGAUUUCUGGGAAGGCGCUUUAUUCCCCAAGACCCGCGAGCCAGGAGACCUGCCUGUUGCAUGAGGGCAUUG hit 46 : 551 314 (rev) 83.43 bits ::::::::::::::[[[[[[,<<<____....____....____>>>,,,,,(((,,,<< 1 uuauauuagccacgugaaGGUcccccca....gaau....gggggggUUAAaAGGGAAuc 52 U U + A C ++:::AGGU: :+CC+ GAAU GG+ : : AAAAGGGAAU: 9807 GUGUCAAACCAUGUGACAGGUUUUGCCGgaacGAAUccccGGCAAUACCAAAAGGGAAUG 9866 <<<___....................____>>>>>,,<<<____>>>,<<<---.<<<<. 53 CGGUGa....................AAAUCCGgaGCUGcCCCCgCAACUGUAA.gcGg. 90 CG: G :CG:AGC:G:CCCC:C:ACUGUA GCGG 9867 CGACGGacggacccacgccgggcgucUUUAUCGCAGCCGACCCCGCGACUGUAGaGCGGa 9926 ------<<<<<<-----............<<<-<<<<<<.____......>>>>>>---> 91 gaaggacccgccAaaau............GCCACUgggc.ucaa......gcccGGGAAG 131 GA+GGA::: :CAA GCCACU:G:: UCA ::C:GGGAAG 9927 GAGGGAAGAGGCAAGCCgggcaaccggcaGCCACUGGAAaUCAGauagauUUCUGGGAAG 9986 >>>>>>>>----------.>>>>---->>>,,,,)))]]]]]]::::::::::::::: 132 GCggcgggaaggaggaaa.cCgcgAGCCAGGAGACCUGCcgugaguguuaacaccccc 188 GCG: ::: + A+A CCGCGAGCCAGGAGACCUGCC:::+G+ U+A+ C + 9987 GCGCUUUAUUCCCCAAGAcCCGCGAGCCAGGAGACCUGCCUGUUGCAUGAGGGCAUUG 10044 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #28814,sp|AE014432.1|AE014432 Brucella suis 1330 chromosome I section 118 of 190 of the complete genome. ----isReversed: 1 ----hitSequence: UCGCAAUUUUCAGGAGACGGUUCCGCCAUUGCGGCGGAUGAAAAGGGAACACGGUGAAGCCAUAGGGCUGAAACCGAGACUGCCCCCGCAACUGUAACCGGAGAGCUAUCCUCCACAGGCCGCGCAAGCGGCCAAAGCCACUGAAAGCAGCAAUAUGCUGCAAUCGGGAAGGCGGAGGCAAAGCGAAGACCCGGAAGUCAGGAGACCUGCCGUAUCCGGUCACCCAUGC hit 47 : 6199 5971 (rev) 119.42 bits ::::::::::::::[[[[[[,<<<________.____>>>,,,,,(((,,,<<<<<___. 1 uuauauuagccacgugaaGGUccccccagaau.gggggggUUAAaAGGGAAucCGGUGa. 58 U A+U++ CA+G GA+GGU:CC+C A U GG+GG:U+AAAAGGGAA: CGGUGA 5283 UCGCAAUUUUCAGGAGACGGUUCCGC--CAUUgCGGCGGAUGAAAAGGGAACACGGUGAa 5340 ...........____>>>>>,,<<<____>>>,<<<---<<<<------<<<<<<----- 59 ...........AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccgccAaaau 107 +AA CCG :+CUGCCCCCGCAACUGUAA:CGG++AG+ : C::C A A 5341 gccauagggcuGAAACCGAGACUGCCCCCGCAACUGUAACCGGAGAGCUAUCCUCCACAG 5400 ..................<<<-<<<<<<...____........>>>>>>--->>>.>>>> 108 ..................GCCACUgggc...ucaa........gcccGGGAAGGC.ggcg 137 GCCACUG: CAA :CGGGAAGGC G::G 5401 gccgcgcaagcggccaaaGCCACUGAAAgcaGCAAuaugcugcAAUCGGGAAGGCgGAGG 5460 >>---------->>>>---->>>,,,,)))]]]]]]::::::::::::::: 138 ggaaggaggaaacCgcgAGCCAGGAGACCUGCcgugaguguuaacaccccc 188 :AAG ++ +A+CCG:+AG+CAGGAGACCUGC+GU + +G U AC+C C 5461 CAAAGCGAAGACCCGGAAGUCAGGAGACCUGCCGUAUCCGGUCACCCAUGC 5511 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #28913,sp|AE014531.1|AE014531 Brucella suis 1330 chromosome II section 27 of 108 of the complete genome. ----isReversed: 0 ----hitSequence: ACCAUAUCUUGUGUUCGAGGUUCUUUCGAUUCGACGAGUCGGGAGCUAAGACGGGAAUCCGGUGCGCUUGCCCAUGGUGGGCGGGCAAUGCCGGAGCUGCCCCCGCAACUGUAAGCGGCGAGCUUUGCGCCCCAUGCCACUGGCGAAAGCCGGGAAGGCGGGUGGAAGCGUUGAGCCGUGAGCCAGGAGACCUGCCUUGAGCGUGAACGUCCAC hit 48 : 11156 11369 (fwd) 121.75 bits ::::::::::::::[[[[[[,.<<<____...____..____>>>,,,,,(.((,,,<<< 1 uuauauuagccacgugaaGGU.cccccca...gaau..gggggggUUAAaA.GGGAAucC 53 + +++U++ + ++U::AGGU C:: C+A GA + GG::G UAA+A GGGAAUCC 11156 ACCAUAUCUUGUGUUCGAGGUuCUUUCGAuucGACGagUCGGGAGCUAAGAcGGGAAUCC 11215 <<___.....................____>>>>>,,<<<____>>>,<<<---<<<<.. 54 GGUGa.....................AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGg.. 90 GGUG+ AA CCGGAGCUGCCCCCGCAACUGUAA:CGG 11216 GGUGCgcuugcccauggugggcgggcAAUGCCGGAGCUGCCCCCGCAACUGUAAGCGGcg 11275 ------<<<<<<-----<<<-<<<<<<____>>>>>>--->>>>>>>>>----------> 91 gaaggacccgccAaaauGCCACUgggcucaagcccGGGAAGGCggcgggaaggaggaaac 150 ++ C :CC A+ GCCACUGG: AA :CCGGGAAGGCGG: G AAG + ++A C 11276 AGCUUUGCGCCCCAU--GCCACUGGC-GAAA-GCCGGGAAGGCGGGUGGAAGCGUUGAGC 11331 >>>---->>>,,,,)))]]]]]]::::::::::::::: 151 CgcgAGCCAGGAGACCUGCcgugaguguuaacaccccc 188 CG:GAGCCAGGAGACCUGCC::GAG+GU+AAC +CC C 11332 CGUGAGCCAGGAGACCUGCCUUGAGCGUGAACGUCCAC 11369 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #28952,sp|AE014570.1|AE014570 Brucella suis 1330 chromosome II section 66 of 108 of the complete genome. ----isReversed: 1 ----hitSequence: CCGUAAUACCGUCAUGACGGUUCCCCGACCGAGAGCGAAGGGGAUUAAUAGGGAACACGGUGAGGACGACCCAUCAAGGGGCCGAGACCGUGGCUGCCCCCGCAACUGUAAGCGGAUUGCCGUUCAUCCUCGUGACGCCGAAAGCGUCAUGCCACUGUGCCCACGGCACGGGAAGGCAGAUGGACGGCGAUUAUCCGCAAGCCAGGAGACCUGCCGUCUUACGUAGUCCAUUG hit 49 : 13585 13353 (rev) 125.17 bits ::::::::::::::[[[[[[,<<<____..____...____>>>,,,,,(((,,,<<<<< 1 uuauauuagccacgugaaGGUcccccca..gaau...gggggggUUAAaAGGGAAucCGG 55 UA+UA C+ C :GA+GGU:CCCC+A GA + GGGG:UUAA+AGGGAA::CGG 60 CCGUAAUACCGUCAUGACGGUUCCCCGAccGAGAgcgAAGGGGAUUAAUAGGGAACACGG 119 ___....................____>>>>>,,<<<____>>>,<<<---<<<<.---- 56 UGa....................AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGg.gaag 94 UGA +A CCG::GCUGCCCCCGCAACUGUAAGCGG ++ 120 UGAggacgacccaucaaggggccGAGACCGUGGCUGCCCCCGCAACUGUAAGCGGaUUGC 179 --<<<<<<-----.................<<<-<<<<<<____.>>>>>>--->>>.>> 95 gacccgccAaaau.................GCCACUgggcucaa.gcccGGGAAGGC.gg 135 + : C::C + +U GCCACUG:GC CA+ GC:CGGGAAGGC G: 180 CGUUCAUCCUCGUgacgccgaaagcgucauGCCACUGUGCCCACgGCACGGGAAGGCaGA 239 >>>>---------->>>>---->>>,,,,)))]]]]]]::::::::::::::: 136 cgggaaggaggaaacCgcgAGCCAGGAGACCUGCcgugaguguuaacaccccc 188 :G :++G +++ A CCGC+AGCCAGGAGACCUGC+GU:+ UA+++C + 240 UGGACGGCGAUUAUCCGCAAGCCAGGAGACCUGCCGUCUUACGUAGUCCAUUG 292 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #29755,sp|AE015411.1|AE015411 Shigella flexneri 2a str. 301 section 374 of 412 of the complete genome. ----isReversed: 0 ----hitSequence: CUGUAGCAUCCACUUGCCGGUCCUGUGAGUUAAUAGGGAAUCCAGUGCGAAUCUAGAGCUGACGCGCAGCGGUAAGGAAAGGUGCGAUGAUUGCGUUAUGCGGACACUGCCAUCCGGUGGGAAGUCAUCAUCUCUUAGUAUCUUAGAUACCCCUCCAAGCCCGAAGACCUGCCGGCCAACGUCGCAUCUGG hit 50 : 8714 8904 (fwd) 85.88 bits ::::::::::::::[[[[[[,.<<<____________>>>,,,,,(((,,,<<<<<____ 1 uuauauuagccacgugaaGGU.ccccccagaaugggggggUUAAaAGGGAAucCGGUGaA 59 U UA+ A+CCAC+:::+GGU C: G+ :GUUAA+AGGGAAUC :GUG++ 8714 CUGUAGCAUCCACUUGCCGGUcCU-----GUG------AGUUAAUAGGGAAUCCAGUGCG 8762 ___>>>>>,,<<<____>>>,<<<---<<<<------<<<<<<-----......<<<-<< 60 AAUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccgccAaaau......GCCACU 113 AAUC: GAGCUG: C C:CA C:GUAAG:: +++ G+:::G:: +U G:CACU 8763 AAUCUAGAGCUGA-CGCGCAGCGGUAAGGAAAGGUGCGAUGAUUGCGUuaugcgGACACU 8821 <<<<____>>>>>>--->>>>>>>>>----------..........>>>>---->>>,,, 114 gggcucaagcccGGGAAGGCggcgggaaggaggaaa..........cCgcgAGCCAGGAG 163 ::: ++ + :::GGGAAG:C::C::: AG+A + ::C+AGCC:G+AG 8822 GCC-AUCC-GGUGGGAAGUCAUCAUCUCUUAGUAUCuuagauacccCUCCAAGCCCGAAG 8879 ,)))]]]]]]::::::::::::::: 164 ACCUGCcgugaguguuaacaccccc 188 ACCUGC+::: + U +CA+C 8880 ACCUGCCGGCCAACGUCGCAUCUGG 8904 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #29868,sp|AE015526.1|AE015526 Shewanella oneidensis MR-1 section 75 of 457 of the complete genome. ----isReversed: 0 ----hitSequence: UUUGAGUCAACCUUCUGUGGUGCUUGCGAUGAUAGCGUCGCGAGAUAAUCGGGAAGCCAGUGAAAUUCUGGCACUGCCCCCGCAACGGUAAAAGGUGAGAGACGGCCGCAUUCGAUAGGUGUUCACGAUGAACCCGUAAAUCGCAGUGUGCAAAGGUCAGUUUCGCGUUUAUCUCUAGUGAGAUGGAUUAUAGCCUAAGUCCGGAGACCGGCCCUAAAGGUGUUUUUGAGA hit 51 : 127 357 (fwd) 81.62 bits ::::::::::::::[[[[[[,.<<<____.____...____>>>,,,,,(((,,,<<<<< 1 uuauauuagccacgugaaGGU.cccccca.gaau...gggggggUUAAaAGGGAAucCGG 55 UU+ A+U+ C+ + + :GGU C::+C+A GA + + G+::G UAA+:GGGAA:CC:G 127 UUUGAGUCAACCUUCUGUGGUgCUUGCGAuGAUAgcgUCGCGAGAUAAUCGGGAAGCCAG 186 _______>>>>>,,<<<____>>>,<<<---.<<<<.------<<<<<<-----<<<-<< 56 UGaAAAUCCGgaGCUGcCCCCgCAACUGUAA.gcGg.gaaggacccgccAaaauGCCACU 113 UGAAA UC:GG:+CUGCCCCCGCAAC:GUAA ::G: ++AG + :C :CA++ G::A 187 UGAAAUUCUGGCACUGCCCCCGCAACGGUAAaAGGUgAGAGACGGCCGCAUUC-GAUAGG 245 <<<<.____..>>>>>>--->>>>>>>>>----------..................... 114 gggc.ucaa..gcccGGGAAGGCggcgggaaggaggaaa..................... 149 G:: +C A ::C AA::CG: G: ++ A+G+ + 246 UGUUcACGAugAACCCGUAAAUCGCAGUGUGCAAAGGUCaguuucgcguuuaucucuagu 305 .............>>>>---->>>,,,,)))]]]]]]::::::::::::::: 150 .............cCgcgAGCCAGGAGACCUGCcgugaguguuaacaccccc 188 :C::+AG+C:GGAGACC:GC: + A++GU++ + + + 306 gagauggauuauaGCCUAAGUCCGGAGACCGGCCCUAAAGGUGUUUUUGAGA 357 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #29890,sp|AE015548.1|AE015548 Shewanella oneidensis MR-1 section 97 of 457 of the complete genome. ----isReversed: 0 ----hitSequence: CCUAUGCUAUUGCAUUAAGGUCAUAAACGCCGGAUCAACCCAAAUAUAAUAGGGAAUCGGGGCGCUGCCCGUCAGCCAGCCCGAACUGUACCCGCAACUGUGAGUAGUUAAAAGAAGCGCCUAGAUUCUAGAUUCUAGAUUCUAGAUUCUAGAUUCUAGAUUCUAAAGCCUAGCACCUUCUUUUCUACAAGUCAGGAGACCUGCCUAUUGCUGUUUUCGCUGC hit 52 : 1057 1279 (fwd) 55.30 bits ::::::::::::::[[[[[[,.<<<____....____.____>>>,,,,,(((,,,<<<< 1 uuauauuagccacgugaaGGU.cccccca....gaau.gggggggUUAAaAGGGAAucCG 54 ++++ + C ++:AGGU :: C+ ++ + + :: UAA+AGGGAAUC:G 1057 CCUAUGCUAUUGCAUUAAGGUcAUAAACGccggAUCAaCCCAAAUAUAAUAGGGAAUCGG 1116 <___...........____>>>>>,,<<<____>>>,<<<---<<<<.....------<< 55 GUGa...........AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGg.....gaaggacc 98 G A CC:GA+CUG: CCC:CAACUGU+AG::G ++A G+ : 1117 GGCGcugcccgucagCCAGCCCGAACUGUACCCGCAACUGUGAGUAGuuaaaAGAAGCGC 1176 <<<<-----....<<<-<<<<<<....____......>>>>>>--->>>>>>>>>----- 99 cgccAaaau....GCCACUgggc....ucaa......gcccGGGAAGGCggcgggaagga 144 C:::A++ U C:A : ::: UC A ::: : AA:G :::G: + 1177 CUAGAUUCUagauUCUAGAUUCUagauUCUAgauucuAGAUUCUAAAGCCUAGCACCUUC 1236 ----->>>>---->>>,,,,)))]]]]]]::::::::::::::: 145 ggaaacCgcgAGCCAGGAGACCUGCcgugaguguuaacaccccc 188 + C::C+AG+CAGGAGACCUGCC:+++G+ U+ ++ C C 1237 UUUU-CUACAAGUCAGGAGACCUGCCUAUUGCUGUUUUCGCUGC 1279 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #30275,sp|AE015938.1|AE015938 Clostridium tetani E88, section 3 of 10 of the complete genome. ----isReversed: 0 ----hitSequence: UGAAUAUGAAAAUAUUCAGGUGCCAUUUUAGGUUUAAAAGGGAAUGUGGUUUAAUUCCACAGCAGCCCCCGCUACUGUAAUUGAGGACGAAUCUUUCACAAACCACUCUUUCAAAAAGGGAAGGGGAAGGGAAAGACAAGGGUGAAUCAUGAGCCAGGAGACCUGCCUGUAUAUGAAAGAUAAAC hit 53 : 141765 141949 (fwd) 110.17 bits ::::::::::::::[[[[[[,<<<____________>>>,,,,,(((,,,<<<<<_____ 1 uuauauuagccacgugaaGGUccccccagaaugggggggUUAAaAGGGAAucCGGUGaAA 60 U A+++U A +::AGGU CC + + GG UUAAAAGGGAAU::GGU AA 141765 UGAAUAUGAAAAUAUUCAGGUGCCAU--UUUA----GGUUUAAAAGGGAAUGUGGUUUAA 141818 __>>>>>,,<<<____>>>,<<<---<<<<------<<<<<<-----<<<-<<<<<<.__ 61 AUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccgccAaaauGCCACUgggc.uc 119 UCC::AGC:GCCCCCGC:ACUGUAA :G:G+A+GA :C::: A A+:CCACU ::: + 141819 UUCCACAGCAGCCCCCGCUACUGUAAUUGAGGACGAAUCUUUCACAAACCACUCUUUcAA 141878 __...>>>>>>--->>>>>>>>>---------->>>>---->>>,,,,)))]]]]]]::: 120 aa...gcccGGGAAGGCggcgggaaggaggaaacCgcgAGCCAGGAGACCUGCcgugagu 176 AA ::: GGGAAGG::::G: AAGG+ GAA :C: GAGCCAGGAGACCUGCC::+A 141879 AAaggGAAGGGGAAGGGAAAGACAAGGGUGAA-UCAUGAGCCAGGAGACCUGCCUGUAUA 141937 :::::::::::: 177 guuaacaccccc 188 AA A+ + C 141938 UGAAAGAUAAAC 141949 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #30275,sp|AE015938.1|AE015938 Clostridium tetani E88, section 3 of 10 of the complete genome. ----isReversed: 0 ----hitSequence: AAUAAUAUGAAUAAAAAAGGUGAAAUAGUUAUUUCUUAAAAGGGAAGCAUGGUGAAAAUCCAUCACGGUCCCGCCACUGUAAUCAGGGAGUUAGGUUUUACCACUGUUAAUUAACGGGAAGGAGAAUCUAUAAAAACUAUGAACUGUAAGUCAGGAGACCUGCCUUUUUUUAAUUAAACAUU hit 54 : 165030 165211 (fwd) 89.36 bits ::::::::::::::[[[[[[,<<<____________>>>,,,,,(((,,,<.<<<<____ 1 uuauauuagccacgugaaGGUccccccagaaugggggggUUAAaAGGGAAu.cCGGUGaA 59 + ++AU +G :::AGGU::: + +AU :::UUAAAAGGGAA: ::GGUGAA 165030 AAUAAUAUGAAUAAAAAAGGUGAAAUAGUUAU----UUCUUAAAAGGGAAGcAUGGUGAA 165085 ___>>>>>,,<<<____>>>,<<<---<<<<.------<<<<<<-----<<<-<<<<<<_ 60 AAUCCGgaGCUGcCCCCgCAACUGUAAgcGg.gaaggacccgccAaaauGCCACUgggcu 118 AAUCC:::+C:G: CCC:C:ACUGUAA C:G GA+ A::::::A CCACUG:: + 165086 AAUCCAUCACGGU-CCCGCCACUGUAAUCAGgGAGUUAGGUUUUA-----CCACUGUU-A 165138 ___>>>>>>--->>>>>>>>>----------.....>>>>---->>>,,,,)))]]]]]] 119 caagcccGGGAAGGCggcgggaaggaggaaa.....cCgcgAGCCAGGAGACCUGCcgug 173 ::CGGGAAGG :::::: A A+ A C:G +AG+CAGGAGACCUGCC::: 165139 AUU-AACGGGAAGG-AGAAUCUAUAAAAACUaugaaCUGUAAGUCAGGAGACCUGCCUUU 165196 ::::::::::::::: 174 aguguuaacaccccc 188 + U + + A C++ 165197 UUUUAAUUAAACAUU 165211 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #30275,sp|AE015938.1|AE015938 Clostridium tetani E88, section 3 of 10 of the complete genome. ----isReversed: 0 ----hitSequence: UUUAAUAUUAUUUUAUUAGGUGCUUUACAAGUUAAAAGGGAAAGUGGUGAAAAUCCACUGCAGCCCACCGUUACUGUAAUGCUGACGAAAUCUUAUAAAAUCCACUAGAUAUAUUUUAUCUGGGAAGGUUAGAAAUUAGGAAGAAGCUAAGCCAGGAAACCUGCCUAAUAAGUGUUAAUUCUU hit 55 : 166402 166584 (fwd) 81.89 bits ::::::::::::::[[[[[[,.<<<____________>>>,,,,,(((,,,<<<<<____ 1 uuauauuagccacgugaaGGU.ccccccagaaugggggggUUAAaAGGGAAucCGGUGaA 59 UU++AU ++ + +:AGGU C:: C ::GUUAAAAGGGAA:::GGUGAA 166402 UUUAAUAUUAUUUUAUUAGGUgCUUUAC---------AAGUUAAAAGGGAAAGUGGUGAA 166452 ___>>>>>,,<<<__.__>>>,<<<---<<<<------<<<<<<-----.<<<-<<<<<< 60 AAUCCGgaGCUGcCC.CCgCAACUGUAAgcGggaaggacccgccAaaau.GCCACUgggc 117 AAUCC:::GC: CCC CCG :ACUGUAA : +A+GA::::: A+AA+ CCACU:G:: 166453 AAUCCACUGCAGCCCaCCGUUACUGUAAUGC-UGACGAAAUCUUAUAAAaUCCACUAGAU 166511 ____...>>>>>>--->>>>>>>>>---------->>>>---->>>,,,,)))]]]]]]: 118 ucaa...gcccGGGAAGGCggcgggaaggaggaaacCgcgAGCCAGGAGACCUGCcguga 174 ++A ::C:GGGAAGG ::::: G++ +AA : +AGCCAGGA ACCUGCC:+ + 166512 AUAUuuuAUCUGGGAAGGUUAGAAAUUAGGAAGAA-GCUAAGCCAGGAAACCUGCCUAAU 166570 :::::::::::::: 175 guguuaacaccccc 188 + GU++ A+ C+ 166571 AAGUGUUAAUUCUU 166584 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #30275,sp|AE015938.1|AE015938 Clostridium tetani E88, section 3 of 10 of the complete genome. ----isReversed: 0 ----hitSequence: GAAUAUUAAAAUUUAUAGAGUUACCCAUUUUUGGGGUUAAAAGGGAAGGGGGUUAGAAUCCUCCACGGUCCGGCCACUGUAAUUGGUAAGUUUAUUCCAUAAGCCAUUGAGAUAUUCUCGAGAAGGUGGAAAUAAAUGAUGAACCAUAAGUCAGGAGACCUGCUUUAUAUUUAAGAUGCAGC hit 56 : 189936 190117 (fwd) 90.90 bits ::::::::::::::[[[[[[,..<<<____________>>>,,,,,(((,,,<<<<<___ 1 uuauauuagccacgugaaGGU..ccccccagaaugggggggUUAAaAGGGAAucCGGUGa 58 AUAUUA + +:::GU CCC ++ U GGGGUUAAAAGGGAA:: GGU A 189936 GAAUAUUAAAAUUUAUAGAGUuaCCC----AUUU-UUGGGGUUAAAAGGGAAGGGGGUUA 189990 ____>>>>>,,<<<____>>>,<<<---<<<<------<<<<<<-----<<<-<<<<<<_ 59 AAAUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccgccAaaauGCCACUgggcu 118 +AAUCC ::+C:G: CC :C:ACUGUAA :GG AAG :::CCA+AA CCA:UG:G: 189991 GAAUCCUCCACGGU-CCGGCCACUGUAAUUGGUAAGUUUAUUCCAUAA-GCCAUUGAGA- 190047 ___>>>>>>--->>>>>>>>>---------->>>>---->>>,,,,)))]]]]]]::::: 119 caagcccGGGAAGGCggcgggaaggaggaaacCgcgAGCCAGGAGACCUGCcgugagugu 178 +A :C:CG:GAAGG GG::: AA ++++AACC: +AG+CAGGAGACCUG:::+ ++U U 190048 UAUUCUCGAGAAGGUGGAAAUAAAUGAUGAACCAUAAGUCAGGAGACCUGCUUUAUAUUU 190107 :::::::::: 179 uaacaccccc 188 A+ C+ C 190108 AAGAUGCAGC 190117 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #30275,sp|AE015938.1|AE015938 Clostridium tetani E88, section 3 of 10 of the complete genome. ----isReversed: 0 ----hitSequence: UUAAAUAUUUAUUUAUAAAGUUUCUUGUAAAAGAGAAUUAAAAGGGAAGGAGGCGAAAAUCCUCCACGGUCCGGCCACUGUAAUUGGUGAGUUUAUUCCAUAAGCCAUUGAGAUAUUCUUGAGAAGGCGGAAAUAAAUGAUGAACCAUAAGUCAGGAGACCUGCUUUAUAAGAAUAAAUAUAC hit 57 : 219824 220006 (fwd) 101.25 bits ::::::::::::::[[[[[[,<<<____________>>>,,,,,(((,,,<<<<<_____ 1 uuauauuagccacgugaaGGUccccccagaaugggggggUUAAaAGGGAAucCGGUGaAA 60 UUA+AU ++ + +:::GU::C + +AA+ G G::UUAAAAGGGAA:::GG GAAA 219824 UUAAAUAUUUAUUUAUAAAGUUUCUUGUAAAA--GAGAAUUAAAAGGGAAGGAGGCGAAA 219881 __>>>>>,,<<<____>>>,<<<---<<<<------<<<<<<-----<<<-<<<<<<___ 61 AUCCGgaGCUGcCCCCgCAACUGUAAgcGggaaggacccgccAaaauGCCACUgggcuca 120 AUCC:::+C:G: CC :C:ACUGUAA :GG +AG :::CCA+AA GCCA:U::G: +A 219882 AUCCUCCACGGU-CCGGCCACUGUAAUUGGUGAGUUUAUUCCAUAA-GCCAUUGAGA-UA 219938 _>>>>>>--->>>>>>>>>---------->>>>---->>>,,,,)))]]]]]]::::::: 121 agcccGGGAAGGCggcgggaaggaggaaacCgcgAGCCAGGAGACCUGCcgugaguguua 180 :C::G:GAAGGCGG::: AA ++++AACC: +AG+CAGGAGACCUG:::+ ++ G+ + 219939 UUCUUGAGAAGGCGGAAAUAAAUGAUGAACCAUAAGUCAGGAGACCUGCUUUAUAAGAAU 219998 :::::::: 181 acaccccc 188 A A+ C 219999 AAAUAUAC 220006 ----endhit ----fastaFile: /projects/bio/zasha/seqs/embl/pro01.dat.fasta.gz ----sequence: #30275,sp|AE015938.1|AE015938 Clostridium tetani E88, section 3 of 10 of the complete genome. ----isReversed: 1 ----hitSequence: AAUAGUAAAUGAAAUUUAGGUGUCCACUUUGUAAAAAUGAUGGAUGAAAAGGGAAUGUGGUUCAAUUCCACAGCAGCCCCCGCUACUGUAAUAGAUGACAAGCCUUUAGUAACCACUCUUUAAAAGGAGGAAGGUAAAGGUUAGAAUGAUUCUUAAGCCAGGAGACCUGCCUAGAUUGUUAAAAUCCUC hit 58 : 189808 189620 (rev) 110.21 bits ::::::::::::::[[[[[[,.<<<____.____...____>>>,,,