AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i006_bsub_mtub_300.orf -o006_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ileS 300 isoleucyl-tRNA synthetase #2 ylyA 77 alternate gene name: ylmK; similar to hypothetical proteins from B. subtilis #3 lsp 102 signal peptidase II #4 pyrR 273 transcriptional attenuator and uracil phosphoribosyltransferase activity (minor) #5 pyrP 171 uracil permease #6 pyrB 145 aspartate carbamoyltransferase Motif number 1 ATAAAAAAAGCCCTCTCATCCCATAAGGGA 1 251 0 CCCTCTCATC 0.949349 -50 ATCCTTCTCAGCCTCTCTGGACTGTTTTAA 4 148 0 GCCTCTCTGG 0.992198 -126 GTCCTAAAACCCCTCTATGCTCTGGCAGGA 4 215 1 CCCTCTATGC 0.98922 -59 CCTCTTTGCAACCTCTCTGGATTGCTTAAA 5 22 0 ACCTCTCTGG 0.987787 -150 TTTGTTGTGCACCTCTTTGCAACCTCTCTG 5 33 0 ACCTCTTTGC 0.980929 -139 GTCTTTGTATGCCTCTTTGCGTAAAAAAGC 5 84 1 GCCTCTTTGC 0.987787 -88 GTATAAAAAAACCTCTTTGCTTTTTTACGC 5 102 0 ACCTCTTTGC 0.980929 -70 ACCCTTCCAAGCCTCTCTGGACTTTCATTA 6 18 0 GCCTCTCTGG 0.992198 -128 ATTGAAGCTTCCTTCTCTTCATAACCCTTC 6 41 0 CCTTCTCTTC 0.920779 -105 TTCAATGCTGCCCTCTATTTAACCATACCC 6 65 1 CCCTCTATTT 0.885282 -81 GTTCTTTCCCCTCTCTTTTCAACTTAAG 6 128 0 CCCTCTCTTT 0.971214 -18 ********** Masking position 6 Map Score: 23.6398 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 123 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 2 CAGAAAATAAAAAAAGCCCTCTCATCCCATA 1 256 0 AAAAACCCTC 0.995216 -45 TGCAAAAGAGCCCGGCGTAAAAGCC 2 5 1 AAAGACCCGG 0.968642 -73 CTTGGCACAAAAAAAGCCCGGCTTTTACGCC 2 24 0 AAAAACCCGG 0.993294 -54 TTTTATCAATAAAAAGCACTGGAGTAAAGAA 3 41 0 AAAAACACTG 0.947849 -62 TATTTCAGAAAAGAAACCCTCTGTCAACCGT 4 94 0 AAGAACCCTC 0.977469 -180 CACCTTGTCCTAAAACCCCTCTATGCTCTGG 4 209 1 TAAAACCCTC 0.966966 -65 ATATAGAAGAAAAAACCCCTCCTGCCAGAGC 4 233 0 AAAAACCCTC 0.995216 -41 AAAGAGGCATACAAAGACCTGCCGAATACTT 5 71 0 ACAAAACCTG 0.88235 -101 ATGACTGTATAAAAAAACCTCTTTGCTTTTT 5 107 0 AAAAAACCTC 0.972945 -65 AAGGCTGAAAAAAAACCCCGGTCTAAGATAG 6 100 0 AAAAACCCGG 0.993294 -46 ***** ***** Masking position 5 Map Score: 20.3711 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 109 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 3 CATAAATTCAGATGAAAAAACGGTTGAAAG 1 19 1 GATGAAAAAA 0.924717 -282 CGATGCTCAAGAGGAAAAAGTGTATGCTTG 1 181 1 GAGGAAAAAG 0.842803 -120 TCCCATAAGGGACGAGAAAGCTTATCTCGC 1 233 0 GACGAGAAAG 0.66102 -68 TTTTTTATTTTCTGAAAAAATGCAGTGGAG 1 273 1 TCTGAAAAAA 0.857913 -28 GTCACTCTTGGCACAAAAAAAGCCCGGCTT 2 31 0 GCACAAAAAA 0.905124 -47 ATCGAAAACCTCAGAAAAAACGGTTGACAG 4 75 1 TCAGAAAAAA 0.839021 -199 GTTTATTATTTCAGAAAAGAAACCCTCTGT 4 101 0 TCAGAAAAGA 0.78191 -173 AATAAACGAAGCTGAATAGATTCTTTAAAA 4 124 1 GCTGAATAGA 0.713123 -150 GTCCAGAGAGGCTGAGAAGGATAACGGATA 4 156 1 GCTGAGAAGG 0.904174 -118 AGTTCATATAGAAGAAAAAACCCCTCCTGC 4 239 0 GAAGAAAAAA 0.913814 -35 TCTCTGGATTGCTTAAAAAGGTGATCTA 5 9 0 GCTTAAAAAG 0.814132 -163 GCAAAGAGGTGCACAACAAAGGCCCAAAAA 5 43 1 GCACAACAAA 0.547482 -129 CACAACAAAGGCCCAAAAAGTATTCGGCAG 5 54 1 GCCCAAAAAG 0.828299 -118 ATGCCTCTTTGCGTAAAAAAGCAAAGAGGT 5 92 1 GCGTAAAAAA 0.705681 -80 GAAGGGTTATGAAGAGAAGGAAGCTTCAAT 6 41 1 GAAGAGAAGG 0.703162 -105 TCAACTTAAGGCTGAAAAAAAACCCCGGTC 6 108 0 GCTGAAAAAA 0.97687 -38 TCAGCCTTAAGTTGAAAAGAGAGGGGAAAG 6 123 1 GTTGAAAAGA 0.6758 -23 ********** Masking position 5 Map Score: 14.8747 Number of sites scoring better than the average of aligned sites = 6171 Number in coding regions = 5544 Number in noncoding regions = 627 Number of orfs with sites within 600 bp upstream = 577 Fraction of orfs with sites within 600 bp upstream = 0.0926759 Motif number 4 TTTTCATCTGAATTTATGAACGTATT 1 5 0 ATTTATGAAG 0.709125 -296 CAGATGAAAAAACGGTTGAAAGGGACAGTCAT 1 27 1 ACGGTTGAAG 0.971667 -274 GAGCATCGTAACGTGATGAACGTCCTAACCTA 1 157 0 AGTGATGAAG 0.928839 -144 CTCGTCCCTTATGGGATGAGAGGGCTTTTTTT 1 247 1 AGGGATGAGG 0.946436 -54 GAAAAAATGCAGTGGAGGAATGAAA 1 286 1 ATGGAGGAAG 0.984694 -15 AATAAAAAGCACTGGAGTAAAGAAATATCAGG 3 33 0 ATGGAGTAAG 0.95941 -70 TAAAATGCATAATGGATTAAAGTAACCGTAAA 3 67 1 ATGGATTAAG 0.974186 -36 GTAACCGTAAACTGGAGGAACGTTT 3 88 1 ATGGAGGAAG 0.984694 -15 CCTCAGAAAAAACGGTTGACAGAGGGTTTCTT 4 83 1 ACGGTTGACG 0.877332 -191 GCCTCTCTGGACTGTTTTAAAGAATCTATTCA 4 136 0 ATGTTTTAAG 0.774162 -138 CAGAGCATAGAGGGGTTTTAGGACAAGGTGCG 4 207 0 AGGGTTTTAG 0.69988 -67 * ******** * Masking position 1 Map Score: 7.9357 Number of sites scoring better than the average of aligned sites = 920 Number in coding regions = 783 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 5 TGAAGGAAACATGACTGTCCCTTTCAACCG 1 39 0 ATGACTGTCC 0.986538 -262 CCCGGAGATGGTGAGAGTCCGGGATGGCCG 1 83 1 GTGAGAGTCC 0.979298 -218 TCGTAACGTGATGAACGTCCTAACCTACTG 1 154 0 ATGAACGTCC 0.982776 -147 CAGTGTCTGTCCGGTTAATATG 3 3 1 GTGTCTGTCC 0.937455 -100 TCATCCTAAAATGAAAGTCAACAATCAGGG 5 142 1 ATGAAAGTCA 0.937689 -30 AACCTTTTAATGAAAGTCCAGAGAGGCTT 6 10 1 ATGAAAGTCC 0.989824 -136 ********** Masking position 8 Map Score: 5.12005 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 80 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 ATGACTGTCCCTTTCAACCGTTTTTTCATC 1 29 0 CTTTCAACCG 0.969814 -272 TTTCATTCCTCCACTGCATTTTT 1 288 0 CATTCCTCCA 0.948839 -13 CCTGATATTTCTTTACTCCAGTGCTTTTTA 3 33 1 CTTTACTCCA 0.973261 -70 TTTACGGTTACTTTAATCCATTATGCATTT 3 69 0 CTTTAATCCA 0.967888 -34 AAACGTTCCTCCAGTTTACGGTT 3 90 0 CGTTCCTCCA 0.964895 -13 AAGAAACCCTCTGTCAACCGTTTTTTCTGA 4 85 0 CTGTCAACCG 0.907965 -189 TGAATAGATTCTTTAAAACAGTCCAGAGAG 4 136 1 CTTTAAAACA 0.750154 -138 ********** Masking position 4 Map Score: 3.12611 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 360 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 7 AGGGACAGTCATGTTTCCTTCAGGCCTTCA 1 47 1 ATGTTTCCTT 0.976667 -254 ATCAGCCCTTTAGTTTCCTTGCTGAACTCA 1 124 1 TAGTTTCCTT 0.791037 -177 GAAAAAGTGTATGCTTGCTTTTTCTAAAAG 1 194 1 ATGCTTGCTT 0.939186 -107 AAGATTTTTCCTTTCGTTCTAAA 2 65 0 ATTTTTCCTT 0.919578 -13 TTTTCGATTAATTCTGCCATATCCTCGGGA 4 53 0 ATTCTGCCAT 0.79676 -221 GGCAGCATTGAAGCTTCCTTCTCTTCATAA 6 47 0 AAGCTTCCTT 0.973344 -99 GGAAGCTTCAATGCTGCCCTCTATTTAACC 6 59 1 ATGCTGCCCT 0.955132 -87 ********** Masking position 5 Map Score: 2.60678 Number of sites scoring better than the average of aligned sites = 579 Number in coding regions = 519 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 8 GCAAAAGAGCCCGGCGTAAAAGCCGGGCTTTT 2 12 1 CCGGGAAAAG 0.966298 -66 CAGTGTCTGTCCGGTTAATATGCCTGATATTT 3 11 1 CCGGTATATG 0.97105 -92 CATCCACGAACAGGAGAATATGTCGAATTTGA 4 12 1 CAGGGATATG 0.986533 -262 AGCGCCGCTTCCCGAGGATATGGCAGAATTAA 4 44 1 CCCGGATATG 0.991254 -230 AGTCAACAATCAGGGGGAAATCATC 5 157 1 CAGGGAAATC 0.953543 -15 TTAACCATACCCCGAGTCTATCTTAGACCGGG 6 83 1 CCCGGCTATC 0.95587 -63 **** * ***** Masking position 10 Map Score: 0.885831 Number of sites scoring better than the average of aligned sites = 311 Number in coding regions = 292 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 9 ********** No masking Map Score: 2.97961e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 10 ********** No masking Map Score: 2.97961e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 11 ********** No masking Map Score: 2.97961e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0