AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i175_biotin_biosynthesis1_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -x5 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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 pgsA 300 phosphatidylglycerophosphate synthase #2 recA 172 multifunctional SOS repair regulator #3 pbpX 167 penicillin-binding protein #4 ymdA 276 similar to hypothetical proteins #5 ymdB 68 similar to hypothetical proteins #6 spoVS 199 spoVS #7 tdh 265 threonine 3-dehydrogenase #8 bioW 251 6-carboxyhexanoate-CoA ligase #9 ytaP 217 ytaP Motif number 1 ATAGGTTTCGTCTTTTTTCAGCGTTCCTTCTTTT 1 63 0 TTTTTTGCGT 0.751609 -238 ATCAGTTATGTCTTTTTTATAGGTTTCGTCTTTT 1 81 0 TTTTTTAGGT 0.552772 -220 CGTTGATTTTTATTTTCAGATTAGGTGCATATCC 1 139 0 TTTTTCTTAG 0.362721 -162 TTACCAGATGACTTTTCTTCACGTCCGAGTATGA 1 262 1 ATTTTCACGT 0.800574 -39 TATTTTCAGCACATTATCCTCCTA 2 1 1 TTTTTCACAT 0.957172 -172 CATATTCGGATTTTTTCTTGGCGTGATTCCTATC 2 71 0 TTTTTCGCGT 0.712397 -102 GCGTTCGCTTTTTTCTTGGCAAATCCCTTCAAAC 2 104 1 TTTCTTAAAT 0.706868 -69 TCTATTTTTTCCTCCTTTATGTTACC 2 157 0 TTTTTTTCCT 0.675464 -16 AAAAAAGCTGAGTTTTTCACTCAGCCTTTTGTAT 3 32 0 ATTTTTTCAG 0.502166 -136 ATTTTTATCATTTTTTTGCAAAATACAAAAAAGC 3 58 0 TTTTTTAAAT 0.852895 -110 AAAATATTGCTTTTTTTGACAACTTTTTTAGGGC 3 87 1 TTTTTTAACT 0.609945 -81 TGCAGGCCAGTCTTCTTTTCACGTGCCGAATGCA 4 35 0 TTTCTTACGT 0.886993 -242 GCTTGACAAGTATTTCCGACACATTTACAATGAA 4 85 1 TTTTCCACAT 0.596854 -192 TTGTAACATTTGTTTTTTTAACATGATTGTTAAA 4 120 1 TTTTTTACAT 0.964667 -157 TACATTGTCTAGTTTTCTCAACATACTAGAACCT 4 199 0 ATTTTCACAT 0.852964 -78 AGCATCACTTTATTTTTTTGACGGCAAGGAATTT 5 23 1 TTTTTTACGG 0.904836 -46 TTCTTTTTAATATTTTTATAAAATAACCATATGT 6 15 0 TTTTTTAAAT 0.85304 -185 GCAAACAGGTTGTTTTTCATTTATTGTGATATTT 7 46 1 TTTTTTTTAT 0.580111 -220 TATTGTGATATTTTCTCCCGATAGTATTTTTAGC 7 67 1 TTTCTCATAG 0.45535 -199 CTCCCGATAGTATTTTTAGCACATAAATGAGCGA 7 81 1 TTTTTTACAT 0.964667 -185 GGGCGGAAATTTTTTTTGAAACGTTTTAGCTCAT 7 131 0 TTTTTTACGT 0.949572 -135 ATTTCCGCCCATTTTTCAAGACAGATACTTTTGT 7 155 1 ATTTTCACAG 0.74463 -111 AACAGAACTGTCTTTTCCAGAAGGACAAAAGTAT 7 179 0 TTTTTCAAGG 0.623328 -87 CTCCTTGAAAAATTCTTGTTATATTCGGATTGTA 7 234 0 ATTCTTATAT 0.345014 -32 GTCTTTTTCGATTTCTTTTTACAG 8 1 0 ATTCTTACAG 0.597043 -251 GTGAAAACGGTCTTTTTGTTTCCTTTTAACCAAC 8 43 1 TTTTTTTCCT 0.675464 -209 ATAAAAAGTTTCTTCTTGCATCATTTCTCGCCCT 8 207 0 TTTCTTTCAT 0.762358 -45 TTAACTCATCTGTTTTTGATAAATTGATATTATC 9 41 1 TTTTTTAAAT 0.852995 -177 TTACAATAATTGTTTTCGAAATATTCCATAATAT 9 91 1 TTTTTCATAT 0.799912 -127 GGTTCCCCTTTATTTTTCCAACATAAATCACATC 9 145 0 TTTTTTACAT 0.964667 -73 * ***** **** Masking position 4 Map Score: 25.3438 Number of sites scoring better than the average of aligned sites = 2316 Number in coding regions = 1812 Number in noncoding regions = 504 Number of orfs with sites within 600 bp upstream = 520 Fraction of orfs with sites within 600 bp upstream = 0.0835207 Motif number 2 TAAGATGACTTTTCTTCCTTTTTATTTACAATC 1 228 0 TTTTCCTTTT 0.940939 -73 TCTATTTTTTCCTCCTTTATGTTACCACTA 2 153 0 TTCTCCTTTT 0.976052 -20 ACTCAGCCTTTTGTATCATTTGAAACTTATTTT 3 15 0 TTATCATTTA 0.824233 -153 AAAGCAATATTTTTATCATTTTTTTGCAAAATA 3 67 0 TTATCATTTT 0.961523 -101 TACAATGAAGTTGTAACATTTGTTTTTTTAACA 4 110 1 TTAACATTTT 0.710945 -167 TTTGTAAATCCTTTCTTCTTGAAAAT 5 53 0 GTATCCTTTT 0.905616 -16 CAAACAGGTTGTTTTTCATTTATTGTGATATTT 7 47 1 GTTTCATTTT 0.805501 -219 ATTTTGTATATTCGCTCATTTATGTGCTAAAAA 7 93 0 TTCTCATTTT 0.971044 -173 TTGAAACGTTTTAGCTCATTTCTGATTTTGTAT 7 117 0 TTCTCATTTT 0.971044 -149 AACGGTCTTTTTGTTTCCTTTTAACCAACTGCC 8 48 1 TTTTCCTTTA 0.749348 -204 ACTGCCATAAATCGATCCTTTCTTCTATTGACA 8 75 1 ATATCCTTTT 0.778652 -177 GAATATATTATTCTCTCCTGTTTCTGTCAATAG 8 99 0 TTCTCCTGTT 0.865381 -153 AAGTTTCTTCTTGCATCATTTCTCGCCCTTTCA 8 203 0 TTATCATTTT 0.961523 -49 TAGTAAAATATTAACTCATCTGTTTTTGATAAA 9 31 1 TTCTCATCTT 0.840999 -187 ** ******* * Masking position 9 Map Score: 14.3301 Number of sites scoring better than the average of aligned sites = 510 Number in coding regions = 406 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 3 TGGCACAAACCATAAAGATTGTAAATAAAAAGGAA 1 212 1 CAAATTGTAA 0.962751 -89 AATAAAGCCCTAAAAAAGTTGTCAAAAAAAGCAAT 3 92 0 TAAATTGTAA 0.864581 -76 ACAAATGTTACAACTTCATTGTAAATGTGTCGGAA 4 98 0 CACTTTGTAA 0.947359 -179 TTTGTTTTTTTAACATGATTGTTAAACCATTTAAA 4 128 1 TACTTTGTAA 0.816778 -149 TGAGTGTGTTCATCGCCCTTGTCAAGTTTAAATGG 4 154 0 CACCTTGTAA 0.975932 -123 AGGAATATAGCAACTCCTTAGTGAATATAGTAAAA 6 53 1 CACCTAGTAA 0.941695 -147 TGAACACTCACTTATCCATTGTAAAACTAAGGGGG 6 168 1 CTACTTGTAA 0.730375 -32 TTGCATTACGCAAACAGGTTGAGAATGCTTTATTT 7 15 0 CAAATTGAAA 0.766578 -251 TAGCGCTTCTCACCTAAATTGTTAACCAATTATAT 8 149 0 CACATTGTAA 0.980063 -103 GTATCCCTCTCATCTATTTAGTAAAATATTAACTC 9 13 1 CACATAGTAA 0.951412 -205 CATCATTTACTAAATATTTAGTAAATATTATGGAA 9 114 0 TAAATAGTAA 0.71832 -104 ** * * **** ** Masking position 14 Map Score: 7.10824 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 155 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 TGAGTGCGCGATGAAGTGGCAGCTCTTTAAAAGAAGG 1 35 1 AAAGGGCTTT 0.791298 -266 CTCGATCCGAAAAAAGTGATGGCACAAACCATAAAGA 1 193 1 AAAGGGCAAA 0.992079 -108 TTTGCCAAGAAAAAAGCGAACGCATATTCGGATTTTT 2 90 0 AAAGGGCAAT 0.985008 -83 GGTATAGTATATGTAGTGGTAACATAAAGGAGGAAAA 2 140 1 ATAGGACAAA 0.866149 -33 TATTCGTCTAACAAAACGTGTGCAAAATGGAATTTAT 3 123 1 AAAAGGCAAA 0.924691 -45 GTTGTTGCTTAAAAAGTGTCGGCATGTACATTGTCTA 4 222 0 AAAGGGCAGT 0.952866 -55 CCATTGTAAAACTAAGGGGGAGCAGAA 6 183 1 AAAGGGCAAA 0.992079 -17 CATGATATGGAATAAGCGTAAACAGAACTGTCTTTTC 7 196 0 AAAGGACAAA 0.976218 -70 ATCATATAAAAGTAAGCGGTTACAATAATTGTTTTCG 9 72 1 AAAGGACATA 0.937607 -146 * *** * *** ** Masking position 5 Map Score: 5.74078 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 189 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 5 AACTGATCAGAAACAAGTTGATATCCGCAC 1 108 1 AAACAAGTTG 0.9666 -193 TCAAATGATACAAAAGGCTGAGTGAAAAAC 3 25 1 CAAAAGGCTG 0.901923 -143 TGCAAAATACAAAAAAGCTGAGTTTTTCAC 3 46 0 AAAAAAGCTG 0.941199 -122 ATAAAGCCCTAAAAAAGTTGTCAAAAAAAG 3 96 0 AAAAAAGTTG 0.950713 -72 TGCATTACGCAAACAGGTTGAGAATGCTTT 7 19 0 AAACAGGTTG 0.977952 -247 TGCGTAATGCAAACAGGTTGTTTTTCATTT 7 38 1 AAACAGGTTG 0.977952 -228 ********** Masking position 5 Map Score: 5.7109 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 192 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 AAGGCATCAGACAGCTCCTGGATTTGAG 1 9 1 AGACAGCTCC 0.95688 -292 AATGGAAGGTAGCCCGCTATTTTTGAAAAG 6 87 1 AGCCCGCTAT 0.84491 -113 CCATTTTTCAAGACAGATACTTTTGTCCTT 7 163 1 AGACAGATAC 0.864541 -103 CTTCTGGAAAAGACAGTTCTGTTTACGCTT 7 190 1 AGACAGTTCT 0.966046 -76 AAATCGAAAAAGACCGTTTTGTGTGAAAAC 8 21 1 AGACCGTTTT 0.940301 -231 GGAAACAAAAAGACCGTTTTCACACAAAAC 8 36 0 AGACCGTTTT 0.940301 -216 CACATTTACGAGACAGATCTGGGTTCCCCT 9 170 0 AGACAGATCT 0.952999 -48 ********** Masking position 1 Map Score: 2.3585 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 117 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 7 CGTTGATTTTTATTTTCAGATTAGGTGCATATC 1 140 0 TTTTTGATTA 0.719454 -161 AACGGTAAGGTTCTTTCATATGAACTCGATCCG 1 169 1 TCTTTTATGA 0.949014 -132 AGAGAAATCATGTTTTCTTAGGAGGATAATGTG 2 20 0 TTTTTTAGGA 0.949084 -153 TACATTATGATATTTTGATAGGAATCACGCCAA 2 55 1 TTTTTTAGGA 0.948778 -118 AAATGGAATTTATTTTGGGAGGAAAAAATGA 3 147 1 TTTTTGAGGA 0.957455 -21 TTGGCGATCTTCTTTTGGATGAATTGCATTCG 4 10 1 TCTTTGATGA 0.957464 -267 TAACATTTGTTTTTTTAACATGATTGTTAAACC 4 123 1 TTTTTCATGA 0.895475 -154 TGTAACCGCTTACTTTTATATGATAATATCAAT 9 63 0 TCTTTTATGA 0.948778 -155 * **** ***** Masking position 10 Map Score: 3.51421 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 219 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 8 CATATCCGGTGCGGATATCAACTTGTTTCT 1 116 0 GCGGATATCA 0.858863 -185 GATATCCGCACCGGATATGCACCTAATCTG 1 127 1 CCGGATATGC 0.980021 -174 TTCTTCACGTCCGAGTATGAAATTGGAGGG 1 276 1 CCGAGTATGA 0.932273 -25 AAGAAAAAATCCGAATATGCGTTCGCTTTT 2 86 1 CCGAATATGC 0.983378 -87 ACATAAATGAGCGAATATACAAAATCAGAA 7 101 1 GCGAATATAC 0.932116 -165 ATGGTACAATCCGAATATAACAAGAATTTT 7 230 1 CCGAATATAA 0.94353 -36 ********** Masking position 6 Map Score: 1.34656 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 147 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 CTCAGCTTTTTTGTATTTTGCAAAAAAATGAT 3 54 1 TTGTATTGCA 0.967415 -114 CCAAAATAAATTCCATTTTGCACACGTTTTGT 3 133 0 TTCCATTGCA 0.977737 -35 TTTGGATGAATTGCATTCGGCACGTGAAAAGA 4 24 1 TTGCATTGCA 0.991592 -253 AACAACCTGTTTGCATTACGCAAACAGGTTGA 7 28 0 TTGCATTGCA 0.991594 -238 ******* *** Masking position 6 Map Score: 0.542973 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 4 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 10 ********** No masking Map Score: -6.60562e-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: -6.60562e-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 12 ********** No masking Map Score: -6.60562e-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