AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i009_Nucleotide_Biosynthes_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 thyA 300 thymidylate synthase A #2 thyB 83 thymidylate synthase B #3 ypjP 259 ypjP #4 ypiP 296 ypiP #5 yphP 106 similar to hypothetical proteins from B. subtilis #6 ilvD 288 dihydroxy-acid dehydratase #7 ypgR 59 similar to hypothetical proteins #8 bsaA 300 glutathione peroxidase Motif number 1 AATAAGATCCTCACTTTATCTGCAAGTGCTT 1 206 1 TCACTTTTCT 0.82903 -95 GGTTCAGAAATGATTTTTTATTGTGTTACAC 2 31 1 TGATTTTTAT 0.546751 -53 TTCATATCACGGGCTTTCTGTTAATCGGTGA 3 11 1 GGGCTTTTGT 0.80659 -249 TCGTTGCTATGCACTTTGTGTAAAAACGCTT 3 135 0 GCACTTTTGT 0.967281 -125 CGTTCTCCGGGCATTTTCTTTTTGGGAGTAC 4 16 1 GCATTTTTTT 0.956945 -281 CTTGTTGTTATCATCTTCTGTACTCCCAAAA 4 35 0 TCATCTTTGT 0.758374 -262 AAGCTGCTTTGCAGTTTTTATGGTGTGTTCA 4 78 0 GCAGTTTTAT 0.840293 -219 AAAGAATTTGGCACCTTGTTTCGTATACAGC 4 216 0 GCACCTTTTT 0.973862 -81 ATAGCTGGGGACACTTTCTTTTATTTTAAGG 5 11 1 ACACTTTTTT 0.821884 -96 ATACTAGAGGGGGCTTTTTTT 5 96 1 GGGCTTTTTT 0.892021 -11 TGCATGATCTGCACCTTTTTTATCT 6 5 0 GCACCTTTTT 0.973862 -284 TGCAGATCATGCACCTTTTTTATGTGAATTC 6 23 1 GCACCTTTTT 0.973862 -266 TTATGTGAATTCACTTTTTATAAAAATTATT 6 42 1 TCACTTTTAT 0.914995 -247 CAGGCCGCCCTCACCTTGTTTTGTTCTTTCG 6 174 0 TCACCTTTTT 0.942467 -115 TTGACAATTTTCAGTTTATTTATGGGCTGTT 6 224 0 TCAGTTTTTT 0.84695 -65 TTGTTTGATTGGATTTTATTTTGACAATTTT 6 244 0 GGATTTTTTT 0.867776 -45 GCGTGTCAGTGCGTTTTATTTAAAGAGTTTT 8 67 0 GCGTTTTTTT 0.913928 -234 TTCATATGGCTCGTTTTTTATCTTATCATTC 8 158 0 TCGTTTTTAT 0.661207 -143 ******* *** Masking position 6 Map Score: 20.443 Number of sites scoring better than the average of aligned sites = 1389 Number in coding regions = 1136 Number in noncoding regions = 253 Number of orfs with sites within 600 bp upstream = 243 Fraction of orfs with sites within 600 bp upstream = 0.0390299 Motif number 2 GAGGAGTTAATCCCCCTCTTTTACACCTGT 1 156 0 TCCCCCTCTT 0.91097 -145 ACTATTCATATCCTTCTTTCATTTTCAGTT 1 280 0 TCCTTCTTTC 0.850399 -21 TTTTTTCATCCTTTAAAAGTAGTCT 2 69 0 TCATCCTTTA 0.812142 -15 TGCCACAGTTTCACTCTTAACATTATTATA 3 59 0 TCACTCTTAA 0.643781 -201 CATGCGGAAAGCCTCCTTTCATGAAATATT 3 103 1 GCCTCCTTTC 0.847088 -157 GACTGCTTATTCCTCTCTATTTTATTGTC 3 241 0 TTCCTCTCTA 0.698322 -19 AGGTTCTTTCTCCCCCTGTAAGAAGCGTTT 4 277 0 TCCCCCTGTA 0.948624 -20 TTGAAATCCGGCCCTCTCTATAGTATCCTT 5 51 1 GCCCTCTCTA 0.945945 -56 AAAAAAAGCCCCCTCTAGTATCCTTCA 5 90 0 GCCCCCTCTA 0.973725 -17 GGTGATCCTCCTAAATTCTTTCAAT 6 274 0 TCCTCCTAAA 0.861379 -15 GATCGTCCTCCTATAGCATATCTGT 7 45 0 TCCTCCTATA 0.936966 -15 TTCTGTTGTTTCCCCCTCAACACGTATAGA 8 39 0 TCCCCCTCAA 0.971152 -262 ACATTACAATTCCCTCTTACATCTTTGAAA 8 122 0 TCCCTCTTAC 0.834227 -179 TTTTATCTTATCATTCTATAAAACATTACA 8 144 0 TCATTCTATA 0.559964 -157 ********** Masking position 7 Map Score: 11.7306 Number of sites scoring better than the average of aligned sites = 814 Number in coding regions = 482 Number in noncoding regions = 332 Number of orfs with sites within 600 bp upstream = 367 Fraction of orfs with sites within 600 bp upstream = 0.0589464 Motif number 3 CCGCAATATCAAACCATTTCGTATAATCCT 1 49 1 AAACCATTTC 0.954685 -252 CTATAAAAAAATCATTTCTGGGTTCAGA 2 9 1 AAATCATTTC 0.962321 -75 ACACAATAAAAAATCATTTCTGAACCCAGA 2 27 0 AAATCATTTC 0.962321 -57 ACAAGGTGCCAAATTCTTTTTTCATCCGAA 4 228 1 AAATTCTTTT 0.816609 -69 CTTTTTATAAAAATTATTTCGAATATTGTT 6 55 1 AAATTATTTC 0.951747 -234 AAATATCCGAAAACTATTTATAGTAAGTAA 6 88 1 AAACTATTTA 0.816791 -201 TGATCCTCCTAAATTCTTTCAATTGTTTGA 6 267 0 AAATTCTTTC 0.94241 -22 AAACAACAGAAAACTCTTTAAATAAAACGC 8 58 1 AAACTCTTTA 0.78646 -243 ACATCTTTGAAAATCATTTTACTGTGAAAC 8 104 0 AAATCATTTT 0.874146 -197 ********** Masking position 7 Map Score: 9.36723 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 169 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 4 CGATAATATTGCATTCGTAATAAATTATGCTTAG 1 245 1 GATCGAAAAA 0.951699 -56 TAGACCGTCTGAACACACCATAAAAACTGCAAAG 4 69 1 GAACACAAAA 0.951946 -228 AGCACCTGCTGAAATCAGCTGAACGTGATTTGCT 4 158 1 GATCACTAAC 0.858124 -139 ACCTTGTTTCGTATACAGCTCAAACCGCTCTTTG 4 201 0 GAACACTAAA 0.951946 -96 GAACATCGCTGTATTCGGATGAAAAAAGAATTTG 4 237 0 GATCGATAAA 0.951699 -60 GATTTCAAATGTTCACGCCTTAAAATAAAAGAAA 5 25 0 GTACGCTAAA 0.751233 -82 TATAAAAAGTGAATTCACATAAAAAAGGTGCATG 6 30 0 GATCAATAAA 0.947881 -259 TTGGAGGGTTCAAATCGAAAGAAAGCTATATAAA 6 130 1 CATCGAAAAA 0.718421 -159 GTGTTGAGGGGGAAACAACAGAAAACTCTTTAAA 8 46 1 GAACACAAAA 0.951946 -255 CATCAATTAAGAACTCATAAGAAACCTAACGATA 8 210 0 GATCAAAAAA 0.947881 -91 * * *** ** *** Masking position 12 Map Score: 4.45379 Number of sites scoring better than the average of aligned sites = 439 Number in coding regions = 386 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 5 TTATACGAAATGGTTTGATATTGCGGTACATAA 1 42 0 TGTTTGTATG 0.98104 -259 TATCTGCAAGTGCTTAGTATTTGCGATAATATT 1 222 1 TGTTAGATTG 0.952619 -79 TAATAAATTATGCTTAGCAACTGAAAATGAAAG 1 262 1 TGTTAGAATG 0.952619 -39 GGTTCAGAAATGATTTTTTATTGTGTTACACTA 2 31 1 TGTTTTTATG 0.870325 -53 ATGACTTGCATGTTTTGGATGTGCTAAAATAAG 3 200 1 TGTTTGATTG 0.969929 -60 CAGCTGAACGTGATTTGCTTGTGGTCGGCAAAG 4 173 1 TGTTTGTTTG 0.98104 -124 ACGAGCCATATGAATTGATAATGAACTGACGCT 8 175 1 TGATTGTATG 0.902654 -126 TCTTAATTGATGTTTACATTTTGAATTGCGATT 8 232 1 TGTTACTTTG 0.861125 -69 ** **** ** ** Masking position 5 Map Score: 4.06013 Number of sites scoring better than the average of aligned sites = 209 Number in coding regions = 182 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 6 TACATAAAAATTCAAATAGTCAGGTGTTTG 1 19 0 TTCAAATAGT 0.86654 -282 GACTATTCATATCCTTCTTTCATTT 1 286 0 TTCATATCCT 0.839762 -15 TTCATATCACGGGCTTTCTG 3 1 1 TTCATATCAC 0.848481 -259 GCATATCAGTTTCATATAGTACATGACTTG 3 178 1 TTCATATAGT 0.925194 -82 AGTTGGAGGGTTCAAATCGAAAGAAAGCTA 6 128 1 TTCAAATCGA 0.834671 -161 TGTTTTTATATTTATATAGCTTTCTTTCGA 6 144 0 TTTATATAGC 0.794412 -145 TCATTATCAATTCATATGGCTCGTTTTTTA 8 169 0 TTCATATGGC 0.919824 -132 TGAACTGACGCTCATATCGTTAGGTTTCTT 8 196 1 CTCATATCGT 0.88093 -105 TTTTACCTTTTTTAAATCGCAATTCAAAAT 8 249 0 TTTAAATCGC 0.8384 -52 ********** Masking position 6 Map Score: 2.27144 Number of sites scoring better than the average of aligned sites = 561 Number in coding regions = 512 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 7 GTATAATCCTCAACAATGTTATCAACGGTG 1 69 1 CAACAATGTT 0.931319 -232 GTTTCACTCTTAACATTATTATACTTTGTC 3 52 0 TAACATTATT 0.894461 -208 GTAAAAACGCTTACAATATTTCATGAAAGG 3 117 0 TTACAATATT 0.894462 -143 GGATATTTTTCAACAATATTCGAAATAATT 6 66 0 CAACAATATT 0.967847 -223 TTATAGTAAGTAACAATATTAATAGTTGGA 6 105 1 TAACAATATT 0.965379 -184 ********** Masking position 5 Map Score: 1.02282 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 20 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 ********** No masking Map Score: -2.70474e-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 9 ********** No masking Map Score: -2.70474e-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 AAATAGTCAGGTGTTTGTGTATACC 1 5 0 GTGTTTGTTA 0.911313 -296 GTTATCAACGGTGTATGTACCAAACTGGCGG 1 86 1 GTGTATGTCC 0.863516 -215 TCTTTTACACCTGTATTTCTCCATAACATAG 1 139 0 CTGTATTTTC 0.888431 -162 ATTCCACTCACTGTGTGTTTAAAGAGGAGTT 1 178 0 CTGTGTGTTA 0.823663 -123 AATATTGTAAGCGTTTTTACACAAAGTGCAT 3 127 1 GCGTTTTTCA 0.815441 -133 AGGTGCTCAACCGTTTGTTTATTCCGGCCGC 4 134 0 CCGTTTGTTA 0.86715 -163 TTGTTCTTTCGTGTTTTTATATTTATATAGC 6 154 0 GTGTTTTTTA 0.904621 -135 TGAGGGCGGCCTGTATTTATCTTATTTGCAA 6 192 1 CTGTATTTTC 0.888431 -97 TATTTATGGGCTGTTTTTGCAAATAAGATAA 6 208 0 CTGTTTTTCA 0.938197 -81 AAAGAGTTTTCTGTTGTTTCCCCCTCAACAC 8 46 0 CTGTTGTTCC 0.774261 -255 ******** ** Masking position 4 Map Score: 1.94571 Number of sites scoring better than the average of aligned sites = 834 Number in coding regions = 717 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 11 AGATCCTCACTTTATCTGCAAGTGCTTAGT 1 210 1 TTTATCTGCA 0.705481 -91 GTAATAAATTATGCTTAGCAACTGAAAATG 1 261 1 ATGCTTAGCA 0.814325 -40 AGGAGATTCGTTGCTATGCACTTTGTGTAA 3 143 0 TTGCTATGCA 0.86643 -117 CTATATGAAACTGATATGCAAATTAGGAGA 3 167 0 CTGATATGCA 0.946579 -93 CATATAGTACATGACTTGCATGTTTTGGAT 3 190 1 ATGACTTGCA 0.887395 -70 CTTTAGAAAGCTGCTTTGCAGTTTTTATGG 4 86 0 CTGCTTTGCA 0.971095 -211 AAAAAGGTGCATGATCTGCACCTTTTTTAT 6 13 0 ATGATCTGCA 0.9578 -276 CTGTATTTATCTTATTTGCAAAAACAGCCC 6 202 1 CTTATTTGCA 0.889141 -87 TCACAGTAAAATGATTTTCAAAGATGTAAG 8 107 1 ATGATTTTCA 0.767799 -194 ********** Masking position 2 Map Score: 3.77765 Number of sites scoring better than the average of aligned sites = 450 Number in coding regions = 390 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 12 CAACGGTGTATGTACCAAACTGGCGGTAACTA 1 91 1 TGTACAACTG 0.898858 -210 CTATGAGCTATGTGACAGACTATGTTATGGAG 1 120 1 TGTGCAACTA 0.98268 -181 GATTTTTTATTGTGTTACACTACTAGAAGACT 2 42 1 TGTGTAACTA 0.964871 -42 AGAGTGAAACTGTGGCAAACAGAGCGTCAATC 3 72 1 TGTGCAACAG 0.934315 -188 ATGTTTTGGATGTGCTAAAATAAGAGAAACAT 3 209 1 TGTGTAAATA 0.882154 -51 AAGAGCTAAATATGCCATACTGCGGCCGGAAT 4 113 1 TATGCAACTG 0.949214 -184 TTGGAGCGACTATGATAGAATAAGTCACAGAT 7 19 1 TATGTAAATA 0.669743 -41 **** ** **** Masking position 7 Map Score: 0.301383 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 158 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 13 ********** No masking Map Score: -2.70474e-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 14 ********** No masking Map Score: -2.70474e-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 15 ********** No masking Map Score: -2.70474e-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