AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i009_bsub_mtub_300.orf -o009_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 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 #9 dfrA 70 dfrA #10 thyA 164 thyA Motif number 1 AAGCACTTGCAGATAAAGTGAGGATCTTATT 1 206 0 AGAAAAGTGA 0.761425 -95 GTGTAACACAATAAAAAATCATTTCTGAACC 2 31 0 ATAAAAATCA 0.495831 -53 TCACCGATTAACAGAAAGCCCGTGATATGAA 3 11 0 ACAAAAGCCC 0.787445 -249 AAGCGTTTTTACACAAAGTGCATAGCAACGA 3 135 1 ACAAAAGTGC 0.944803 -125 GTACTCCCAAAAAGAAAATGCCCGGAGAACG 4 16 0 AAAAAAATGC 0.933849 -281 TTTTGGGAGTACAGAAGATGATAACAACAAG 4 35 1 ACAAAGATGA 0.657705 -262 TGAACACACCATAAAAACTGCAAAGCAGCTT 4 78 1 ATAAAACTGC 0.816087 -219 GCTGTATACGAAACAAGGTGCCAAATTCTTT 4 216 1 AAAAAGGTGC 0.956541 -81 CCTTAAAATAAAAGAAAGTGTCCCCAGCTAT 5 11 0 AAAAAAGTGT 0.745597 -96 AAAAAAAGCCCCCTCTAGTAT 5 96 0 AAAAAAGCCC 0.889507 -11 AGATAAAAAAGGTGCAGATCATGCA 6 5 1 AAAAAGGTGC 0.956541 -284 GAATTCACATAAAAAAGGTGCATGATCTGCA 6 23 0 AAAAAGGTGC 0.956541 -266 AATAATTTTTATAAAAAGTGAATTCACATAA 6 42 0 ATAAAAGTGA 0.876311 -247 CGAAAGAACAAAACAAGGTGAGGGCGGCCTG 6 174 1 AAAAAGGTGA 0.916676 -115 AACAGCCCATAAATAAACTGAAAATTGTCAA 6 224 1 AAAAAACTGA 0.853374 -65 AAAATTGTCAAAATAAAATCCAATCAAACAA 6 244 1 AAAAAAATCC 0.837748 -45 AAAACTCTTTAAATAAAACGCACTGACACGC 8 67 1 AAAAAAACGC 0.89309 -234 GAATGATAAGATAAAAAACGAGCCATATGAA 8 158 1 ATAAAAACGA 0.614069 -143 ACTCGCCGCCAAACAAACCCAGCGGGCGATC 10 88 0 AAAAAACCCA 0.557453 -77 *** ******* Masking position 6 Map Score: 19.0591 Number of sites scoring better than the average of aligned sites = 1555 Number in coding regions = 1259 Number in noncoding regions = 296 Number of orfs with sites within 600 bp upstream = 284 Fraction of orfs with sites within 600 bp upstream = 0.0456152 Motif number 2 CTTATTCTATCATAGTCGCTCCAAGCCTTCTA 7 11 0 CTAGCGCTCC 0.965195 -49 ACTTCATTGTCGTCGGCGCGCC 9 1 0 CTCGCGCGCC 0.998726 -70 GGAATACACCCAGATCCGCGCCACAGGAGTAC 10 21 0 CGATCGCGCC 0.949138 -144 GGTGTATTCCCGTCGACTCGCTGTGCCCGGCT 10 43 1 CTCGCTCGCT 0.990432 -122 CTGTGCCCGGCTTCGCCGCGCTTGCGATCGCC 10 63 1 CTCGCGCGCT 0.997372 -102 GAAGCCGCCGCAGCGACTCGCCGCCAAACAAA 10 102 0 CGCGCTCGCC 0.993097 -63 GCTGCGGCGGCTTCGCCGCGCTTGCGATCGCC 10 120 1 CTCGCGCGCT 0.997372 -45 * *** ****** Masking position 7 Map Score: 12.5478 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 48 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 3 GAGGAGTTAATCCCCCTCTTTTACACCTGT 1 156 0 TCCCCCTCTT 0.879347 -145 ACTATTCATATCCTTCTTTCATTTTCAGTT 1 280 0 TCCTTCTTTC 0.80194 -21 TTTTTTCATCCTTTAAAAGTAGTCT 2 69 0 TCATCCTTTA 0.754862 -15 TGCCACAGTTTCACTCTTAACATTATTATA 3 59 0 TCACTCTTAA 0.562801 -201 CATGCGGAAAGCCTCCTTTCATGAAATATT 3 103 1 GCCTCCTTTC 0.797812 -157 GACTGCTTATTCCTCTCTATTTTATTGTC 3 241 0 TTCCTCTCTA 0.62247 -19 AGGTTCTTTCTCCCCCTGTAAGAAGCGTTT 4 277 0 TCCCCCTGTA 0.929339 -20 TTGAAATCCGGCCCTCTCTATAGTATCCTT 5 51 1 GCCCTCTCTA 0.925732 -56 AAAAAAAGCCCCCTCTAGTATCCTTCA 5 90 0 GCCCCCTCTA 0.963499 -17 GGTGATCCTCCTAAATTCTTTCAAT 6 274 0 TCCTCCTAAA 0.815705 -15 GATCGTCCTCCTATAGCATATCTGT 7 45 0 TCCTCCTATA 0.913702 -15 TTCTGTTGTTTCCCCCTCAACACGTATAGA 8 39 0 TCCCCCTCAA 0.959966 -262 ACATTACAATTCCCTCTTACATCTTTGAAA 8 122 0 TCCCTCTTAC 0.781873 -179 TTTTATCTTATCATTCTATAAAACATTACA 8 144 0 TCATTCTATA 0.475456 -157 ********** Masking position 7 Map Score: 9.96753 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 4 TTGTCGTCATGGAGGTCACCGATTAACAGA 3 27 0 GGAGGTCACC 0.701507 -233 TATGCCATACTGCGGCCGGAATAAACAAAC 4 123 1 TGCGGCCGGA 0.822994 -174 GAGCACCTGCTGAAATCAGCTGAACGTGAT 4 157 1 TGAAATCAGC 0.59314 -140 GTGATTTGCTTGTGGTCGGCAAAGAGCGGT 4 182 1 TGTGGTCGGC 0.984757 -115 CAAAACAAGGTGAGGGCGGCCTGTATTTAT 6 182 1 TGAGGGCGGC 0.961725 -107 CCGACTTCATTGTCGTCGGCGCGCC 9 6 0 TGTCGTCGGC 0.906955 -65 CCGACGACAATGAAGTCGGCTCGGACAGCC 9 17 1 TGAAGTCGGC 0.963847 -54 GTCGACTCGCTGTGCCCGGCTTCGCCGCGC 10 54 1 TGTGCCCGGC 0.858535 -111 TCGCCGCGCTTGCGATCGCCCGCTGGGTTT 10 75 1 TGCGATCGCC 0.784739 -90 GCAAGCGCGGCGAAGCCGCCGCAGCGACTC 10 115 0 CGAAGCCGCC 0.766246 -50 TCGCCGCGCTTGCGATCGCCGCTAGGCTGA 10 132 1 TGCGATCGCC 0.784739 -33 GATTGACACGCGGTCAGCCTAGCGGCGA 10 147 0 CGCGGTCAGC 0.921237 -18 ********** Masking position 7 Map Score: 8.3713 Number of sites scoring better than the average of aligned sites = 1178 Number in coding regions = 1127 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 5 AGGATTATACGAAATGGTTTGATATTGCGG 1 49 0 GAAATGGTTT 0.948257 -252 TCTGAACCCAGAAATGATTTTTTTATAG 2 9 0 GAAATGATTT 0.956928 -75 TCTGGGTTCAGAAATGATTTTTTATTGTGT 2 27 1 GAAATGATTT 0.956928 -57 TTCGGATGAAAAAAGAATTTGGCACCTTGT 4 228 0 AAAAGAATTT 0.794896 -69 AACAATATTCGAAATAATTTTTATAAAAAG 6 55 0 GAAATAATTT 0.944998 -234 TTACTTACTATAAATAGTTTTCGGATATTT 6 88 0 TAAATAGTTT 0.795049 -201 TCAAACAATTGAAAGAATTTAGGAGGATCA 6 267 1 GAAAGAATTT 0.934361 -22 GCGTTTTATTTAAAGAGTTTTCTGTTGTTT 8 58 0 TAAAGAGTTT 0.762105 -243 GTTTCACAGTAAAATGATTTTCAAAGATGT 8 104 1 AAAATGATTT 0.858081 -197 ********** Masking position 4 Map Score: 8.23418 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 6 GTGGCAAACAGAGCGTCAATCATGCGGAAA 3 83 1 GAGCGTCAAT 0.963901 -177 AAACCAAAAGGCGTGTCAGTGCGTTTTATT 8 78 0 GCGTGTCAGT 0.9819 -223 CTAACGATATGAGCGTCAGTTCATTATCAA 8 189 0 GAGCGTCAGT 0.976361 -112 CGTCACACGCGTCACTCCTTGATTCC 9 55 0 ACGCGTCACT 0.949773 -16 TTGTTTGGCGGCGAGTCGCTGCGGCGGCTT 10 103 1 GCGAGTCGCT 0.918361 -62 TAGGCTGACCGCGTGTCAATC 10 154 1 GCGTGTCAAT 0.972277 -11 ********** Masking position 6 Map Score: 3.08276 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 70 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 CTAAGCATAATTTATTACGAATGCAATATTATCG 1 245 0 TTTTTCGATC 0.938674 -56 CTTTGCAGTTTTTATGGTGTGTTCAGACGGTCTA 4 69 0 TTTTGTGTTC 0.938982 -228 AGCAAATCACGTTCAGCTGATTTCAGCAGGTGCT 4 158 0 GTTAGTGATC 0.824516 -139 CAAAGAGCGGTTTGAGCTGTATACGAAACAAGGT 4 201 1 TTTAGTGTTC 0.938982 -96 CAAATTCTTTTTTCATCCGAATACAGCGATGTTC 4 237 1 TTTATCGATC 0.938674 -60 TTTCTTTTATTTTAAGGCGTGAACATTTGAAATC 5 25 1 TTTAGCGTAC 0.701126 -82 CATGCACCTTTTTTATGTGAATTCACTTTTTATA 6 30 1 TTTATTGATC 0.933896 -259 TTTATATAGCTTTCTTTCGATTTGAACCCTCCAA 6 130 0 TTTTTCGATG 0.664652 -159 TTTAAAGAGTTTTCTGTTGTTTCCCCCTCAACAC 8 46 0 TTTTGTGTTC 0.938982 -255 TATCGTTAGGTTTCTTATGAGTTCTTAATTGATG 8 210 1 TTTTTTGATC 0.933896 -91 *** ** *** * * Masking position 3 Map Score: 3.21551 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 8 GTCAGGTGTTTGTGTATACC 1 1 0 TGTGTATACC 0.903673 -300 GTTATCATCTTCTGTACTCCCAAAAAGAAA 4 30 0 TCTGTACTCC 0.945806 -267 CTCAACCGTTTGTTTATTCCGGCCGCAGTA 4 130 0 TGTTTATTCC 0.772931 -167 AGCGGTTTGAGCTGTATACGAAACAAGGTG 4 206 1 GCTGTATACG 0.908165 -91 TCTGAACATCGCTGTATTCGGATGAAAAAA 4 244 0 GCTGTATTCG 0.958096 -53 GGCCTCCGTTGTACTCCTGTGGCGCGG 10 8 1 GTTGTACTCC 0.886333 -157 CGCGGATCTGGGTGTATTCCCGTCGACTCG 10 33 1 GGTGTATTCC 0.962416 -132 ********** Masking position 6 Map Score: 1.94296 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 204 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 ACTAAGCACTTGCAGATAAAGTGAGGATCT 1 210 0 TGCAGATAAA 0.688399 -91 CATTTTCAGTTGCTAAGCATAATTTATTAC 1 261 0 TGCTAAGCAT 0.801782 -40 TTACACAAAGTGCATAGCAACGAATCTCCT 3 143 1 TGCATAGCAA 0.856789 -117 TCTCCTAATTTGCATATCAGTTTCATATAG 3 167 1 TGCATATCAG 0.942337 -93 ATCCAAAACATGCAAGTCATGTACTATATG 3 190 0 TGCAAGTCAT 0.879055 -70 CCATAAAAACTGCAAAGCAGCTTTCTAAAG 4 86 1 TGCAAAGCAG 0.968736 -211 ATAAAAAAGGTGCAGATCATGCACCTTTTT 6 13 1 TGCAGATCAT 0.954407 -276 GGGCTGTTTTTGCAAATAAGATAAATACAG 6 202 0 TGCAAATAAG 0.880914 -87 CTTACATCTTTGAAAATCATTTTACTGTGA 8 107 0 TGAAAATCAT 0.753067 -194 ********** Masking position 9 Map Score: 2.6446 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 10 TAATTTATTACGAATGCAATATTATCGCAA 1 242 0 CGAATGCAAT 0.892709 -59 TGTGTAAAAACGCTTACAATATTTCATGAA 3 120 0 CGCTTACAAT 0.954594 -140 GGCTTCGCCGCGCTTGCGATCGCCCGCTGG 10 71 1 CGCTTGCGAT 0.99232 -94 GGCTTCGCCGCGCTTGCGATCGCCGCTAGG 10 128 1 CGCTTGCGAT 0.99232 -37 ********** Masking position 5 Map Score: 0.680097 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 43 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 11 TATAATCCTCAACAATGTTATCAACGGTGT 1 70 1 AACAATGTTA 0.767613 -231 AAAATGAAAGAAGGATATGAATAGTC 1 285 1 AAGGATATGA 0.872865 -16 TTTCACTCTTAACATTATTATACTTTGTCG 3 51 0 AACATTATTA 0.690275 -209 ATCTGAAGTAAAGGATACTATAGAGAGGGC 5 61 0 AAGGATACTA 0.872847 -46 ACTTCAGATGAAGGATACTAGAGGGGGCTT 5 82 1 AAGGATACTA 0.872847 -25 GATATTTTTCAACAATATTCGAAATAATTT 6 65 0 AACAATATTC 0.767613 -224 TATAGTAAGTAACAATATTAATAGTTGGAG 6 106 1 AACAATATTA 0.925575 -183 TAAGAAACCTAACGATATGAGCGTCAGTTC 8 197 0 AACGATATGA 0.917832 -104 ********** Masking position 2 Map Score: 0.116487 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 134 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 12 ********** No masking Map Score: 3.26382e-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 13 ********** No masking Map Score: 3.26382e-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: 3.26382e-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