AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -ifruR_hpyl_opreg_300.orf -g0.389 -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 = 0.389 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HP0027 198 isocitrate dehydrogenase (icd) #2 HP0088 223 RNA polymerase sigma-70 factor (rpoD) #3 HP0090 300 malonyl coenzyme A-acyl carrier protein transacylase (fabD) #4 HP0121 186 phosphoenolpyruvate synthase (ppsA) #5 HP0921 143 glyceraldehyde-3-phosphate dehydrogenase (gap) #6 HP1100 65 6-phosphogluconate dehydratase #7 HP1346 88 glyceraldehyde-3-phosphate dehydrogenase (gap) #8 HP1350 209 protease #9 HP1352 300 adenine specific DNA methyltransferase (HINFIM) Motif number 1 TTCAACTCCTAATTATAAGCCAAAAAATTAAATG 1 36 1 AATTATAAAA 0.807055 -163 TAGCGGTTGGAAATAACTTGAAAAAACGCAATGT 1 83 0 AAATAACAAA 0.841565 -116 AAAAATACTATATAACCCTTAAAAATCTTTTTTT 1 134 0 TATAACCAAA 0.54665 -65 CTCAAACTTTAGAAAAAGGATAAACA 1 183 1 AGAAAAAAAA 0.77601 -16 ACAAAATGTAAAAAATACTAAAAAGCTTTTTTAC 2 50 0 AAAAATAAAA 0.874624 -174 TATTCTACTAAAAAATAGCTTAAATTCTAATTAT 2 122 0 AAAAATAAAA 0.874624 -102 GGTGTCTCGTTAATACATTCTAAACAAAAAGTTT 3 37 1 TAATACAAAA 0.863968 -264 CACAAAGTAGAATTATAGTAAAAATAAGTTAAAA 3 184 1 AATTATAAAA 0.807055 -117 AAATAAGTTAAAATAAACCTTAAACTTTAATGGT 3 205 1 AAATAAAAAA 0.923738 -96 AATTATGGATTAATAAAACTTAAAGGATAACACC 3 277 1 TAATAAAAAA 0.797715 -24 CCCATTATACAATAAAATCATAAACCAAAAAGAA 4 47 1 AATAAAAAAA 0.83985 -140 CTAGGTCCAATATAATAGCGCAAAATGTAGTAAA 5 61 1 TATAATAAAA 0.536428 -83 AAATGTAGTAAAATACCAAACAAAACCCCCTAAA 5 83 1 AAATACCAAA 0.895341 -61 ATAATAACTCAAAAACACTCTAAAAGGGTTATTG 6 11 0 AAAAACAAAA 0.943107 -55 TTTGAGTTATTATTATATATTAAATCTTAATTAA 6 32 1 TATTATAAAA 0.576462 -34 GGTGATTTTTAAATAAAGGGAAAAC 7 74 1 AAATAAAAAA 0.923738 -15 TGCCCGTTACAAAAACATTAGAAATGGGGCTTAC 8 21 0 AAAAACAAAA 0.943107 -189 TGAGCCTAAACGATACAACAAAAACGCGTAACTC 8 86 0 CGATACAAAA 0.676943 -124 TTTTAGATAGAATAAACGCAAAAATTGAATAAAA 8 152 1 AATAAACAAA 0.69694 -58 GCAAAAATTGAATAAAACCTTAAAGGTGATTCTT 8 169 1 AATAAAAAAA 0.83985 -41 CGAGATTAGGCAATACAGAATAAAGGGAAGGC 9 9 0 CAATACAAAA 0.861598 -292 TGTTCGTTACAAAAACATTAGAAATGGGGCTTAC 9 69 0 AAAAACAAAA 0.943107 -232 CTATTTTAAACGATACAACAAAAACGCATAACTC 9 134 0 CGATACAAAA 0.676943 -167 TTAAACATTAAGATAACCTTAAAACGCTTGTGTT 9 238 1 AGATAACAAA 0.64131 -63 ******* *** Masking position 5 Map Score: 23.893 Number of sites scoring better than the average of aligned sites = 1226 Number in coding regions = 894 Number in noncoding regions = 332 Number of orfs with sites within 600 bp upstream = 212 Fraction of orfs with sites within 600 bp upstream = 0.0340508 Motif number 2 AACTCCTAATTATAAGCCAAAAAATTAAATGATTTCTT 1 39 1 TACCAAATTA 0.593952 -160 AATAACTTGAAAAAACGCAATGTTTTTAAAAGAAATCA 1 68 0 AAGCATTTTA 0.864402 -131 AAAGCGGGGAAAAATTCCAATAATATAATTAGAATTTA 2 98 1 AACCATTATA 0.689333 -126 TTATCTTATGGATCTAGCTTTTGATTGAAAGCATGGGT 2 175 1 GAGCTTATTA 0.900086 -49 AATAAGTTAAAATAAACCTTAAACTTTAATGGTTTCTA 3 206 1 AACCTACTTA 0.75033 -95 AACCACCCTTTCTATTCAAAAATACCTA 4 1 1 AACCTTATTA 0.978696 -186 AACCAAAAAGAATACACCCTCTTATTAAAAAGCTTAGT 4 69 1 AACCTCATTA 0.887467 -118 ATGATAGCATGATAGAGCTTTAGTTTTAGCTAGTTTGT 4 110 0 GAGCTTTTTA 0.774418 -77 AAAACTCCCTTAAAATGATCATTAAGTT 4 169 0 AACCTTAATA 0.881174 -18 AATACCAAACAAAACCCCCTAAAATTGAAATTGAAGTC 5 94 1 AACCTAATTA 0.945964 -50 GAATACCCCTTTAATTAAGATTTAATAT 6 48 0 GACCTTATTA 0.951036 -18 AGAACCCCTTAAGAATGCCTTTATTTAAGAGCATTTGT 7 28 1 AAGCTTTTTA 0.890345 -61 AAAAACGCGTAACTCCCCGATCCATTCACATGCAAATC 8 63 0 AACCATATTA 0.973024 -147 AAATTTAGATAACATGCCCATTCATTCACTCATTTTGA 8 117 0 AACCATATTA 0.973024 -93 AAAAACGCATAACTCCCCGATCCATTCACATGCAAATC 9 111 0 AACCATATTA 0.973024 -190 ATTTGATGAGAACAAAGCTAAAGATTAAACATTAAGAT 9 214 1 AAGCAAATTA 0.864412 -87 ** ** ** *** * Masking position 16 Map Score: 15.0608 Number of sites scoring better than the average of aligned sites = 421 Number in coding regions = 343 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 3 AAATCTTTTTTTGAATGCGTGTTTAAAAGTAGCG 1 112 0 TGAAGCGTTT 0.756741 -87 TATAGAGGGGTGGAATGGAGGGGTGGAATGTAAA 2 21 1 TGAAGGAGGT 0.90079 -203 TATTTTTGAATAGAAAGGGTGGTT 4 1 0 TGAAGGGTTT 0.969574 -186 GATTTTATTGTATAATGGGCGGTTAGTTAGGTAT 4 32 0 TTAAGGGCTT 0.934075 -155 TAATGATCATTTTAAGGGAGTTTT 4 173 1 TTAAGGAGTT 0.89202 -14 TCAATTTCAATTTTAGGGGGTTTTGTTTGGTATT 5 94 0 TTTAGGGGTT 0.863523 -50 TTAAATCTTAATTAAAGGGGTATTC 6 51 1 ATAAGGGGTT 0.923918 -15 GCATTTGTGATAGAATGGTGATTTTTAAATAAAG 7 58 1 TGAAGGTGTT 0.94219 -31 ACAAAAACATTAGAAATGGGGCTTACTTTAGAGC 8 13 0 TGAATGGGTT 0.963196 -197 TGCATGTGAATGGATCGGGGAGTTACGCGTTTTT 8 67 1 TGATGGGGTT 0.976877 -143 AAATGAGTGAATGAATGGGCATGTTATCTAAATT 8 120 1 AGAAGGGCGT 0.760802 -90 ACAAAAACATTAGAAATGGGGCTTACTTTAGAGC 9 61 0 TGAATGGGTT 0.963196 -240 TGCATGTGAATGGATCGGGGAGTTATGCGTTTTT 9 115 1 TGATGGGGTT 0.976877 -186 * *** **** ** Masking position 14 Map Score: 12.7386 Number of sites scoring better than the average of aligned sites = 472 Number in coding regions = 418 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 4 CTATCAAAACTTAAGGAAGTCAA 1 4 0 TTAAGGAAGT 0.659797 -195 GTTTGTTTTTATAGAGGGGTGGAATGGAGG 2 12 1 ATAGAGGGGT 0.951038 -212 GAGGGGTGGAATGGAGGGGTGGAATGTAAA 2 25 1 ATGGAGGGGT 0.837639 -199 AAGCTTTTTAATAAGAGGGTGTATTCTTTT 4 74 0 ATAAGAGGGT 0.756344 -113 AATGATCATTTTAAGGGAGTTTT 4 174 1 TTAAGGGAGT 0.960959 -13 TTGAGTTGAATTCAAGGAGTAAAAC 5 6 0 TTCAAGGAGT 0.86557 -138 AATTTCAATTTTAGGGGGTTTTGTTTGGTA 5 96 0 TTAGGGGGTT 0.906357 -48 TAAATCTTAATTAAAGGGGTATTC 6 52 1 TTAAAGGGGT 0.945055 -14 AAAGGCATTCTTAAGGGGTTCTGTCTCATT 7 20 0 TTAAGGGGTT 0.878232 -69 ATGTGAATGGATCGGGGAGTTACGCGTTTT 8 70 1 ATCGGGGAGT 0.951903 -140 ATGTGAATGGATCGGGGAGTTATGCGTTTT 9 118 1 ATCGGGGAGT 0.951903 -183 ********** Masking position 2 Map Score: 10.0394 Number of sites scoring better than the average of aligned sites = 749 Number in coding regions = 657 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 5 TATATAGTATTTTTGCGCTAGTATAGTTAC 1 154 1 TTTTGCGCTA 0.964196 -45 TTTTACTACATTTTGCGCTATTATATTGGA 5 66 0 TTTTGCGCTA 0.964196 -78 TTTAGAGTGTTTTTGAGTTATTATTATATA 6 21 1 TTTTGAGTTA 0.826534 -45 TGGGGCTTACTTTAGAGCCT 8 1 0 TTTAGAGCCT 0.746442 -209 AACGGGCATGCTTTGCGATTTGCATGTGAA 8 47 1 CTTTGCGATT 0.910257 -163 CATTCACTCATTTTGAGCCTAAACGATACA 8 103 0 TTTTGAGCCT 0.929274 -107 TTTATTCAATTTTTGCGTTTATTCTATCTA 8 155 0 TTTTGCGTTT 0.953043 -55 CCATTTTTGAGATTAGAAAGAATC 8 196 0 TTTTGAGATT 0.922854 -14 TCTCGCTCTCATTTGCGATAGAGGCTCTAA 9 38 1 ATTTGCGATA 0.658542 -263 TGGGGCTTACTTTAGAGCCTCTATCGCAAA 9 49 0 TTTAGAGCCT 0.746442 -252 AACGAACATGCTTTGCGATTTGCATGTGAA 9 95 1 CTTTGCGATT 0.910257 -206 GATCGGGGAGTTATGCGTTTTTGTTGTATC 9 127 1 TTATGCGTTT 0.701566 -174 ********** Masking position 2 Map Score: 10.8449 Number of sites scoring better than the average of aligned sites = 700 Number in coding regions = 632 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 6 TGGCTTATAATTAGGAGTTGAATGCTATCAAAA 1 25 0 TTGATTGAAT 0.968003 -174 TTTAAGCTATTTTTTAGTAGAATAACAAAGGAT 2 132 1 TTTATAGAAT 0.929022 -92 TTTAAAAACTTTTTGTTTAGAATGTATTAACGA 3 43 0 TTGTTAGAAT 0.913858 -258 AAGCCCTTAGTTTTGTTTAGAAACCATTAAAGT 3 228 0 TTGTTAGAAA 0.83075 -73 ACTAAGGGCTTTTATATTACAATTTTAAATTAT 3 250 1 TTTATACAAT 0.807713 -51 AGTTAGGTATTTTTGAATAGAAAGGGTGGTT 4 9 0 TTGATAGAAA 0.952217 -178 ATTAAAAAGCTTAGTAATACAAACTAGCTAAAA 4 92 1 TTTATACAAA 0.63199 -95 TAAAATTATTTATTGAGTTGAATTCAAGGAGTA 5 15 0 TAGATTGAAT 0.763022 -129 TTATCCTATTTTCAGACTTCAATTTCAATTTTA 5 113 0 TTGATTCAAT 0.904505 -31 TTTAAGAGCATTTGTGATAGAATGGTGATTTTT 7 51 1 TTTGTAGAAT 0.718581 -38 CGGGCATGCTTTGCGATTTGCATGTGAATGGAT 8 49 1 TTGATTGCAT 0.90518 -161 CCATTTTTGAGATTAGAAAGAATCACCTT 8 191 0 TTGATAGAAA 0.95505 -19 CGAACATGCTTTGCGATTTGCATGTGAATGGAT 9 97 1 TTGATTGCAT 0.90518 -204 ** ** ****** Masking position 12 Map Score: 8.69796 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 149 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 7 AATGCTATCAAAACTTAAGGAAGTCAA 1 8 0 AAACTTAAGG 0.663635 -191 AATACATTCTAAACAAAAAGTTTTTAAAGG 3 48 1 AAACAAAAAG 0.892727 -253 AACCCTCGGTAACCTTGACGGCTACGCATC 3 108 1 AACCTTGACG 0.695423 -193 AGTTAAAATAAACCTTAAACTTTAATGGTT 3 210 1 AACCTTAAAC 0.639186 -91 AATGGTTTCTAAACAAAACTAAGGGCTTTT 3 233 1 AAACAAAACT 0.661881 -68 TGGATTAATAAAACTTAAAGGATAACACC 3 282 1 AAACTTAAAG 0.865084 -19 TAAAATCATAAACCAAAAAGAATACACCCT 4 59 1 AACCAAAAAG 0.921557 -128 AAGTTTCTTAAAACAAAAATATAACAATGA 4 144 0 AAACAAAAAT 0.512894 -43 TTGTTTTAAGAAACTTAATGATCATTTTAA 4 158 1 AAACTTAATG 0.571032 -29 GTAAAATACCAAACAAAACCCCCTAAAATT 5 90 1 AAACAAAACC 0.751736 -54 TAAACGATACAACAAAAACGCGTAACTCCC 8 84 0 AACAAAAACG 0.784244 -126 ACTCATTTTGAGCCTAAACGATACAACAAA 8 98 0 AGCCTAAACG 0.869545 -112 AATTTTAGATAGAATAAACGCAAAAATTGA 8 150 1 AGAATAAACG 0.440027 -60 AATTGAATAAAACCTTAAAGGTGATTCTTT 8 174 1 AACCTTAAAG 0.900514 -36 TAAACGATACAACAAAAACGCATAACTCCC 9 132 0 AACAAAAACG 0.784244 -169 ********** Masking position 8 Map Score: 6.04194 Number of sites scoring better than the average of aligned sites = 965 Number in coding regions = 864 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 8 GAATGCGTGTTTAAAAGTAGCGGTTGGAAATAAC 1 100 0 TTAAAATGGT 0.877901 -99 AATAATATAATTAGAATTTAAGCTATTTTTTAGT 2 116 1 TTAGAATGCT 0.986452 -108 CTCCATAAAGTAAGAACCCATGCTTTCAATCAAA 2 194 0 TAAGAACGCT 0.948062 -30 AAAGGAATGCTTAGAAACTATGGTGTCTCGTTAA 3 16 1 TTAGAACGGT 0.985281 -285 CAGGGAGGGATTCGAACCCTCGGTAACCTTGACG 3 94 1 TTCGAACGGT 0.953698 -207 TACAAAAACATTAGAAATGGGGCTTACTTTAGAG 8 14 0 TTAGAATGCT 0.986452 -196 TACAAAAACATTAGAAATGGGGCTTACTTTAGAG 9 62 0 TTAGAATGCT 0.986452 -239 ****** * *** Masking position 6 Map Score: 3.77426 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 47 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 CGCATTCAAAAAAAGATTTTTAAGGGTTATA 1 127 1 AAAAGTTTTT 0.885344 -72 TGGAATGTAAAAAAGCTTTTTAGTATTTTTT 2 44 1 AAAAGTTTTT 0.885344 -180 GTAGAATAACAAAGGATTAGGTGTATCTTAT 2 148 1 AAAGGTTAGG 0.90353 -76 CATTAAAGTTTAAGGTTTATTTTAACTTATT 3 206 0 TAAGGTTATT 0.865719 -95 CCTCTTATTAAAAAGCTTAGTAATACAAACT 4 86 1 AAAAGTTAGT 0.956944 -101 AAACACTCTAAAAGGGTTATTG 6 2 0 AAAGGTTATT 0.972944 -64 AATCTTAATTAAAGGGGTATTC 6 54 1 AAAGGGTATT 0.905251 -12 TAGCAGATATAAAAGGTTAGTTAATC 9 285 1 AAAAGTTAGT 0.956944 -16 ***** ***** Masking position 3 Map Score: 4.26708 Number of sites scoring better than the average of aligned sites = 273 Number in coding regions = 228 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 10 TTGACTTCCTTAAGTTTTGATAGCATTCA 1 10 1 TTAAGTTTTG 0.593682 -189 TTTAAAAACATTGCGTTTTTTCAAGTTATT 1 76 1 TTGCGTTTTT 0.972469 -123 TTACTACATTTTGCGCTATTATATTGGACC 5 64 0 TTGCGCTATT 0.803203 -80 TAGAGTGTTTTTGAGTTATTATTATATATT 6 23 1 TTGAGTTATT 0.785328 -43 CGGGCATGCTTTGCGATTTGCATGTGAATG 8 49 1 TTGCGATTTG 0.965925 -161 TATTCAATTTTTGCGTTTATTCTATCTAAA 8 153 0 TTGCGTTTAT 0.917778 -57 CCATTTTTGAGATTAGAAAGAATCAC 8 194 0 TTGAGATTAG 0.745927 -16 CGAACATGCTTTGCGATTTGCATGTGAATG 9 97 1 TTGCGATTTG 0.965925 -204 TCGGGGAGTTATGCGTTTTTGTTGTATCGT 9 129 1 ATGCGTTTTT 0.847754 -172 ********** Masking position 7 Map Score: 4.87698 Number of sites scoring better than the average of aligned sites = 431 Number in coding regions = 394 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 11 AAATTGTAATATAAAAGCCCTTAGTTTTGTT 3 244 0 ATAAAGCCCT 0.959018 -57 ACCAAAAAGAATACACCCTCTTATTAAAAAG 4 70 1 ATACACCTCT 0.868597 -117 ACTAGCTAAAACTAAAGCTCTATCATGCTAT 4 114 1 ACTAAGCTCT 0.871569 -73 AAAATACCAAACAAAACCCCCTAAAATTGAA 5 92 1 ACAAACCCCC 0.858349 -52 GCTTAATGAGACAGAACCCCTTAAGAATGCC 7 16 1 ACAGACCCCT 0.964971 -73 CCATTCTATCACAAATGCTCTTAAATAAAGG 7 45 0 ACAAAGCTCT 0.974271 -44 CTCATTTGCGATAGAGGCTCTAAAGTAAGCC 9 45 1 ATAGAGCTCT 0.966172 -256 GCATCAAATGATAGAAGCTATCTATCCCCAC 9 168 0 ATAGAGCTAT 0.759685 -133 ***** ***** Masking position 5 Map Score: 1.32134 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 172 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 12 ********** No masking Map Score: -1.73129e-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: -1.73129e-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: -1.73129e-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