AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i180_ecoli_mtub_300.orf -o180_ecoli_mtub_300.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -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 = 0.58 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 talB 278 transaldolase B #2 mog 114 required for the efficient incorporation of molybdate into molybdoproteins #3 moaA 300 molybdopterin biosynthesis, protein A #4 moaB 21 molybdopterin biosynthesis, protein B #5 moeA 203 molybdopterin biosynthesis #6 Rv3108 98 hypothetical protein Rv3108 #7 moaA 148 moaA #8 moaB 50 moaB #9 Rv3113 122 hypothetical protein Rv3113 #10 Rv3115 161 hypothetical protein Rv3115 #11 moeB 77 moeB #12 cysA3 28 cysA3 Motif number 1 CGTTTACACAGGAAAGTCATCGCGACCGGCAAT 1 24 0 GGAGTCACGC 0.993013 -255 AAAATGGCGGGCGATATCAACGCAGTGTCAGAA 1 133 1 GCGATCACGC 0.940582 -146 GGCGATAACCGTCTTGTCGGCGGTTGCGCTGAC 1 185 1 GTCGTCGCGG 0.914377 -94 ATATCACGACGCAACGTCAGCGCAACCGCCGAC 1 200 0 GCAGTCACGC 0.948291 -79 GCTTGTTAGGGGGATGTAACCGGTCTGCCCTGA 1 235 0 GGGGTAACGG 0.958898 -44 ATCTTTACGAGCATTGTCACGGCCAAAGCACCG 3 223 0 GCAGTCAGGC 0.935738 -78 AGATGGATATGGCATGTAAAGGCAGGACCCAGC 5 98 1 GGCGTAAGGC 0.964935 -106 CAGCGTTTGAGGACGATCATGGCTCCGCCGACG 6 22 1 GGAATCAGGC 0.938451 -77 CTGGTGCTGGTGGTCGTCGGCGGAGCCATGATC 6 36 0 TGGGTCGCGG 0.895656 -63 GGTGCTGGATGGGCTATCGTCGCGGCCCTGGTG 6 63 0 GGGATCGCGC 0.983161 -36 CAACGCGCCATAAACGCAGGCTCATGC 7 5 1 GCGATAACGC 0.900055 -144 GAAATGCATCGGCGCATCGTGGCGCAGCGCATG 7 33 0 GGCATCGGGC 0.966027 -116 GCGCATTCACGGCCGGTCATCCCCTTGT 9 6 0 GGCGTCACCC 0.965715 -117 GAATGCGCTCTCATCGTCGCCGCTGTTCGGCAA 9 31 1 TCAGTCGCGC 0.85881 -92 TCCTGGGTCAGTGAGGTAGTCGGCAAGCCGAG 10 10 0 GTGGTAGCGG 0.754055 -152 GTGGTGTACGGGCAGGTAAGGCCGGTGGGCGTG 10 63 1 GGCGTAAGCC 0.796783 -99 AAGGCCGGTGGGCGTGTCGTAGCCCAGTAGTGG 10 80 1 GGCGTCGAGC 0.946037 -82 GCCCAGTAGTGGGCGGTCATCGCGTGATCCTTC 10 101 1 GGGGTCACGC 0.987755 -61 *** **** *** Masking position 7 Map Score: 28.9232 Number of sites scoring better than the average of aligned sites = 2868 Number in coding regions = 2675 Number in noncoding regions = 193 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 2 GGAAAGTCATCGCGACCGGCAATAAGAGGGATATGC 1 10 0 CGCGCCAAGA 0.88752 -269 GCAACGTCAGCGCAACCGCCGACAAGACGGTTATCGC 1 186 0 CGCACCGAGA 0.860396 -93 GCCTGTCTGTCACTCCCTTCGCAGTGTATCATTCTGT 2 57 1 CACTCCGTGT 0.725827 -58 ATGCACGCTATGCCTCCCTGATGATGTATATCAAAGT 3 28 1 TGCCCCATGT 0.914411 -273 CCGTATCAGTTGACCCAGGTGCAGAGGCTAGAGTGTT 3 189 0 TGACCAGAGG 0.866229 -112 CGAGCATTGTCACGGCCAAAGCACCGTATCAGTTGAC 3 212 0 CACGCCGCGT 0.862952 -89 TCGTAAAGATTGCCACCAGGGCGAAGGAAGAAATGAC 3 246 1 TGCCCCGAGG 0.995598 -55 ACAGACTGTATGCCACCTCGGGCGTAGCGCTGGGTCC 5 122 0 TGCCCCGTAG 0.897979 -82 AATTCGATTTTGCCTCCGCAGGAGTGTTTTC 5 183 1 TGCCCCGTGT 0.986794 -21 GGGCTATCGTCGCGGCCCTGGTGCTGGTGGTCGTCGG 6 49 0 CGCGCCGTGG 0.996454 -50 CAACGCGCCATAAACGCAGGCTCATGCGCT 7 4 1 CGCGCAAAGG 0.91117 -145 TCTAACCGACTGCGTCCAAAGTGGAGGATCGAAAAGA 7 112 1 TGCGCCGAGG 0.994988 -37 GATTGATCAACGACTCCACAGTTGAGGAAGGAACC 8 26 1 CGACCCGAGG 0.98314 -25 GACCGAAATTCGCCGCACCCGAATAGTCGGGTCGCAT 9 94 1 CGCCCAGAGT 0.971745 -29 ACTACCTCACTGACCCAGGAGGAGAGTTACGTCCAGG 10 23 1 TGACCAGAGT 0.731549 -139 GGAGGAGAGTTACGTCCAGGGGTGTGGTGTACGGGCA 10 40 1 TACGCCGTGG 0.968915 -122 ACTCGTACACCACGTCCCTGGCCTTGGCCAGGAGGAG 11 44 1 CACGCCGTGG 0.982558 -34 **** ** * *** Masking position 6 Map Score: 23.2385 Number of sites scoring better than the average of aligned sites = 2409 Number in coding regions = 2312 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 3 ACCTCTAAAGGACGATGCACGCTATGCCTCCCTGA 3 14 1 GACGACGCTT 0.90996 -287 TAGTGGTTATGCCGATACTAGCGTGTAAATGAGAT 3 154 0 GCCGACGCGG 0.994294 -147 TGACCCAGGTGCAGAGGCTAGAGTGTTTAGTGGTT 3 181 0 GCAGACGAGG 0.982984 -120 GCATGTAAAGGCAGGACCCAGCGCTACGCCCGAGG 5 109 1 GCAGGCGCGT 0.994998 -95 GTGGTCGTCGGCGGAGCCATGATCGTCCTCAAACG 6 25 0 GCGGACGATG 0.873784 -74 GTGGTGGCTAGCCGGTGCTGGATGGGCTATCGTCG 6 74 0 GCCGGCGATG 0.982794 -25 CGCCATAAACGCAGGCTCATGCGCTGCGCCACGAT 7 16 1 GCAGGCGCGT 0.994998 -133 CGTTCTGCACGCCGGCACTGGAACTCCCACGTTGC 9 60 0 GCCGGCGAAT 0.934105 -63 TGGTCGTTTCGAAGGATCACGCGATGACCGCCCAC 10 109 0 GAAGGCGCGT 0.982494 -53 ACTGCCACCCGAAGGATCACGCGAGGAACCTTCAC 11 11 1 GAAGGCGCGG 0.988951 -67 ***** * *** * Masking position 8 Map Score: 14.2888 Number of sites scoring better than the average of aligned sites = 812 Number in coding regions = 779 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 4 AAAGTCATCGCGACCGGCAATAAGAGGGAT 1 15 0 CGACCGGCAA 0.838773 -264 TGGCGATAACCGTCTTGTCGGCGGTTGCGC 1 184 1 CGTCTTGTCG 0.570908 -95 GTAGCGTGACCGACTTCCCGGTCACGCTAA 2 17 0 CGACTTCCCG 0.914651 -98 GCTCCGCCGACGACCACCAGCACCAGGGCC 6 43 1 CGACCACCAG 0.947252 -56 CATCCAGCACCGGCTAGCCACCAC 6 85 1 CGGCTAGCCA 0.63986 -14 GCCGAACGAACAGTCGATTGATCAAC 8 7 1 CGAACAGTCG 0.791768 -44 AGCGCATTCACGGCCGGTCATCCCCTTGT 9 10 0 CGGCCGGTCA 0.585094 -113 CCCACGTTGCCGAACAGCGGCGACGATGAG 9 40 0 CGAACAGCGG 0.884488 -83 GTTCCAGTGCCGGCGTGCAGAACGACCGAA 9 71 1 CGGCGTGCAG 0.81142 -52 TCGCCGCACCCGAATAGTCGGGTCGCATAG 9 103 1 CGAATAGTCG 0.615622 -20 CTCGGCTTGCCGACTACCTCAC 10 3 1 CGGCTTGCCG 0.542833 -159 GGCTACGACACGCCCACCGGCCTTACCTGC 10 74 0 CGCCCACCGG 0.824522 -88 TCCTTCGAAACGACCAGCAAAAGTCAATCG 10 128 1 CGACCAGCAA 0.924681 -34 ACTGCCACCCGAAGGATCACG 11 2 1 CTGCCACCCG 0.719913 -76 ********** Masking position 1 Map Score: 8.39639 Number of sites scoring better than the average of aligned sites = 5555 Number in coding regions = 5359 Number in noncoding regions = 196 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 5 GGGATGTAACCGGTCTGCCCTGATGATATC 1 228 0 CGGTCTGCCC 0.942115 -51 GGACGATGCACGCTATGCCTCCCTGATGAT 3 23 1 CGCTATGCCT 0.902693 -278 ACACTCTAGCCTCTGCACCTGGGTCAACTG 3 190 1 CTCTGCACCT 0.768141 -111 CAGGACCCAGCGCTACGCCCGAGGTGGCAT 5 120 1 CGCTACGCCC 0.988913 -84 ACGCCACAGACTGTATGCCACCTCGGGCGT 5 134 0 CTGTATGCCA 0.418449 -70 GGACGATCATGGCTCCGCCGACGACCACCA 6 32 1 GGCTCCGCCG 0.890308 -67 CAGGCTCATGCGCTGCGCCACGATGCGCCG 7 27 1 CGCTGCGCCA 0.982465 -122 CGCTGCGCCACGATGCGCCGATGCATTTCG 7 37 1 CGATGCGCCG 0.923638 -112 ATCATCTTTTCGATCCTCCACTTTGGACGC 7 123 0 CGATCCTCCA 0.870155 -26 CATTCACGGCCGGTCATCCCCTTGT 9 6 0 CGGTCATCCC 0.679904 -117 GACCGAAATTCGCCGCACCCGAATAGTCGG 9 94 1 CGCCGCACCC 0.855463 -29 CTGGACGTAACTCTCCTCCTGGGTCAGTGA 10 29 0 CTCTCCTCCT 0.901306 -133 TACTGGGCTACGACACGCCCACCGGCCTTA 10 79 0 CGACACGCCC 0.866706 -83 GATTGCTCTCCTCCTGGCCAAGGCC 11 63 0 CTCTCCTCCT 0.901306 -15 ********** Masking position 8 Map Score: 9.77211 Number of sites scoring better than the average of aligned sites = 3727 Number in coding regions = 3546 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 6 TGATATCGCCCGCCATTTTTATACAAAACC 1 122 0 CGCCATTTTT 0.945359 -157 TATCGCCAGGCGAGACTGTTTCGGATTTCT 1 162 0 CGAGACTGTT 0.95642 -117 TTCTGTTTAACGAGACTGTTTAAACGGAAA 2 88 1 CGAGACTGTT 0.95642 -27 AAAGTAAAACCGCCATTTTCCCTTATTCTG 3 60 1 CGCCATTTTC 0.907383 -241 TTTTTACCATCCACACTTTCGCTATGTAAT 3 125 0 CCACACTTTC 0.855569 -176 AAGGGTGGTTCGCCACTTTTGCTATAAATA 5 25 1 CGCCACTTTT 0.986952 -179 CTCTCATCGTCGCCGCTGTTCGGCAACGTG 9 38 1 CGCCGCTGTT 0.960415 -85 CTATGCGACCCGACTATTCGGGTGCGGC 9 105 0 CCCGACTATT 0.833323 -18 ********** Masking position 7 Map Score: 4.30141 Number of sites scoring better than the average of aligned sites = 1027 Number in coding regions = 947 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 7 TGTATAAAAATGGCGGGCGATATCAACGCA 1 127 1 TGGCGGGCGA 0.95999 -152 GATAACCGTCTTGTCGGCGGTTGCGCTGAC 1 188 1 TTGTCGGCGG 0.841361 -91 TCTACCTCTAAAGGACGATGCACGCTAT 3 9 1 TAAAGGACGA 0.694719 -292 GAACCACCCTTAATGGACGAATACT 5 6 0 TAATGGACGA 0.834043 -198 GTGTCAGCGTTTGAGGACGATCATGGCTCC 6 18 1 TTGAGGACGA 0.93657 -81 GCCCTGGTGCTGGTGGTCGTCGGCGGAGCC 6 42 0 TGGTGGTCGT 0.882866 -57 GACTCCACAGTTGAGGAAGGAACC 8 37 1 TTGAGGAAGG 0.599749 -14 TCCAGGGGTGTGGTGTACGGGCAGGTAAGG 10 54 1 TGGTGTACGG 0.943026 -108 CAGGTAAGGCCGGTGGGCGTGTCGTAGCCC 10 75 1 CGGTGGGCGT 0.881056 -87 CGTAGCCCAGTAGTGGGCGGTCATCGCGTG 10 97 1 TAGTGGGCGG 0.978489 -65 GCCAGGGACGTGGTGTACGAGTGAAGGTTC 11 36 0 TGGTGTACGA 0.927817 -42 ********** Masking position 9 Map Score: 3.5938 Number of sites scoring better than the average of aligned sites = 1572 Number in coding regions = 1515 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 8 GACCGGCAATAAGAGGGATATGC 1 3 0 AAGAGGATAT 0.985498 -276 CCAATTGTTTAAGAAGTATATACGCTACGAG 1 60 1 AAGAGTATAT 0.977383 -219 AACCGCCGACAAGACGGTTATCGCCAGGCGA 1 179 0 AAGAGGTTAT 0.943686 -100 TGCCTCCCTGATGATGTATATCAAAGTAAAA 3 38 1 ATGAGTATAT 0.958612 -263 TCGCTATGTAATCATGTATATAGCGTCATGA 3 106 0 ATCAGTATAT 0.841542 -195 TGAATATAGAAAGATGGATATGGCATGTAAA 5 87 1 AAGAGGATAT 0.985498 -117 **** ****** Masking position 4 Map Score: 4.66804 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 23 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 TCAAGTACCTCGTAGCGTATATACTTCTTA 1 69 0 CGTAGCGTAT 0.921534 -210 GCGATATCAACGCAGTGTCAGAAATCCGAA 1 143 1 CGCAGTGTCA 0.555404 -136 TCTTGTCGGCGGTTGCGCTGACGTTGCGTC 1 196 1 GGTTGCGCTG 0.814137 -83 GTTGCGCTGACGTTGCGTCGTGATATCATC 1 207 1 CGTTGCGTCG 0.956969 -72 TCACTCCCTTCGCAGTGTATCATTCTGTTT 2 66 1 CGCAGTGTAT 0.723286 -49 CCACCTCGGGCGTAGCGCTGGGTCCTGCCT 5 117 0 CGTAGCGCTG 0.984726 -87 GGGCTATCGTCGCGGCCCTGGTGCTGGTGG 6 56 0 CGCGGCCCTG 0.87206 -43 CGCATCGTGGCGCAGCGCATGAGCCTGCGT 7 24 0 CGCAGCGCAT 0.972551 -125 CGCTGCGCCACGATGCGCCGATGCATTTCG 7 37 1 CGATGCGCCG 0.926532 -112 GTGGGCGTGTCGTAGCCCAGTAGTGGGCGG 10 87 1 CGTAGCCCAG 0.957339 -75 ********** Masking position 5 Map Score: 3.29907 Number of sites scoring better than the average of aligned sites = 4295 Number in coding regions = 4051 Number in noncoding regions = 244 Number of orfs with sites within 600 bp upstream = 191 Fraction of orfs with sites within 600 bp upstream = 0.0306778 Motif number 10 TCAACGCAGTGTCAGAAATCCGAAACAGTCT 1 149 1 GTCAGAATCC 0.885145 -130 CCTTCGCCCTGGTGGCAATCTTTACGAGCAT 3 242 0 GGTGGAATCT 0.724202 -59 GTCCATTAAGGGTGGTTCGCCACTTTTGCTA 5 18 1 GGTGGTCGCC 0.966254 -186 GTGGTGGCTAGCCGGTGCTGGAT 6 86 0 GGTGGTAGCC 0.983205 -13 GGTAACGATTGTTAGTTAACCCTTGTACGAA 7 66 1 GTTAGTAACC 0.703183 -83 GACGCAGTCGGTTAGAGCGCCTCAAGAGAGT 7 97 0 GTTAGGCGCC 0.850514 -52 CACCCGAATAGTCGGGTCGCATAG 9 109 1 GTCGGTCGCA 0.847083 -14 CAGTGAGGTAGTCGGCAAGCCGAG 10 4 0 GTCGGAAGCC 0.983589 -158 GGCGGGAATCCTTTCGCATAG 12 18 0 GGCGGAATCC 0.967896 -11 ***** ***** Masking position 10 Map Score: 2.72738 Number of sites scoring better than the average of aligned sites = 1498 Number in coding regions = 1413 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 11 GCATATCCCTCTTATTGCCGGTC 1 2 1 CATCCCTCTT 0.900705 -277 GGCATAACCACTAAACACTCTAGCCTCTGCAC 3 176 1 CAACACTCTA 0.892414 -125 CTGATCTCTCCTTTTGACGTT 4 10 0 CATCTCTCCT 0.960828 -12 GCAAAAGTGGCGAACCACCCTTAATGGACGAA 5 15 0 CACCACCCTT 0.905517 -189 GAAAACACTCCTGCGGAGGCAA 5 192 0 GAACACTCCT 0.923962 -12 AACCCTTGTACGAAACTCTCTTGAGGCGCTCT 7 83 1 CAACTCTCTT 0.972638 -66 CACCCCTGGACGTAACTCTCCTCCTGGGTCAG 10 32 0 CAACTCTCCT 0.982573 -130 CCTGCCCGTACACCACACCCCTGGACGTAACT 10 47 0 CCACACCCCT 0.91696 -115 * ********* Masking position 6 Map Score: 1.80665 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 99 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 12 GGTACTTGATAACTTCTGCGTAGCATACAT 1 90 1 AACTTCTGCG 0.690176 -189 CAAGATTTTTCCGTTTAAACAGT 2 102 0 GATTTTTCCG 0.916925 -13 AGGAAGAAATGACTTCGCCTCCCGTATCTG 3 270 1 GACTTCGCCT 0.978045 -31 CTGATCTCTCCTTTTGACGTT 4 10 0 GATCTCTCCT 0.825904 -12 AGGCAAAATCGAATTTGCCTATTATGTCAG 5 168 0 GAATTTGCCT 0.925733 -36 AGGCAAATTCGATTTTGCCTCCGCAGGAGT 5 178 1 GATTTTGCCT 0.94698 -26 AGAACGACCGAAATTCGCCGCACCCGAATA 9 89 1 AAATTCGCCG 0.815923 -34 TCCTTCGATTGACTTTTGCTGGTCGTTTCG 10 133 0 GACTTTTGCT 0.862343 -29 ********** Masking position 2 Map Score: 0.698066 Number of sites scoring better than the average of aligned sites = 980 Number in coding regions = 922 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 13 ********** No masking Map Score: 3.32777e-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: 3.32777e-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: 3.32777e-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