AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i180_ecoli_mtub_100.orf -o180_ecoli_mtub_100.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 mog 114 required for the efficient incorporation of molybdate into molybdoproteins #2 moaA 300 molybdopterin biosynthesis, protein A #3 moaB 21 molybdopterin biosynthesis, protein B #4 moeA 203 molybdopterin biosynthesis #5 moaA 148 moaA #6 moaB 50 moaB #7 Rv3115 161 hypothetical protein Rv3115 #8 moeB 77 moeB #9 cysA3 28 cysA3 Motif number 1 TGATACACTGCGAAGGGAGTGACAGACAGGCTTC 1 54 0 CGAAGGATCA 0.972321 -61 GCCACCAGGGCGAAGGAAGAAATGACTTCGCCTC 2 257 1 CGAAGGAATG 0.985287 -44 AACACTCCTGCGGAGGCAAAATCGAATTTGCCTA 4 177 0 CGGAGGAACG 0.994489 -27 GCGCCATAAACGCAGGCTCATGCGCTGCGCCACG 5 15 1 CGCAGGTACG 0.978411 -134 GCCGAACGAACAGTCGATTGATCAAC 6 3 1 CGAACGAACG 0.976342 -48 CTGGTCGTTTCGAAGGATCACGCGATGACCGCCC 7 111 0 CGAAGGTACG 0.993148 -51 AAAAGTCAATCGAAGGAAATGACGCA 7 146 1 CGAAGGATCG 0.99716 -16 ACTGCCACCCGAAGGATCACGCGAGGAACCTTC 8 10 1 CGAAGGTACG 0.993148 -68 CCGAACTATGCGAAAGGATTCCCGCC 9 13 1 CGAAAGATCG 0.975268 -16 ****** * * ** Masking position 4 Map Score: 19.2867 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 131 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 2 AGGACGATGCACGCTATGCCTCCCTGATGAT 2 22 1 ACGCTATGCT 0.879345 -279 CACGATCATGACGCTATATACATGATTACAT 2 101 1 ACGCTATAAC 0.95837 -200 TAACCACTAAACACTCTAGCCTCTGCACCTG 2 180 1 ACACTCTACC 0.834367 -121 CTGCCTTTACATGCCATATCCATCTTTCTAT 4 92 0 ATGCCATACC 0.909364 -112 GCAGGACCCAGCGCTACGCCCGAGGTGGCAT 4 119 1 GCGCTACGCC 0.984767 -85 TGTCAGAAAAACGCCACAGACTGTATGCCAC 4 143 0 ACGCCACAAC 0.980666 -61 CAACGCGCCATAAACGCAGGCTCAT 5 5 1 GCGCCATAAC 0.956718 -144 CTCTCTTGAGGCGCTCTAACCGACTGCGTCC 5 98 1 GCGCTCTACC 0.927396 -51 ACCTGCCCGTACACCACACCCCTGGACGTAA 7 49 0 ACACCACACC 0.972322 -113 CTACTGGGCTACGACACGCCCACCGGCCTTA 7 79 0 ACGACACGCC 0.941375 -83 TCGAAGGATCACGCGATGACCGCCCACTACT 7 105 0 ACGCGATGCC 0.986748 -57 CCGAAGGATCACGCGAGGAACCTTCACTCGT 8 19 1 ACGCGAGGAC 0.850399 -59 CTTCACTCGTACACCACGTCCCTGGCCTTGG 8 40 1 ACACCACGCC 0.979812 -38 ******** ** Masking position 4 Map Score: 16.1349 Number of sites scoring better than the average of aligned sites = 2727 Number in coding regions = 2274 Number in noncoding regions = 453 Number of orfs with sites within 600 bp upstream = 173 Fraction of orfs with sites within 600 bp upstream = 0.0277867 Motif number 3 CGTATCAGTTGACCCAGGTGCAGAGGCTAGAGT 2 192 0 GCCCAGGCAG 0.973438 -109 GCATTGTCACGGCCAAAGCACCGTATCAGTTGA 2 213 0 GCCAAAGCCG 0.961892 -88 TTGCCACCAGGGCGAAGGAAGAAATGACTTCGC 2 255 1 GCGAAGGGAA 0.846328 -46 CACCTTTCCAGATACGGGAGGCGAAGTCATTTC 2 275 0 GTACGGGGCG 0.800259 -26 AACGTCAAAAGGAGAGATCAG 3 4 1 GCAAAAGGAG 0.975507 -18 TGATATTTATAGCAAAAGTGGCGAACCACCCTT 4 25 0 ACAAAAGGCG 0.755866 -179 CCAGCGCTACGCCCGAGGTGGCATACAGTCTGT 4 126 1 GCCGAGGGCA 0.9463 -78 AACCGACTGCGTCCAAAGTGGAGGATCGAAAAG 5 115 1 GCCAAAGGAG 0.990859 -34 CTACCTCACTGACCCAGGAGGAGAGTTACGTCC 7 24 1 GCCCAGGGAG 0.99417 -138 GGAGAGTTACGTCCAGGGGTGTGGTGTACGGGC 7 43 1 GCCAGGGGTG 0.986325 -119 TCCTGGCCAAGGCCAGGGACGTGGTGTACGAGT 8 44 0 GCCAGGGGTG 0.986325 -34 CCTGGCCTTGGCCAGGAGGAGAGCAATC 8 60 1 GCAGGAGGAG 0.941231 -18 * ****** *** Masking position 8 Map Score: 12.4306 Number of sites scoring better than the average of aligned sites = 1231 Number in coding regions = 1169 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 4 ACCGACTTCCCGGTCACGCTAAGAATGA 1 9 0 CGGTCACGCT 0.980704 -106 ACCGGGAAGTCGGTCACGCTACCTCTTCTG 1 25 1 CGGTCACGCT 0.980704 -90 AAGGGAGTGACAGACAGGCTTCAGAAGAGG 1 46 0 CAGACAGGCT 0.940333 -69 TCCGTTTAAACAGTCTCGTTAAACAGAATG 1 86 0 CAGTCTCGTT 0.85419 -29 TATACATCATCAGGGAGGCATAGCGTGCAT 2 28 0 CAGGGAGGCA 0.967274 -273 CCTCCTGGGTCAGTGAGGTAGTCGGCAAGC 7 15 0 CAGTGAGGTA 0.939138 -147 GTGTGGTGTACGGGCAGGTAAGGCCGGTGG 7 61 1 CGGGCAGGTA 0.967444 -101 TGGCCAAGGCCAGGGACGTGGTGTACGAGT 8 44 0 CAGGGACGTG 0.916167 -34 ********** Masking position 3 Map Score: 5.73383 Number of sites scoring better than the average of aligned sites = 840 Number in coding regions = 785 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 5 AGACAGGCTTCAGAAGAGGTAGCGTGACCGAC 1 33 0 CGAAGAGGAG 0.980014 -82 GAATGATACACTGCGAAGGGAGTGACAGACAG 1 59 0 CGCGAAGGAG 0.921272 -56 GTGCATCGTCCTTTAGAGGTAGA 2 2 0 CTTAGAGGAG 0.956888 -299 TACACCTTTCCAGATACGGGAGGCGAAGTCAT 2 278 0 CGATACGGAG 0.879594 -23 GGCGAACCACCCTTAATGGACGAATACT 4 7 0 CTTAATGGCG 0.838858 -197 TGGATATGGCATGTAAAGGCAGGACCCAGCGC 4 101 1 AGTAAAGGAG 0.895648 -103 AACGACTCCACAGTTGAGGAAGGAACC 6 34 1 CGTTGAGGAG 0.985967 -17 GGTGTACGGGCAGGTAAGGCCGGTGGGCGTGT 7 65 1 CGGTAAGGCG 0.942725 -97 TGTCGTAGCCCAGTAGTGGGCGGTCATCGCGT 7 94 1 CGTAGTGGCG 0.971458 -68 * ******* ** Masking position 8 Map Score: 3.44811 Number of sites scoring better than the average of aligned sites = 925 Number in coding regions = 862 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 6 GGAGGCATAGCGTGCATCGTCCTTTAGAGG 2 15 0 CGTGCATCGT 0.899957 -286 GCAATCTTTACGAGCATTGTCACGGCCAAA 2 229 0 CGAGCATTGT 0.652086 -72 GTCCATTAAGGGTGGTTCGCCACTTTTGCT 4 18 1 GGTGGTTCGC 0.872248 -186 TGCCACCTCGGGCGTAGCGCTGGGTCCTGC 4 119 0 GGCGTAGCGC 0.979134 -85 GGCGCATCGTGGCGCAGCGCATGAGCCTGC 5 26 0 GGCGCAGCGC 0.99285 -123 GAAATGCATCGGCGCATCGTGGCGCAGCGC 5 36 0 GGCGCATCGT 0.990056 -113 CGTCCAAAGTGGAGGATCGAAAAGATGATA 5 124 1 GGAGGATCGA 0.939339 -25 CACTGACCCAGGAGGAGAGTTACGTCCAGG 7 30 1 GGAGGAGAGT 0.930511 -132 AAGGCCGGTGGGCGTGTCGTAGCCCAGTAG 7 80 1 GGCGTGTCGT 0.887134 -82 GCCTTGGCCAGGAGGAGAGCAATC 8 64 1 GGAGGAGAGC 0.945175 -14 ********** Masking position 4 Map Score: 8.66537 Number of sites scoring better than the average of aligned sites = 1941 Number in coding regions = 1858 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 7 TGCTCGTAAAGATTGCCACCAGGGCGAAGG 2 243 1 GATTGCCACC 0.983508 -58 GCCACAGACTGTATGCCACCTCGGGCGTAG 4 132 0 GTATGCCACC 0.927447 -72 CTCGGCTTGCCGACTACCTCACTG 7 5 1 GCTTGCCGAC 0.963983 -157 AGGATCACGCGATGACCGCCCACTACTGGG 7 102 0 GATGACCGCC 0.966031 -60 TATGCGAAAGGATTCCCGCC 9 19 1 GATTCCCGCC 0.98958 -10 ********** Masking position 6 Map Score: 1.12211 Number of sites scoring better than the average of aligned sites = 823 Number in coding regions = 778 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 8 AGCGTGCATCGTCCTTTAGAGGTAGA 2 7 0 GTCCTTTAGA 0.960573 -294 CCTGGTGGCAATCTTTACGAGCATTGTCAC 2 236 0 ATCTTTACGA 0.879711 -65 TTTGGACGCAGTCGGTTAGAGCGCCTCAAG 5 102 0 GTCGGTTAGA 0.899076 -47 TTTCCTATCATCTTTTCGATCCTCCACTT 5 130 0 ATCTTTTCGA 0.967367 -19 ACTTTTGCTGGTCGTTTCGAAGGATCACGC 7 122 0 GTCGTTTCGA 0.986321 -40 GGCGGGAATCCTTTCGCATAGTTCGGT 9 12 0 ATCCTTTCGC 0.943714 -17 ********** Masking position 6 Map Score: 1.83691 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 85 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 9 ********** No masking Map Score: 1.08956e-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 ********** No masking Map Score: 1.08956e-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: 1.08956e-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