AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00120_ecoli_reg_100.orf -o00120_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 caiA 30 probable carnitine operon oxidoreductase #2 caiT 300 probable carnitine transporter #3 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #4 mhpA 76 3-(3-hydroxyphenyl)propionate hydroxylase #5 adhC 34 alcohol dehydrogenase class III; formaldehyde dehydrogenase, glutathione-dependent #6 yaiN 166 putative alpha helix chain #7 adhE 300 CoA-linked acetaldehyde dehydrogenase and iron-dependent alcohol dehydrogenase; pyruvate-formate-lyase deactivase #8 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #9 rspA 205 starvation sensing protein #10 gatD 47 galactitol-1-phosphate dehydrogenase #11 gatB 30 galactitol-specific enzyme IIB of phosphotransferase system #12 gatZ 28 putative tagatose 6-phosphate kinase 1 #13 gatY 197 tagatose-bisphosphate aldolase 1 #14 pdxB 98 erythronate-4-phosphate dehyrogenase #15 pepP 25 proline aminopeptidase P II #16 ygfB 161 orf, hypothetical protein #17 yiaY 189 putative oxidoreductase #18 rfe 239 UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase; synthesis of enterobacterial common antigen (ECA) #19 fadB 189 4-enzyme protein: 3-hydroxyacyl-CoA dehydrogenase; 3-hydroxybutyryl-CoA epimerase; delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase; enoyl-CoA hydratase Motif number 1 CTTTCAACCTCTTGATATTTTGGGGGTTAA 1 9 0 TACCGTTTTG 0.955121 -22 TTGTTTCGGGTGAATAGAGGGCGTTTTTTCGTTAATTTT 2 114 0 TATAGTTTTT 0.905133 -187 ACTGATTACGTGATCCAAATCAAATTTTTGCAAAGCTGA 7 58 0 TACCCTTTTT 0.804515 -243 CCTTTTTTTGTGATCACTCCGGCTTTTTTCGATCTTTAT 9 110 1 TACAGTTTTT 0.986913 -96 GTTATCCCCCTTAACAATCAGGAGTTTTT 10 29 1 TACAGTTTTT 0.986911 -19 CCTCGAATAATTTTCATATTGTCGTTTTTGTGATCGTTA 13 108 1 TTCAGTTTTT 0.889196 -90 TTGTATTCATTAAACAATGTGCTTTTTTTAAATTCATAA 17 54 0 TACAGTTTTT 0.986911 -136 CATTGTTTAATGAATACAATGTGCTTTTTATTAGATTAA 17 74 1 TATAGTTTTT 0.905134 -116 AAATCCTCAGTAAGCTGCCCGCCCTTTTTTACACTTTCA 17 151 1 TACTGTTTTT 0.913873 -39 AAACGCCACGTAAACACGTGGCGTTTTTGGCATAAGACA 18 14 0 TACAGTTTTG 0.974404 -226 AGCAGAAGTATAACCACGAAGACCTTTATTCAGAAGGGA 18 185 0 TACAGTTTAT 0.897272 -55 TTTTTACCCTTCTGTTTTTTTGACCTTAAGTC 19 4 1 TACCGTTTTG 0.955121 -186 CTGCCGAGCGTGATCAGATCGGCATTTCTTTAATCTTTT 19 81 1 TACAGTTTCT 0.928292 -109 * * ** * ***** Masking position 15 Map Score: 14.4678 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 89 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 2 ATCGTAAGAATGAGACAGGCCGTAAAGTTTGG 3 29 0 TGAGCAGCCG 0.934152 -76 TTCTTACGATTGCGGCAGGCCGTGTTATTATT 3 51 1 TGCGCAGCCG 0.980498 -54 ATTACCATATTGAGGAAGAGCGAGAG 5 19 1 TGAGAAGGCG 0.905246 -16 AATCACAGTGAGTGTGAGCGCGAGTAAGCTTT 7 180 1 AGTGGAGGCG 0.877235 -121 ATACGAGAGTATAGTCAGTGCGGTGATGATTT 7 231 0 ATAGCAGGCG 0.956311 -70 AGGTAAGTGATTCGGGGGAGCGAACGCAGCCA 8 119 1 TTCGGGGGCG 0.949389 -156 GGGCGCAGAGATCCCCGGGCCGTATGCCCGTT 8 204 0 ATCCCGGCCG 0.77894 -71 GCAGTTTGTGAACGTCAGGGCGCAGAGATCCC 8 221 0 AACGCAGGCG 0.94154 -54 TCCTTGTTAAATGGCAGGTGCG 12 1 0 ATGGAGGGCG 0.881017 -28 CGGCTTCCCTATCGGGAGGCCGTTTTTTTGCC 13 69 1 ATCGGAGCCG 0.962028 -129 ACCCATGGTCTGCGAAGGGGCGACACTATAGC 16 52 1 TGCGAGGGCG 0.961331 -110 TTTTCCTAACATCGCCAGCGCGGCATTAAGAT 18 69 0 ATCGCAGGCG 0.987252 -171 TTTATTCAGAAGGGAAAGTCCGTTCCAAACCC 18 168 0 AGGGAAGCCG 0.910935 -72 **** *** *** Masking position 11 Map Score: 10.8989 Number of sites scoring better than the average of aligned sites = 1810 Number in coding regions = 1728 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 3 GCCCTCTATTCACCCGAAACAAAAATGTGA 2 131 1 CACCCGAAAC 0.871325 -170 GGGAAGGCCGCCCCGGATAGCGGGCGGCAG 6 17 0 CCCCGGATAG 0.965314 -150 CGACCACATTCACCGGATAAATTTTATTCT 6 83 1 CACCGGATAA 0.682629 -84 CAATGCATACCCCCCTATAGTATATAACAC 6 116 0 CCCCCTATAG 0.9104 -51 TATAGAATACCCCCCTATAGTATATTGC 6 149 1 CCCCCTATAG 0.9104 -18 AATGCTCTCCTGATAATGTTAAACTT 7 285 0 CTCCTGATAA 0.856401 -16 TGCGTTCGCTCCCCCGAATCACTTACCTGA 8 117 0 CCCCCGAATC 0.888669 -158 AAAAACTCCTGATTGTTAAGGGGGA 10 33 0 CTCCTGATTG 0.912171 -15 AAAAAACGGCCTCCCGATAGGGAAGCCGTA 13 67 0 CTCCCGATAG 0.980836 -131 AACACACTCCTGAAAGTGTAAAAAAG 17 174 0 CTCCTGAAAG 0.938925 -16 GTCAGTCTCCTGAATCCGCAAGGTGA 19 174 0 CTCCTGAATC 0.759368 -16 ********** Masking position 7 Map Score: 8.30783 Number of sites scoring better than the average of aligned sites = 295 Number in coding regions = 251 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 4 TTTGTTTTATTTTTGTTAACATTTAATATA 2 237 0 TTTTGTTAAC 0.858383 -64 TTGCGTTCCCGTTTGTTTTATTTTTGTTAA 2 248 0 GTTTGTTTTA 0.602175 -53 CGTTCCATCTTTTGTTCGCCAAACTTTAC 3 10 1 TTTTGTTCGC 0.824544 -95 GCGCAACTTATTTTGTTAAAAACATGTAA 4 10 0 TTTTGTTAAA 0.682189 -67 CGCAACGACATTTTGTCCGAGTCGTGAGGT 4 51 1 TTTTGTCCGA 0.578545 -26 GATATATGCAGTTTGTGAACGTCAGGGCGC 8 230 0 GTTTGTGAAC 0.843592 -45 ATAGAATACCTTTTGTCAGCTGACACTTCC 9 43 0 TTTTGTCAGC 0.88802 -163 CTATTTCATCTTTTGTCAACCATTCACAGC 9 69 1 TTTTGTCAAC 0.833322 -137 ATACGCCTTTTTTTGTGATCACTCCGGCTT 9 105 1 TTTTGTGATC 0.922533 -101 ATATTGTCGTTTTTGTGATCGTTATCTCGA 13 123 1 TTTTGTGATC 0.922533 -75 ATCCTGTCGTTTGTTTTCGATTTCAAAA 13 180 0 GTTTGTTTTC 0.810399 -18 GTTTGTGTTACCTGTATGAG 14 89 0 GTTTGTGTTA 0.67011 -10 TTCTTTAATCTTTTGTTTGCATATTTTTAA 19 106 1 TTTTGTTTGC 0.874746 -84 GAAGTGTGTATTTTGTGTTAAAAATATGCA 19 123 0 TTTTGTGTTA 0.753905 -67 ********** Masking position 6 Map Score: 7.8128 Number of sites scoring better than the average of aligned sites = 673 Number in coding regions = 516 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 5 CTTCCCTGCCGATTAGCCCCCCCCCCTTTCC 6 41 1 GTTAGCCCCC 0.979923 -126 ATATGTCAATGCATACCCCCCTATAGTATAT 6 121 0 GATACCCCCC 0.993721 -46 TTGACATATAGAATACCCCCCTATAGTATAT 6 143 1 GATACCCCCC 0.993721 -24 GAGTAATCTTGCTTACGCCACCTGGAAGTGA 7 107 1 GTTACGCCAC 0.943095 -194 GGCGCATTGCGCTTACCCGGCTTACAGAACA 8 17 0 GTTACCCGGC 0.946612 -258 AAATAAACGGGCATACGGCCCGGGGATCTCT 8 199 1 GATACGGCCC 0.917029 -76 CTGAGGGGGAGGTTATCCCCCTTAACAATCA 10 18 1 GTTATCCCCC 0.970528 -30 TGCCACGTATGTTTACACCGCATCCGGCATA 13 18 1 GTTACACCGC 0.943095 -180 * ********* Masking position 5 Map Score: 6.07302 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 94 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 CGCCCCGGATAGCGGGCGGCAGAAGGAA 6 9 0 AGCGGGCGGC 0.918363 -158 CGCCCGCTATCCGGGGCGGCCTTCCCTGCC 6 21 1 CCGGGGCGGC 0.989215 -146 AAGAGGAAAGGGGGGGGGGCTAATCGGCAG 6 46 0 GGGGGGGGGC 0.947049 -121 ATGCGTCACTTCCAGGTGGCGTAAGCAAGA 7 113 0 TCCAGGTGGC 0.849231 -188 TCAAGTTGCATCAAGGCGGCAAGTGAGCGA 8 71 1 TCAAGGCGGC 0.953241 -204 GGTAAGTGATTCGGGGGAGCGAACGCAGCC 8 120 1 TCGGGGGAGC 0.850694 -155 GCAGCCAAGGCAGAGGCGGCTTGAAGGATG 8 144 1 CAGAGGCGGC 0.843773 -131 TCAATCAGCAGGAAGGTGGC 16 1 0 GGAAGGTGGC 0.853482 -161 GGTCTAAAGACGAAGGCAGCGCAGTCAATC 16 25 0 CGAAGGCAGC 0.897399 -137 TCTCTTCTCATCAGGGTAGCTATAGTGTCG 16 72 0 TCAGGGTAGC 0.803907 -90 TGTAAAAAAGGGCGGGCAGCTTACTGAGGA 17 154 0 GGCGGGCAGC 0.935071 -36 CCTAACATCGCCAGCGCGGCATTAAGATTA 18 67 0 CCAGCGCGGC 0.881897 -173 ********** Masking position 10 Map Score: 8.70606 Number of sites scoring better than the average of aligned sites = 2626 Number in coding regions = 2488 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 7 GGCGGCCTTCCCTGCCGATTAGCCCCCCCC 6 35 1 CCTGCCGATT 0.978487 -132 ATCTCTGCGCCCTGACGTTCACAAACTGCA 8 224 1 CCTGACGTTC 0.83104 -51 CGCACCTGCCATTTAACAAGGAAA 12 5 1 CCTGCCATTT 0.908896 -24 ATCCTGTCGTTTGTTTTCGATT 13 186 0 CCTGTCGTTT 0.936755 -12 AACACTCTCCTTACGTTTTTTGTTT 15 8 0 CCTTACGTTT 0.866124 -18 GCCACCTTCCTGCTGATTGACTGCGCTG 16 9 1 CCTGCTGATT 0.918478 -153 CAGTAAGCTGCCCGCCCTTTTTTACACTTT 17 158 1 CCCGCCCTTT 0.735769 -32 CACGTAAACACGTGGCGTTTTTGGCATAAG 18 17 0 CGTGGCGTTT 0.905904 -223 CACGTGTTTACGTGGCGTTTTGCTTTTATA 18 33 1 CGTGGCGTTT 0.905904 -207 ACGGACTTTCCCTTCTGAATAAAGGTCTTC 18 177 1 CCTTCTGAAT 0.261776 -63 TTTTTACCCTTCTGTTTTTTTGACCTT 19 8 1 CCTTCTGTTT 0.875102 -182 ********** Masking position 1 Map Score: 4.13586 Number of sites scoring better than the average of aligned sites = 1276 Number in coding regions = 1179 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 8 AAAAGAAATTTTCAATATTGTTTTATGGATC 2 18 1 TTAATATTGT 0.775948 -283 CGTTCCATCTTTTGTTCGCCAAA 3 3 1 TTCATCTTTT 0.967391 -102 TTACATGTTTTTAACAAAATA 4 1 1 TTCATGTTTT 0.917127 -76 AGGTATTCTATTTCATCTTTTGTCAACCATT 9 62 1 TTCATCTTTT 0.967391 -144 CTCGAATAATTTTCATATTGTCGTTTTTGTG 13 109 1 TTCATATTGT 0.926983 -89 TCGGCATTTCTTTAATCTTTTGTTTGCATAT 19 99 1 TTAATCTTTT 0.890022 -91 AATCTTTTGTTTGCATATTTTTAACACAAAA 19 112 1 TTCATATTTT 0.949664 -78 ** ******** Masking position 5 Map Score: 2.6328 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 43 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 9 TAGCCATTAACGCGTCCACGAGGTTAATAA 2 203 1 CGCGTCCACG 0.976325 -98 TCTAATGCGTCACTTCCAGGTGGCGTAAGC 7 117 0 CACTTCCAGG 0.97745 -184 GGGGAGCGAACGCAGCCAAGGCAGAGGCGG 8 133 1 CGCAGCCAAG 0.914154 -142 ATAGCACTGCCACGTATGTTTACA 13 5 1 CACTGCCACG 0.978764 -193 GCCATAATCTCGCGGCCAGGCATACTTGCG 14 36 0 CGCGGCCAGG 0.984458 -63 CCCTTTTTTACACTTTCAGGAGTGTGTT 17 172 1 CACTTTCAGG 0.870227 -18 ********** Masking position 8 Map Score: 2.41359 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 337 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 10 TTCAGTACCTCACGACTCGGAC 4 65 0 TCAGTACTCA 0.811927 -12 TTAAACTCTTTTAGTAAATCACAGTGAGTGT 7 164 1 TTAGTAATCA 0.9612 -137 TTTCATAGGTTAAGCAAATCATCACCGCACT 7 216 1 TAAGCAATCA 0.890826 -85 TTAAACTTTTTTAGTAAATCATCTGCTCGAA 7 262 0 TTAGTAATCA 0.9612 -39 TACTTGTATGGTAGTAGCTCAGTTGCGTAGA 9 148 1 GTAGTACTCA 0.888192 -58 GCCCAAAGTGGTAGCATATCATGAATATTCC 16 126 1 GTAGCAATCA 0.957006 -36 TGTTATGCAATTTGCATATCAAATGGTTAAT 18 120 1 TTTGCAATCA 0.875689 -120 TCTCCGCATCTTAGCACATCGTTCATCCAGA 19 41 1 TTAGCAATCG 0.912592 -149 ****** **** Masking position 6 Map Score: 1.71407 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 49 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 TGATTATTAATCAAAATTAACGAAAAAACG 2 102 1 TCAAAATTAA 0.920236 -199 AAACGGGAACGCAAAATAAATATTCGTTTT 2 264 1 GCAAAATAAA 0.887659 -37 ACTCTTCCTGTCAAAATATAAGAAACGACA 3 82 0 TCAAAATATA 0.920519 -23 GTTTTCGATTTCAAAATATAATGAAATTAT 13 166 0 TCAAAATATA 0.920519 -32 TAATTAAGTTTTAAAATAAATTAATACAAA 17 20 1 TTAAAATAAA 0.769586 -170 TTATTGATTATCAAAATTAATCTAATAAAA 17 99 0 TCAAAATTAA 0.920236 -91 ********** Masking position 5 Map Score: 0.974673 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 25 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 12 ATGCTGAAAGGTGTCAGCTTTGCAAAAATT 7 45 1 GTGTCAGCTT 0.949014 -256 ACCCAGAAGTGAGTAATCTTGCTTACGCCA 7 97 1 GAGTAATCTT 0.907623 -204 GTGTGAGCGCGAGTAAGCTTTTGATTTTCA 7 191 1 GAGTAAGCTT 0.972984 -110 TCACTTACCTGAGTAAGCTCATCGGGATTC 8 99 0 GAGTAAGCTC 0.941887 -176 ATAAGAGGAAGTGTCAGCTGACAAAAGGTA 9 37 1 GTGTCAGCTG 0.939139 -169 TGAAAATCCTCAGTAAGCTGCCCGCCCTTT 17 148 1 CAGTAAGCTG 0.926426 -42 GCTTTTATATCTGTAATCTTAATGCCGCGC 18 54 1 CTGTAATCTT 0.760998 -186 ********** Masking position 6 Map Score: 2.7493 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 43 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 13 ********** No masking Map Score: -1.57497e-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: -1.57497e-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: -1.57497e-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