AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00280_ecoli_reg_100.orf -o00280_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 hlpA 121 histone-like protein, located in outer membrane or nucleoid #2 lnt 24 apolipoprotein N-acyltransferase, copper homeostasis protein, inner membrane #3 ybeX 89 putative transport protein #4 ybeZ 113 putative ATP-binding protein in pho regulon #5 htrB 224 heat shock protein #6 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #7 ydbO 284 orf, hypothetical protein #8 ydcH 72 orf, hypothetical protein #9 rimL 62 acetylation of N-terminal serine of 30S ribosomal subunit protein L7; acetyl transferase #10 msbB 119 suppressor of htrB, heat shock protein #11 wcaA 34 putative regulator #12 BIME92 24 BIME #13 wza 300 putative polysaccharide export protein #14 sbm 203 methylmalonyl-CoA mutase (MCM) #15 ilvM 300 acetolactate synthase II, valine insensitive, small subunit #16 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 CAATATAAGATCGCCGGGCCACGCAAAGAACTGCACCCTCCGG 1 62 1 TCCCGGCAAG 0.988065 -60 TTTGCCAGGCATTTGACTGGCAGACGTCCCCGCC 3 2 1 TTCCGGCAGA 0.981622 -88 CTGGGCGAAATTGCCGCGCTTGTAAATAACAAATAATTTTTAA 5 109 0 TTCCCGCAAA 0.951093 -116 CGCATTGCGCTTACCCGGCTTACAGAACAAAAAGA 6 3 0 TTCCGGCGAA 0.980294 -272 TAAGCGCAATGCGCCCGGCAATCTATACACAAAATCATTCAAG 6 33 1 GCCCGGCAAA 0.991776 -242 GGCGCAGAGATCCCCGGGCCGTATGCCCGTTTATTTCTGGCGA 6 192 0 TCCCGGCGGA 0.969149 -83 GTTAAAAAAGCCGCCTGGCTGGCGGCTTAGGAAAGT 9 4 0 CCCCGGCGAA 0.952523 -59 CTTATCTCCAGTCAATCCATGCAGTTGTTAAAAAAGC 9 36 0 TCCCGTCAAG 0.813984 -27 GCGGCGCAACTTGCCCCGCACCAAATAAAAAAAGCCGGTACTG 10 40 0 TTCCCGCAAA 0.951093 -80 AGGTTGTTCTCCCGGCTTATGAGCTGGTTTGCTT 11 5 0 TCCCGGCAGT 0.967446 -30 ACACGCTACCGCCCCTGGCTTTTTAGCTACCAATACACTGATT 13 91 0 GCCCGGCAAA 0.991775 -210 ATTGATTTCATCCGCAGGCTATTGACAGAATAATTCAGACTGG 13 150 0 TCGCGGCAAA 0.977781 -151 CCATGCACATTTACCTTGCAGTTAATTGAATAAAAATTTAACT 13 211 0 TTCCTGCAAA 0.926321 -90 ATGCATTTTTTTTGCTGGCGACAAACCCACGTAAAAAGCTCAC 14 124 1 TTGCGGCAAA 0.943495 -80 TGAATTACTGGCGCCAGGCGGCACCAGCGGCCAGACGTTCTCA 15 248 0 GCCCGGCCGA 0.954865 -53 TACGACCAGATCACCTTGCGGATTCAGGAGACTGAC 16 164 1 TCCCTGCCAT 0.662603 -26 ** ** *** * * * Masking position 9 Map Score: 18.5966 Number of sites scoring better than the average of aligned sites = 949 Number in coding regions = 880 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 2 CGTCGTTAATCACCAACGGCGGGGACGTCT 3 32 0 CACCAACGGC 0.978505 -58 CGTTGGTGATTAACGACGGCGTTTTGATTA 3 44 1 TAACGACGGC 0.937185 -46 GCAGCCAAGGCAGAGGCGGCTTGAAGGATG 6 144 1 CAGAGGCGGC 0.94111 -131 CCCTGACGTTCACAAACTGCATATATCTGA 6 233 1 CACAAACTGC 0.912662 -42 GCGATCTGTATAGCAACTGCGGAAAACATT 7 102 1 TAGCAACTGC 0.901554 -183 GCGGCTTTTTTAACAACTGCATGGATTGAC 9 33 1 TAACAACTGC 0.853459 -30 ACTGACTGCGTACCGGCTGCGAATGGATGT 10 14 0 TACCGGCTGC 0.970543 -106 AAAAAGCCGGTACTGACTGCGTACCGGCTG 10 25 0 TACTGACTGC 0.760544 -95 CCTTTCTCATCAACGACTGCATGCTGAGAG 13 42 1 CAACGACTGC 0.937185 -259 ATAGACAAATCTCAGGCGGCAAAAAACGAC 14 88 1 CTCAGGCGGC 0.874181 -116 AAAGACCAGGTTGAAGCGGCACTCGACACC 15 168 1 TTGAAGCGGC 0.582935 -133 CGCCAGGCGGCACCAGCGGCCAGACGTTCT 15 250 0 CACCAGCGGC 0.98139 -51 ********** Masking position 7 Map Score: 11.2727 Number of sites scoring better than the average of aligned sites = 2986 Number in coding regions = 2895 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 3 TGCACCCTCCGGTGCAAATGGGATGGTAAG 1 93 1 GGTGCAAATG 0.894451 -29 ACAGGAAAAAGGCGCAAGCATTGCAATAAA 4 64 0 GGCGCAAGCA 0.845868 -50 TTTTTCCTGTGGCGTGAATAATTTCCTTAT 4 84 1 GGCGTGAATA 0.735382 -30 TAATTTTTAATGCGCAAATGTAGCGTAAAA 5 89 0 TGCGCAAATG 0.864659 -136 CTGAAGACTGGGCGAAATTGCCGCGCTTGT 5 129 0 GGCGAAATTG 0.885992 -96 TTTGGTTGCGGGCGAAAAAATGCGACAATA 5 167 1 GGCGAAAAAA 0.67566 -58 GGCGAAAAAATGCGACAATACATACAATTG 5 177 1 TGCGACAATA 0.566787 -48 GTGATTCGGGGGAGCGAACGCAGCCAAGGC 6 125 1 GGAGCGAACG 0.706119 -150 GGGGCGGTGCGAATGCAGGCGTCG 12 10 0 GGTGCGAATG 0.841462 -15 AAATGTGCATGGCGACATTGCTATTAATAG 13 242 1 GGCGACATTG 0.829566 -59 GCTCACCGTAGGCGCAAATACCCTCATTTT 14 161 1 GGCGCAAATA 0.978383 -43 TGCGTTTTACGGAGCAAATA 14 194 1 GGAGCAAATA 0.909019 -10 GGTGCCGCCTGGCGCCAGTAATTCAGAAAT 15 266 1 GGCGCCAGTA 0.915823 -35 CAGAAATGTTGGAGAAATTATC 15 289 1 GGAGAAATTA 0.585332 -12 ********** Masking position 7 Map Score: 7.77521 Number of sites scoring better than the average of aligned sites = 2021 Number in coding regions = 1870 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 4 CGCAAGCATTGCAATAAAGATGGGGATAAAG 4 51 0 GCAAAAAGAT 0.90377 -63 CTACATTTGCGCATTAAAAATTATTTGTTAT 5 96 1 GCATAAAAAT 0.928288 -129 TTTTTCGCCCGCAACCAAAATTTGTGGCTGA 5 155 0 GCAACAAAAT 0.982483 -70 TTAACTATTAGCAACAGAAATGTGAAACATC 7 23 0 GCAAAGAAAT 0.90377 -262 CACAGTTCAAACATACAAAATTTGTGATTTT 7 179 1 ACATCAAAAT 0.69631 -106 TTTGTCGCCAGCAAAAAAAATGCATTCAGAC 14 118 0 GCAAAAAAAT 0.972497 -86 TCCGTAAAACGCAATCAAAATGAGGGTATTT 14 176 0 GCAACAAAAT 0.982483 -28 TTAAAAATATGCAAACAAAAGATTAAAGAAA 16 105 0 GCAACAAAAG 0.937094 -85 **** ****** Masking position 8 Map Score: 5.81388 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 68 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 5 TAAAGAGAGAAAAAACAAGGCCCACCGGAACGGC 4 22 0 AAAAAAAGCA 0.886504 -92 ATGGGAAAGTAAAAATCCGCGGCATGATATAGCA 5 30 1 AAAAACCGCA 0.947766 -195 GAATAGGTTGAAAAACAGGATTGAT 5 210 1 AAAAAAGGGA 0.770565 -15 AATGATTTATAAAAATAGGGTGCGAAATCCGTCA 7 147 1 AAAAAAGGCG 0.84315 -138 TGAATTAATTAAAAACACGAATCACATTGTTTTA 7 233 0 AAAAAACGCA 0.865332 -52 GCAGTTGTTAAAAAAGCCGCCTGGCTGGCGGCTT 9 19 0 AAAAACCGGG 0.966713 -44 CACCAAATAAAAAAAGCCGGTACTGACTGCGTAC 10 31 0 AAAAACCGCT 0.869153 -89 CGGATAAGGCAAAAATCAATCTGGTGATAGTGTA 10 83 0 AAAAACAAGG 0.682429 -37 TTGGTAGCTAAAAAGCCAGGGGCGGTAGCGTGTC 13 101 1 AAAAGCAGCG 0.837388 -200 TGGATGCCTGAAAGACCAGTCTGAATTATTCTGT 13 135 1 AAAGACAGGA 0.864903 -166 CAAGGAATACAAAAAGAAGTGAGGACAACGCCTG 14 40 0 AAAAAAAGGG 0.925935 -164 ATCGTTCCTGAAAAAACAGTTGCTGCCATTGTCG 15 51 0 AAAAACAGCT 0.8898 -250 CATCACCCGGAAAGACCAGGTTGAAGCGGCACTC 15 158 1 AAAGACAGGA 0.864903 -143 CTTAAGGTCAAAAAAACAGAAGGGTAAAAA 16 7 0 AAAAACAGGG 0.972453 -183 ***** *** ** Masking position 3 Map Score: 9.24681 Number of sites scoring better than the average of aligned sites = 706 Number in coding regions = 551 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 6 TTCTCAGGCCTGCCGTTCCGGTGGGCCTTGT 4 11 1 TGCCGTTCCG 0.894669 -103 GGTGTACGGTTCCTGCGAGATGGGA 5 5 1 TACGGTTCCG 0.967017 -220 TACTCAGGTAAGTGATTCGGGGGAGCGAACG 6 114 1 AGTGATTCGG 0.796831 -161 TATGACTCCTGTTTCACGTCT 6 264 0 TATGACTCCG 0.912363 -11 CTTTGCTTTTTATGATTCGCGATTTAACTAT 7 46 0 TATGATTCGG 0.962487 -239 CATAAAACAATGTGATTCGTGTTTTTAATTA 7 231 1 TGTGATTCGG 0.965275 -54 TCATCACCTTTACGATTCCAGTTTTCGTGAA 7 263 0 TACGATTCCG 0.972636 -22 AGGGAGTGCGTATGTTTCCAGAATACCGAGA 8 15 1 TATGTTTCCG 0.912006 -58 TATTTTGTGATGTGATTCAAGGAATACAAAA 14 60 0 TGTGATTCAG 0.875239 -144 GGTTTCGCTGTATCGTTCCTGAAAAAACAGT 15 65 0 TATCGTTCCG 0.916744 -236 ********* * Masking position 7 Map Score: 6.31381 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 194 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 7 TCTGCCAGTCAAATGCCTGGCAAA 3 5 0 AAATGCCTGG 0.699963 -85 CCAACGGCGGGGACGTCTGCCAGTCAAATG 3 20 0 GGACGTCTGC 0.955045 -70 AGGCCCACCGGAACGGCAGGCCTGAGAA 4 9 0 GAACGGCAGG 0.521427 -105 TACGGCCCGGGGATCTCTGCGCCCTGACGT 6 212 1 GGATCTCTGC 0.296064 -63 TGCAGTTTGTGAACGTCAGGGCGCAGAGAT 6 224 0 GAACGTCAGG 0.74873 -51 TTGTTAAAAAAGCCGCCTGGCTGGCGGCTT 9 19 0 AGCCGCCTGG 0.884232 -44 CGACGCCTGCATTCGCACCG 12 1 1 CGACGCCTGC 0.973105 -24 CCTTTCTCATCAACGACTGCATGCTGAGAG 13 42 1 CAACGACTGC 0.659953 -259 TAGCGTGTCTGGATGCCTGAAAGACCAGTC 13 126 1 GGATGCCTGA 0.907432 -175 TCCATCAAATAATGCCTGATAGCACATAT 14 10 1 TAATGCCTGA 0.637361 -194 GAAGTGAGGACAACGCCTGATATGTGCTAT 14 29 0 CAACGCCTGA 0.938937 -175 CGTCGTTTTTTGCCGCCTGAGATTTGTCTA 14 89 0 TGCCGCCTGA 0.851945 -115 CGGCAAAAAACGACGTCTGAATGCATTTTT 14 104 1 CGACGTCTGA 0.917829 -100 ACGAACTTGAGAACGTCTGGCCGCTGGTGC 15 241 1 GAACGTCTGG 0.944962 -60 TGGCCGCTGGTGCCGCCTGGCGCCAGTAAT 15 258 1 TGCCGCCTGG 0.916279 -43 ********** Masking position 7 Map Score: 9.88047 Number of sites scoring better than the average of aligned sites = 3236 Number in coding regions = 3047 Number in noncoding regions = 189 Number of orfs with sites within 600 bp upstream = 170 Fraction of orfs with sites within 600 bp upstream = 0.0273049 Motif number 8 CTTTGCGTGGCCCGGCGATCTTATATTGATC 1 59 0 CCCGGGATCT 0.993129 -63 CATACAATTGCCCGAATAGGTTGAAAAACAG 5 197 1 CCCGATAGGT 0.657735 -28 GCGCAATGCGCCCGGCAATCTATACACAAAA 6 36 1 CCCGGAATCT 0.934077 -239 GTGAGCGAATCCCGATGAGCTTACTCAGGTA 6 93 1 CCCGAGAGCT 0.977868 -182 GGGCATACGGCCCGGGGATCTCTGCGCCCTG 6 207 1 CCCGGGATCT 0.993129 -68 AGCTAAAAAGCCAGGGGCGGTAGCGTGTCTG 13 106 1 CCAGGGCGGT 0.841766 -195 TATTTGCGCCTACGGTGAGCTTTTTACGTGG 14 150 0 TACGGGAGCT 0.702823 -54 CCTGGTCTTTCCGGGTGATGTGTTGGCCATG 15 147 0 CCGGGGATGT 0.924969 -154 GCACCAGCGGCCAGACGTTCTCAAGTTCGTC 15 240 0 CCAGAGTTCT 0.678144 -61 CCTGAATCCGCAAGGTGATCTGGTCGTACCA 16 161 0 CAAGGGATCT 0.891172 -29 ***** ***** Masking position 11 Map Score: 5.3331 Number of sites scoring better than the average of aligned sites = 752 Number in coding regions = 697 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 9 CGGTGCAAATGGGATGGTAAGGAGTTTATT 1 102 1 GGGATGGTAA 0.97357 -20 CCTGCGAGATGGGAAAGTAAAAATCCGCGG 5 22 1 GGGAAAGTAA 0.885285 -203 GTAAAATGTGTGGATGTTAATTATCGATAA 5 65 0 TGGATGTTAA 0.950978 -160 TTTTTCAGACGGGATATTAAATCTCGGTAT 8 37 0 GGGATATTAA 0.892718 -36 CGGCTGCGAATGGATGTTAA 10 1 0 TGGATGTTAA 0.950978 -119 CTTATATTCGGAAGTTAATTTCCGTAAT 13 9 1 CGGAAGTTAA 0.89732 -292 TTCAATTAACTGCAAGGTAAATGTGCATGG 13 224 1 TGCAAGGTAA 0.775718 -77 ********** Masking position 4 Map Score: 2.11179 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 163 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 10 CTTTGCGTGGCCCGGCGATCTTATATTGAT 1 60 0 CCCGGCGATC 0.988477 -62 GTTCTGTAAGCCGGGTAAGCGCAATGCGCC 6 18 1 CCGGGTAAGC 0.956424 -257 GCGCAATGCGCCCGGCAATCTATACACAAA 6 36 1 CCCGGCAATC 0.951504 -239 GTGAGCGAATCCCGATGAGCTTACTCAGGT 6 93 1 CCCGATGAGC 0.914644 -182 GGTAAGTGATTCGGGGGAGCGAACGCAGCC 6 120 1 TCGGGGGAGC 0.920431 -155 GGGCATACGGCCCGGGGATCTCTGCGCCCT 6 207 1 CCCGGGGATC 0.988477 -68 AGCTCATAAGCCGGGAGAACAACCT 11 20 1 CCGGGAGAAC 0.905292 -15 CCTGGTCTTTCCGGGTGATGTGTTGGCCAT 15 148 0 CCGGGTGATG 0.929337 -153 ********** Masking position 8 Map Score: 5.40998 Number of sites scoring better than the average of aligned sites = 404 Number in coding regions = 379 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 11 ********** No masking Map Score: -9.07063e-13 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 12 ********** No masking Map Score: -9.07063e-13 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: -9.07063e-13 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