AlignACE version 2.2 July 7, 1998 alignACE -z/skink1/amcguire/genomes/ecoli.fna -a/home/amcguire/alignace/lib/ORF_ecoli.txt -b/home/amcguire/alignace/lib/bimes_ecoli.txt -k0 -l300 -jrpoH.reg -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 155 Input sequences: #1 dnaK 300 bp dnaK 638 1-1917 CDS #2 clpP 245 bp clpP 207 1-624 CDS #3 lon 187 bp lon 784 1-2355 CDS #4 htpG 109 bp htpG 624 1-1875 CDS #5 gapA 300 bp gapA 331 1-996 CDS #6 clpB 129 bp clpB 857 1-2574 CDS #7 grpE 122 bp grpE 197 1-594 CDS #8 rpoD 194 bp rpoD 613 1-1842 CDS #9 ftsJ 125 bp ftsJ 209 1-630 CDS #10 hslT 230 bp hslT 137 1-414 CDS #11 hslV 92 bp hslV 176 1-531 CDS #12 mopB 275 bp mopB 97 1-294 CDS Motif number 1 GCAAAAGCACAAAAAATTTTTGCATCTCCCCCTTGATGACGTG 1 130 1 AAATCCCCCT 0.975746 -171 TCTCCCCCTTGATGACGTGGTTTACGACCCCATTTAGTAGTCA 1 154 1 GATTCCCCAT 0.922925 -147 TTGGGCAGTTGAAACCAGACGTTTCGCCCCTATTACAGACTCA 1 229 1 GAAGCCCTAT 0.916995 -72 GTTATGCTTGAAATATGGTGATGCCGTACCCATAACACAGGGA 2 142 1 AAAGACCCAT 0.919774 -104 AGGAAAAATTAAAGGGGAGATAAAATCCCCCCTTTTTGGTTAA 3 33 0 AAAACCCCCT 0.878141 -155 TCTCGGCGTTGAATGTGGGGGAAACATCCCCATATACTGACGT 3 80 1 GAAGCCCCAT 0.994904 -108 CTCTCGCTTGAAATTATTCTCCCTTGTCCCCATCTCTCCCACA 4 34 1 AAATCCCCAT 0.985197 -76 ATTGCCCTTTAAAATTCGGGGCGCCGACCCCATGTGGTCTCAA 5 115 1 AAAGCCCCAT 0.990724 -186 CAATAACCTTGAATAATTGAGGGATGACCTCATTTAATCTCCA 6 66 1 GAATCCTCAT 0.873161 -64 TGCTTCCCTTGAAACCCTGAAACTGATCCCCATAATAAGCGAA 7 52 1 GAATCCCCAT 0.991848 -71 CTTAAGTGCCGAAGAGCGATCGGGAAGCCCCCGACAGCCGCAC 8 19 1 GAAGCCCCCG 0.941219 -176 GTTGGGATTGAAAACGGGTCATTCTACCGCCATCTCCCATATA 9 27 1 AAAGCGCCAT 0.899568 -99 GATAAGGCTTGAAAAGTTCATTTCCAGACCCATTTTTACATCG 10 103 1 GAATACCCAT 0.928873 -128 GTGCTGATCAGAATTTTTTTTCTTTTTCCCCCTTGAAGGGGCG 12 146 1 GAATCCCCCT 0.986584 -130 TTCCCCCTTGAAGGGGCGAAGCCTCATCCCCATTTCTCTGGTC 12 171 1 AAGGCCCCAT 0.934681 -105 *** * ****** Masking position 2 Map Score: 21.2784 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 108 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 2 GTCTTGTCCTGCCATATCGCGAAATTTCTGCGCAA 1 99 1 GAATCGCGAT 0.815691 -202 GCGGTTGACTACTAAATGGGGTCGTAAACCACGTC 1 167 0 AAATGGGGGT 0.969399 -134 CTGCAAAAAAATGAAATTGGGCAGTTGAAACCAGA 1 213 1 AAATTGGGGT 0.814868 -88 TTTACGCAGCATAACGCGCTAAATTCGCACAA 2 8 1 AAAACGCGAA 0.759342 -238 AAAAAAGCCCACCACCTGGCGGTGACGGGCCTTTG 2 40 0 AACTGGCGGA 0.945327 -206 CATGTACGTCAGTATATGGGGATGTTTCCCCCACA 3 93 0 AAATGGGGGT 0.9694 -95 CGTACATGTTAATAGATGGCGTGAAGCACAGTCGT 3 120 1 AAATGGCGAA 0.976224 -68 GTGTCATCTGATTACCTGGCGGAAATTAAACTAAG 3 153 1 AACTGGCGAA 0.905505 -35 CAGGATGTGGGAGAGATGGGGACAAGGGAGAATAA 4 47 0 GAATGGGGAA 0.962386 -63 TGGGCTTGAGACCACATGGGGTCGGCGCCCCGAAT 5 128 0 AAATGGGGGG 0.96332 -173 GATGAATGCGAAAAAAACGCGGAGAAATTC 7 103 1 AAAACGCGGA 0.850596 -20 TAACGGCTGAAGGACATCGGGTCAATCGCCCAACA 8 137 1 AAATCGGGAA 0.959126 -58 GGTGATATATGGGAGATGGCGGTAGAATGACCCGT 9 40 0 GAATGGCGAG 0.878105 -86 ATAATGCAATTATAGATGGGGGGGATTTTGAGGGT 11 12 0 TAATGGGGGA 0.898442 -81 GACGGCGATGAAGAAATTGCGATGAAATGTGAGGT 12 87 1 AAATTGCGGA 0.911453 -189 TCTGATCAGCACAAAATCGGGTGAAAACCCTGATT 12 123 0 AAATCGGGAA 0.959126 -153 CTGGTGACCAGAGAAATGGGGATGAGGCTTCGCCC 12 184 0 GAATGGGGGA 0.978798 -92 * * ****** ** Masking position 4 Map Score: 20.7199 Number of sites scoring better than the average of aligned sites = 734 Number in coding regions = 658 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 3 TGACTACTAAATGGGGTCGTAAACCACGTC 1 167 0 ATGGGGTCGT 0.981964 -134 TTCGGTCATCATGTGGTTGTGAGTCTGTAA 1 261 0 ATGTGGTTGT 0.72776 -40 TCCCTGTGTTATGGGTACGGCATCACCATA 2 155 0 ATGGGTACGG 0.902713 -91 AACTAATTGTATGGGAATGGTTAA 3 5 0 ATGGGAATGG 0.852551 -183 ACGTCAGTATATGGGGATGTTTCCCCCACA 3 93 0 ATGGGGATGT 0.978109 -95 TGTGGGAGAGATGGGGACAAGGGAGAATAA 4 47 0 ATGGGGACAA 0.953726 -63 TTGAGACCACATGGGGTCGGCGCCCCGAAT 5 128 0 ATGGGGTCGG 0.990738 -173 TGGAGATTAAATGAGGTCATCCCTCAATTA 6 79 0 ATGAGGTCAT 0.756541 -51 TTCGCTTATTATGGGGATCAGTTTCAGGGT 7 65 0 ATGGGGATCA 0.85263 -58 CACTTATTTCATGAGGTTGGTGTTGGGCGA 8 162 0 ATGAGGTTGG 0.929926 -33 TAACTTTCCCATGGGGATAACTCATCGTAA 9 105 0 ATGGGGATAA 0.927762 -21 ATCGTAGCCGATGAGGACGCGCCTGATGGG 10 142 1 ATGAGGACGC 0.865424 -89 ATTCGTAACCAAGGGGTCAGCTC 11 80 1 AAGGGGTCAG 0.751633 -13 GACCAGAGAAATGGGGATGAGGCTTCGCCC 12 184 0 ATGGGGATGA 0.978109 -92 ********** Masking position 1 Map Score: 14.7453 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 398 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 4 CACGTCATCAAGGGGGAGATGCAAAAATTTTTTGT 1 138 0 AGGGGGGAAA 0.904076 -163 GAGTCTGTAATAGGGGCGAAACGTCTGGTTTCAAC 1 236 0 TAGGGGGAGC 0.850011 -65 GCCCACCACCTGGCGGTGACGGGCCTTTGTGCGAA 2 34 0 TGGCGGGAGC 0.980282 -212 TTAACCAAAAAGGGGGGATTTTATCTCCCCTTTAA 3 33 1 AGGGGGATAC 0.795219 -155 GCGTTGAATGTGGGGGAAACATCCCCATATACTGA 3 85 1 TGGGGGAACC 0.982168 -103 TCTGATTACCTGGCGGAAATTAAACTAAGAGAGAG 3 159 1 TGGCGGAAAC 0.981226 -29 GTGGGAGAGATGGGGACAAGGGAGAATAATTTCAA 4 41 0 TGGGGAAAAA 0.834464 -69 TAATTATCGTTGGCGGTAAACAACCGTTGGATTTC 8 97 1 TGGCGGAAAC 0.981226 -98 ATATGGGAGATGGCGGTAGAATGACCCGTTTTCAA 9 34 0 TGGCGGAGGC 0.942042 -92 AACTTTCCCATGGGGATAACTCATCGTAACCAATT 9 99 0 TGGGGAAAAC 0.945452 -27 CGTCGCACTGTGGCGGCTATCGCACTTTAACGTTT 10 13 1 TGGCGGTACC 0.764419 -218 GCATAGACTGAGGGGGCAGCACGAAACGTTAAAGT 10 36 0 AGGGGGAGGA 0.781113 -195 CAATTATAGATGGGGGGGATTTTGAGGGTT 11 6 0 TGGGGGGATA 0.894809 -87 GCCCAAAATTTGGGCGCAATCGGACATCAACCC 12 9 0 TGGGCGAAGC 0.910926 -267 CGCCCCTTCAAGGGGGAAAAAGAAAAAAAATTCTG 12 154 0 AGGGGGAAAA 0.919841 -122 ACCAGAGAAATGGGGATGAGGCTTCGCCCCTTCAA 12 178 0 TGGGGAGATC 0.818133 -98 ****** ** * * Masking position 3 Map Score: 13.9503 Number of sites scoring better than the average of aligned sites = 934 Number in coding regions = 866 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 5 GACTACTAAATGGGGTCGTAAACCACGTCATCAA 1 162 0 TGGGGTCGCC 0.978231 -139 GCGTTGAATGTGGGGGAAACATCCCCATATACTG 3 85 1 TGGGGGAACC 0.837596 -103 CCTTTAAAATTCGGGGCGCCGACCCCATGTGGTC 5 120 1 TCGGGGCGCC 0.980027 -181 GCCGACCCCATGTGGTCTCAAGCCCAAAGGAAGA 5 137 1 TGTGGTCTCC 0.822962 -164 TTCACATTAATCTGGTCAATAACCTTGAATAATT 6 50 1 TCTGGTCACC 0.98475 -80 GGAGATTAAATGAGGTCATCCCTCAATTATTCAA 6 74 0 TGAGGTCATC 0.693274 -56 CTGAAGGACATCGGGTCAATCGCCCAACACCAAC 8 143 1 TCGGGTCACC 0.995649 -52 GGGATTGAAAACGGGTCATTCTACCGCCATCTCC 9 30 1 ACGGGTCAAC 0.888602 -96 TCCACAATGGACAGGTCAGGTAGCCAGAACACCC 10 169 0 ACAGGTCAGC 0.810762 -62 GTACAAAAGTACGGGGCATAATGCAATTATAGAT 11 30 0 ACGGGGCAGC 0.924032 -63 CAGCACAAAATCGGGTGAAAACCCTGATTCACCT 12 118 0 TCGGGTGACC 0.963934 -158 TCCCCATTTCTCTGGTCACCAGCCGGGAAACCAC 12 197 1 TCTGGTCACC 0.98475 -79 ******** ** Masking position 14 Map Score: 9.43502 Number of sites scoring better than the average of aligned sites = 404 Number in coding regions = 374 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 6 GTCAAGCGGAATCGTGTCAATCATTGCGAC 5 215 0 ATCGTGTCAA 0.906969 -86 TTTCACATTAATCTGGTCAATAACCTTGAA 6 49 1 ATCTGGTCAA 0.906969 -81 CTCCTCCCATAACGGATCAAAGTTGCTACT 6 108 0 AACGGATCAA 0.931063 -22 TTTAACGGCTTAAGTGCCGAAGA 8 4 1 AACGGCTTAA 0.850726 -191 TTTCAGCGTTAACGGCTGAAGGACATCGGG 8 128 1 AACGGCTGAA 0.939555 -67 GCTGAAGGACATCGGGTCAATCGCCCAACA 8 142 1 ATCGGGTCAA 0.988675 -53 TGGGATTGAAAACGGGTCATTCTACCGCCA 9 29 1 AACGGGTCAT 0.939923 -97 TCAGCACAAAATCGGGTGAAAACCCTGATT 12 123 0 ATCGGGTGAA 0.97357 -153 ********** Masking position 9 Map Score: 6.68862 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 164 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 CTGCCATATCGCGAAATTTCTGCGCAAAAGC 1 107 1 GCGAAATTCT 0.961425 -194 AGGGGGAGATGCAAAAATTTTTTGTGCTTTT 1 132 0 GCAAAATTTT 0.73955 -169 TGTAATAGGGGCGAAACGTCTGGTTTCAACT 1 235 0 GCGAAAGTCT 0.975329 -66 ATGGAACCGTGCGAAAAGCCTCTTTCGGTGT 2 91 1 GCGAAAGCCT 0.95724 -155 CGAGTCAGTCGCGTAATGCTTAGGCACAGGA 5 177 1 GCGTAAGCTT 0.958052 -124 GCTTGACGCTGCGTAAGGTTTTTGTAATTTT 5 238 1 GCGTAAGTTT 0.975806 -63 GTAACCAATTGCGTAAATTTTTACGCGCCTA 9 78 0 GCGTAATTTT 0.962161 -48 TTGGGCAACTGCGTAGATTTTCGATGGTAGC 12 38 1 GCGTAGTTTT 0.87103 -238 ****** **** Masking position 5 Map Score: 5.42037 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 190 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 8 AGGCATTCATCAAAAAATTGTAATAAAAAG 1 22 0 CAAAAAATTG 0.967967 -279 CGCAAAAGCACAAAAAATTTTTGCATCTCC 1 129 1 CAAAAAATTT 0.824294 -172 AGTGAGTCTGCAAAAAAATGAAATTGGGCA 1 206 1 CAAAAAAATG 0.958825 -95 AAATTCATGACAAAAAAAAGCCCACCACCT 2 58 0 CAAAAAAAAG 0.94705 -188 AGCGTAACAACAAAAGATTGTTATGCTTGA 2 123 1 CAAAAGATTG 0.903102 -123 CCAACGTAAGCAAAAAATACG 9 2 0 CAAAAAATAC 0.84227 -124 CCATAAACTGCAAAAAAAAGTCCGCTGATA 10 77 1 CAAAAAAAAG 0.94705 -154 ********** Masking position 5 Map Score: 4.48126 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 65 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 9 GGGCCTTTGTGCGAATTTAGCGCGTTATGCTGCGTA 2 13 0 GCGATTGGGT 0.99296 -233 CGAAATGGCTGCACCTAAATCGTGATGAAAATCACA 5 68 1 GCACTATGGT 0.817662 -233 CCCATAATAAGCGAAGTTAGCGAGATGAATGCGAAA 7 80 1 GCGAGTGGGT 0.977478 -43 GCCTCTCAGTGCGGCTGTCGGGGGCTTCCCGATCGC 8 34 0 GCGCTTGGGT 0.996579 -161 AAATTTTTACGCGCCTATTTGGTGATATATGGGAGA 9 59 0 GCGCTTTGGT 0.987573 -67 CGATGAGGACGCGCCTGATGGGTGTTCTGGCTACCT 10 150 1 GCGCTAGGGT 0.992171 -81 TATAGATGGGGGGGATTTTGAGGGTT 11 1 0 GGGATTGGGT 0.964434 -92 *** ** * * * * * Masking position 16 Map Score: 3.81022 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 163 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 10 ATTCGCACAAAGGCCCGTCACCGCCAGGTG 2 33 1 AGGCCCGTCA 0.977748 -213 CGTGAAGCACAGTCGTGTCATCTGATTACC 3 139 1 AGTCGTGTCA 0.966438 -49 AGGAAGAGTGAGGCGAGTCAGTCGCGTAAT 5 164 1 AGGCGAGTCA 0.97971 -137 CGTCAAGCGGAATCGTGTCAATCATTGCGA 5 216 0 AATCGTGTCA 0.816875 -85 ATCACCAAATAGGCGCGTAAAAATTTACGC 9 69 1 AGGCGCGTAA 0.96743 -57 AACACCCATCAGGCGCGTCCTCATCGGCTA 10 146 0 AGGCGCGTCC 0.984767 -85 ********** Masking position 8 Map Score: 3.765 Number of sites scoring better than the average of aligned sites = 269 Number in coding regions = 258 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 AAATTAAACTAAGAGAGAGCTCT 3 175 1 AAGAGAGAGC 0.940951 -13 GCAAACGAGAGCAGGATCACCT 4 3 1 AAACGAGAGC 0.945268 -107 GAATAATTTCAAGCGAGAGCAGGTGATCCT 4 23 0 AAGCGAGAGC 0.984451 -87 AGATGGGGACAAGGGAGAATAATTTCAAGC 4 39 0 AAGGGAGAAT 0.934649 -71 CTCAAGCCCAAAGGAAGAGTGAGGCGAGTC 5 153 1 AAGGAAGAGT 0.871801 -148 CTCCTGAAATCAGCGAGAATGTAAGACCTT 10 202 0 CAGCGAGAAT 0.814839 -29 GGACTTTCTCAAAGGAGAGTTATCA 12 261 1 AAAGGAGAGT 0.934649 -15 ********** Masking position 6 Map Score: 2.57107 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 93 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 12 GCCCACCACCTGGCGGTGACGGGCCTTTGT 2 39 0 TGGCGGTGAC 0.862119 -207 GCTTGAAATATGGTGATGCCGTACCCATAA 2 147 1 TGGTGATGCC 0.96708 -99 ATCACGATTTAGGTGCAGCCATTTCGTCGA 5 64 0 AGGTGCAGCC 0.904981 -237 TTAAAATTCGGGGCGCCGACCCCATGTGGT 5 123 1 GGGCGCCGAC 0.956562 -178 CTTATATATTTGCCGCTGCCTCTCAGTGCG 8 57 0 TGCCGCTGCC 0.93957 -138 CTTTAACGTTTCGTGCTGCCCCCTCAGTCT 10 37 1 TCGTGCTGCC 0.909443 -194 CCCCTTGAAGGGGCGAAGCCTCATCCCCAT 12 174 1 GGGCGAAGCC 0.967457 -102 TATCTGTTATGGGTGACGCCGGAGCTTACG 12 230 0 GGGTGACGCC 0.966879 -46 ********** Masking position 5 Map Score: 3.13607 Number of sites scoring better than the average of aligned sites = 1297 Number in coding regions = 1245 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 13 GAAAAGCCTCTTTCGGTGTTAGCGTAACAA 2 103 1 TTTCGGTGTT 0.922741 -143 TTTCCTCTATTCTCGGCGTTGAATGTGGGG 3 70 1 TCTCGGCGTT 0.975211 -118 TGGGGATCAGTTTCAGGGTTTCAAGGGAAG 7 54 0 TTTCAGGGTT 0.967926 -69 GAATTTCTCCGCGTTTTTTTCGCAT 7 108 0 TCTCCGCGTT 0.95531 -15 AACCGTTGGATTTCAGCGTTAACGGCTGAA 8 118 1 TTTCAGCGTT 0.977757 -77 TGGGGGGGATTTTGAGGGTT 11 1 0 TTTGAGGGTT 0.873727 -92 ********** Masking position 3 Map Score: 2.29842 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 129 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 14 AGCATAACGCGCTAAATTCGCACAAAGGCC 2 18 1 GCTAAATTCG 0.951535 -228 TTGTTGTTACGCTAACACCGAAAGAGGCTT 2 106 0 GCTAACACCG 0.966165 -140 CGTCCATAAGGTTACAATCGGTACAGCAGG 2 198 1 GTTACAATCG 0.853363 -48 CATTCATCTCGCTAACTTCGCTTATTATGG 7 81 0 GCTAACTTCG 0.977894 -42 ATCTGATTGTGCTACCATCGAAAATCTACG 12 49 0 GCTACCATCG 0.985596 -227 ********** Masking position 4 Map Score: 0.595758 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 113 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 15 ATAAAGAATGAATCGCAGCCAAGGCATTCA 1 43 0 AATCGCAGCC 0.961799 -258 TGTCATCAATCTTCGCAACAAGGACCTCGG 7 15 0 CTTCGCAACA 0.87543 -108 GGGGATAACTCATCGTAACCAATTGCGTAA 9 93 0 CATCGTAACC 0.979871 -33 CCCATTTTTACATCGTAGCCGATGAGGACG 10 131 1 CATCGTAGCC 0.981326 -100 TGTACTCTGTATTCGTAACCAAGGGGTCAG 11 70 1 ATTCGTAACC 0.937804 -23 ********** Masking position 7 Map Score: 0.0623116 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 90 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987