AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i060_Diaminopimelate_Pathway_hpyl_reg_300.orf -o060_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -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 = 0.39 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RHP01430 21 AE000511 Input sequences: #1 RHP01419 228 AE000511 #2 RHP01422 57 AE000511 #3 RHP01712 45 AE000511 #4 RHP01424 88 AE000511 #5 RHP01425 140 AE000511 #6 RHP01426 203 AE000511 #7 RHP00416 300 AE000511 #8 RHP00417 36 AE000511 #9 RHP00589 61 AE000511 #10 RHP00623 73 AE000511 #11 RHP00624 150 AE000511 Motif number 1 TAATGAAATTTTCTTAAAATTATACAATAT 1 29 1 TTCTTAAAAT 0.84095 -200 TTTTTAGGTATTTTTAAAGTGGGTTTTTTC 1 100 1 TTTTTAAAGT 0.680585 -129 AATCTTAAGATCTTTAAAGATTTTAAAAAC 1 133 1 TCTTTAAAGA 0.49137 -96 TCTTTAAAGATTTTAAAAACTAATACAGCA 1 143 1 TTTTAAAAAC 0.519546 -86 TCCTTGTCAATGATTAAAATTAAAGAGCGA 1 194 0 TGATTAAAAT 0.853785 -35 TTGGGAGTGGCGATTAAAATCCC 3 4 0 CGATTAAAAT 0.88354 -42 AAAGCGTTTATTATTAAAGCATCACACTTG 4 14 0 TTATTAAAGC 0.796164 -75 CTTTAGTTAATCCTAAAAGAGAAAATTATG 4 40 1 TCCTAAAAGA 0.792135 -49 TATGATGTCCCCATTAAAGATAAAGAAAAA 5 37 1 CCATTAAAGA 0.919591 -104 TATTTTTCATCTTTTAAAGTAGTGAGTTCA 5 69 0 CTTTTAAAGT 0.802507 -72 TATCATTAGCCCCTAAAAAATGATATTTTT 5 92 0 CCCTAAAAAA 0.838057 -49 TGATACGGATTGATTAAAAAGAAAATACCC 6 14 1 TGATTAAAAA 0.892181 -190 CTTCATAAAGCTATAAAAACAAGGCCAGGC 6 103 1 CTATAAAAAC 0.657094 -101 ATAACATAAGCCATTAAAGAAAAACGATAC 6 142 0 CCATTAAAGA 0.919591 -62 AAACGCTAAAAAAATTTTAAGCG 7 4 1 CGCTAAAAAA 0.82182 -297 CCTAAAAGATCGCTTAAAATTTTTTTAGCG 7 14 0 CGCTTAAAAT 0.899634 -287 CTTCATTTAACCCTAAAAGATCGCTTAAAA 7 25 0 CCCTAAAAGA 0.832504 -276 GCTTAGTTGTTGTTTAAAAACTCTTTTTTG 7 79 0 TGTTTAAAAA 0.798246 -222 CATTGAAGCTTTTTTAAAAAGTCATGGTCG 7 212 0 TTTTTAAAAA 0.484788 -89 TAAATCATCATGTTTAAAAATCAGTTTGTT 7 270 0 TGTTTAAAAA 0.798246 -31 ATCGTTCAAATCATAAAAGATAAGGATTTA 8 16 1 TCATAAAAGA 0.763428 -21 TAGCTTAAAATCTTTAAAAAAGGGCTATTG 9 11 0 TCTTTAAAAA 0.503994 -51 GTTTAAGTTTTGCTTAAAATGAA 10 4 0 TGCTTAAAAT 0.8734 -70 CCAAATAACGCTATTAAAACGGAGAGGGT 11 10 0 CTATTAAAAC 0.841853 -141 TATTTGGGCGCTATTAAAATGAGTTTCAAG 11 33 1 CTATTAAAAT 0.854068 -118 TTTAAGAATGCCATTAAAATCAAAAATTAA 11 73 0 CCATTAAAAT 0.894859 -78 TTTAATGGCATTCTTAAAGCTAGTATACAC 11 85 1 TTCTTAAAGC 0.821735 -66 ********** Masking position 6 Map Score: 31.4548 Number of sites scoring better than the average of aligned sites = 3204 Number in coding regions = 2716 Number in noncoding regions = 488 Number of orfs with sites within 600 bp upstream = 327 Fraction of orfs with sites within 600 bp upstream = 0.0525217 Motif number 2 AAATACCTAAAAAATACAGAGCAACGCCCT 1 83 0 AAAATACAGA 0.966113 -146 TCAATGATTAAAATTAAAGAGCGATGTCCT 1 188 0 AAATTAAAGA 0.849265 -41 CTTTTAYGCTATAATTAAGACCAAAAATTC 2 20 1 ATAATTAAGA 0.834437 -38 GTCCCCATTAAAGATAAAGAAAAATTTGAA 5 43 1 AAGATAAAGA 0.977468 -98 TTAGGGGCTAATGATAAAGTAAAAACTCTT 5 106 1 ATGATAAAGT 0.734323 -35 CAATGATACGGATTGATTAAAA 6 3 1 ATGATACGGA 0.857422 -201 TTATACTAATAAAATACAGATTTGATTGAA 6 168 1 AAAATACAGA 0.966113 -36 CAAATCATAAAAGATAAGGATTTAA 8 22 1 AAGATAAGGA 0.949117 -15 ATTAAAATCAAAAATTAAGAAAAAAGGGCT 11 61 0 AAAATTAAGA 0.917564 -90 AGAAAGAGCTAAAATAAAGACCT 11 138 1 AAAATAAAGA 0.975634 -13 ********** Masking position 5 Map Score: 10.3146 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 191 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 3 ATTTTAAGAAAATTTCATTATTTAAGTAAGGGG 1 16 0 AATCTTATTT 0.935456 -213 GGTATTTTTAAAGTGGGTTTTTTCTTAAATCTT 1 106 1 AAGGTTTTTT 0.951142 -123 AAAAGCGTTCTTTTAYGCTATAA 2 1 1 AAGCTTCTTT 0.96615 -57 CCAAAAATTCAAGGGGATTATTTTAACT 2 40 1 AAGGTTATTT 0.900126 -18 CTTTAATAATAAACGCTTTAGTTAATCCTAAAA 4 25 1 AAGCTTAGTT 0.902398 -64 AAAGATGAAAAATATCATTTTTTAGGGGCTAAT 5 85 1 AATCTTTTTT 0.969046 -56 TAGCTTTATGAAGCGCGTTTTATTGATGCATGG 6 83 0 AAGCTTTTAT 0.871965 -121 GTTTTTCTTTAATGGCTTATGTTATACTAATAA 6 147 1 AAGCTATGTT 0.646429 -57 TTTTTTGTAAAACTTCATTTTTTGAATAAAACT 7 53 0 AATCTTTTTT 0.969041 -248 TGTTGTTTAAAAACTCTTTTTTGTAAAACTTCA 7 69 0 AATCTTTTTG 0.831591 -232 CTCGCGCTACAATCTCCCTTTTTGATTGCGGAG 7 112 1 AATCCTTTTT 0.893669 -189 CACACCAAACAAACTGATTTTTAAACATGATGA 7 263 1 AATGTTTTTA 0.605896 -38 CAATAGCCCTTTTTTAAAGATTTT 9 2 1 AAGCCTTTTT 0.952312 -60 TCTCCGTTTTAATAGCGTTATTTGGGCGCTATT 11 15 1 AAGCTTATTT 0.971783 -136 TTTTGATTTTAATGGCATTCTTAAAGCTAGTAT 11 78 1 AAGCTTCTTA 0.842716 -73 ** ** ****** Masking position 2 Map Score: 15.9867 Number of sites scoring better than the average of aligned sites = 1863 Number in coding regions = 1571 Number in noncoding regions = 292 Number of orfs with sites within 600 bp upstream = 192 Fraction of orfs with sites within 600 bp upstream = 0.0308384 Motif number 4 ATTCCCCTTACTTAAATAATGAAATTTTCT 1 13 1 CTTAAATAAT 0.798199 -216 TGAAATTTTCTTAAAATTATACAATATGTA 1 32 1 TTAAAATTAT 0.843292 -197 TGGGTTTTTTCTTAAATCTTAAGATCTTTA 1 119 1 CTTAAATCTT 0.927906 -110 GTATTAGTTTTTAAAATCTTTAAAGATCTT 1 139 0 TTAAAATCTT 0.916076 -90 CGCTCTTTAATTTTAATCATTGACAAGGAG 1 195 1 TTTTAATCAT 0.768969 -34 AGTTAAAATAATCCCCTTGAAT 2 46 0 TTAAAATAAT 0.770351 -12 CTCTCGCTGATTTAAATGTTTGGGAGTGGC 3 23 0 TTTAAATGTT 0.768416 -23 AAGTGTGATGCTTTAATAATAAACGCTTTA 4 15 1 CTTTAATAAT 0.460964 -74 CAAGATGAGCCTTTAATCATC 4 78 1 CTTTAATCAT 0.775399 -11 AAGTAGTGAGTTCAAATTTTTCTTTATCTT 5 53 0 TTCAAATTTT 0.755403 -88 TTCACTCAATTCATAAAGAGTTTT 5 127 0 CTCAATTCAT 0.586172 -14 AAAAGATCGCTTAAAATTTTTTTAGCGTTT 7 11 0 TTAAAATTTT 0.812649 -290 TAGAAATCCTTTAAATCATCATGTTTAAA 7 282 0 TTTAAATCAT 0.939006 -19 GGGTTATCGTTCAAATCATAAAAGATAAG 8 10 1 TTCAAATCAT 0.906036 -27 AAATTTTAGCTTAAAATCTTTAAAAAAGGG 9 17 0 TTAAAATCTT 0.916076 -45 AGATTTTAAGCTAAAATTTTAGCATACAAA 9 28 1 CTAAAATTTT 0.81815 -34 CAAAATGATCTTAAAATGATACAATTACAA 10 34 0 TTAAAATGAT 0.783606 -40 GCCCTTTTTTCTTAATTTTTGATTTTAATG 11 62 1 CTTAATTTTT 0.420078 -89 ********** Masking position 7 Map Score: 16.3427 Number of sites scoring better than the average of aligned sites = 1044 Number in coding regions = 868 Number in noncoding regions = 176 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 5 TTAAATAATGAAATTTTCTTAAAATTATAC 1 24 1 AAATTTTCTT 0.610236 -205 TTTAAAGTGGGTTTTTTCTTAAATCTTAAG 1 112 1 GTTTTTTCTT 0.965489 -117 TAATGCCATAATTTTCTCTTTTAGGATTAA 4 46 0 ATTTTCTCTT 0.858759 -43 AGTGAGTTCAAATTTTTCTTTATCTTTAAT 5 49 0 AATTTTTCTT 0.829836 -92 TTCATAAAGAGTTTTTACTTTATCATTAGC 5 112 0 GTTTTTACTT 0.79743 -29 ATAGCGTTGGGTATTTTCTTTTTAATCAAT 6 22 0 GTATTTTCTT 0.899818 -182 GATGCATGGTGGTTTCTCATAAATGGTTTT 6 62 0 GGTTTCTCAT 0.392559 -142 AAACTTGTATCGTTTTTCTTTAATGGCTTA 6 136 1 CGTTTTTCTT 0.915039 -68 AATCAAATCTGTATTTTATTAGTATAACAT 6 165 0 GTATTTTATT 0.531928 -39 TACAATCTCCCTTTTTGATTGCGGAGTATG 7 119 1 CTTTTTGATT 0.548799 -182 GTATGCTAAAATTTTAGCTTAAAATCTTTA 9 25 0 ATTTTAGCTT 0.554797 -37 TACAAGTTTAAGTTTTGCTTAAAATGAA 10 9 0 AGTTTTGCTT 0.859998 -65 GTTTCAAGCCCTTTTTTCTTAATTTTTGAT 11 55 1 CTTTTTTCTT 0.945042 -96 ********** Masking position 5 Map Score: 4.83978 Number of sites scoring better than the average of aligned sites = 1302 Number in coding regions = 1146 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 6 GCCAAGATGAGCCTTTAATCATC 4 76 1 GCCTTTAATC 0.909952 -13 AACAAGGCCAGGCTTTAAACTTGTATCGTT 6 120 1 GGCTTTAAAC 0.991525 -84 TTTGATTGAAGGCATTAAACAACTGC 6 188 1 GGCATTAAAC 0.972664 -16 CGGAGTAGCGGGATTCAAACCCACGACCTC 7 184 0 GGATTCAAAC 0.929368 -117 AAGAAAAAAGGGCTTGAAACTCATTTTAAT 11 45 0 GGCTTGAAAC 0.985641 -106 ********** Masking position 5 Map Score: 2.03818 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 84 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 7 TCATTATTTAAGTAAGGGGAATTA 1 5 0 AGTAAGGGGA 0.864372 -224 ATACAGCAATAGTTGGACGATTAAGGACAT 1 165 1 AGTTGGACGA 0.846365 -64 AAAGGGAGATTGTAGCGCGAGTTTGCTTAG 7 103 0 TGTAGCGCGA 0.93914 -198 TTGATTGCGGAGTATGGCGCAGCCTGATTA 7 133 1 AGTATGGCGC 0.948022 -168 GCGCAGCCTGATTAGCGCGCACCCTTGGGG 7 149 1 ATTAGCGCGC 0.960762 -152 TCATGGTCGGAGTAGCGGGATTCAAACCCA 7 191 0 AGTAGCGGGA 0.969101 -110 TAATAGCGTTATTTGGGCGCTATTAAAATG 11 24 1 ATTTGGGCGC 0.933294 -127 ********** Masking position 3 Map Score: 1.06234 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 159 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 ACTTAACTATAGTATAATCTAAGGGCGTTGCTC 1 62 1 AGATACTAAG 0.883315 -167 AACCCACTTTAAAAATACCTAAAAAATACAGAG 1 92 0 AAAAACTAAA 0.945909 -137 TTTTGGTCTTAATTATAGCTAAAAGAACGCTT 2 13 0 AATAACTAA 0.0504725 -45 TTTCTCTTTTAGGATTAACTAAAGCGTTTATTA 4 31 0 AGATACTAAA 0.937482 -58 CCAACGCTATAAGACGAGATAAAACCATTTATG 6 42 1 AAACAATAAA 0.60405 -162 GTATTTTATTAGTATAACATAAGCCATTAAAGA 6 152 0 AGATAATAAG 0.538371 -52 AAACGCTAAAAAAATTTTAAGCGATCTTTT 7 8 1 AAAAATTTAA 0.632553 -293 AGAGTTTTTAAACAACAACTAAGCAAACTCGCG 7 85 1 AAAAACTAAG 0.89825 -216 TGTATGCTAAAATTTTAGCTTAAAATCTTTAAA 9 23 0 AATTACTTAA 0.6576 -39 TTCATTTTAAGCAAAACTTAAACTTGTAATTG 10 10 1 AGAAATTAAA 0.732996 -64 TCTACTTATCAAAATGATCTTAAAATGATACAA 10 40 0 AAATACTTAA 0.903876 -34 TATACACTATAATACCATCTTAATCAAACAAGA 11 108 1 AAACACTTAA 0.863529 -43 TAATCAAACAAGAAAGAGCTAAAATAAAGACCT 11 128 1 AGAAACTAAA 0.946864 -23 ** ** * ***** Masking position 7 Map Score: 5.28515 Number of sites scoring better than the average of aligned sites = 551 Number in coding regions = 416 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 9 ********** No masking Map Score: -1.94446e-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: -1.94446e-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: -1.94446e-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