AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i250_fts_cell_wall_hpyl_reg_100.orf -o250_hpyl_100.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: RHP00808 16 AE000511 Input sequences: #1 RHP01415 124 AE000511 #2 RHP00058 119 AE000511 #3 RHP00136 179 AE000511 #4 RHP00164 146 AE000511 #5 RHP00165 77 AE000511 #6 RHP00389 128 AE000511 #7 RHP00391 130 AE000511 #8 RHP00553 130 AE000511 #9 RHP00809 24 AE000511 #10 RHP00810 101 AE000511 #11 RHP00873 138 AE000511 #12 RHP00934 155 AE000511 Motif number 1 AAAAGATTCCTAAAAATTAAAATAAG 1 6 1 ATCCTAAAAA 0.902647 -119 GCAAATTGATTTACTTAAAAATAGCATGAAT 1 52 0 TTCTTAAAAA 0.97147 -73 TAAAATCGCCATGCTTGAAATTTAGAAAAAA 1 95 0 ATCTTGAAAT 0.558566 -30 AAAATCCCCTAAAATCGCCATGCTT 1 110 0 TCCCTAAAAT 0.900741 -15 ATAGTTAATCTTACCTAAAATTTAAGCGTTA 2 74 0 TTCCTAAAAT 0.883852 -46 ACCCTTTAAAAGGGTGTCTTT 3 1 1 ACCTTTAAAA 0.947621 -179 CGCCCAAAAGTTTCTTTATAATCAATTTTAG 3 90 0 TTCTTTATAA 0.674713 -90 ACAATCCCCTTAAAACCCTTAGATG 3 165 0 TCCCTTAAAA 0.97173 -15 ACTTTTAAATTCTCTCAAAAATTAAAGGTTA 4 17 0 TCCTCAAAAA 0.856498 -130 AAAAAGCGATTTTCTTAAACAATAAGGCTTA 4 73 0 TTCTTAAACA 0.747704 -74 AGCATTTTATTTGCATTAAAAAGCGATTTTC 4 90 0 TTCATTAAAA 0.850208 -57 TCATTGCCTTAAATTCTTTTTAAA 4 133 0 TTCCTTAAAT 0.899551 -14 CTATCTATATTTACCTAAAAAAAGGCTTTTG 5 24 0 TTCCTAAAAA 0.960773 -54 GATCAAACTCCCTAAAAACGATTGCAA 5 61 0 ACCCCTAAAA 0.656666 -17 AGAACTCTAATCCCTTTAAAAAATCAAAAAT 6 107 0 TCCTTTAAAA 0.979504 -22 GGCGTTTTTATCGCATAAAGAAATGGCTGTA 7 13 0 TCCATAAAGA 0.572976 -118 AAATAGAGCGTTCCTTAAAAAATGGTTGGAT 8 21 1 TTCTTAAAAA 0.971472 -110 ACAAATTCCTTAAAAAGAGTGGTGGC 10 6 1 TTCTTAAAAA 0.971472 -96 ATTTTACCCTATTCTTTAAGTTTTTATCCAT 10 75 0 ATCTTTAAGT 0.523718 -27 CCCTTGAGCCACTCTTAAAAAGCGTTGTTTG 11 60 1 ACCTTAAAAA 0.938922 -79 CTTTAAAATTTTACTTTAAGATACCATATAA 11 105 0 TTCTTTAAGA 0.903375 -34 TTTTTAAAACTCTCTTTAAAATTTTACTTTA 11 118 0 TCCTTTAAAA 0.979503 -21 TTAAGTGGCTTCTCTTTAAATGATCGCTTGG 12 15 1 TCCTTTAAAT 0.936899 -141 CAACAAACCCTCTCTTTAAAAAGGACCAAGC 12 40 0 TCCTTTAAAA 0.979503 -116 TGATGGTAAAATCCGTTAAAATGGGGTGTAG 12 74 0 ATCGTTAAAA 0.64362 -82 AAGCACTTACTTGAAAATGGCGTGGCG 12 139 0 TTCTTGAAAA 0.914954 -17 ** ******** Masking position 8 Map Score: 39.4018 Number of sites scoring better than the average of aligned sites = 1251 Number in coding regions = 1017 Number in noncoding regions = 234 Number of orfs with sites within 600 bp upstream = 187 Fraction of orfs with sites within 600 bp upstream = 0.0300353 Motif number 2 TAAAAATTAAAATAAGCTTCTATCCTACCCTA 1 21 1 AAAGCTTCTA 0.59441 -104 AAAATCCCCTAAAATCGCCATGCT 1 111 0 AACCCTAAAA 0.661395 -14 GTTTCATACCATAACGCTTAAATTTTAGGTAA 2 63 1 ATAGCTTAAA 0.893127 -57 TAAGGACTAAAAAGGGCTTAAAGACACCCTTT 3 19 0 AAGGCTTAAA 0.850449 -161 AGTCCTTATAAAAAGGGTTTTAGTTTGGATTT 3 43 1 AAAGGTTTTA 0.565691 -137 TTAGCTTTTTAAGATGCGAAAATCCAAACTAA 3 62 0 AAAGCGAAAA 0.7591 -118 TTCGCATCTTAAAAAGCTAAAATTGATTATAA 3 74 1 AAAGCTAAAA 0.955031 -106 CAATCCCCTTAAAACCCTTAGATGAATTTTCC 3 157 0 AAACCTTAGA 0.791837 -23 TAAAATTAACCTTTAATTTTTGAGAG 4 5 1 ATACCTTTAA 0.729753 -142 ATCATACTAAAACGTGCTTAAAATTAAGCCTT 4 49 1 AAGGCTTAAA 0.85045 -98 TTCTTAAACAATAAGGCTTAATTTTAAGCACG 4 61 0 ATAGCTTAAT 0.672197 -86 TAATGCAAATAAAATGCTAAAATGCCATGATT 4 103 1 AAAGCTAAAA 0.955429 -44 AAGAAAATTCAAAAGCCTTTTTTTAGGTAAAT 5 15 1 AAACCTTTTT 0.567693 -63 GATCAAACTCCCTAAAAACGATTGCAA 5 61 0 AATCCTAAAA 0.699152 -17 GGTTATTAAAATTATCCTTATTATAGAGAGTT 6 17 0 ATACCTTATT 0.490417 -112 AGTAAAATCAAATAACCTTATTTTAACCAAAG 6 48 0 AAACCTTATT 0.555624 -81 TTCAGGTTTAAACAACCTTATAGTAAAATCAA 6 69 0 AAACCTTATA 0.941958 -60 AAAGCCAGAAAACATGGTATAATCCTTTAGCT 7 57 1 AAAGGTATAA 0.631792 -74 TATTATCCTAAAATAGAGCGTTC 8 2 1 ATACCTAAAA 0.842315 -129 CGCAACAATTAAAAGCGTAAAAGCAAAAGGCG 8 58 0 AAACGTAAAA 0.840022 -73 ACAAATTCCTTAAAAAGAGTGGTG 10 3 1 AATCCTTAAA 0.786153 -99 GCTGAATGCTAACATGCTAAAACTAAAACCCT 10 35 1 AAAGCTAAAA 0.955434 -67 TGCTAAAACTAAAACCCTTATAAGTTATGGAT 10 49 1 AAACCTTATA 0.941606 -53 AAACTTAAAGAATAGGGTAAAATAAACGC 10 83 1 AAAGGTAAAA 0.840009 -19 CCACTATTAGAACAAGGTTTTTATGACGAT 11 9 0 AAAGGTTTTT 0.23312 -130 TTTTGATGGTAAAATCCGTTAAAATGGGGTGT 12 76 0 AAACCGTTAA 0.619612 -80 ** * ******* Masking position 1 Map Score: 23.907 Number of sites scoring better than the average of aligned sites = 3146 Number in coding regions = 2695 Number in noncoding regions = 451 Number of orfs with sites within 600 bp upstream = 311 Fraction of orfs with sites within 600 bp upstream = 0.0499518 Motif number 3 TCTTACCTAAAATTTAAGCGTTATGGTATGAA 2 65 0 AATTTAGGTT 0.75474 -55 TTAAAATGGAATAGTTAATCTTACCTAAAATT 2 83 0 ATAGTAACTT 0.609038 -37 AAAAGGGCTTAAAGACACCCTTTTAAAGGGT 3 10 0 AAAGAACCTT 0.817214 -170 TTTAGTCCTTATAAAAAGGGTTTTAGTTTGGA 3 40 1 ATAAAAGGTT 0.603993 -140 CTTTATAATCAATTTTAGCTTTTTAAGATGCG 3 76 0 AATTTAGTTT 0.653594 -104 AATTGATTATAAAGAAACTTTTGGGCGTAACC 3 94 1 AAAGAACTTT 0.769116 -86 ATTCTCTCAAAAATTAAAGGTTAATTTTA 4 8 0 AAATTAAGTT 0.75847 -139 TTTTTGAGAGAATTTAAAAGTTATCATACTAA 4 27 1 AATTTAAGTT 0.420766 -120 AACGTGCTTAAAATTAAGCCTTATTGTTTAAG 4 59 1 AAATTAGCTT 0.917681 -88 ATATTTACCTAAAAAAAGGCTTTTGAATTTTC 5 17 0 AAAAAAGCTT 0.797946 -61 TTAGGTAAATATAGATAGACTTTATTGCAATC 5 37 1 ATAGAAGCTT 0.880915 -41 TATCCTTATTATAGAGAGTTTTTAAC 6 5 0 ATAGAAGTTT 0.846446 -124 CAAAAATATGAAATTCAGGTTTAAACAACCTT 6 82 0 AAATTAGTTT 0.892565 -47 TATTATCCTAAAATAGAGCGTTCCTTAAAAAA 8 11 1 AAATAAGGTT 0.937124 -120 ATGGTATCTTAAAGTAAAATTTTAAAGAGAGT 11 109 1 AAAGTAATTT 0.75655 -30 GTAAAATTTTAAAGAGAGTTTTAAAAA 11 122 1 AAAGAAGTTT 0.944488 -17 GGTCCTTTTTAAAGAGAGGGTTTGTTGTTGCT 12 44 1 AAAGAAGGTT 0.964597 -112 ***** ** *** Masking position 7 Map Score: 11.4259 Number of sites scoring better than the average of aligned sites = 1145 Number in coding regions = 959 Number in noncoding regions = 186 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 4 TAGTTAATCTTACCTAAAATTTAAGCGTTA 2 74 0 TACCTAAAAT 0.63792 -46 GGCTACTTTAATCTTAAAATGGAATAGTTA 2 98 0 ATCTTAAAAT 0.865244 -22 GCTTTTTAAGATGCGAAAATCCAAACTAAA 3 61 0 ATGCGAAAAT 0.910865 -119 GCATCTTAAAAAGCTAAAATTGATTATAAA 3 77 1 AAGCTAAAAT 0.88479 -103 AAAAGTTATCATACTAAAACGTGCTTAAAA 4 42 1 ATACTAAAAC 0.655363 -105 TACTAAAACGTGCTTAAAATTAAGCCTTAT 4 53 1 TGCTTAAAAT 0.612016 -94 TGCAAATAAAATGCTAAAATGCCATGATTT 4 106 1 ATGCTAAAAT 0.976048 -41 TAACCAAAGGTTATTAAAATTATCCTTATT 6 27 0 TTATTAAAAT 0.643602 -102 TAATAACCTTTGGTTAAAATAAGGTTATTT 6 41 1 TGGTTAAAAT 0.793228 -88 AAACAACCTTATAGTAAAATCAAATAACCT 6 62 0 ATAGTAAAAT 0.806436 -67 GCCAGAAAACATGGTATAATCCTTTAGCTA 7 60 1 ATGGTATAAT 0.627099 -71 AGTTTAAGATTTGCAAAAATCGTATCTCAA 7 98 1 TTGCAAAAAT 0.676402 -33 TATTATCCTAAAATAGAGCGTTCC 8 5 1 ATCCTAAAAT 0.943812 -126 GAATGCTAACATGCTAAAACTAAAACCCTT 10 38 1 ATGCTAAAAC 0.905226 -64 CTTAAAGAATAGGGTAAAATAAACGC 10 86 1 AGGGTAAAAT 0.898503 -16 TGAATTTTTGATGGTAAAATCCGTTAAAAT 12 83 0 ATGGTAAAAT 0.954318 -73 CTCTCATGCGTTGTGAAAATCCAACGCCAC 12 115 1 TTGTGAAAAT 0.693776 -41 ********** Masking position 6 Map Score: 14.3992 Number of sites scoring better than the average of aligned sites = 814 Number in coding regions = 647 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 5 CTACCCTATTCATGCTATTTTTAAGTAAAT 1 45 1 CATGCTATTT 0.738861 -80 AAATTTCAAGCATGGCGATTTTAGGGGATT 1 103 1 CATGGCGATT 0.729139 -22 CTTTTTAAATCATGGCATTTTAGCATTTTA 4 112 0 CATGGCATTT 0.969209 -35 TTACCTAAAAAAAGGCTTTTGAATTTTCTT 5 15 0 AAAGGCTTTT 0.828314 -63 TGATAACCATCAAGGCGTTTTTATCGCATA 7 27 0 CAAGGCGTTT 0.96823 -104 TTGGATTTGGAACGCCTTTTGCTTTTACGC 8 46 1 AACGCCTTTT 0.783112 -85 AATTATACAACAAAGCATTTAAATTAAAAA 8 101 1 CAAAGCATTT 0.828796 -30 ACTATTAGAACAAGGTTTTTATGACGAT 11 9 0 CAAGGTTTTT 0.863397 -130 TTTTATCAAACAACGCTTTTTAAGAGTGGC 11 67 0 CAACGCTTTT 0.903941 -72 GTTGTTGCTACACCCCATTTTAACGGATTT 12 67 1 CACCCCATTT 0.885346 -89 AATCCAACGCCACGCCATTTTCAAGTAAGT 12 132 1 CACGCCATTT 0.966531 -24 ********** Masking position 2 Map Score: 7.56411 Number of sites scoring better than the average of aligned sites = 703 Number in coding regions = 655 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 6 ACCCTTTAAAAGGGTGTCTTTAAGCCC 3 7 1 TAAAAGGTGT 0.809142 -173 AAACCCTTTTTATAAGGACTAAAAAGGGCTT 3 32 0 TATAAGGCTA 0.776005 -148 GGAAAATTCATCTAAGGGTTTTAAGGGGATT 3 157 1 TCTAAGGTTT 0.922928 -23 TTTCTTAAACAATAAGGCTTAATTTTAAGCA 4 63 0 AATAAGGTTA 0.956257 -84 ATTTACCTAAAAAAAGGCTTTTGAATTTTCT 5 16 0 AAAAAGGTTT 0.911554 -62 AACTCTCTATAATAAGGATAATTTTAATAAC 6 17 1 AATAAGGTAA 0.873547 -112 CTTTGGTTAAAATAAGGTTATTTGATTTTAC 6 48 1 AATAAGGTAT 0.921362 -81 TTGATTTTACTATAAGGTTGTTTAAACCTGA 6 69 1 TATAAGGTGT 0.938466 -60 AGACAAAAGACTAAGGATTAATCA 9 10 1 ACTAAGGTTA 0.893505 -15 ATCCATAACTTATAAGGGTTTTAGTTTTAGC 10 50 0 TATAAGGTTT 0.968945 -52 CCACTATTAGAACAAGGTTTTTATGACGAT 11 10 0 AACAAGGTTT 0.896508 -129 ******* *** Masking position 5 Map Score: 10.7631 Number of sites scoring better than the average of aligned sites = 424 Number in coding regions = 346 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 7 AAGGGTTTTAGTTTGGATTTTCGCATCTTA 3 55 1 GTTTGGATTT 0.932182 -125 TTATAATCAATTTTAGCTTTTTAAGATGCG 3 76 0 TTTTAGCTTT 0.838864 -104 CACCCAATGGTGTTGGTTTTGTTTGGTTAC 3 120 0 TGTTGGTTTT 0.863518 -60 AAAAAAAGGCTTTTGAATTTTCTTAAAA 5 9 0 TTTTGAATTT 0.816228 -69 AAAATAAGGTTATTTGATTTTACTATAAGG 6 56 1 TATTTGATTT 0.682596 -73 GAATTTCATATTTTTGATTTTTTAAAGGGA 6 98 1 TTTTTGATTT 0.931704 -31 ATACCATGTTTTCTGGCTTTTGATAACCAT 7 47 0 TTCTGGCTTT 0.796222 -84 CTTAAAAAATGGTTGGATTTGGAACGCCTT 8 34 1 GGTTGGATTT 0.895931 -97 TTTGGAACGCCTTTTGCTTTTACGCTTTTA 8 51 1 CTTTTGCTTT 0.80682 -80 TGGACTATCCTTTTTAATTTAAATGCTTTG 8 111 0 TTTTTAATTT 0.65463 -20 CTTATAAGGGTTTTAGTTTTAGCATGTTAG 10 43 0 TTTTAGTTTT 0.697933 -59 AATGGCGTGGCGTTGGATTTTCACAACGCA 12 121 0 CGTTGGATTT 0.895931 -35 ********** Masking position 4 Map Score: 6.29322 Number of sites scoring better than the average of aligned sites = 1390 Number in coding regions = 1222 Number in noncoding regions = 168 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 8 ATGCTTGAAATTTAGAAAAAAGAAAATTGT 1 86 0 TTTAGAAAAA 0.757536 -39 CTTTTTAGTCCTTATAAAAAGGGTTTTAGT 3 37 1 CTTATAAAAA 0.380586 -143 TTGGGTGGGCGTTTGGAAAATTCATCTAAG 3 143 1 GTTTGGAAAA 0.828953 -37 GCACGTTTTAGTATGATAACTTTTAAATTC 4 36 0 GTATGATAAC 0.481378 -111 AAAGCCTTTTTTTAGGTAAATATAGATAGA 5 26 1 TTTAGGTAAA 0.576985 -52 ATAAGGATAATTTTAATAACCTTTGGTTAA 6 28 1 TTTTAATAAC 0.505733 -101 ACTCTAATCCCTTTAAAAAATCAAAAATAT 6 105 0 CTTTAAAAAA 0.652477 -24 GTTTTCTGGCTTTTGATAACCATCAAGGCG 7 40 0 TTTTGATAAC 0.840062 -91 AAATCTTAAACTTTGATAAATAGCTAAAGG 7 80 0 CTTTGATAAA 0.915488 -51 TGTTGTATAATTTTGAAAAAATACGCAACA 8 83 0 TTTTGAAAAA 0.870234 -48 AAAAAGCGTTGTTTGATAAAAATGGCTCAT 11 76 1 GTTTGATAAA 0.92432 -63 TTTAAAGAGAGTTTTAAAAA 11 129 1 GTTTTAAAAA 0.498748 -10 ********** Masking position 8 Map Score: 2.80916 Number of sites scoring better than the average of aligned sites = 1601 Number in coding regions = 1447 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 9 ATGCTATTTTTAAGTAAATCAATTTGCGCT 1 56 1 TAAGTAAATC 0.889097 -69 AATTTAGAAAAAAGAAAATTGTAGCGCAAA 1 78 0 AAAGAAAATT 0.947484 -47 AATTGATTATAAAGAAACTTTTGGGCGTAA 3 94 1 AAAGAAACTT 0.86837 -86 CCTTATTGTTTAAGAAAATCGCTTTTTAAT 4 77 1 TAAGAAAATC 0.937335 -70 TTTTAAGAAAATTCAAAAGCCTT 5 4 1 TAAGAAAATT 0.947486 -74 ATGGTATCTTAAAGTAAAATTTTAAAGAGA 11 109 1 AAAGTAAAAT 0.704634 -30 ********** Masking position 6 Map Score: 1.2402 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 113 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 10 ********** No masking Map Score: 2.98671e-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: 2.98671e-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 12 ********** No masking Map Score: 2.98671e-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