AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i064_Histidine_Biosynthesis_mthe_reg_100.orf -o064_mthe_100.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTH01080 300 M.thermo #2 RTH02062 231 M.thermo #3 RTH02127 159 M.thermo #4 RTH01004 66 M.thermo #5 RTH01088 218 M.thermo #6 RTH00777 35 M.thermo #7 RTH00316 57 M.thermo #8 RTH00321 44 M.thermo #9 RTH01047 56 M.thermo #10 RTH02145 30 M.thermo #11 RTH00013 16 M.thermo #12 RTH00133 56 M.thermo #13 RTH01743 127 M.thermo #14 RTH00602 189 M.thermo #15 RTH00576 116 M.thermo #16 RTH00954 31 M.thermo #17 RTH00250 30 M.thermo #18 RTH00057 21 M.thermo #19 RTH01659 205 M.thermo Motif number 1 GGTCCATTAGATGCCCCCTAATCCAAATTA 1 66 1 ATGCCCCCTA 0.978263 -235 ATGATCCGGTGTGCCCCCTAAATTCTTAAA 1 230 1 GTGCCCCCTA 0.922802 -71 GGCACAGCCTCTCGCCCATA 2 1 0 CTCGCCCATA 0.846232 -231 TGCCCAGGGGATGGCCCATGATTCCGGTTA 2 27 1 ATGGCCCATG 0.937252 -205 TTATCAGTTTATCACCCCGGCATTACAGGC 2 72 1 ATCACCCCGG 0.942995 -160 GTCACACTCTCCCCTGGATTATAGGT 2 216 0 CTCTCCCCTG 0.972977 -16 GGGGGTTCAAATCCCCCCGGGTCCGCTTTT 5 28 0 ATCCCCCCGG 0.979982 -191 AAGCTGTCTGCTGTCCCCTGAGTCTGGTCT 5 171 0 CTGTCCCCTG 0.984555 -48 TTTATACTAAATGCCCCTTAATTAATAAAT 5 199 1 ATGCCCCTTA 0.763549 -20 GAGGATGACCCTGTCCCCGGCGGATACATC 7 11 0 CTGTCCCCGG 0.983045 -47 TGTAGAACCTATGGCGCCGGTTCTTTATAT 8 25 0 ATGGCGCCGG 0.912665 -20 CCTCCACCACCTCACCCCTACTGATTTTTT 12 14 1 CTCACCCCTA 0.922273 -43 CGTTTCTGGATGGCTCCGGGAGAAAAAAA 12 38 0 ATGGCTCCGG 0.876117 -19 ATGGCTGGAACTGGTCCCTACTGATGAAAT 13 100 0 CTGGTCCCTA 0.8242 -28 ********** Masking position 2 Map Score: 15.5867 Number of sites scoring better than the average of aligned sites = 968 Number in coding regions = 920 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 2 TTGGAATTCATCCCATGGATATGACTACCA 1 130 0 TCCCATGGAT 0.717827 -171 CCCTAACTTTTTCACTGGAGG 1 290 1 TTCACTGGAG 0.909043 -11 TCAGTTTATCACCCCGGCATTACAGGCAAA 2 75 1 ACCCCGGCAT 0.771411 -157 GTCACACTCTCCCCTGGATTATAGGTAAC 2 213 0 TCCCCTGGAT 0.922063 -19 CTTTATAAAGTTTCATGGAGATAAACT 3 8 0 TTTCATGGAG 0.666842 -152 AGTATTCTGCACTACTGCAGATGTAACCCT 3 36 1 ACTACTGCAG 0.579411 -124 CTGCAGATGTAACCCTGCAGCTACAGAAAC 3 50 1 AACCCTGCAG 0.95433 -110 TCAAGATTGTAACCCTGTAGCTACAGAAAC 3 85 1 AACCCTGTAG 0.700046 -75 TAAAAAAGCGGACCCGGGGGGATTTGAACC 5 25 1 GACCCGGGGG 0.770314 -194 GATGACCCTGTCCCCGGCGGATACATC 7 8 0 TCCCCGGCGG 0.845613 -50 TGTTGGGGCATTCCGTGGAGCATTTCAGGG 9 27 1 TTCCGTGGAG 0.828817 -30 TTTCTGGATGGCTCCGGGAGAAAAAAATCA 12 35 0 GCTCCGGGAG 0.844393 -22 AAATCATCATTTCCATGCAGTAAGATATCT 13 74 0 TTCCATGCAG 0.883505 -54 TCTATCATTCTTCACTGGAGATTAACTTAT 14 98 0 TTCACTGGAG 0.909043 -92 AAGAATGATAGATCCTGCAGATGAACGGAT 14 116 1 GATCCTGCAG 0.808257 -74 TGAACGGATAAACCCTGCAGGAGCTTAATG 14 137 1 AACCCTGCAG 0.95433 -53 ATATTAATCAATCCATGGATATGAATCATG 15 34 1 ATCCATGGAT 0.421284 -83 GTTAACTCAGGTCACTGGAGAG 16 3 0 GTCACTGGAG 0.891567 -29 ********** Masking position 7 Map Score: 13.552 Number of sites scoring better than the average of aligned sites = 3184 Number in coding regions = 3017 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 3 TAAACTTATTATTTAAAAATTTTGGTCCATTA 1 43 1 ATTAAAATTT 0.951458 -258 CCACAGATTAATATAAAAATTGCAAATGGTAG 1 104 1 AATAAAATTG 0.956769 -197 ATATGCTTTCACTTAAACATTGGTTGATGGTT 1 158 0 ATTAAAATTG 0.963375 -143 AATTCCAGTAATATAAACATTTATTTATATGC 1 184 0 AATAAAATTT 0.942799 -117 ACACCGGATCATTTAATAATTTGAAGAATTCC 1 210 0 ATTAATATTT 0.713477 -91 CGCTGATGGTAAATAAATATTGTAAGTACCAT 2 162 0 AATAAAATTG 0.94665 -70 TTACCATCAGCGATAAATATTGTTGCCATAGG 2 182 1 CATAAAATTG 0.806202 -50 AAAGTTAACCATTTAAATATTTTCTCATCAAC 5 128 1 ATTAAAATTT 0.951414 -91 GAATCACCAGAAATAAAGAGTTGACGGAT 10 8 0 AATAAAAGTT 0.756401 -23 TTAAAGAACTATTTAAAACTTTACTGTACATA 13 42 0 ATTAAACTTT 0.882668 -86 ATAAGGGAGTATTTAAATCTTGACATGGTGGT 19 56 0 ATTAAACTTG 0.909873 -150 * ***** **** Masking position 6 Map Score: 9.97077 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 15 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 4 CCATGATTCCGGTTACATGTGTTTTTCCAGT 2 42 1 GGTTACATTG 0.981842 -190 TGTTGCCATAGGTTACCTATAATCCAGGGGA 2 202 1 GGTTACCTTA 0.972551 -30 GTAGCTGCAGGGTTACATCTGCAGTAGTGCA 3 43 0 GGTTACATTG 0.981842 -117 ATATTTAAATGGTTAACTTTAAATAGAGATG 5 117 0 GGTTAACTTA 0.964938 -102 CTCGATGACTGGTTAAATTTATTTTACATTA 14 162 0 GGTTAAATTA 0.95531 -28 TCATTTAGAAGCTTACATATATA 15 3 0 GCTTACATTA 0.799952 -114 ACAATCTCGGTTAACTCAGGTCACTGGAG 16 13 0 GGTTAACTAG 0.895 -19 ATATTTAACTGGTTAACCATGATTTAGAGTT 19 123 0 GGTTAACCTG 0.92665 -83 ATGGTTAACCAGTTAAATATGAATTTTTTGA 19 134 1 AGTTAAATTG 0.804586 -72 ******** ** Masking position 5 Map Score: 7.47734 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 71 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 CCTTAATTTGGATTAGGGGGCATCTAATGGA 1 68 0 GTTAGGGGGC 0.990457 -233 CCTTTTAAGAATTTAGGGGGCACACCGGATC 1 232 0 ATTAGGGGGC 0.987748 -69 CCAGTGAAAAAGTTAGGGCGAATGGTTAGTT 1 277 0 ATTAGGGCGA 0.920972 -24 ATAGAGATGTGTGTAGGGGGCCCGTAGTCTA 5 95 0 GGTAGGGGGC 0.960396 -124 ATTTATTAATTAAGGGGCATTTAGTATA 5 201 0 ATTAAGGGGC 0.963532 -18 GAAAAAAATCAGTAGGGGTGAGGTGGTGGAG 12 15 0 ATAGGGGTGA 0.770841 -42 AACCACAGACATTTGAGGTGACGTAAT 15 100 1 ATTGAGGTGA 0.874896 -17 TGACATGGTGGTTTGGGGTGCTGTGTGGTCA 19 37 0 GTTGGGGTGC 0.981809 -169 CGGTGTTAAAGATTAAGGTGATATA 19 191 1 GTTAAGGTGA 0.916076 -15 * ********* Masking position 7 Map Score: 7.01564 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 86 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 ATTTTTATATTAATCTGTGGTCATTCCTTAATTTGGATT 1 85 0 TTGCATTCCT 0.986893 -216 CATTGGTTGATGGTTGGAATTCATCCCATGGATATGACT 1 134 0 TTACATCCCT 0.986893 -167 GAATGGTTAGTTTTATGGAGCCATTCCCTTTTAAGAATT 1 250 0 TTACATTCCT 0.983189 -51 CATGTAACCGGAATCATGGGCCATCCCCTGGGCACAGCC 2 22 0 GTGCATCCCT 0.967561 -210 CTTAATGGTTATTCCTCCCTTTTTATGATCC 4 46 0 TTACCTCCCT 0.946214 -21 CATTCAGTGTCATTGTTGGGGCATTCCGTGGAGCATTTC 9 14 1 CTGCATTCCT 0.977084 -43 TGTTTATTAACCATTCCCTTTGATGTACA 13 1 1 TTACATTCCT 0.983189 -127 GCTGGAACCATGATGCAAATCCATCCCATGATTCATATC 15 51 0 TTACATCCCT 0.986893 -66 CTCCCTTATCCTATTATAGAGTATTCCATACTGGCGGTG 19 79 1 CTGTATTCCT 0.806945 -127 * * * ****** * Masking position 14 Map Score: 8.17053 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 43 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 ACATTGGTTGATGGTTGGAATTCATCCCAT 1 144 0 ATGGTTGGAA 0.908646 -157 AAATGTTTATATTACTGGAATTCTTCAAAT 1 194 1 ATTACTGGAA 0.91497 -107 TGATAAACTGATAACTGGAAAAACACATGT 2 56 0 ATAACTGGAA 0.964525 -176 ATCACCTCATGGCTGGAACTGGTCCCTA 13 110 0 ATGGCTGGAA 0.988898 -18 AAATCCCTCGATGACTGGTTAAATTTATTT 14 169 0 ATGACTGGTT 0.879039 -21 GTTATGCAACATGGCTGGAACCATGATGCA 15 73 0 ATGGCTGGAA 0.988898 -44 CCCGCATAACTGGCTGTTCATATTC 19 6 1 ATAACTGGCT 0.839098 -200 CACCGTAAAAACAGCTGGATTTAACATAAA 19 166 0 ACAGCTGGAT 0.877152 -40 ********** Masking position 1 Map Score: 5.36491 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 126 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 CATGTAACCGGAATCATGGGCCATCCCCTG 2 31 0 GAATCATGGG 0.985355 -201 CCGAAGACCAGACTCAGGGGACAGCAGACA 5 167 1 GACTCAGGGG 0.933024 -52 ATCACCTCATGGCTGGAACTGGT 13 115 0 ACCTCATGGC 0.910773 -13 CCATGGATATGAATCATGGGATGGATTTGC 15 46 1 GAATCATGGG 0.985355 -71 GGATGGATTTGCATCATGGTTCCAGCCATG 15 64 1 GCATCATGGT 0.973014 -53 CTGTGGTTATGCAACATGGCTGGAACCATG 15 78 0 GCAACATGGC 0.920297 -39 ATGTAACTCTAAATCATGGTTAACCAGTTA 19 119 1 AAATCATGGT 0.890662 -87 ********** Masking position 6 Map Score: 4.71721 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 126 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 9 GTATAGAATCTGATTTTTTTTCTCATGGTA 2 138 1 TGATTTTTTT 0.95947 -94 CAATCTTGAGTGATGTTTCTGTAGCTGCAG 3 64 0 TGATGTTTCT 0.965011 -96 TTATCTTGACTGATGTTTCTGTAGCTACAG 3 99 0 TGATGTTTCT 0.965011 -61 TCACCCCTACTGATTTTTTTCTCCCGGAGC 12 25 1 TGATTTTTTT 0.95947 -32 CAGTTAAATATGAATTTTTTGAATTTATGT 19 143 1 TGAATTTTTT 0.877974 -63 ********** Masking position 6 Map Score: 2.54446 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 22 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 10 CATTGGTTGATGGTTGGAATTCATCCCATG 1 143 0 TGGTTGGAAT 0.936963 -158 AGAGATTCTTTGCCTGTAATGCCGGGGTGA 2 83 0 TGCCTGTAAT 0.923076 -149 CCCGTAGTCTAGCCTGGAATATGACGTGGG 5 76 0 AGCCTGGAAT 0.950338 -143 GATATCTTACTGCATGGAAATGATGATTTC 13 75 1 TGCATGGAAA 0.854706 -53 ATCACCTCATGGCTGGAACTGGTCCCTAC 13 109 0 TGGCTGGAAC 0.988198 -19 TTATGCAACATGGCTGGAACCATGATGCAA 15 72 0 TGGCTGGAAC 0.988198 -45 ********** Masking position 5 Map Score: 2.50586 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 63 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 11 TCTCCATGAAACTTTATAAAGTATTCTGCACTACTGCA 3 17 1 ACTTTATTCG 0.922159 -143 TAAGTTGTGGAATTTATCTTGACTGATGTTTCTGTAGC 3 104 0 AATTTATTAG 0.969589 -56 TATAAGTTAGAACTTATAAGTTATAAGGTGGTTCC 14 8 0 AACTTATTAG 0.974684 -182 TATAAGTTCTAACTTATAATCGGTCAGGGACCGGACTC 14 28 1 AACTTATTAG 0.974684 -162 ACTGGAGATTAACTTATATCTCTTTCAGGAAACCTATA 14 77 0 AACTTATTCG 0.978945 -113 TGACTGGTTAAATTTATTTTACATTAAGCTCCTGCAGG 14 150 0 AATTTATTAG 0.969589 -40 GAATTTTTTGAATTTATGTTAAATCCAGCTGTTTTTAC 19 154 1 AATTTATTCG 0.974684 -52 ******* * * * Masking position 6 Map Score: 2.75214 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 4 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 TAATACACACTTATAAGGAGACTGAGGCTG 1 15 0 TTATAAGGAG 0.830255 -286 AATTATTAAATGATCCGGTGTGCCCCCTAA 1 221 1 TGATCCGGTG 0.94555 -80 GAATGGTTAGTTTTATGGAGCCATTCCCTT 1 259 0 TTTTATGGAG 0.786163 -42 CTTTATAAAGTTTCATGGAGATAAACT 3 8 0 TTTCATGGAG 0.752011 -152 TCCCTTTTTATGATCCGGTGAACTTCAGAG 4 32 0 TGATCCGGTG 0.94555 -35 GGTCTTCGGCTGACACGTTGATGAGAAAAT 5 146 0 TGACACGTTG 0.741788 -73 AACTTATAAGTTATAAGGTGGTTCC 14 6 0 TTATAAGGTG 0.903141 -184 ATTTAAATCTTGACATGGTGGTTTGGGGTG 19 48 0 TGACATGGTG 0.93416 -158 ATCCAGCTGTTTTTACGGTGTTAAAGATTA 19 176 1 TTTTACGGTG 0.935381 -30 ********** Masking position 1 Map Score: 2.9088 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 169 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 13 AATTAAGGAATGACCACAGATTAATATAAA 1 91 1 TGACCACAGA 0.979447 -210 TGTAACCCTGCAGCTACAGAAACATCACTC 3 57 1 CAGCTACAGA 0.905016 -103 TGTAACCCTGTAGCTACAGAAACATCAGTC 3 92 1 TAGCTACAGA 0.954855 -68 CCATGTTGCATAACCACAGACATTTGAGGT 15 89 1 TAACCACAGA 0.97785 -28 TTCATATTCATGACCACACAGCACCCCAAA 19 27 1 TGACCACACA 0.931197 -179 ********** Masking position 6 Map Score: 0.20888 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 39 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 14 ********** No masking Map Score: 6.31916e-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 TAAGGAGACTGAGGCTGGTAA 1 2 0 GAGGCTGGTA 0.913561 -299 GATGGCCCATGATTCCGGTTACATGTGTTT 2 36 1 GATTCCGGTT 0.879417 -196 AAATCCCCCCGGGTCCGCTTTTTTATTAAC 5 20 0 GGGTCCGCTT 0.925239 -199 ATGTGTGTAGGGGGCCCGTAGTCTAGCCTG 5 90 0 GGGGCCCGTA 0.923841 -129 GCTGTCCCCTGAGTCTGGTCTTCGGCTGAC 5 162 0 GAGTCTGGTC 0.920882 -57 TAGAACCTATGGCGCCGGTTCTTTATATCT 8 23 0 GGCGCCGGTT 0.968678 -22 GTTTCTGGATGGCTCCGGGAGAAAAAAATC 12 36 0 GGCTCCGGGA 0.893396 -21 AATAGGTTTGGAGTCCGGTCCCTGACCGAT 14 46 0 GAGTCCGGTC 0.980725 -144 ********** Masking position 5 Map Score: 2.11434 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 392 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357