AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -ifruR_mthe_opreg_300.orf -g0.495 -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 = 0.495 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MTH184 125 isocitrate dehydrogenase #2 MTH1040 300 unknown #3 MTH1041 195 triosephosphate isomerase #4 MTH1119 132 ribosomal protein L10 #5 MTH1386 300 3-isopropylmalate dehydratase, LeuD subunit Motif number 1 AAAAATCTGAAAGCCTTTTAAATTAAATCA 2 14 0 AAGCCTTTTA 0.98541 -287 GGAAAAAATAAAACCTTTTAACAGAGTATT 2 67 1 AAACCTTTTA 0.977045 -234 ATGCTGAAAAAAGCATTATATAAGCCTTTT 2 134 1 AAGCATTATA 0.905924 -167 AGCATTATATAAGCCTTTTTGTCTTATTCC 2 145 1 AAGCCTTTTT 0.976785 -156 CACTATATATAAACCTTTGTTTCCGGAATA 2 169 0 AAACCTTTGT 0.87577 -132 ATTAAATTGTAAACATTATA 3 1 0 AAACATTATA 0.858565 -195 GGAGCTCACCAAGTCTTTTATAGACGGGGC 5 38 0 AAGTCTTTTA 0.939204 -263 CTATATATTTAAATCTTATTATCAAAGTAT 5 88 1 AAATCTTATT 0.790977 -213 ********** Masking position 2 Map Score: 6.7655 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 86 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 2 CCCCATATTCATTCTTTGGAAAAAATAAAACC 2 50 1 ATCTTTGGAA 0.916037 -251 GATTCTAATCATGAATTGATAATGGCGCCCCA 2 96 0 ATAATTGAAA 0.706 -205 GATGATGTTAAACCAGTGAAAAATTAAATTGT 3 21 0 AACAGTGAAA 0.918234 -175 ATTATAAAATATGCTGTGACATCCGTGCGGGA 3 139 0 ATCTGTGAAT 0.974193 -57 CACCTCAACCATACTATGAGATATCCCATTAA 3 172 1 ATCTATGAAT 0.853775 -24 TCCTCCTGTGATCCTGTGAGAATAACTATGAA 4 105 0 ATCTGTGAAA 0.991699 -28 GGCCCTATAAATACTTTGATAATAAGATTTAA 5 96 0 ATCTTTGAAA 0.979034 -205 AAAGACAGTTATCCAGTGAACATATGGGGACA 5 178 1 ATCAGTGACA 0.936067 -123 TCCATGGGGCAGTCTGTGAAAATTAGAGCCTC 5 223 0 AGCTGTGAAA 0.969447 -78 ** ****** ** Masking position 7 Map Score: 5.53846 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 158 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 3 TTTATGATGTCTTCATATTCCCTTTTAT 1 4 0 CTTATCCCTT 0.874522 -122 AATATGAAGACATCATAAAAACCCCCAGCTTCCAA 1 20 1 CATATAACCC 0.876454 -106 GATCATTCAGCTTCATGAGAACACTTCAAGAGGAA 1 96 1 CTTATAACCT 0.925743 -30 TACCATGAACCTTAATCACATCACCACTATATATA 2 188 0 CTTATATCCC 0.918803 -113 CCACTGATGGCAGGATCTACCCGCCGACCTTACCA 2 218 0 CAGATCCCCC 0.95491 -83 GCGAGTGTCTCTTAATCTTACCGCCTCCACTGATG 2 244 0 CTTATACCCC 0.992338 -57 ACTGGTTTAACATCATCCAACAGCTTTCTGCATTT 3 36 1 CATATACACT 0.928687 -160 CAACAGCTTTCTGCATTTAACACCTTCACTATGTG 3 53 1 CTGATACACT 0.96788 -143 TGGGGATGCGCTGGATATTACAGGCAAATTCATTC 3 86 1 CTGATACAGC 0.861977 -110 TCACAGCATATTTTATAATACACCTCAACCATACT 3 152 1 TTTATACACT 0.72438 -44 AAAAACTCGTCTGAATTTTACATCTATATTTTCAC 5 130 0 CTGATACACT 0.96788 -171 TTGCTGGAACCTTTATGAACCCTTCAATTATTCTG 5 259 1 CTTATCCCTC 0.91773 -42 *** ** *** ** Masking position 5 Map Score: 7.29866 Number of sites scoring better than the average of aligned sites = 616 Number in coding regions = 566 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 4 ATTTTTATCATTACAGCCTTAAAATATTATCC 1 58 1 TTAACCTTAA 0.837348 -68 CCTTAAAATATTATCCCATGCAGATCATTCAG 1 74 1 TTACCATGCA 0.901817 -52 CAGCTTCATGAGAACACTTCAAGAGGAATTTA 1 103 1 AGACCTTCAA 0.859585 -23 TCTCTTAATCTTACCGCCTCCACTGATGGCAG 2 240 0 TTACCCTCCA 0.975673 -61 CTTTCTGCATTTAACACCTTCACTATGTGGGG 3 59 1 TTACCCTTCA 0.970177 -137 AATTCATTCATGAACCCCTTCAACAACTCCCG 3 112 1 TGACCCTTCA 0.980802 -84 ATACTATGAGATATCCCATTAATC 3 182 1 ATACCATTAA 0.760705 -14 AAGAGTTAATAGATAACCTGAAAATATAAGGA 4 29 0 AGAACCTGAA 0.822283 -104 AAAGACTTGGTGAGCTCCTGAAAACTAATAAG 5 50 1 TGACCCTGAA 0.983363 -251 GGAACCTTTATGAACCCTTCAATTATTCTGCT 5 264 1 TGACCTTCAA 0.931037 -37 *** * ****** Masking position 9 Map Score: 6.36635 Number of sites scoring better than the average of aligned sites = 849 Number in coding regions = 786 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 5 AAAGAATGAATATGGGGCCCTAAAAAAATC 2 37 0 TATGGGGCCC 0.991184 -264 TTTAACAGAGTATTGGGGCGCCATTATCAA 2 83 1 TATTGGGGCG 0.965869 -218 TCAAAGTATTTATAGGGCCGGGTGAAAATA 5 109 1 TATAGGGCCG 0.986989 -192 CCAGTGAACATATGGGGACATCAGAAGGTT 5 190 1 TATGGGGACA 0.950233 -111 GCAAGTGGTCCATGGGGCAGTCTGTGAAAA 5 233 0 CATGGGGCAG 0.962987 -68 ********** Masking position 3 Map Score: 1.46872 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 74 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 6 TTAAAAGGTTTTATTTTTTCCAAAGAATGA 2 58 0 TTATTTTTTC 0.967477 -243 GCTTATATAATGCTTTTTTCAGCATTCAGA 2 129 0 TGCTTTTTTC 0.900176 -172 TGTTTACAATTTAATTTTTCACTGGTTTAA 3 16 1 TTAATTTTTC 0.900414 -180 ATATGTATCCTTATATTTTCAGGTTATCTA 4 22 1 TTATATTTTC 0.94098 -111 AATTTTACATCTATATTTTCACCCGGCCCT 5 122 0 CTATATTTTC 0.929665 -179 AAAATTCAGACGAGTTTTTCAGTATGAAGG 5 146 1 CGAGTTTTTC 0.902062 -155 ********** Masking position 6 Map Score: 1.10191 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 34 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 7 TCTTGAAGTGTTCTCATGAAGCTGAATGAT 1 97 0 TTCTCATGAA 0.832838 -29 CAGAGGATTCTAATCATGAATTGATAATGG 2 103 0 TAATCATGAA 0.962202 -198 CCCGCCGACCTTACCATGAACCTTAATCAC 2 204 0 TTACCATGAA 0.958053 -97 CAGGCAAATTCATTCATGAACCCCTTCAAC 3 106 1 CATTCATGAA 0.807633 -90 ATTTTCAGGTTATCTATTAACTCTTTGCTG 4 36 1 TATCTATTAA 0.677108 -97 AGTATCTCGGTAACCATTAATAAATATTGT 4 72 0 TAACCATTAA 0.93482 -61 CCTGTGAGAATAACTATGAAATGAGTATCT 4 95 0 TAACTATGAA 0.934767 -38 ********** Masking position 6 Map Score: 0.93729 Number of sites scoring better than the average of aligned sites = 412 Number in coding regions = 360 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 8 ********** No masking Map Score: 1.46615e-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 9 ********** No masking Map Score: 1.46615e-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: 1.46615e-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