AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -ityrR_mjan_opreg_300.orf -g0.314 -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 = 0.314 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MJ0611 300 conserved hypothetical integral membrane protein #2 MJ0612 94 chorismate mutase/prephenate dehydratase (tyrA) #3 MJ1392 300 2-isopropylmalate synthase (leuA) #4 MJ1393 247 conserved hypothetical protein Motif number 1 GAAATACAACAACTCTTAAATGTGGAGCTA 1 84 0 AACTCTTAAA 0.874827 -217 CAATCCCAGTAAATATAAGAGTGGCAGTAA 1 120 1 AAATATAAGA 0.478456 -181 GAGTAGAATTAAATCTATAAGTGCAAATAT 1 152 0 AAATCTATAA 0.91367 -149 TCTACTCCCTTACTCTTTAAAAACTGGAAT 1 175 1 TACTCTTTAA 0.625546 -126 GTAGTTTTCCAAATATTAATCCAGTTATAA 1 231 0 AAATATTAAT 0.734929 -70 CTAACAATGAAACTTTTAGAAAAAGTTTCA 2 35 1 AACTTTTAGA 0.692591 -60 AGTTTCATCAAAATATATATACTACAATCC 2 58 1 AAATATATAT 0.543184 -37 ATTAAATCTTTAATGCGAGTATT 3 4 1 AAATCTTTAA 0.970158 -297 AATCTTTATAAAATTTTTATTATTTTTGAA 3 56 0 AAATTTTTAT 0.911593 -245 ACTTTATTAATAATCTTTATAAAATTTTTA 3 67 0 TAATCTTTAT 0.750132 -234 CGCAGGAATAAAATCTTTAAAAGAAATCTT 3 109 1 AAATCTTTAA 0.970158 -192 TCTTTAAAAGAAATCTTAATTTATAAATTT 3 122 1 AAATCTTAAT 0.926252 -179 CTTTAAATTTAAATTTATAAATTAAGATTT 3 132 0 AAATTTATAA 0.867925 -169 TTGGTAATATACATCTTTAAATTTAAATTT 3 146 0 ACATCTTTAA 0.90719 -155 TTTCCCACATAAATTTTAAATATACAATAT 3 194 1 AAATTTTAAA 0.938522 -107 ACAATATCAAATATCTTTGAGATGATTCAA 3 217 1 ATATCTTTGA 0.560883 -84 TAATTTAATGAAATTTAAATACTCATAATG 3 262 0 AAATTTAAAT 0.717426 -39 ACCTAATAAAACATTTTAAAATAAGCAAAA 4 14 0 ACATTTTAAA 0.821115 -234 TAGGTATTGATAATTTTAATATCAAAAGGT 4 39 1 TAATTTTAAT 0.585021 -209 TTCTTTTTCTAAATTTTTGAAAAATCAAAA 4 120 1 AAATTTTTGA 0.912891 -128 CATTTTTTAGACATTTTTGATTTTTCAAAA 4 134 0 ACATTTTTGA 0.759093 -114 ********** Masking position 6 Map Score: 21.6131 Number of sites scoring better than the average of aligned sites = 2691 Number in coding regions = 2012 Number in noncoding regions = 679 Number of orfs with sites within 600 bp upstream = 477 Fraction of orfs with sites within 600 bp upstream = 0.0766142 Motif number 2 TCTGGGGCAATATTTGGAATAATGGGAGCTT 1 44 1 TATTTGAATA 0.709439 -257 CTAAGTGTGTTATGTGTGCAATTCCAGTTTT 1 194 0 TATGTTGCAA 0.872252 -107 ACTGGATTAATATTTGGAAAACTACTATATA 1 236 1 TATTTGAAAA 0.958073 -65 GGAAAACTACTATATAGGAAAATGGATGTAA 1 251 1 TATATGGAAA 0.881538 -50 TTGATGAAACTTTTTCTAAAAGTTTCATTGT 2 38 0 TTTTTTAAAA 0.831908 -57 AAATTTTTATTATTTTTGAAAGATACTATAC 3 45 0 TATTTTGAAA 0.958504 -256 TTATTAATAATCTTTATAAAATTTTTATTAT 3 63 0 TCTTTTAAAA 0.810188 -238 ATTTAAAATTTATGTGGGAAATAGTTCTGGA 3 184 0 TATGTGGAAA 0.956564 -117 TTTGATATTGTATATTTAAAATTTATGTGGG 3 197 0 TATATTAAAA 0.877535 -104 ATTTTTCAAAAATTTAGAAAAAGAACCCAAA 4 114 0 AATTTGAAAA 0.825166 -134 AAAAATCAAAAATGTCTAAAAAATGTTCCAT 4 139 1 AATGTTAAAA 0.812448 -109 TTCCATAAATTATTTATACAAACGGAAGACA 4 164 1 TATTTTACAA 0.877515 -84 ACCTCATGCATTTGTGTGAAATAGGGGAACA 4 221 0 TTTGTTGAAA 0.828829 -27 ***** ***** Masking position 11 Map Score: 11.2018 Number of sites scoring better than the average of aligned sites = 447 Number in coding regions = 330 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 3 TTCACTGGGGATTACAACCCATC 1 2 1 TCATGGGATT 0.954995 -299 CACTCTTATATTTACTGGGATTGGTAAGGGAA 1 111 0 TTTCGGGATT 0.930254 -190 CATAACACACTTAGCTGGGCTTATAACTGGAT 1 211 1 TTACGGGCTT 0.976828 -90 TACAATCCTATAAAGGGGGAATATT 2 80 1 TAAGGGGAAT 0.891793 -15 ATTAATAAAGTTAATGGGGCTTTCGCAGGAAT 3 86 1 TTATGGGCTT 0.975032 -215 TATTTAAAATTTATGTGGGAAATAGTTCTGGA 3 184 0 TTAGGGGAAA 0.876758 -117 AAATTATTTTTTATGAGGGATTGTT 3 286 1 TTAGGGGATT 0.990862 -15 TTAAAATGTTTTATTAGGTATTGATAATTTTA 4 25 1 TTATGGTATT 0.885071 -223 *** * ****** Masking position 1 Map Score: 4.13476 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 119 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 4 CATTGGATTTTTAATAGTATCTTACATCCAT 1 272 0 TTAATATATC 0.828042 -29 CATTGTTAGGTTTTTATTTTCCATGAATTTC 2 13 0 TTTTTATTTC 0.851239 -82 TGCGAGTATTTTATGACTTTCGTATAGTATC 3 24 1 TTATGATTTC 0.961517 -277 TATAAAATTTTTATTATTTTTGAAAGATACT 3 49 0 TTATTATTTT 0.923812 -252 CCCATTAACTTTATTAATAATCTTTATAAAA 3 73 0 TTATTATAAT 0.646467 -228 AATTTATAAATTAAGATTTCTTTTAAAGATT 3 120 0 TTAAGATTCT 0.698866 -181 ATCAGATTCATTATGAGTATTTAAATTTCAT 3 254 1 TTATGATATT 0.917046 -47 GATATTAAAATTATCAATACCTAATAAAACA 4 31 0 TTATCATACC 0.809589 -217 ATATCGGCTGTTATTATTTTCAAATTGAAAA 4 73 1 TTATTATTTC 0.958441 -175 TTTTAGACATTTTTGATTTTTCAAAAATTTA 4 129 0 TTTTGATTTT 0.765231 -119 AGACATTACATTATTACTACCTACTTAAGAA 4 190 1 TTATTATACC 0.932515 -58 ****** **** Masking position 6 Map Score: 5.88872 Number of sites scoring better than the average of aligned sites = 680 Number in coding regions = 502 Number in noncoding regions = 178 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 5 TTCACTGGGGATTACAACCCATCAGT 1 7 1 GGGGATTACA 0.931253 -294 GGAGCTTCTGGGGCAATATTTGGAATAATG 1 38 1 GGGCAATATT 0.972535 -263 GGATTGGTAAGGGAAATACAACAACTCTTA 1 96 0 GGGAAATACA 0.960589 -205 TCCTATAAAGGGGGAATATT 2 85 1 GGGGAATATT 0.989575 -10 AAATTTATGTGGGAAATAGTTCTGGACTAA 3 180 0 GGGAAATAGT 0.961107 -121 GTGTGAAATAGGGGAACATTCTTAAGTAGG 4 209 0 GGGGAACATT 0.971995 -39 ********** Masking position 5 Map Score: 4.50124 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 52 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 AGCTCCCATTATTCCAAATATTGCCCCAGA 1 44 0 ATTCCAAATA 0.942037 -257 ATATAGTAGTTTTCCAAATATTAATCCAGT 1 236 0 TTTCCAAATA 0.950769 -65 TCACCATTGGATTTTTAATAGTATCTTACA 1 277 0 ATTTTTAATA 0.495466 -24 TTAATAATCTTTATAAAATTTTTATTATTT 3 61 0 TTATAAAATT 0.533642 -240 AAGATGTATATTACCAACTTTTTAGTCCAG 3 159 1 TTACCAACTT 0.55838 -142 TCCCACATAAATTTTAAATATACAATATCA 3 196 1 ATTTTAAATA 0.797103 -105 TAAATATACAATATCAAATATCTTTGAGAT 3 210 1 ATATCAAATA 0.877159 -91 TAATAAAACATTTTAAAATAAGCAAAAATA 4 11 0 TTTTAAAATA 0.766324 -237 AAAATTATCAATACCTAATAAAACATTTTA 4 26 0 ATACCTAATA 0.703938 -222 GCTGTTATTATTTTCAAATTGAAAACCTTG 4 79 1 TTTTCAAATT 0.894487 -169 TTGGGTTCTTTTTCTAAATTTTTGAAAAAT 4 115 1 TTTCTAAATT 0.788613 -133 ********** Masking position 7 Map Score: 3.53275 Number of sites scoring better than the average of aligned sites = 1183 Number in coding regions = 1005 Number in noncoding regions = 178 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 7 ACTGGGGATTACAACCCATCAGTCGGAGCT 1 14 1 ACAACCCATC 0.965069 -287 TAAGGGAAATACAACAACTCTTAAATGTGG 1 89 0 ACAACAACTC 0.965986 -212 AAATATGATTACTGCCACTCTTATATTTAC 1 128 0 ACTGCCACTC 0.963228 -173 AACAATCCCTCATAAAAAATA 3 290 0 ACAATCCCTC 0.965069 -11 AACTTCACCTCATGCATTTGT 4 237 0 ACTTCACCTC 0.946449 -11 ********** Masking position 9 Map Score: 0.0399434 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 102 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 8 ********** No masking Map Score: -3.13817e-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: -3.13817e-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: -3.13817e-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