AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i057_Chorismate_Biosynthes_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 aroI 275 shikimate kinase #2 tyrA 48 prephenate dehydrogenase #3 trpE 215 anthranilate synthase #4 aroB 61 3-dehydroquinate synthase #5 aroF 69 chorismate synthase #6 cheR 236 methyl-accepting chemotaxis proteins (MCPs) methyltransferase #7 aroC 111 3-dehydroquinate dehydratase #8 yqhS 86 similar to 3-dehydroquinate dehydratase #9 yqhR 226 yqhR #10 yqeG 300 similar to hypothetical proteins #11 aroA 235 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase Motif number 1 ACTTCGACGCAAAAAAGCGTTAAAACCTTC 1 89 0 AAAAAAGCGT 0.960515 -187 GTCATTCAGGCAAAAATGGCTACAACAAAG 1 153 1 CAAAAATGGC 0.845906 -123 AAATGGCTACAACAAAGCGCACTATAAGCT 1 166 1 AACAAAGCGC 0.86482 -110 CAAAACAGAACAAAAACCGGCGGCGTTATA 6 44 0 CAAAAACCGG 0.736121 -193 AATAGCAACTAAAAAAGAGCCTTAAAGGGC 7 16 0 AAAAAAGAGC 0.857169 -96 AAATTTTCAAAAAAAAGTTGTACGTGTATA 7 56 1 AAAAAAGTTG 0.838969 -56 TTTCTCATGTAAAAAATGTTCACTTCTCGT 8 44 0 AAAAAATGTT 0.490903 -43 TGACAGGCTGAAAAAATTGCCATAGCCTTG 9 94 1 AAAAAATTGC 0.942284 -133 TCGCAGCTGCCAAAAAGTGTGAGCTTTTTT 9 165 1 CAAAAAGTGT 0.912489 -62 AAATGTCAATAAAAAAGCTCACACTTTTTG 9 175 0 AAAAAAGCTC 0.934845 -52 TTATCCACACCAAAAAGTGGATAACTTGTG 10 95 1 CAAAAAGTGG 0.930673 -206 AAAATTTCGACAAAAATTGGGTTTCTTCAC 10 199 0 CAAAAATTGG 0.867447 -102 AAACTGAGCAAAAAAATTTCGACAAAAATT 10 211 0 AAAAAATTTC 0.813378 -90 TGATTGTCGAAAAAAATCGAACTTGCGCCT 10 247 0 AAAAAATCGA 0.745272 -54 AAAAAAGCGTCCAGATATCA 11 1 1 AAAAAAGCGT 0.960515 -235 TTTTTTACAAAAAAAAGCGCCAGATGATAT 11 25 0 AAAAAAGCGC 0.981732 -211 ACTGAAATACAAAAAATTTTATAAAAACTC 11 135 0 AAAAAATTTT 0.663219 -101 ********** Masking position 5 Map Score: 14.8953 Number of sites scoring better than the average of aligned sites = 2430 Number in coding regions = 2020 Number in noncoding regions = 410 Number of orfs with sites within 600 bp upstream = 385 Fraction of orfs with sites within 600 bp upstream = 0.0618375 Motif number 2 ATACACAAGAGTGTGTATAAAGCAATTAGA 3 32 1 GTGTGTATAA 0.987691 -184 CCACTTTTTGGTGTGGATAACAGAACGATT 10 85 0 GTGTGGATAA 0.989785 -216 TGTGAGTATCGTGTTTATAATTTGTCTAAA 10 121 1 GTGTTTATAA 0.956313 -180 AGAGTGGATAGTGTGTGTAAATTTATCCAC 10 164 1 GTGTGTGTAA 0.981817 -137 TCTTCACCAGGTGTGGATAAATTTACACAC 10 176 0 GTGTGGATAA 0.989785 -125 ACTTAAAAGCGTTTGGGTAATAAAGTAGAG 11 108 1 GTTTGGGTAA 0.946775 -128 ATAAAGTAGAGTTTTTATAAAATTTTTTGT 11 127 1 GTTTTTATAA 0.856561 -109 ********** Masking position 9 Map Score: 9.67041 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 17 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 3 CGCCATTCCTCCCTTCCTATTTATCAT 1 8 1 CCTCCCTTCC 0.946142 -268 ATCTTCTCATTCTCCTTGCCATAAGGAGTG 3 190 1 TCTCCTTGCC 0.951252 -26 GACTTCTTCTCCCTTCATCGCATTAAC 5 53 0 TCTCCCTTCA 0.869062 -17 GCATCAGACCTCTGCCTTTCCCAACGATCT 6 117 1 TCTGCCTTTC 0.970013 -120 AATAAAAAAATCAGCTTTTCAGCTGATTTT 6 147 0 TCAGCTTTTC 0.870851 -90 CTCTACTCTCCCAGTCTCGCTGTCTT 6 221 0 TCTCCCAGTC 0.88178 -16 ACAATCTCTCCTTTTCGCGAGGGTTT 8 71 0 TCTCCTTTTC 0.939571 -16 ATTATCAACCTGCCTATTTCTTTA 9 5 1 TCAACCTGCC 0.895821 -222 GGCAATTTTTTCAGCCTGTCAATCTAGAGG 9 85 0 TCAGCCTGTC 0.962204 -142 AACCCGCACCCTTCCCTTTTTCTTT 10 286 0 GCACCCTTCC 0.936641 -15 TTTTTTCATCCTTTCCCTGCACATT 11 221 0 TCATCCTTTC 0.872637 -15 ********** Masking position 5 Map Score: 9.08523 Number of sites scoring better than the average of aligned sites = 690 Number in coding regions = 532 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 4 TAGTATTTTATCCTCTCATGCCATCTTCTCATTC 3 168 1 TCTCTCAGCT 0.982187 -48 TGCTCTCACTCCTTATGGCAAGGA 3 202 0 TCTCTCATCT 0.931779 -14 TCTCCACATTTTCTCTAATGCGGTCAATTTGAT 4 10 0 TCTCTAAGCT 0.959235 -52 ATAGTAGTCTTACTTAAAAGCGTTAATGCGATGA 5 32 1 TCTTAAAGCT 0.954902 -38 AAAGAGCCCTTTAAGGCTCTTTTTTAGTTG 7 7 1 CCTTTAAGCT 0.906164 -105 TCGTCTCAAATCCTTTCAATCTTTACCTTGTTTT 7 88 0 TCTTTCATCT 0.935917 -24 GCTAACCATTTCCTTTCACTCTATTGTACAGGAA 9 40 1 TCTTTCATCT 0.935917 -187 AGCCTTGCTTTTCCTACATGCATTATACCCGTTA 9 117 1 TCCTACAGCT 0.903323 -110 AGAACGATTGTTCTTATATGCATTTCATGGTAGA 10 60 0 TCTTATAGCT 0.865513 -241 ATAAACACGATACTCACAAGTTATCCACTTTTTG 10 105 0 TCTCACAGTT 0.785227 -196 ATTACTTTATCACTTAAAAGCGTTTGGGTAATAA 11 97 1 CCTTAAAGCT 0.890429 -139 * ****** ** * Masking position 8 Map Score: 8.1257 Number of sites scoring better than the average of aligned sites = 310 Number in coding regions = 278 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 5 GAAGGGTCTTTTTCTGTATGATAAATAGGA 1 25 0 TTTCTGTATG 0.923256 -251 TTGTACAACATTTCTGCAGGTATTTTAATA 1 118 0 TTTCTGCAGG 0.931364 -158 AAAAGAAAGACTTCTTTTGGGTAGAATAAA 3 122 0 CTTCTTTTGG 0.939345 -94 AAAAGAAGTCTTTCTTTTGGGTTTATTTGT 3 134 1 TTTCTTTTGG 0.980519 -82 CCAGTCTCGCTGTCTTTTTGTCCTAGTATA 6 207 0 TGTCTTTTTG 0.808602 -30 AACCTGCCTATTTCTTTAGGATTGCTAACC 9 17 1 TTTCTTTAGG 0.984971 -210 TTGCTCAGTTTTTCTTTAGGCGCAAGTTCG 10 230 1 TTTCTTTAGG 0.984971 -71 ********** Masking position 5 Map Score: 5.1507 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 190 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 TCCCTTCCTATTTATCATACAGAAAAAGAC 1 20 1 TTTATCATAC 0.912345 -256 CTGAATGACATTCATTGTACAACATTTCTG 1 132 0 TTCATTGTAC 0.90706 -144 GAATTATATATTCATTATATGCTTATTTAG 1 230 0 TTCATTATAT 0.748707 -46 AGACATTATGTTTATTCTACCCAAAAGAAG 3 112 1 TTTATTCTAC 0.932007 -104 TTTGAAAATTTCTATTATATGAATAGCAAC 7 37 0 TCTATTATAT 0.671639 -75 TTTACCTTGTTTTATTATACACGTACAACT 7 71 0 TTTATTATAC 0.960328 -41 TCGTGAACATTTTATCATACTGGAAAAGGA 8 18 0 TTTATCATAC 0.912345 -69 TTCCTTTCACTCTATTGTACAGGAAACACC 9 49 1 TCTATTGTAC 0.870133 -178 TTTTCCTACATGCATTATACCCGTTATTTT 9 125 1 TGCATTATAC 0.820715 -102 TGAAGTTATCTTTAATCTACCATGAAATGC 10 45 1 TTTAATCTAC 0.658557 -256 ********** Masking position 4 Map Score: 4.51424 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 130 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 7 ATAACATATTTTTCAGCAAAAAG 5 4 0 TTTCAGCAAA 0.874272 -66 AATTGTATTGTTTCAATAAAAAAATCAGCT 6 161 0 TTTCAATAAA 0.862969 -76 TAATAGAAATTTTCAAAAAAAAGTTGTACG 7 50 1 TTTCAAAAAA 0.921736 -62 GTATAATGCATGTAGGAAAAGCAAGGCTAT 9 115 0 TGTAGGAAAA 0.546404 -112 AAAAATGAAATGTCAATAAAAAAGCTCACA 9 182 0 TGTCAATAAA 0.838963 -45 TACATCACTCTTTAGACAAATTATAAACAC 10 131 0 TTTAGACAAA 0.782666 -170 AGCAAAAAAATTTCGACAAAAATTGGGTTT 10 205 0 TTTCGACAAA 0.948196 -96 TCAAAATGATTGTCGAAAAAAATCGAACTT 10 253 0 TGTCGAAAAA 0.926009 -48 CAAGGGTTTTTTACAAAAAAAAGCGCCAGA 11 31 0 TTACAAAAAA 0.650091 -205 ********** Masking position 8 Map Score: 2.01145 Number of sites scoring better than the average of aligned sites = 775 Number in coding regions = 599 Number in noncoding regions = 176 Number of orfs with sites within 600 bp upstream = 199 Fraction of orfs with sites within 600 bp upstream = 0.0319627 Motif number 8 ATAAAGCAATTAGAATGAGTTGAGTTAGAG 3 48 1 TAGAATGAGT 0.868361 -168 TAGGGTAGCAGAGAATGAGTTTAGTTGAGC 3 80 1 GAGAATGAGT 0.980716 -136 TTATGGCAAGGAGAATGAGAAGATGGCATG 3 184 0 GAGAATGAGA 0.975035 -32 GACCGCATTAGAGAAAATGTGGAGAATATG 4 19 1 GAGAAAATGT 0.765028 -43 AGAAAATGTGGAGAATATGAGAAAACTGTC 4 30 1 GAGAATATGA 0.891617 -32 GCGATGAAGGGAGAAGAAGTC 5 59 1 GAGAAGAAGT 0.953301 -11 AAACCCTCGCGAAAAGGAGAGATTGT 8 71 1 GAAAAGGAGA 0.80769 -16 ********** Masking position 5 Map Score: 1.77396 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 229 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 9 TAACGCTTTTAAGTAAGACTACTATAACATA 5 26 0 AAGTAAGCTA 0.935542 -44 CTGATAAAACAAGCTATACTAGGACAAAAAG 6 193 1 AAGCTATCTA 0.964903 -44 AGGAAATGGTTAGCAATCCTAAAGAAATAGG 9 23 0 TAGCAATCTA 0.902998 -204 CATGTAGGAAAAGCAAGGCTATGGCAATTTT 9 106 0 AAGCAAGCTA 0.975325 -121 GTAATCTATGAAGCTATCCTACATGATGTGA 11 71 0 AAGCTATCTA 0.965536 -165 ATCTTACTATAAGTAATTCCAAATGGAAATA 11 164 0 AAGTAATCCA 0.866205 -72 ******* *** Masking position 6 Map Score: 1.29104 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 28 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 10 ATCATACAGAAAAAGACCCTTCCATCGAAG 1 33 1 AAAAGACCCT 0.972068 -243 CTATATAACAAATAAACCCAAAAGAAAGAC 3 141 0 AATAAACCCA 0.899032 -75 TAGCAACTAAAAAAGAGCCTTAAAGGGCTC 7 14 0 AAAAGAGCCT 0.888633 -98 TTTTTTACATGAGAAACCCTCGCGAAAAGG 8 58 1 GAGAAACCCT 0.943082 -29 ACACCTGGTGAAGAAACCCAATTTTTGTCG 10 192 1 AAGAAACCCA 0.960454 -109 TTTTTTTTGTAAAAAACCCTTGAACATTGC 11 39 1 AAAAAACCCT 0.976732 -197 ********** Masking position 6 Map Score: 1.93718 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 69 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 11 ********** No masking Map Score: 6.83075e-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: 6.83075e-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 13 ********** No masking Map Score: 6.83075e-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