AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00300_mthe_reg_100.orf -o00300_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 MTH415 199 conserved protein #2 MTH531 291 UDP-N-acetylmuramyl tripeptide synthetase related protein #3 MTH532 28 UDP-N-acetylmuramyl tripeptide synthetase related protein #4 MTH533 41 unknown #5 MTH800 52 dihydrodipicolinate reductase #6 MTH802 49 aspartokinase II alpha subunit #7 MTH804 40 chorismate mutase, subunit A #8 MTH805 240 conserved protein (homoserine kinase related) #9 MTH1231 40 conserved protein #10 MTH1232 25 homoserine dehydrogenase #11 MTH1335 73 diaminopimelate decarboxylase #12 MTH1542 37 conserved protein #13 MTH1543 229 thiamine biosynthesis protein Motif number 1 AACATGGCCTCAGATTCAGCAGAGGGAACATGGA 1 45 0 CAACAGCGAG 0.919378 -155 ATCACCTCTAACACTCCAGGGAGTTCATGGA 2 8 1 CTACTCCGGG 0.983667 -284 TGGGTGGATACATATCCTCCCGGGTGAGGATCTT 2 118 1 CAACTCCGGG 0.997669 -174 AGATCAGTGCCAGTTCCTCCAGGACCATCATGAG 5 15 0 CATCTCCGGA 0.962551 -38 TCTGATATAACAAAAACTCCTGAAAACATGACTG 8 32 0 CAACTCCGAA 0.987334 -209 CTCAAGCTCTCAAACACTGCAAAGTGTATTCATC 8 155 0 CAACTGCAAG 0.888207 -86 AGTGAACGATCATAGAATCCTGGA 8 227 1 CAAATCCGGA 0.941033 -14 TCATGTTTGTCAGAGTCTGGGGGGGCCCCA 13 7 0 CAACTGGGGG 0.965027 -223 GGGGAGACATCAAAGACTCCTTAAGAGTATTAAC 13 83 1 CAACTCCTAA 0.884288 -147 TGATCCAGATCATACCCTCACGGGTTAAGGGTCA 13 188 1 CAACTCAGGG 0.976724 -42 ** * **** *** Masking position 1 Map Score: 10.0174 Number of sites scoring better than the average of aligned sites = 491 Number in coding regions = 465 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 2 CCCATGTCTGCAGTGGTCATCCTGT 1 5 1 TGTCTGAGTG 0.968528 -195 TATAAGGCTTAGTCTATCGTGCTACAATGAT 1 116 0 AGTCTACGTG 0.835889 -84 AAACACATAAAGTCTATGGTGCTGCAGTGAT 1 146 0 AGTCTAGGTG 0.956923 -54 ATCCATGAACTCCCTGGAGTGTTAGAGGTGA 2 12 0 TCCCTGAGTG 0.972714 -280 TCCTTAAAGAGCAGTTAACGG 3 1 1 TCCTTAAGAG 0.644417 -28 TGATGAATACACTTTGCAGTGTTTGAGAGCT 8 154 1 ACTTTGAGTG 0.933021 -87 AGTGTTTGAGAGCTTGAGGTGCTCTCTGGAG 8 171 1 AGCTTGGGTG 0.962592 -70 CTTGAGGTGCTCTCTGGAGTGCTTTGCAGCC 8 183 1 TCTCTGAGTG 0.968528 -58 ATAAATTAAATGCCTGATGTGACTATAAATC 9 18 0 TGCCTGTGTG 0.897905 -23 ACAATATAAGTCCTTAGGGTGTGAAGAT 11 8 0 TCCTTAGGTG 0.920935 -66 ATTTGATTAAACTTTAGGGAGGATCAACACT 11 52 1 ACTTTAGGAG 0.713868 -22 TGTTTGTCAGAGTCTGGGGGGGCCCCA 13 7 0 AGTCTGGGGG 0.910991 -223 ****** **** Masking position 5 Map Score: 8.94821 Number of sites scoring better than the average of aligned sites = 880 Number in coding regions = 829 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 3 TTCATGGATTACTGAGCCAGATGCCTGACCC 2 34 1 ACTGACCAGA 0.972177 -258 GAGCCAGATGCCTGACCCGGGATCTGATAGC 2 47 1 CCTGACCGGG 0.97843 -245 ACCTAAAGATCCTCACCCGGGAGGATATGTA 2 126 0 CCTCACCGGG 0.98588 -166 TGGCACCCGTCCTGACCGAGGTAGTGGGTGT 2 198 0 CCTGACGAGG 0.857882 -94 AGGAACTGGCACTGATCTAGGGGGTGTGATG 5 31 1 ACTGACTAGG 0.97742 -22 AGCCGTGGCCCCTCAACTAGGGGAGACATCA 13 64 1 CCTCACTAGG 0.977884 -166 TCTCATTTCCGCTGATCCAGATCATACCCTC 13 176 1 GCTGACCAGA 0.9672 -54 ***** ***** Masking position 5 Map Score: 8.53701 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 204 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 4 CTGCAGTGGTCATCCTGTCACACAGGATCCA 1 18 1 CATCCTGTAC 0.828195 -182 CTGGCTCAGTAATCCATGAACTCCCTGGAGT 2 23 0 AATCCATGAC 0.598359 -269 GATATGTATCCACCCATAGACACTCTACCTA 2 103 0 CACCCATAAC 0.952193 -189 TCCATAGGTACACCCACTACCTCGGTCAGGA 2 189 1 CACCCACTCC 0.948874 -103 TTAAATGCACCCATAAACGTTTTTATTA 2 274 0 CACCCATAAC 0.952193 -18 AGTGCCAGTTCCTCCAGGACCATCATGAGCC 5 13 0 CCTCCAGGCC 0.954582 -40 GACCTTTTTACCTCCAGTCATGTTTTCAGGA 8 18 1 CCTCCAGTAT 0.916965 -223 TTATATCAGACATCCATGTACCATCCTAAAT 8 56 1 CATCCATGAC 0.954051 -185 ACAAAAACCTCCACATATTTTCTGT 10 8 0 CCTCCACAAT 0.846375 -18 ACCACCCACTCCTTTTTTTAGAG 12 3 1 CACCCACTCT 0.856861 -35 TGGGGCCCCCCCAGACTCTGACAAACAT 13 8 1 CCCCCAGATC 0.835386 -222 TGATTGGTTCCATCCAGTTATAAAAACTACT 13 129 0 CATCCAGTAT 0.93067 -101 ******** ** Masking position 5 Map Score: 7.88566 Number of sites scoring better than the average of aligned sites = 1295 Number in coding regions = 1225 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 5 ATCAGACTCCTCTCAACTTG 1 190 0 ATCAGACTCC 0.954678 -10 CTATATAGCTATCAGATCCCGGGTCAGGCA 2 55 0 ATCAGATCCC 0.954678 -237 GCATCACACCCCCTAGATCAGT 5 41 0 ATCACACCCC 0.991449 -12 TAACCTTCACAACCTTTTAAATGTT 6 35 0 TTCACAACCT 0.775623 -15 GGTATCAGACCTTTTTACCTCCA 8 4 1 ATCAGACCTT 0.949763 -237 TTTTTGTTATATCAGACATCCATGTACCAT 8 50 1 ATCAGACATC 0.805745 -191 ATCTTCACACCCTAAGGACTTAT 11 4 1 TTCACACCCT 0.968707 -70 AAACTACTGTTTCAGTCCCCGTTAATACTC 13 107 0 TTCAGTCCCC 0.939754 -123 GCTGATCCAGATCATACCCTCACGGGTTAA 13 186 1 ATCATACCCT 0.93692 -44 ********** Masking position 4 Map Score: 8.56599 Number of sites scoring better than the average of aligned sites = 389 Number in coding regions = 351 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 TCTCTGTGGCAAGGTTTATATCATTGTAGCA 1 97 1 AGGTTTATAT 0.915475 -103 ACGATAGACTAAGCCTTATATCACTGCAGCA 1 127 1 AGCCTTATAT 0.841122 -73 CTCACCCGGGAGGATATGTATCCACCCATAG 2 115 0 AGATATGTAT 0.814039 -177 GTAAGATATATATTGTATGATTA 4 3 1 AGATATATAT 0.954525 -39 ATATTGTATGATTATTTATATAAAATTGAGG 4 20 1 ATATTTATAT 0.889056 -22 ATCTAAGTGCAATATTTATATAGTGGTAGAA 8 113 0 ATATTTATAT 0.889056 -128 ATGAAAAGATTTATAGTCACATCAGG 9 6 1 AGATTTATAG 0.906257 -35 TCACACCCTAAGGACTTATATTGTCATTTGG 11 15 1 AGACTTATAT 0.957733 -59 TTTTTTAGAGAAGATTAATATATT 12 24 1 AGATTAATAT 0.867069 -14 ATCAGCGGAAATGAGATATATGGATATCATA 13 161 0 AGAGATATAT 0.847912 -69 * ********* Masking position 9 Map Score: 5.79786 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 29 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 7 AGATTCAGCAGAGGGAACATGGATCCTGTG 1 38 0 GAGGGAACAT 0.947904 -162 TAACACTCCAGGGAGTTCATGGATTACTGA 2 19 1 GGGAGTTCAT 0.870207 -273 ATCCTCACCCGGGAGGATATGTATCCACCC 2 119 0 GGGAGGATAT 0.952037 -173 TGGATCATTCGGTGGGATATCTACCAGAGG 2 163 0 GGTGGGATAT 0.952037 -129 AAAAATTTAGGATGGTACATGGATGTCTGA 8 61 0 GATGGTACAT 0.898061 -180 TTTATATAGTGGTAGAACATTCTATTAATA 8 100 0 GGTAGAACAT 0.939891 -141 CCCTCAACTAGGGGAGACATCAAAGACTCC 13 73 1 GGGGAGACAT 0.951203 -157 ********** Masking position 9 Map Score: 1.98205 Number of sites scoring better than the average of aligned sites = 540 Number in coding regions = 509 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 8 CTCTCTGTGACAGGTCTCTGTGGCAAGGTTT 1 83 1 CAGGTCTCTT 0.927625 -117 ATCAAGTTGAGAGGAGTCTGAT 1 188 1 GAGGAGTCTA 0.855979 -12 CGGGTGCCATCAGGTGACTCTTATTCACAGA 2 220 1 CAGGTGACTT 0.898086 -72 GACAGAATTTTTTTCATTTTTTC 6 3 1 CAGAATTTTT 0.70305 -47 GTCATGTTTTCAGGAGTTTTTGTTATATCAG 8 34 1 CAGGAGTTTT 0.981888 -207 TCCAGGATTCTATGATCGTTCAC 8 228 0 CAGGATTCTT 0.976556 -13 AAAATATGTGGAGGTTTTTGT 10 15 1 GAGGTTTTTT 0.797357 -11 TAATACTCTTAAGGAGTCTTTGATGTCTCCC 13 84 0 AAGGAGTCTT 0.93051 -146 GGGACTGAAACAGTAGTTTTTATAACTGGAT 13 118 1 CAGTAGTTTT 0.858295 -112 ********* * Masking position 9 Map Score: 3.02525 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 314 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 9 TCTCAACTTGATGGATACATGTGAAACACA 1 170 0 ATGGATACAT 0.905055 -30 GCTATATAGGATGAGAACATATCTTTATAG 2 76 1 ATGAGAACAT 0.91238 -216 GTGTCTATGGGTGGATACATATCCTCCCGG 2 111 1 GTGGATACAT 0.896705 -181 AAAAACGTTTATGGGTGCATTTAA 2 278 1 ATGGGTGCAT 0.809966 -14 ACAAAAACTCCTGAAAACATGACTGGAGGT 8 27 0 CTGAAAACAT 0.925252 -214 TATTTAATTGATGAATACACTTTGCAGTGT 8 146 1 ATGAATACAC 0.864591 -95 TGATCGTTCACTGAATAGATTATTAGGCTG 8 209 0 CTGAATAGAT 0.875557 -32 ATGAAAAGATTTATAGTCAC 9 1 1 ATGAAAAGAT 0.866974 -40 ********** Masking position 9 Map Score: 1.93823 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 167 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 10 CCCTGGAGTGTTAGAGGTGAT 2 2 0 TTAGAGGTGA 0.759125 -290 TAATCTGTGAATAAGAGTCACCTGATGGCA 2 224 0 ATAAGAGTCA 0.552522 -68 TCCTTAAAGAGCAGTTAACGGTG 3 4 1 TTAAAGAGCA 0.650356 -25 TAAAGAGCAGTTAACGGTGAATCA 3 15 1 TTAACGGTGA 0.959418 -14 TTTCTTCCATTCAAGGGTCACTGGAG 7 7 0 TCAAGGGTCA 0.905411 -34 CTTGAATGGAAGAAAGGGGAATGTAATTT 7 22 1 AGAAAGGGGA 0.800745 -19 ATCTATTCAGTGAACGATCATAGAATCCTG 8 219 1 TGAACGATCA 0.760825 -22 CTTAAGAGTATTAACGGGGACTGAAACAGT 13 102 1 TTAACGGGGA 0.944188 -128 CCCTCACGGGTTAAGGGTCAAACCAGAAGG 13 202 1 TTAAGGGTCA 0.968944 -28 GGGTCAAACCAGAAGGGTGATTAC 13 216 1 AGAAGGGTGA 0.920991 -14 ********** Masking position 3 Map Score: 2.37427 Number of sites scoring better than the average of aligned sites = 618 Number in coding regions = 560 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 11 ********** No masking Map Score: -1.57497e-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: -1.57497e-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: -1.57497e-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