AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00290_mthe_reg_300.orf -o00290_mthe_300.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 MTH723 149 2-isopropylmalate synthase #2 MTH725 149 conserved protein #3 MTH726 92 unknown #4 MTH767 83 valyl-tRNA synthetase #5 MTH829 61 3-isopropylmalate dehydratase, LeuD subunit #6 MTH831 25 molybdenum cofactor biosynthesis MoaA homolog #7 MTH1375 22 isoleucyl-tRNA synthetase #8 MTH1376 65 conserved protein #9 MTH1386 300 3-isopropylmalate dehydratase, LeuD subunit #10 MTH1430 300 branched-chain amino-acid aminotransferase #11 MTH1442 75 ketol-acid reductoisomerase #12 MTH1444 64 acetolactate synthase, large subunit #13 MTH1449 135 dihydroxy-acid dehydratase #14 MTH1477 127 unknown #15 MTH1478 135 conserved protein #16 MTH1480 144 conserved protein #17 MTH1481 142 isopropylmalate synthase #18 MTH1510 109 NH(3)-dependent NAD+ synthetase #19 MTH1602 63 acetolactate synthase, large subunit homolog #20 MTH1628 220 unknown #21 MTH1629 90 conserved protein #22 MTH1630 191 2-isopropylmalate synthase Motif number 1 GGTATCAGATACCAGCCTCCACCTGACGTA 1 10 0 ACCAGCCCCA 0.764448 -140 CCATGGATTCATCACCGCGCCTATCCACCAC 2 33 0 ATCACCGGCC 0.979577 -117 TTATGGATTCATCACCGCGCCTATCCACCGC 2 81 0 ATCACCGGCC 0.979577 -69 CATCTATATTTTCACCCGGCCCTATAAATAC 9 114 0 TTCACCCGCC 0.945463 -187 AGTTCGAATCTCGTCCGGCCCACTGGATTTT 10 42 0 TCGTCCGCCC 0.937927 -259 ATACCCCTAGACCACCGGCCCCTCTGAAGCC 10 102 1 ACCACCGCCC 0.9938 -199 AGTTCGAATCTCGTCCGGCCCATTTATTATT 10 138 0 TCGTCCGCCC 0.937927 -163 ATACCCCTAGACCACCGGCCCTCAGTGTGAC 10 198 1 ACCACCGCCC 0.9938 -103 ATTGATATAAACCTCCGACCATAACATACCC 10 270 1 ACCTCCGCCA 0.943222 -31 ACCTTGATGTCCACCATGCAGCACCGGCGG 15 10 1 TCCACCAGCA 0.66792 -126 CACCTCATATTTGACCCTCCCAGTGGAATCT 16 36 1 TTGACCCCCC 0.939209 -109 AATGCATCTGATGACCGTGCCATGCCCGCAT 16 82 0 ATGACCGGCC 0.964397 -63 ATGCTACCACCCTTCAGTGCTCTAAC 21 75 0 ACCACCCTCA 0.779077 -16 ATAACACGTAATGACCCACCATATTTCAGCC 22 71 1 ATGACCCCCA 0.905597 -121 ******* *** Masking position 6 Map Score: 18.6275 Number of sites scoring better than the average of aligned sites = 428 Number in coding regions = 398 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 2 TATGGTTTTGGGGTGATGATATAAATAAGTA 8 35 0 GGGTATGATA 0.97187 -31 TTTTATAGACGGGGCGTGATATTATTAATCA 9 22 0 GGGGGTGATA 0.987946 -279 CGGTGGTCTAGGGGTATGATACCTCGCTCAC 10 88 0 GGGGATGATA 0.99626 -213 CGGTGGTCTAGGGGTATGATACCTCGCTTAC 10 184 0 GGGGATGATA 0.99626 -117 AACTTTAGTGGGGTATGTTATGGTCGGAGG 10 281 0 GGGGATGTTA 0.991444 -20 CAGCACCGGCGGGGGATGTTATGATGACAGG 15 29 1 GGGGATGTTA 0.991444 -107 TTTTTCAATTGAGGAATGATAAACGCTGAAT 20 113 0 GAGGATGATA 0.97187 -108 **** ****** Masking position 11 Map Score: 14.8531 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 = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 3 TCACCGCGCCTATCCACCACAAACTTACCGTC 2 21 0 TATCCACCCA 0.906905 -129 TCACCGCGCCTATCCACCGCAAACTTACCGTC 2 69 0 TATCCACCCA 0.906905 -81 TTATTTATATCATCACCCCAAAACCATAAACC 8 38 1 CATCACCCAA 0.938923 -28 AGCGAGGTATCATACCCCTAGACCACCGGCCC 10 91 1 CATACCCCAA 0.960668 -210 AGCGAGGTATCATACCCCTAGACCACCGGCCC 10 187 1 CATACCCCAA 0.960668 -114 CCGACCATAACATACCCCACTAAAGTT 10 284 1 CATACCCCCA 0.979586 -17 TTCCCGGCCACATCCACCTGAGGGAACTTGCA 13 96 1 CATCCACCGG 0.937247 -40 GTCATCATAACATCCCCCGCCGGTGCTGCATG 15 25 0 CATCCCCCCG 0.9869 -111 CCCATCACCCTGTACTCAATACTC 15 122 0 CATCACCCGA 0.948886 -14 AGATGCATTGCAGCCCTCGACAGACATACCTC 16 104 1 CAGCCCTCAA 0.73343 -41 TTCATCCCCCTCTATTCATTAAGT 20 207 0 CATCCCCCCA 0.995421 -14 CACCATATTTCAGCCACCGGAATATGGATGCA 22 87 1 CAGCCACCGA 0.937247 -105 ******** * * Masking position 2 Map Score: 14.7057 Number of sites scoring better than the average of aligned sites = 561 Number in coding regions = 523 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 4 TACGTCAGGTGGAGGCTGGTATC 1 1 1 TCTCAGTGGA 0.975501 -149 GTGTTTCTCCCTCAGCTGGATA 7 3 0 TCTCAGTGGA 0.948222 -20 TAACTTATTAGTTTTCAGGAGCTCACCAAGTCT 9 52 0 GTTCAGAGCT 0.595089 -249 TTCAGACGAGTTTTTCAGTATGAAGGCGAAAGA 9 150 1 TTTCAGATGA 0.551324 -151 AACATATGGGGACATCAGAAGGTTAAAGAGGCT 9 196 1 GCTCAGAGGT 0.951704 -105 GGATTTTCATTTTTTCAGAGGCACACGCCACTC 10 16 0 TTTCAGGGCA 0.824661 -285 TTATTCTTCGGGCTTCAGAGGGGCCGGTGGTCT 10 110 0 GCTCAGGGGG 0.983715 -191 TAGACCACCGGCCCTCAGTGTGACTTTAAATTT 10 205 1 GCTCAGGTGA 0.89922 -96 CAGGCCGCAGGCCCTCAGGAGGGATCG 13 5 0 GCTCAGAGGG 0.983109 -131 CTCTGCAAGTTCCCTCAGGTGGATGTGGCCGGG 13 98 0 TCTCAGTGGA 0.948222 -38 AAATGATGATTTCATCAGTAGGGACCAGTTCCA 14 24 0 TCTCAGAGGG 0.979582 -104 TACATATATGTACATCAAAGGGAATGGTTAATA 14 101 1 TCTCAAGGGA 0.87995 -27 GTGGAATCTATTCTTCAATAGCGTATGCGGGCA 16 58 1 TCTCAAAGCG 0.696296 -87 GCATGGCACGGTCATCAGATGCATTGCAGCCCT 16 88 1 GCTCAGTGCA 0.951626 -57 * * **** **** Masking position 7 Map Score: 14.663 Number of sites scoring better than the average of aligned sites = 546 Number in coding regions = 509 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 5 TTCATCGTCTGTGGTACCGGTATCAGATACC 1 28 0 GTGGTACGGT 0.915683 -122 GTTCCAGCAAGTGGTCCATGGGGCAGTCTGT 9 238 0 GTGGTCATGG 0.948874 -63 TCACACCGAGGTGGTCACGAGTTCGAATCTC 10 61 0 GTGGTCCGAG 0.989821 -240 AGAGGGGCCGGTGGTCTAGGGGTATGATACC 10 96 0 GTGGTCAGGG 0.994019 -205 TTACAACGAGGTGGTCACGAGTTCGAATCTC 10 157 0 GTGGTCCGAG 0.989821 -144 CTGAGGGCCGGTGGTCTAGGGGTATGATACC 10 192 0 GTGGTCAGGG 0.994019 -109 AAAATTTATGGGAGTCCCGGTCTGATCCGGA 11 29 0 GGAGTCCGGT 0.860134 -47 GTTATAACCCGGGTTCCCGGGTGCCAGGTAA 17 25 0 GGGTTCCGGG 0.964141 -118 ****** **** Masking position 5 Map Score: 9.09506 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 178 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 CATATATACCATTTAAAACCAAACTCTACATAA 1 96 1 ATTTAAAAAA 0.955052 -54 CAACCATTACATATAAAAACATATACAACAAAT 3 15 1 ATATAAAAAA 0.729712 -78 TGATAATAAGATTTAAATATATAGTAATAACTT 9 79 0 ATTTAAATAA 0.935538 -222 TATTGTGAAAATTTAAAGTCACACTGAGGGCCG 10 213 0 ATTTAAAGAA 0.867337 -88 TTAACAGCTCATTTAAAATAAAATTTATGGGAG 11 46 0 ATTTAAAAAA 0.955044 -30 TTATTTGAAAGTATATATTTTATAG 12 3 1 ATTTGAAAAA 0.800055 -62 TTAAAGAACTATTTAAAACTTTACTGTACATAT 14 75 1 ATTTAAAATA 0.840561 -53 TCTGCCAACTATTTAAATCATGAATTAAAAAAA 19 27 0 ATTTAAATTA 0.782655 -37 ATATAGGTGCATTTAAATTTATATGTAGGTTTA 20 32 0 ATTTAAATAA 0.935537 -189 CTTGGCATTTATTTAAAATTAGATATATTAGTA 22 134 0 ATTTAAAAAA 0.955052 -58 TTAATGCTTTATTAAAATGAATACTTGGCATTT 22 157 0 ATTAAAATAA 0.648389 -35 ******** * * Masking position 7 Map Score: 8.15807 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 11 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 ATCCACTGCACATAAATGGGCACTTAACCA 1 68 1 CATAAATGGG 0.806318 -82 ATTTAAGAGATACAGAAGGGAGGGCAGGG 2 131 1 TACAGAAGGG 0.936974 -19 CCAAGTCTTTTATAGACGGGGCGTGATATT 9 30 0 TATAGACGGG 0.877468 -271 TTATCCAGTGAACATATGGGGACATCAGAA 9 186 1 AACATATGGG 0.872996 -115 TTAGCAGAATAATTGAAGGGTTCATAAAGG 9 268 0 AATTGAAGGG 0.923493 -33 CCCGAAGAATAATAAATGGGCCGGACGAGA 10 131 1 AATAAATGGG 0.880266 -170 TTTAAAATAAAATTTATGGGAGTCCCGGTC 11 38 0 AATTTATGGG 0.74544 -38 AAAAAATATTAACAGAAGGGGG 19 3 0 AACAGAAGGG 0.965917 -61 GTTGGCAGAATATAGATGGGTGC 19 51 1 TATAGATGGG 0.95142 -13 ATACTTAATGAATAGAGGGGGATGAA 20 205 1 AATAGAGGGG 0.931748 -16 TGTGTTAGAGCACTGAAGGGTGGTAGCAT 21 72 1 CACTGAAGGG 0.86471 -19 ********** Masking position 6 Map Score: 7.982 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 149 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 TGTATCTCCCTTACTGGTGTTCTATC 5 46 0 CTCCCTACTG 0.844442 -16 AATTTCTCCTGAACTGGATGTATATA 8 6 1 CTCCTAACTG 0.961653 -60 AAATTAGAGCCTCTTTAACCTTCTGATGTCC 9 205 0 CTCTTAACCT 0.896213 -96 TATATCAATGCTCCCAAACCGGAAAACTTTA 10 248 0 CTCCCAACCG 0.985559 -53 ACCCTCCTTAACAGCCTCTGCAAG 13 122 0 CTCCTAACAG 0.972657 -14 ACAGACATACCTCCTCAACATGGGGGAGTGA 16 123 1 CTCCTAACAT 0.933548 -22 TACCTGGATGCTCTAAAACAGTTTCAGAAAC 21 15 0 CTCTAAACAG 0.809165 -76 TATGGATGCACTCTCAAACCTTTTATACTAA 22 109 1 CTCTCAACCT 0.912498 -83 ***** ***** Masking position 8 Map Score: 4.06173 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 153 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 CCACAAACTTACCGTCAGATTCCTTC 2 4 0 ACGCAGATCC 0.988165 -146 CCGCAAACTTACCGTCAGATCCCATGGATTCAT 2 52 0 ACGCAGACCC 0.987929 -98 CATTATTATTAATGACATATTTCCTATAAAATA 12 26 0 AAGCATATTC 0.908783 -39 CATTAATAATAATGACAGATTCCGTTCAAG 12 45 1 AAGCAGATCC 0.970272 -20 CAACAGTTACACTGACATAGTTCCCGGCCACAT 13 76 1 ACGCATATTC 0.962247 -60 GCAGCCCTCGACAGACATACCTCCTCAACATGG 16 113 1 ACGCATACTC 0.961513 -32 AAGCAGATAAAATGCCAGACCACGGGGAATCAA 17 119 1 AAGCAGACAC 0.859752 -24 GTGCTCTAACACAGACATAATCATAAAGTAGAG 21 52 0 ACGCATATCA 0.854618 -39 ** * **** *** Masking position 7 Map Score: 4.10774 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 95 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 AGGAATCTGACGGTAAGTTTGTGGTGGATAGGCGCGG 2 13 1 CGTAGGGTGG 0.99789 -137 TGGGATCTGACGGTAAGTTTGCGGTGGATAGGCGCGG 2 61 1 CGTAGGGTGG 0.997913 -89 TATGATACCTCGCTCACACCGAGGTGGTCACGAGTTC 10 68 0 CGTAGGGTGG 0.997668 -233 TATGATACCTCGCTTACAACGAGGTGGTCACGAGTTC 10 164 0 CGTAGGGTGG 0.997905 -137 TCTGCAAGTTCCCTCAGGTGGATGTGGCCGGGAACTA 13 93 0 CCTAGTGTGG 0.974559 -43 GTCACTCCCCCATGTTGAGGAGGTATGTCTGTC 16 122 0 CCCAGGGAGG 0.949964 -23 ** * * * ***** Masking position 6 Map Score: 6.44718 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 24 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 11 ATACAACAAATTAATCCTCATTGTAGTTAA 3 37 1 TTAATCCTCA 0.816504 -56 CTTCTATCCTCCTTTAGCAGAA 9 289 0 TCTATCCTCC 0.954546 -12 GAGGTTTATATCAATGCTCCCAAACCGGAA 10 255 0 TCAATGCTCC 0.96947 -46 CACCCTATACTCAATACTCCTTATGAGACC 15 67 0 TCAATACTCC 0.974212 -69 CACCCTGTACTCAATACTCCAGCAAAACAA 15 111 0 TCAATACTCC 0.974212 -25 TCAGCGTTTATCATTCCTCAATTGAAAAAT 20 115 1 TCATTCCTCA 0.876481 -106 ********** Masking position 5 Map Score: 2.24603 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 85 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 12 TGGGCACTTAACCATATATACCATTTAAAA 1 84 1 ACCATATATA 0.75789 -66 TTAAAACCAAACTCTACATAACTATTTTCC 1 108 1 ACTCTACATA 0.716144 -42 AGAGTATTCAAACATCTTTATAAAGATTGG 4 61 1 AACATCTTTA 0.532084 -23 ACTTCGAGAAACCATTCATAGGTATAGCCA 13 48 1 ACCATTCATA 0.817096 -88 ACCCTCCTTAACAGCCTCTG 13 126 0 ACCCTCCTTA 0.973807 -10 TATAAAATATACCCTACTTACTTTTAACCA 18 90 1 ACCCTACTTA 0.96653 -20 GGTGAAGTTAAACCTACATATAAATTTAAA 20 24 1 AACCTACATA 0.890685 -197 TATTTTAAGCACCATCCTTAAATAATTTAA 20 174 1 ACCATCCTTA 0.95887 -47 TAAATAATTTAACATACTTAATGAATAGAG 20 192 1 AACATACTTA 0.836316 -29 ACACGTAATGACCCACCATATTTCAGCCAC 22 74 1 ACCCACCATA 0.839518 -118 ********** Masking position 9 Map Score: 3.60775 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 164 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 13 AATATATAGTAATAACTTATTAGTTTTCAG 9 67 0 AATAACTTAT 0.801206 -234 ACTATATATTTAAATCTTATTATCAAAGTA 9 87 1 TAAATCTTAT 0.871214 -214 TCATTTAAAATAAAATTTATGGGAGTCCCG 11 41 0 TAAAATTTAT 0.808644 -35 TTTGAAAGTATATATTTTATAGGAAATATG 12 14 1 TATATTTTAT 0.808669 -51 GAACCCGGGTTATAACTTATAAGATATAAC 17 40 1 TATAACTTAT 0.935483 -103 ACTTATAAGATATAACTTATAACATACTGT 17 54 1 TATAACTTAT 0.935483 -89 ACTCCTCCTGTAAAATTAATCATCGATCCA 18 14 1 TAAAATTAAT 0.540182 -96 AAAGAGGTAGAAAAACTTATATCAGTGATG 18 51 0 AAAAACTTAT 0.733514 -59 GTAAGTAGGGTATATTTTATATAACTATCA 18 81 0 TATATTTTAT 0.808669 -29 TTTATACTAATATATCTAATTTTAAATAAA 22 130 1 TATATCTAAT 0.733553 -62 ********** Masking position 4 Map Score: 4.54383 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 10 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 14 GATACCAGCCTCCACCTGACGTA 1 4 0 TCCACCTGAC 0.85974 -146 ATCGCCAGTATCCACTGCACATAAATGGGC 1 59 1 TCCACTGCAC 0.948758 -91 ACCGCGCCTATCCACCACAAACTTACCGTC 2 21 0 TCCACCACAA 0.91561 -129 ACCGCGCCTATCCACCGCAAACTTACCGTC 2 69 0 TCCACCGCAA 0.988186 -81 CTCCTTAACAGCCTCTGCAAGTTCCCTCAG 13 113 0 GCCTCTGCAA 0.768416 -23 AAGAATAGATTCCACTGGGAGGGTCAAATA 16 43 0 TCCACTGGGA 0.948549 -102 TAGGTTTAACTTCACCGGGAGGTATCTAG 20 10 0 TTCACCGGGA 0.840677 -211 CCATATTTCAGCCACCGGAATATGGATGCA 22 89 1 GCCACCGGAA 0.979311 -103 ********** Masking position 5 Map Score: 1.79371 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 229 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 15 TACCACAGACGATGAAATCGCCAGTATCCA 1 43 1 GATGAAATCG 0.949663 -107 TAGGCGCGGTGATGAATCCATGGGATCTGA 2 41 1 GATGAATCCA 0.964328 -109 TAGGCGCGGTGATGAATCCATAATGGAGAG 2 89 1 GATGAATCCA 0.964328 -61 CCTGACAGATGATGACTTCGAGAAACCATT 13 34 1 GATGACTTCG 0.924115 -102 GGTCCCTACTGATGAAATCATCATTTCCAT 14 31 1 GATGAAATCA 0.945877 -97 ********** Masking position 5 Map Score: 0.782298 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 65 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701