AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00770_mthe_reg_100.orf -o00770_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 MTH1193 146 transcriptional regulator #2 MTH1194 35 acetylpolyamine aminohydolase #3 MTH1430 300 branched-chain amino-acid aminotransferase #4 MTH1442 75 ketol-acid reductoisomerase #5 MTH1444 64 acetolactate synthase, large subunit #6 MTH1449 135 dihydroxy-acid dehydratase #7 MTH1602 63 acetolactate synthase, large subunit homolog Motif number 1 AAAATCCAGTGGGCCGGACGAGATTCGAAC 3 42 1 GGGCCGGACG 0.974171 -259 GGCTTCAGAGGGGCCGGTGGTCTAGGGGTA 3 103 0 GGGCCGGTGG 0.998618 -198 AATAATAAATGGGCCGGACGAGATTCGAAC 3 138 1 GGGCCGGACG 0.974171 -163 GTCACACTGAGGGCCGGTGGTCTAGGGGTA 3 199 0 GGGCCGGTGG 0.998618 -102 GGGTATGTTATGGTCGGAGGTTTATATCAA 3 271 0 TGGTCGGAGG 0.983519 -30 TCCCTCCTGAGGGCCTGCGGCCTGACAGAT 6 14 1 GGGCCTGCGG 0.994801 -122 ********** Masking position 5 Map Score: 19.2632 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 23 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 2 GACGAGATTCGAACTCGTGACCACCTCGGTGTGAG 3 58 1 GACTCGCACC 0.997989 -243 AGGGGTATGATACCTCGCTCACACCGAGGTGGTCA 3 75 0 TACTCGCACC 0.998029 -226 CGAGGTATCATACCCCTAGACCACCGGCCCCTCTG 3 93 1 TACCCTCACC 0.991268 -208 GACGAGATTCGAACTCGTGACCACCTCGTTGTAAG 3 154 1 GACTCGCACC 0.997989 -147 AGGGGTATGATACCTCGCTTACAACGAGGTGGTCA 3 171 0 TACTCGCAAC 0.987395 -130 CGAGGTATCATACCCCTAGACCACCGGCCCTCAGT 3 189 1 TACCCTCACC 0.991268 -112 CTATGAATGGTTTCTCGAAGTCATCATCTGTCAGG 6 34 0 TTCTCGCATC 0.980595 -102 CACTGACATAGTTCCCGGCCACATCCACCTGAGGG 6 85 1 GTCCCGCATC 0.978893 -51 ** **** **** Masking position 13 Map Score: 16.2587 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 55 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 3 TCTTCAGATAAACATTTATAAGGGAACATCCC 1 38 1 AAATTATAAG 0.938368 -109 AGAAGTCATCAACTTTTATAAGATAGGGGATG 1 64 0 AATTTATAAG 0.94772 -83 TTATATTATAAAGTTTTTTAAGTGAATATAAG 1 102 0 AATTTTTAAG 0.718382 -45 TTTATAATATAACTTTCATAGGCATACATTGT 1 122 1 AATTTATAGG 0.980136 -25 AGCCCGAAGAATAATAAATGGGCCGGACGAGA 3 129 1 ATATAATGGG 0.909421 -172 AACTTTAGTGGGGTATGTTATG 3 289 0 AATTTGTGGG 0.932477 -12 CATTTAAAATAAAATTTATGGGAGTCCCGGTC 4 38 0 AAATTATGGG 0.982368 -38 CATAAATTTTATTTTAAATGAGCTGTTAATTA 4 50 1 ATTTAATGAG 0.814327 -26 TTGAAAGTATATATTTTATAGGAAATATGTCA 5 15 1 ATTTTATAGG 0.95716 -50 ACTTCGAGAAACCATTCATAGGTATAGCCAAC 6 48 1 ACATTATAGG 0.916632 -88 TAGTTGGCAGAATATAGATGGGTGC 7 49 1 AAATAATGGG 0.956884 -15 ** *** ***** Masking position 1 Map Score: 11.4313 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 111 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 4 TAAACAATGTATGCCTATGAAAGTTATATTA 1 126 0 ATCCTATGAA 0.965027 -21 ATTATTTATCCCCTGAATCAGAAAATG 2 7 1 TACCCCTGAA 0.863513 -29 AGAGTGGCGTGTGCCTCTGAAAAAATGAAAA 3 15 1 GTCCTCTGAA 0.973414 -286 GCGAGGTATCATACCCCTAGACCACCGGCCC 3 92 1 ATCCCCTAGA 0.957347 -209 TAGACCACCGGCCCCTCTGAAGCCCGAAGAA 3 109 1 GCCCTCTGAA 0.96795 -192 GCGAGGTATCATACCCCTAGACCACCGGCCC 3 188 1 ATCCCCTAGA 0.957347 -113 ACCATAACATACCCCACTAAAGTT 3 287 1 ACCCACTAAA 0.8919 -14 TCAGACCGGGACTCCCATAAATTTTATTTTA 4 35 1 ACCCCATAAA 0.948386 -41 TAATGACATATTTCCTATAAAATATATACTT 5 19 0 TTCCTATAAA 0.863655 -46 ACTGTTGGCTATACCTATGAATGGTTTCTCG 6 52 0 ATCCTATGAA 0.965027 -84 ** ******** Masking position 8 Map Score: 10.3261 Number of sites scoring better than the average of aligned sites = 514 Number in coding regions = 466 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 5 TTATAAGATAGGGGATGTTCCCTTATAAAT 1 51 0 GGGGATGTTC 0.983828 -96 GGTGGTCTAGGGGTATGATACCTCGCTCAC 3 88 0 GGGTATGATA 0.988831 -213 GGTGGTCTAGGGGTATGATACCTCGCTTAC 3 184 0 GGGTATGATA 0.988831 -117 AACTTTAGTGGGGTATGTTATGGTCGGAGG 3 281 0 GGGTATGTTA 0.988831 -20 ATGGGAGTCCCGGTCTGATCCGGAATTTTT 4 23 0 CGGTCTGATC 0.933119 -53 GGAACTTGCAGAGGCTGTTAAGGAGGGT 6 118 1 GAGGCTGTTA 0.903971 -18 ********** Masking position 6 Map Score: 7.17919 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 112 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 6 AAAATGAAAATCCAGTGGGCCGGACGAGAT 3 36 1 TCCAGTGGGC 0.979404 -265 TTTAAAGTCACACTGAGGGCCGGTGGTCTA 3 205 0 CACTGAGGGC 0.988339 -96 CGATCCCTCCTGAGGGCCTGCGGCCTG 6 8 1 TCCTGAGGGC 0.995553 -128 ATGTCAGTGTAACTGTTGGCTATACCTATG 6 64 0 AACTGTTGGC 0.930968 -72 GGCCACATCCACCTGAGGGAACTTGCAGAG 6 101 1 ACCTGAGGGA 0.977436 -35 ********** Masking position 5 Map Score: 3.97281 Number of sites scoring better than the average of aligned sites = 395 Number in coding regions = 383 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 CCAGTGGGCCGGACGAGATTCGAACTCGTGAC 3 47 1 GGACGGTTCG 0.988327 -254 TAAATGGGCCGGACGAGATTCGAACTCGTGAC 3 143 1 GGACGGTTCG 0.988327 -158 TGCTCAATGCGGAAAAATTCCGGATCAGACCG 4 11 1 GGAAAATCCG 0.939216 -65 TTATTATTAATGACATATTTCCTATAAAATAT 5 25 0 TGACAATTCC 0.937824 -40 TTAATAATAATGACAGATTCCGTTCAAG 5 47 1 TGACAATCCG 0.985023 -18 ACAGTTACACTGACATAGTTCCCGGCCACATC 6 78 1 TGACAATTCC 0.973463 -58 ***** * **** Masking position 9 Map Score: 3.05708 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 43 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 8 TTACCCTCCTTTTTTATTTTCCCATCTTCA 1 14 1 TTTTTATTTT 0.967874 -133 ATGGTTATCATTTTCTGATTCAGG 2 22 0 TTATCATTTT 0.899496 -14 GCCCACTGGATTTTCATTTTTTCAGAGGCA 3 26 0 TTTTCATTTT 0.944633 -275 TCCGGCCCATTTATTATTCTTCGGGCTTCA 3 126 0 TTATTATTCT 0.786902 -175 TCAGTGTGACTTTAAATTTTCACAATATAT 3 219 1 TTTAAATTTT 0.835447 -82 ACCGGAAAACTTTATATATTGTGAAAATTT 3 232 0 TTTATATATT 0.793941 -69 ACTCCCATAAATTTTATTTTAAATGAGCTG 4 45 1 ATTTTATTTT 0.826026 -31 TATTTGAAAGTATATATTTTATAGGAAATA 5 12 1 TATATATTTT 0.792712 -53 CCCCCTTCTGTTAATATTTTTTTAATTCAT 7 11 1 TTAATATTTT 0.927318 -53 ********** Masking position 6 Map Score: 6.25656 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 59 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 9 TAATTACCCTCCTTTTTTATTTTCCC 1 7 1 CCCTCCTTTT 0.945559 -140 TTTTTATTTTCCCATCTTCAGATAAACATT 1 24 1 CCCATCTTCA 0.91659 -123 AGGGGATGTTCCCTTATAAATGTTTATCTG 1 42 0 CCCTTATAAA 0.735988 -105 GGGAACATCCCCTATCTTATAAAAGTTGAT 1 59 1 CCTATCTTAT 0.680636 -88 AGACCACCGGCCCCTCTGAAGCCCGAAGAA 3 110 1 CCCCTCTGAA 0.942361 -191 TCTCGTCCGGCCCATTTATTATTCTTCGGG 3 131 0 CCCATTTATT 0.598509 -170 CGATCCCTCCTGAGGGCCTGCGGC 6 5 1 CCCTCCTGAG 0.92089 -131 ACCCTCCTTAACAGCCTCTGC 6 125 0 CCCTCCTTAA 0.963455 -11 CCCCCTTCTGTTAATATTTTTT 7 3 1 CCCTTCTGTT 0.967168 -61 GCACCCATCTATATTCTGCCAAC 7 51 0 CCCATCTATA 0.949326 -13 ********** Masking position 7 Map Score: 5.25877 Number of sites scoring better than the average of aligned sites = 1194 Number in coding regions = 1099 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 10 ACACCGAGGTGGTCACGAGTTCGAATCTCGT 3 59 0 GGCACGAGTT 0.990189 -242 CCACCTCGGTGTGAGCGAGGTATCATACCCC 3 78 1 GTAGCGAGGT 0.990189 -223 ACAACGAGGTGGTCACGAGTTCGAATCTCGT 3 155 0 GGCACGAGTT 0.990189 -146 CCACCTCGTTGTAAGCGAGGTATCATACCCC 3 174 1 GTAGCGAGGT 0.990189 -127 ** ******** Masking position 8 Map Score: 1.20131 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 7 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 11 TTTATAGGAAATATGTCATTAATAATAATG 5 29 1 ATATGTCATT 0.969585 -36 CTTGAACGGAATCTGTCATTATTATTAATG 5 45 0 ATCTGTCATT 0.980124 -20 CGAAGTCATCATCTGTCAGGCCGCAGGCCC 6 24 0 ATCTGTCAGG 0.978138 -112 TGGCCGGGAACTATGTCAGTGTAACTGTTG 6 76 0 CTATGTCAGT 0.966583 -60 ********** Masking position 6 Map Score: 1.14375 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 24 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 12 ********** No masking Map Score: 1.72905e-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: 1.72905e-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 14 ********** No masking Map Score: 1.72905e-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