AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00340_mthe_reg_100.orf -o00340_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 MTH119 43 ATP phosphoribosyltransferase related protein #2 MTH120 21 NADPH-oxidoreductase #3 MTH225 300 histidinol dehydrogenase #4 MTH243 231 conserved protein #5 MTH669 145 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase related protein #6 MTH1193 146 transcriptional regulator #7 MTH1194 35 acetylpolyamine aminohydolase #8 MTH1343 218 imidazoleglycerol-phosphate synthase (cyclase) #9 MTH1348 139 precorrin-2 methyltransferase #10 MTH1468 35 ferredoxin #11 MTH1469 57 molybdenum transport ATP-binding protein homolog #12 MTH1470 44 molybdenum transport protein ModA related protein #13 MTH1471 56 O-antigen transporter homolog #14 MTH1472 30 O-antigen transporter homolog #15 MTH1475 56 unknown #16 MTH1476 127 tryptophan synthase, beta subunit homolog #17 MTH1506 189 ATP phosphoribosyltransferase #18 MTH1514 125 precorrin-6Y methylase #19 MTH1522 116 nitrogenase alpha chain (NifD) related protein #20 MTH1587 31 histidinol-phosphate aminotransferase #21 MTH1591 30 phosphonopyruvate decarboxylase #22 MTH1592 21 conserved protein #23 MTH1593 205 ribosomal protein S3a Motif number 1 TGGTTGGAATTCATCCCATGGATATGACTA 3 133 0 TCATCCCATG 0.884915 -168 TTTTATGGAGCCATTCCCTTTTAAGAATTT 3 249 0 CCATTCCCTT 0.952103 -52 GAATCATGGGCCATCCCCTGGGCACAGCCT 4 21 0 CCATCCCCTG 0.996923 -211 GTCACACTCTCCCCTGGATTATAGGT 4 216 0 CTCTCCCCTG 0.969339 -16 ATTATTTATCCCCTGAATCAGAAAA 7 6 1 TTATCCCCTG 0.948286 -30 AAGCTGTCTGCTGTCCCCTGAGTCTGGTCT 8 171 0 CTGTCCCCTG 0.988338 -48 TTATATAGTTCCACCCCCTTAAATAGGTCC 9 11 0 CCACCCCCTT 0.943617 -129 GAGGATGACCCTGTCCCCGGCGGATACATC 11 11 0 CTGTCCCCGG 0.941028 -47 TGTTTATTAACCATTCCCTTTGATGTACAT 16 11 1 CCATTCCCTT 0.952103 -117 GGTTTGGAGTCCGGTCCCTGACCGATTATA 17 42 0 CCGGTCCCTG 0.922489 -148 TGATGCAAATCCATCCCATGATTCATATCC 19 50 0 CCATCCCATG 0.980358 -67 ********** Masking position 6 Map Score: 15.1027 Number of sites scoring better than the average of aligned sites = 564 Number in coding regions = 521 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 2 TAAACTTATTATTTAAAAATTTTGGTCCATTA 3 43 1 ATTAAAATTT 0.943726 -258 CCACAGATTAATATAAAAATTGCAAATGGTAG 3 104 1 AATAAAATTG 0.94372 -197 ATATGCTTTCACTTAAACATTGGTTGATGGTT 3 158 0 ATTAAAATTG 0.951045 -143 AATTCCAGTAATATAAACATTTATTTATATGC 3 184 0 AATAAAATTT 0.935366 -117 ACACCGGATCATTTAATAATTTGAAGAATTCC 3 210 0 ATTAATATTT 0.640876 -91 CGCTGATGGTAAATAAATATTGTAAGTACCAT 4 162 0 AATAAAATTG 0.938444 -70 TTACCATCAGCGATAAATATTGTTGCCATAGG 4 182 1 CATAAAATTG 0.725534 -50 TGTATGGAATACTTAAAGCTTCATGTAAATAG 5 84 0 ATTAAACTTC 0.692179 -62 TCCCATCTTCAGATAAACATTTATAAGGGAAC 6 33 1 AATAAAATTT 0.935366 -114 AAAGTTAACCATTTAAATATTTTCTCATCAAC 8 128 1 ATTAAAATTT 0.943707 -91 GAATCACCAGAAATAAAGAGTTGACGGAT 14 8 0 AATAAAAGTT 0.695394 -23 TTAAAGAACTATTTAAAACTTTACTGTACATA 16 42 0 ATTAAACTTT 0.89436 -86 ATAAGGGAGTATTTAAATCTTGACATGGTGGT 23 56 0 ATTAAACTTG 0.907468 -150 * ***** **** Masking position 6 Map Score: 11.85 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 16 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 3 AGTTTAATACACACTTATAAGGAGACTGAG 3 19 0 ACACTTATAA 0.898883 -282 AGTGTGTATTAAACTTATTATTTAAAAATT 3 34 1 AAACTTATTA 0.851785 -267 CCGGGGTGATAAACTGATAACTGGAAAAAC 4 62 0 AAACTGATAA 0.814928 -170 GGACCGCCTTTCACTTATTTCCACAGCAAG 5 12 1 TCACTTATTT 0.591304 -134 GAACATCCCCTATCTTATAAAAGTTGATGA 6 61 1 TATCTTATAA 0.683354 -86 GACTTCTTCTAAACTTATATTCACTTAAAA 6 89 1 AAACTTATAT 0.962476 -58 TATGCCTATGAAAGTTATATTATAAAGTTT 6 118 0 AAAGTTATAT 0.731741 -29 GGCACTCTCTAAACTTATATAGTTCCACCC 9 25 0 AAACTTATAT 0.962476 -115 AACCACCTTATAACTTATAAGTTCTAACTT 17 13 1 TAACTTATAA 0.949063 -177 TTATAAGTTCTAACTTATAATCGGTCAGGG 17 27 1 TAACTTATAA 0.949063 -163 CTCTTTCAGGAAACCTATATAATAGGTTTG 17 66 0 AAACCTATAT 0.814928 -124 CACTGGAGATTAACTTATATCTCTTTCAGG 17 86 0 TAACTTATAT 0.949063 -104 ********** Masking position 7 Map Score: 8.98343 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 29 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 4 GGTCCATTAGATGCCCCCTAATCCAAATTAA 3 66 1 AGCCCCCTAA 0.726514 -235 ATGATCCGGTGTGCCCCCTAAATTCTTAAAA 3 230 1 GGCCCCCTAA 0.971194 -71 GAAGCTTTAAGTATTCCATACACATAAAATA 5 94 1 GATTCCATAC 0.911493 -52 GGGGGGATTTGAACCCCCGACCTTGGGATCC 8 40 1 GACCCCCGAC 0.972206 -179 GCTAGACTACGGGCCCCCTACACACATCTCT 8 93 1 GGCCCCCTAC 0.992706 -126 AGTTTAGAGAGTGCCACAGAAAAATAATGAT 9 40 1 GGCCACAGAA 0.730807 -100 GTCAGGGACCGGACTCCAAACCTATTATATA 17 50 1 GACTCCAAAC 0.898827 -140 ATTAAAGAGAGTGTCCCATACCAACATTTTA 18 39 0 GGTCCCATAC 0.981631 -87 TGACCACACAGCACCCCAAACCACCATGTCA 23 37 1 GACCCCAAAC 0.960287 -169 CTATTATAGAGTATTCCATACTGGCGGTGTA 23 89 1 GATTCCATAC 0.911493 -117 CCATGATTTAGAGTTACATACACCGCCAGTA 23 107 0 GGTTACATAC 0.751649 -99 * ********* Masking position 10 Map Score: 7.05438 Number of sites scoring better than the average of aligned sites = 311 Number in coding regions = 289 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 5 ACCATGAGAAAAAAAATCAGATTCTATACT 4 137 0 AAAAAATCAG 0.9336 -95 GTCTACAATAAAAAGAGCAGTACTTGCTGT 5 34 0 AAAAGAGCAG 0.957405 -112 AGGGATCTAAAAAATAGGGGTCTACAATAA 5 53 0 AAAATAGGGG 0.842709 -93 AAGCTTCATGTAAATAGCAGGGATCTAAAA 5 71 0 TAAATAGCAG 0.907321 -75 ATGGGAAAATAAAAAAGGAGGGTAATTA 6 9 0 AAAAAAGGAG 0.956041 -138 TAAAAAGCAGTTAATAAAAA 8 1 1 TAAAAAGCAG 0.957454 -218 AGCAGTTAATAAAAAAGCGGACCCGGGGGG 8 16 1 AAAAAAGCGG 0.972075 -203 CTCCGGGAGAAAAAAATCAGTAGGGGTGAG 15 24 0 AAAAAATCAG 0.9336 -33 ********** Masking position 6 Map Score: 6.23962 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 37 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 TTTGGATTAGGGGGCATCTAATGGACCAAA 3 63 0 GGGGCATCTA 0.940131 -238 ACTGACCGGTGCAGCATCTAAACCCGAAGA 4 110 0 GCAGCATCTA 0.910927 -122 AGCGGACCCGGGGGGATTTGAACCCCCGAC 8 31 1 GGGGGATTTG 0.943945 -188 TATTAATTAAGGGGCATTTAGTATAAAGCT 8 196 0 GGGGCATTTA 0.939063 -23 TATTTAAGGGGGTGGAACTATATAAGTTTA 9 16 1 GGTGGAACTA 0.798079 -124 GGCATTCCGTGGAGCATTTCAGGGCATATA 13 33 1 GGAGCATTTC 0.713981 -24 TCACCTCATGGCTGGAACTGGTCCCTACTG 16 107 0 GCTGGAACTG 0.649447 -21 CCGTTCATCTGCAGGATCTATCATTCTTCA 17 114 0 GCAGGATCTA 0.952358 -76 TTAAGCTCCTGCAGGGTTTATCCGTTCATC 17 135 0 GCAGGGTTTA 0.755745 -55 ACCAGTCATCGAGGGATTTA 17 180 1 GAGGGATTTA 0.873252 -10 TGAATCATGGGATGGATTTGCATCATGGTT 19 55 1 GATGGATTTG 0.70831 -62 ATAGGATAAGGGAGTATTTAAATCTTGACA 23 63 0 GGAGTATTTA 0.69639 -143 CGTAAAAACAGCTGGATTTAACATAAATTC 23 163 0 GCTGGATTTA 0.940908 -43 ********** Masking position 9 Map Score: 6.49806 Number of sites scoring better than the average of aligned sites = 259 Number in coding regions = 231 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 7 CAAATGGTAGTCATATCCATGGGATGAATTC 3 126 1 TCATATCCAG 0.985381 -175 AAGTCCCACGTCATATTCCAGGCTAGACTAC 8 72 1 TCATATTCCG 0.92795 -147 GATGAAATCATCATTTCCATGCAGTAAGATA 16 77 0 TCATTTCCAG 0.933307 -51 AGATATAAGTTAATCTCCAGTGAAGAATGAT 17 94 1 TAATCTCCAT 0.711263 -96 GTTTATCCGTTCATCTGCAGGATCTATCATT 17 119 0 TCATCTGCAG 0.897456 -71 CATTTTATTATAATATCCCGGCACTACTTAT 18 15 0 TAATATCCCG 0.915244 -111 ATGGATTGATTAATATTCATTTAGAAGCTTA 19 19 0 TAATATTCAT 0.629688 -98 ATCCCATGATTCATATCCATGGATTGATTAA 19 37 0 TCATATCCAG 0.985381 -80 AACTGGCTGTTCATATTCATGACCACACAGC 23 18 1 TCATATTCAG 0.963435 -188 ********* * Masking position 6 Map Score: 5.91432 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 165 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 CTCCAGTATGATGGTTGATTGAGTCCTA 1 26 0 CCGATATGTA 0.938513 -18 ACACATGTAACCGGAATCATGGGCCATCCCCTGGGC 4 28 0 CCGATATGGA 0.992737 -204 GTTTATCACCCCGGCATTACAGGCAAAGAATCTCTT 4 78 1 CCGATACGGA 0.993978 -154 CACACTCTCCCCTGGATTATAGGTAACCTATGGCAA 4 204 0 CCGATATGGA 0.992737 -28 CAGCCGAAGACCAGACTCAGGGGACAGCAGACAGCT 8 164 1 CCGCTAGGGA 0.942378 -55 TAAATCCCTCGATGACTGGTTAAATTTATTTT 17 168 0 CCCATACGGA 0.983164 -22 CCCGCATAACTGGCTGTTCATATTCA 23 1 1 CCGATACGGG 0.977698 -205 AGTATGGAATACTCTATAATAGGATAAGGGAGTATT 23 75 0 ACCATATGGA 0.843755 -131 ** * ** ** ** * Masking position 9 Map Score: 6.42745 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 = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 AAATTAAGGAATGACCACAGATTAATATAA 3 90 1 ATGACCACAG 0.98558 -211 CCTTTCACTTATTTCCACAGCAAGTACTGC 5 18 1 ATTTCCACAG 0.868277 -128 GTGTCAGCCGAAGACCAGACTCAGGGGACA 8 160 1 AAGACCAGAC 0.882756 -59 TTCTCTGGAAATATCCAGACCCGCCTTTAT 9 72 0 ATATCCAGAC 0.877216 -68 CCAGAGAAGGATGACCAGACCATCATCATG 9 94 1 ATGACCAGAC 0.976752 -46 GACCATCATCATGTCTACAGAGTTATTAAA 9 111 1 ATGTCTACAG 0.826297 -29 GCCATGTTGCATAACCACAGACATTTGAGG 19 88 1 ATAACCACAG 0.949102 -29 GTTCATATTCATGACCACACAGCACCCCAA 23 26 1 ATGACCACAC 0.98558 -180 ********** Masking position 7 Map Score: 6.24487 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 76 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 10 GGTTAGTTTTATGGAGCCATTCCCTTTTAA 3 255 0 ATGGAGCCAT 0.721103 -46 ACACATGTAACCGGAATCATGGGCCATCCC 4 34 0 CCGGAATCAT 0.852173 -198 GGCTAGACTACGGGCCCCCTACACACATCT 8 92 1 CGGGCCCCCT 0.941526 -127 ATATAAAGAACCGGCGCCATAGGTTCTACA 12 25 1 CCGGCGCCAT 0.976093 -20 TTTTTTTCTCCCGGAGCCATCCAGAAACG 15 38 1 CCGGAGCCAT 0.989547 -19 TGCAACATGGCTGGAACCATGATGCAAATC 19 69 0 CTGGAACCAT 0.950942 -48 TCAAATGGATCGGGACCCCTC 22 11 1 CGGGACCCCT 0.968617 -11 ********** Masking position 10 Map Score: 3.9195 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 140 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 11 ACATTGGTTGATGGTTGGAATTCATCCCAT 3 144 0 ATGGTTGGAA 0.952371 -157 AAATGTTTATATTACTGGAATTCTTCAAAT 3 194 1 ATTACTGGAA 0.92099 -107 TGATAAACTGATAACTGGAAAAACACATGT 4 56 0 ATAACTGGAA 0.92099 -176 ATCACCTCATGGCTGGAACTGGTCCCTA 16 110 0 ATGGCTGGAA 0.990508 -18 GTTATGCAACATGGCTGGAACCATGATGCA 19 73 0 ATGGCTGGAA 0.990508 -44 ********** Masking position 6 Map Score: 4.0543 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 20 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 12 TTACCAGCCTCAGTCTCCTTATAAGTG 3 7 1 GCCCAGTCTC 0.894894 -294 CCATCCCCTGGGCACAGCCTCTCGCCCATA 4 10 0 GGCCAGCCTC 0.985815 -222 CCGGAATCATGGGCCATCCCCTGGGCACAGC 4 23 0 GGGCATCCCC 0.952984 -209 TATACTGACCGGTGCAGCATCTAAACCCGAA 4 112 0 GGTCAGCATC 0.759018 -120 GTCACACTCTCCCCTGGATTA 4 221 0 GTCCACTCTC 0.950163 -11 AACTTATATAGTTCCACCCCCTTAAATAGGT 9 13 0 GTTCACCCCC 0.89042 -127 TTATTTTTCTGTGGCACTCTCTAAACTTATA 9 36 0 GTGCACTCTC 0.961503 -104 GCCGGGGACAGGGTCATCCTCCTTGTTGAAC 11 20 1 GGGCATCCTC 0.976986 -38 ATGTTGGTATGGGACACTCTCTTTAATGGAG 18 43 1 GGGCACTCTC 0.98404 -83 *** ******* Masking position 6 Map Score: 6.18728 Number of sites scoring better than the average of aligned sites = 375 Number in coding regions = 354 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 13 ATTTGGATTAGGGGGCATCTAATGGACCAA 3 64 0 GGGGGCATCT 0.876043 -237 AAGCGGACCCGGGGGGATTTGAACCCCCGA 8 30 1 GGGGGGATTT 0.826693 -189 GATGTGTGTAGGGGGCCCGTAGTCTAGCCT 8 91 0 GGGGGCCCGT 0.988762 -128 AAAATCAGTAGGGGTGAGGTGGTGGAGGGG 15 12 0 GGGGTGAGGT 0.975905 -45 TAATAGGTTTGGAGTCCGGTCCCTGACCGA 17 47 0 GGAGTCCGGT 0.877659 -143 ACAGACATTTGAGGTGACGTAAT 19 104 1 GAGGTGACGT 0.868214 -13 GAGGGGTCCCGATCCATTTGA 22 10 0 GGGGTCCCGA 0.943704 -12 ATGGTGGTTTGGGGTGCTGTGTGGTCATGA 23 34 0 GGGGTGCTGT 0.983474 -172 ********** Masking position 4 Map Score: 2.15892 Number of sites scoring better than the average of aligned sites = 384 Number in coding regions = 364 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 14 AGTTAGGGCGAATGGTTAGTTTTATGGAGC 3 268 0 AATGGTTAGT 0.92939 -33 AAAATATTTAAATGGTTAACTTTAAATAGA 8 121 0 AATGGTTAAC 0.96927 -98 GAAAGGTTAATGCGTTTTGAG 10 25 0 AAAGGTTAAT 0.898793 -11 CATCAAAGGGAATGGTTAATAAACA 16 6 0 AATGGTTAAT 0.966907 -122 AACTCTAAATCATGGTTAACCAGTTAAATA 23 123 1 CATGGTTAAC 0.934249 -83 ********** Masking position 6 Map Score: 1.24214 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 4 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 15 CCTCCAGTGAAAAAGTTAGGGCGA 3 287 0 CCAGTGAAAA 0.987262 -14 TAAAAAGCAGTTAATAAAAAAGCGGAC 8 7 1 GCAGTTAAAA 0.802558 -212 TTAGAGAGTGCCACAGAAAAATAATGATAAT 9 43 1 CCACAGAAAA 0.866348 -97 CTGGATATTTCCAGAGAAGGATGACCAGACC 9 84 1 CCAGAGAAGA 0.924975 -56 AAGTTAATCTCCAGTGAAGAATGATAGATCC 17 100 1 CCAGTGAAAA 0.987262 -90 TTGCTGAGACCCAGTGAATATCTGCCTCCGT 18 77 1 CCAGTGAAAT 0.94149 -49 TCATGGTTAACCAGTTAAATATGAATTTTTT 23 132 1 CCAGTTAATA 0.839131 -74 ******** ** Masking position 7 Map Score: 2.02188 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 65 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542