AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -imodE_mthe_opreg_300.orf -g0.495 -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 = 0.495 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MTH150 75 conserved protein #2 MTH806 240 protease IV #3 MTH807 75 thioredoxin #4 MTH808 34 cobalamin biosynthesis protein D #5 MTH809 138 molybdenum cofactor biosynthesis protein MoaC #6 MTH922 67 unknown #7 MTH923 21 unknown #8 MTH925 32 conserved protein #9 MTH927 139 ferredoxin #10 MTH928 300 cobalamin biosynthesis protein N #11 MTH1550 40 molybdenum cofactor biosynthesis MoaA #12 MTH1551_MTH1552 139 MTH1551: molybdopterin-guanine dinucleotide biosynthesis protein B related, MTH1552: formate dehydrogenase, alpha subunit homolog #13 MTH1553 71 tungsten formylmethanofuran dehydrogenase, subunit H #14 MTH1560 107 nitrogenase NifH subunit #15 MTH1563 37 nitrogenase NifD subunit #16 MTH1567 235 catalytic subunit of nitrate reductase (flp) #17 MTH1861 300 molybdenum cofactor biosynthesis MoaB Motif number 1 TCCTAAATTTTTAACCATTTTTATTAATAGAATGTT 2 147 0 TACTTTTATA 0.789912 -94 CTTCTTTTTCAATTAATTTTTAAGGATTTTTCT 4 8 1 TAAATTTTTA 0.50511 -27 AATCCATCAAAGAAATTCATGAGTGATGATAA 5 7 1 TAAATTCATA 0.964851 -132 AAATACATGGGTGAATTCTTTCATTATCATCACTCA 5 30 0 GAATTTCATA 0.951985 -109 TTAGAATCCATCAAAGAAATTCATGAGTGATGATAA 5 65 1 TAAATTCATA 0.964851 -74 AAATACATGGGTGAATTCTTTCATTATCATCACTCA 5 88 0 GAATTTCATA 0.951985 -51 TTAGAATCCATCAAAGAAATTCATGA 5 123 1 TAAATTCATA 0.964851 -16 CAAGGTAATCTGAAAGTAATTCAGCACACCTTTCAG 6 40 0 TAAATTCAGA 0.930735 -28 CATGTAAAACAGTACTGTTTTCATGAGGTCCATTAA 9 79 1 AACTTTCATA 0.64359 -61 CAGGTCCATATATAAATCTTTCTTAATGGACCTCAT 9 101 0 TAATTTCTTA 0.856481 -39 GTTAAAGCCCTTTAAACGTTTCAGAAAAATTCTGAA 10 45 0 TAATTTCAGA 0.958575 -256 ACTCAAGAAATTAAAAATTTTTATAAATATAACGGC 10 84 0 TAATTTTATA 0.881239 -217 CATAAATGCAGATAAAATATTCATTAATTATGCAAT 10 137 1 GAAATTCATA 0.920087 -164 TATATGAAAATTTAATACATTCATCACGCGTTATTG 10 169 0 TAAATTCATA 0.964874 -132 AAGACTTTTTATTAATTTTTTTATTACATATTCTTG 10 229 0 AAATTTTATA 0.663982 -72 CTTTTTATGGTGAAACTTTATCATGATGCACAGATA 12 83 1 TAATATCATA 0.744105 -57 ATGGGAAAAATAGAATTTATTTAGGATCGGAC 14 7 0 TAAATTTAGA 0.798528 -101 AAGCAAAAACTGAACAGTTTTCATGAGAAGAAAATG 14 40 0 TACTTTCATA 0.927271 -68 CTATTTAAATTTTTTGGTAAATGGTTAAA 14 89 0 TAATTTTGGA 0.57116 -19 CTTCAGATCGGTTAAAGATTTCAGTACAGTACCTTG 16 170 0 GAATTTCAGA 0.906534 -66 CAGCACTATTTATAAAGTTTTCGTTAGGTTATTTAA 17 25 0 TAATTTCGTA 0.902258 -276 GACCAAATCGTCATAAATTTTTATTACTTTTCTCTC 17 163 1 TTATTTTATA 0.372455 -138 * ** ****** * Masking position 11 Map Score: 24.4785 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 152 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 2 ATGTCAGTAAAACTATTAGAACTATGGTGCTTCTA 1 37 0 ACTTGAACAT 0.66273 -39 CTTAGATACTATTTAATTGATGAATACACTTTGCA 2 90 0 ATTTGATGAT 0.978784 -151 TCACTCATGAATTTCTTTGATGGATT 5 2 0 ATTTGATGAT 0.9788 -137 ATAATGAAAGAATTCACCCATGTATTTTAGAATCC 5 39 1 ATTCCATGAT 0.902395 -100 TCACTCATGAATTTCTTTGATGGATTCTAAAATAC 5 60 0 ATTTGATGAT 0.9788 -79 ATAATGAAAGAATTCACCCATGTATTTTAGAATCC 5 97 1 ATTCCATGAT 0.902395 -42 TCATGAATTTCTTTGATGGATTCTAAAATAC 5 118 0 ATTTGATGAT 0.9788 -21 TGGCCTCTTCAGTTGATTGATCGATTCAGAATTTT 10 21 1 ATTTGATCAT 0.964172 -280 TTATATGAAAATTTAATACATTCATCACGCGTTAT 10 171 0 ATTTCATTAT 0.765693 -130 CCATATAATAATTTTCTACAAAAATCAAATAGAAA 13 32 0 ATTTCAAAAT 0.602024 -40 AATTGAATGGACTTACTTGAAGGATGATTTAAA 15 15 1 ATTTGAAGAT 0.955314 -23 TATTTAGTTAAATTAATTGAACTATCTTCAGATCG 16 196 0 ATTTGAACAT 0.925697 -40 CACATAAATAAATTGTTACATCCATAATTCAGTAT 17 265 1 ATTTCATCAT 0.94461 -36 * ** * **** ** Masking position 10 Map Score: 15.5722 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 33 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 3 TGAACGATCATAGAATCCTGGA 2 1 0 TAGACCTGGA 0.806951 -240 TGATATAACAAAAACTCCTGAAAACATGACTG 2 198 1 AAAACCTGAA 0.98506 -43 ACTGGAGGTAAAAAGGTCTGATACC 2 226 1 AAAATCTGAT 0.62746 -15 CAGAAAAATCCTTAAAAATTAATTG 4 20 0 AAAACCTTAA 0.935713 -15 AACGTTTCAGAAAAATTCTGAATCGATCAATC 10 35 0 AAAATCTGAA 0.935715 -266 ACGGCAAGGTTAAAGCCCTTTAAACGTTTCAG 10 57 0 TAAACCTTTA 0.673585 -244 AAAAATTAATAAAAAGTCTTAAATAATCTTCA 10 245 1 AAAATCTTAA 0.762568 -56 GAAATACGTTAAAATACCTGTAGATGGGGATA 16 14 1 AAAACCTGTA 0.95418 -222 TTAATTTAACTAAATACCTGGATGTAAATCA 16 215 1 TAAACCTGGA 0.960546 -21 AATAAGTTTTAAAAGTCCTGGACCCTACCCGT 17 75 0 AAAACCTGGA 0.97914 -226 ATTCCAATTTAAAAGACCAGAATAAGTTTTAA 17 95 0 AAAACCAGAA 0.936601 -206 TTCGGTAAGCTAAAAACCAGAAGACTTATAAA 17 226 1 TAAACCAGAA 0.884557 -75 **** ****** Masking position 4 Map Score: 11.2031 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 195 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 GAAATTCATGAGTGATGATAATGAAAGAATT 5 22 1 AGTGAGATAA 0.977861 -117 GAAATTCATGAGTGATGATAATGAAAGAATT 5 80 1 AGTGAGATAA 0.977861 -59 GAGCGTTTCCAGTGCAGTGAACTGTCCTA 6 9 0 AGTGCGTGAA 0.960617 -59 GTAATACATAAATGCAGATAAAATATTCATT 10 131 1 AATGCGATAA 0.892852 -170 TAAAAAGGACACTGAAGATAACATGAAGGGG 12 59 0 ACTGAGATAA 0.89464 -81 ATGAGTAGAGAGTGAGGTGAAGAGG 12 125 1 AGTGAGTGAA 0.967289 -15 AGTGAATTGAATGGACTTACT 15 1 1 AGTGATTGAA 0.853435 -37 CTTTATAAATAGTGCTGTTAATATATAGTAA 17 44 1 AGTGCGTTAA 0.967289 -257 GCTTACCGAAAATGATTATAATCCCCTTTCT 17 205 0 AATGATATAA 0.665475 -96 ***** ***** Masking position 3 Map Score: 7.70324 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 52 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 5 TTACTGACATAATAACTTTATGCG 1 62 1 AATAATTTAT 0.738416 -14 ATCTAAGTGCAATATTTATATAGTGGTAGAA 2 118 1 AATATTATAT 0.889655 -123 AGGGGAAGAAGATAATTATATTACTCTCACG 3 44 1 GATAATATAT 0.413442 -32 TTTCAATTTTTTTATTTTTCAGGAA 9 5 1 AATTTTTTAT 0.944972 -135 CATTAAGAAAGATTTATATATGGACCTGTGG 9 109 1 GATTTTATAT 0.810892 -31 AGAAATTAAAAATTTTTATAAATATAACGGC 10 84 0 AATTTTATAA 0.821986 -217 GAATGTATTAAATTTTCATATAATTATTACT 10 183 1 AATTTCATAT 0.870386 -118 ACTTTTTATTAATTTTTTTATTACATATTCT 10 231 0 AATTTTTTAT 0.944972 -70 CAAATAGAAAAATATATATATAGGTGTGTGG 13 11 0 AATATTATAT 0.889655 -61 TTTTGTAGAAAATTATTATATGGACGGCGGC 13 44 1 AATTATATAT 0.857398 -28 GGAAAAATAGAATTTATTTAGGATCGGAC 14 9 0 AATTTTTTAG 0.730353 -99 TATTAAATTCAATTTTTATAAGAGTATCCCC 16 39 0 AATTTTATAA 0.821986 -197 TTATTTAAGGAATATCCTTATTAAATTCAAT 16 57 0 AATATCTTAT 0.759197 -179 TATCCCATCAAATTTCCTTATTTAAGGAATA 16 74 0 AATTTCTTAT 0.870386 -162 AAGATAGTTCAATTAATTTAACTAAATACCT 16 203 1 AATTATTTAA 0.617839 -33 TGGATGTAACAATTTATTTATGTGGGCGTGA 17 258 0 AATTTTTTAT 0.944972 -43 ***** ***** Masking position 3 Map Score: 14.7743 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 44 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 6 GAACTATGGTGCTTCTAGTATATATTCATGGAGC 1 20 0 GCTCTTATAA 0.967675 -56 TTCTTTGATGGATTCTAAAATACATGGGTGAATT 5 49 0 GATCTAATAA 0.950867 -90 TTCTTTGATGGATTCTAAAATACATGGGTGAATT 5 107 0 GATCTAATAA 0.950867 -32 GGTATCAGATCCTGGTTTAAA 7 1 0 GATCTTTTAA 0.950867 -21 TTTTCTATTTGATTTTTGTAGAAAATTATTATAT 13 31 1 GATTTTAGAA 0.762559 -41 TGTAGATGGGGATACTCTTATAAAAATTGAATTT 16 32 1 GATCTTATAA 0.981435 -204 TCCCAGATGCTGATTTAAATAACCTAACG 17 6 1 GATCTTTTAA 0.950867 -295 TATAAATAGTGCTGTTAATATATAGTAAACGGGT 17 47 1 GCTTTTATAA 0.872558 -254 *** ** **** * Masking position 12 Map Score: 3.30267 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 10 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 TAGGACAGTTCACTGCACTGGAAACG 6 6 1 CAGTCACTGC 0.984195 -62 ATAATGTTTCAGTCACCTGCTTGACTGAGC 11 21 0 CAGTACCTGC 0.984195 -20 GTTCAGCCTCAAGTTCCCTTCCATCTATTCT 12 16 1 AAGTCCCTTC 0.965081 -124 CTAAATTTAACAGTCCCCTTCATGTTATCTT 12 45 1 CAGTCCCTTC 0.993114 -95 GATTTCAGTACAGTACCTTGCCACATATACA 16 159 0 CAGTCCTTGC 0.984195 -77 **** ****** Masking position 4 Map Score: 2.75145 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 100 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 ATTAGAACTATGGTGCTTCTAGTATATATT 1 28 0 TGGTGCTTCT 0.969478 -48 GCCATTATACTGGTGCTATT 8 23 1 TGGTGCTATT 0.952507 -10 GTCCTTTTTATGGTGAAACTTTATCATGAT 12 80 1 TGGTGAAACT 0.970054 -60 TACCTGTAGATGGGGATACTCTTATAAAAA 16 28 1 TGGGGATACT 0.954393 -208 AATGATAATGTGGTGCAACTCATAAAATTA 16 117 1 TGGTGCAACT 0.985849 -119 ********** Masking position 1 Map Score: 1.87326 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 17 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 9 TGTATTCATCAATTAAATAGTATCTAAGTG 2 97 1 AATTAAATAG 0.777898 -144 TAAGTGCAATATTTATATAGTGGTAGAACA 2 121 1 ATTTATATAG 0.948299 -120 ATAAGTATTTATCTAAAAAGGGGAAGAAGA 3 26 1 ATCTAAAAAG 0.836842 -50 TTAAAAATTAATTGAAAAAGAAG 4 4 0 ATTGAAAAAG 0.70011 -31 ATTAAGAAAGATTTATATATGGACCTGTGG 9 110 1 ATTTATATAT 0.538089 -30 TTGCCGTTATATTTATAAAAATTTTTAATT 10 82 1 ATTTATAAAA 0.683773 -219 CAATTGTAAAAACTATAAAGGAG 10 288 1 AACTATAAAG 0.54828 -13 ATAGAAAAATATATATATAGGTGTGTGG 13 9 0 ATATATATAG 0.712967 -63 GAAAAATAGAATTTATTTAGGATCGGAC 14 9 0 ATTTATTTAG 0.802194 -99 TTACCAAAAAATTTAAATAG 14 98 1 ATTTAAATAG 0.944811 -10 TAAAAATTGAATTTAATAAGGATATTCCTT 16 52 1 ATTTAATAAG 0.751436 -184 CCAGATGCTGATTTAAATAACCTAACGAAA 17 13 1 ATTTAAATAA 0.704305 -288 TAACAGCACTATTTATAAAGTTTTCGTTAG 17 34 0 ATTTATAAAG 0.916972 -267 ********** Masking position 5 Map Score: 6.37846 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 29 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 10 GCCTAATAATCTATTCAGTGAACGATCATA 2 21 0 CTATTCAGTG 0.927173 -220 CTCTGGAGTGCTTTGCAGCCTAATAATCTA 2 38 0 CTTTGCAGCC 0.803631 -203 TTGAGGTGCTCTCTGGAGTGCTTTGCAGCC 2 48 0 CTCTGGAGTG 0.889442 -193 GATGAATACACTTTGCAGTGTTTGAGAGCT 2 77 0 CTTTGCAGTG 0.968853 -164 GGAGCGTTTCCAGTGCAGTGAACTGTCCTA 6 11 0 CAGTGCAGTG 0.747966 -57 ACTAAATGGCCTCTTCAGTTGATTGATCGA 10 15 1 CTCTTCAGTT 0.931772 -286 CCTTCATGTTATCTTCAGTGTCCTTTTTAT 12 61 1 ATCTTCAGTG 0.830521 -79 CTCATGAAAACTGTTCAGTTTTTGCTTTTT 14 49 1 CTGTTCAGTT 0.904718 -59 ATTATCATTTCTTTTCAGTCTTATCCCATC 16 96 0 CTTTTCAGTC 0.931541 -140 ********** Masking position 4 Map Score: 4.28523 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 273 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 11 CTATTAATAAAAATGGTTAAAAATTTAGGAT 2 153 1 AAATGGTAAA 0.954359 -88 TGAAGGTGGAAAAGGATAAGTATTTATCTA 3 10 1 AAAAGGTAAG 0.915297 -66 TATTTATCTAAAAAGGGGAAGAAGATAATTA 3 31 1 AAAAGGGAAG 0.863734 -45 TACAAAAATCAAATAGAAAAATATATATATA 13 20 0 AAATAGAAAA 0.850839 -52 CATGAGAAGAAAATGGGAAAAATAGAATTTA 14 24 0 AAATGGAAAA 0.954359 -84 ATAAAGAACAAAAAAGCAAAAACTGAACAGT 14 58 0 AAAAAGAAAA 0.81415 -50 ATTTTTTGGTAAATGGTTAAAATAAAGAACA 14 79 0 AAATGGTAAA 0.954359 -29 ****** **** Masking position 3 Map Score: 1.45611 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 69 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 12 TCCATGTACCATCCTAAATTTTTAACCATT 2 164 0 ATCCTAAATT 0.94754 -77 TCTTTGATGGATTCTAAAATACATGGGTGA 5 52 0 ATTCTAAAAT 0.895192 -87 TCTTTGATGGATTCTAAAATACATGGGTGA 5 110 0 ATTCTAAAAT 0.895192 -29 TTTCAGAAAAATTCTGAATCGATCAATCAA 10 33 0 ATTCTGAATC 0.84283 -268 CCTTCCATCTATTCTAAATTTAACAGTCCC 12 32 1 ATTCTAAATT 0.9557 -108 GTCCGATCCTAAATAAATTCTATTT 14 6 1 ATCCTAAATA 0.816771 -102 CGTCTACTTAATACTGAATTATGGATGTAA 17 280 0 ATACTGAATT 0.816771 -21 ********** Masking position 7 Map Score: 1.78207 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 15 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 13 TGAATTCTTTCATTATCATCACTCATGAAT 5 25 0 CATTATCATC 0.98163 -114 TGAATTCTTTCATTATCATCACTCATGAAT 5 83 0 CATTATCATC 0.98163 -56 CTATTTTTCCCATTTTCTTCTCATGAAAAC 14 30 1 CATTTTCTTC 0.895786 -78 AGTTGCACCACATTATCATTTCTTTTCAGT 16 107 0 CATTATCATT 0.932039 -129 ********** Masking position 6 Map Score: 0.976475 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 9 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 14 CTAGTATATATTCATGGAGCCGGTGGCGA 1 8 0 TTATGGACCG 0.899291 -68 TTTAGGATGGTACATGGATGTCTGATATAACA 2 176 1 TAATGGAGTC 0.963467 -65 TAAATCTTTCTTAATGGACCTCATGAAAACAG 9 93 0 TTATGGACTC 0.937855 -47 GAAAGATTTATATATGGACCTGTGGAATATAC 9 115 1 TAATGGACTG 0.978525 -25 AAATTTAGAATAGATGGAAGGGAACTTGAGGC 12 21 0 TAATGGAGGG 0.966398 -119 AGAAAATTATTATATGGACGGCGGCTAAATGT 13 50 1 TAATGGAGGC 0.956324 -22 CTCATAAAATTAGATGAATCTGACTGTATATG 16 135 1 TAATGAACTG 0.855228 -101 ** ***** *** Masking position 8 Map Score: 1.32389 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 49 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 15 ********** No masking Map Score: -4.23951e-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