AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00450_mthe_reg_100.orf -o00450_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 MTH278 300 ferredoxin #2 MTH384 249 unknown #3 MTH387 24 conserved protein #4 MTH388 35 unknown #5 MTH393 41 NADH dehydrogenase (ubiquinone), subunit 1 related protein #6 MTH394 55 unknown #7 MTH397 40 formate hydrogenlyase, subunit 7 #8 MTH399 23 polyferredoxin #9 MTH400 33 polyferredoxin #10 MTH405 130 polyferredoxin #11 MTH587 263 methionyl-tRNA synthetase #12 MTH927 139 ferredoxin #13 MTH1032 229 ferredoxin (putative 2-oxoglutarate oxidoreductase, delat subunit) #14 MTH1133 21 polyferredoxin (MvhB) #15 MTH1136 171 methyl viologen-reducing hydrogenase, delta subunit #16 MTH1246 30 NADH dehydrogenase I, subunit N #17 MTH1251 147 conserved protein #18 MTH1468 35 ferredoxin #19 MTH1469 57 molybdenum transport ATP-binding protein homolog #20 MTH1470 44 molybdenum transport protein ModA related protein #21 MTH1471 56 O-antigen transporter homolog #22 MTH1472 30 O-antigen transporter homolog #23 MTH1475 56 unknown #24 MTH1476 127 tryptophan synthase, beta subunit homolog #25 MTH1636 101 S-adenosylhomocysteine hydrolase #26 MTH1819 134 ferredoxin Motif number 1 TTGATAGGAGATGGGAGCACTCAGGTCAACCTCGCG 1 36 0 AGGGACACGT 0.992114 -265 ACATATAAACATAGGATGAGGCAGTTCCCGCAAACA 1 108 1 AAGGAGACGT 0.969911 -193 ACATATAAACATAGGATGAGGCAGTTCCCGCAAACA 1 152 1 AAGGAGACGT 0.969911 -149 ATGTGACTCCATAGGAACCTCCAGGACATGATGGGG 2 18 0 AAGGACCCGA 0.90247 -232 ATCTTCTGTAGAGGGACCCTTCAGATATCAGTAAAA 2 121 1 GGGGACCCGT 0.98837 -129 AAGTTTCTGTAGAGAAACCTCCAGATATTAGTAAAA 2 159 1 AAGAACCCGT 0.95827 -91 GTTTATGATAATAGAATCATTCCGGTGTTAATGGTG 5 11 1 AAGAACACGT 0.95751 -31 GGTCATAATCACGGCAACACGCCGCTGAGGTACTGG 11 119 0 AGGCACACGT 0.942168 -145 CATGGCAGCTGAGGACCCCCGCAGTTATAATGGATA 12 47 0 GGGACCCCGT 0.780917 -93 ACCTCTGGTGAAGGGAACACCCTGATAATTTATTAT 13 123 1 AGGGACACGT 0.992114 -107 GTTTCATAGGAGCCTTCTGGTGGAAGGGGAG 15 6 1 AAGGACCCGT 0.987628 -166 TAAAATGAGGAATCTAACAGGTGAGGAATT 16 7 1 GGGAACTCGT 0.790804 -24 AAACACTTGAAGGGGAAGAGGCTGCCGTAATAACCC 17 21 0 AGGGAGACGC 0.942342 -127 GGTTCAACAAGGAGGATGACCCTGTCCCCGGCGGAT 19 16 0 GAGGAGACGC 0.871019 -42 * **** ** * * * Masking position 12 Map Score: 18.044 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 253 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 2 ACTGCCTTGATAGGAGATGGGAGCACTCAG 1 48 0 TAGGAGATGG 0.942031 -253 CCTATGTTTATATGTTATGGCTCTGATTCG 1 93 0 TATGTTATGG 0.942984 -208 CATATAAACATAGGATGAGGCAGTTCCCGC 1 109 1 TAGGATGAGG 0.858267 -192 CCTATGTTTATATGTTATGGCTCTGTTTGC 1 137 0 TATGTTATGG 0.942984 -164 CATATAAACATAGGATGAGGCAGTTCCCGC 1 153 1 TAGGATGAGG 0.858267 -148 TATATGTTTATATGTTATGGCTCTGTTTGC 1 181 0 TATGTTATGG 0.942984 -120 TCCAGGACATGATGGGGTGGGAAT 2 5 0 GATGGGGTGG 0.857598 -245 AAGACATGATGTGGAATGAAAATG 6 5 1 CATGATGTGG 0.788407 -51 ACTGCGGTTCGATGTGATGGAACACTTCGA 11 45 0 GATGTGATGG 0.932726 -219 ATCTGGCCTTGAGGTTGTGGTTTCCCTGAA 11 88 1 GAGGTTGTGG 0.979178 -176 CAGTAGGGGTGAGGTGGTGGAGGGGT 23 7 0 GAGGTGGTGG 0.979559 -50 CTGTAGATAATAGGTTGTGGGTCATCACTT 25 48 0 TAGGTTGTGG 0.982807 -54 CTAAAAATAGTTGGTGATGGATGGAGCAGC 26 69 0 TTGGTGATGG 0.769283 -66 ********** Masking position 4 Map Score: 16.3585 Number of sites scoring better than the average of aligned sites = 361 Number in coding regions = 340 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 3 CCGGTCCCGAATCAGAGCCATAACATATAAAC 1 86 1 ACAGGCCATA 0.986703 -215 AGTTCCCGCAAACAGAGCCATAACATATAAAC 1 130 1 ACAGGCCATA 0.986703 -171 AGTTCCCGCAAACAGAGCCATAACATATAAAC 1 174 1 ACAGGCCATA 0.986703 -127 CACCCAGATTCCCGGATCCAGCACATTAAAGA 10 18 0 CCGGTCCAGC 0.956175 -113 AAACCACAACCTCAAGGCCAGATCAGCATGCC 11 79 0 CCAAGCCAGA 0.833366 -185 TCGTATATTCCACAGGTCCATATATAAATCTT 12 117 0 CCAGTCCATA 0.971679 -23 GATATAAAGAACCGGCGCCATAGGTTCTACA 20 24 1 ACGGGCCATA 0.983867 -21 ATTTTTTTCTCCCGGAGCCATCCAGAAACG 23 37 1 CCGGGCCATC 0.986248 -20 ATCAGTAGGGACCAGTTCCAGCCATGAGGTGA 24 105 1 ACAGTCCAGC 0.960674 -23 CACAACCATCAGCTGCTCCATCCATCACCAAC 26 58 1 ACTGTCCATC 0.876893 -77 * *** ****** Masking position 10 Map Score: 13.2641 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 = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 4 CTGCCTCATCCTATGTTTATATGTTATGGCTC 1 100 0 CTATTTATAT 0.939335 -201 CTGCCTCATCCTATGTTTATATGTTATGGCTC 1 144 0 CTATTTATAT 0.939335 -157 AGGAGTATTTATATGTTTATATGTTATGGCTC 1 188 0 ATATTTATAT 0.942699 -113 CCTTTTTTAAAAAGATTTATAT 2 238 1 AAATTTATAT 0.965609 -12 ATGGACTCAAATAAATTTATATAGAAGTAAAC 11 162 1 ATATTTATAT 0.941565 -102 TTTCAATTTTTTTATTTTTCAGGAA 12 4 1 CAATTTTTAT 0.769446 -136 GTCCATTAAGAAAGATTTATATATGGACCTGT 12 106 1 AAATTTATAT 0.965609 -34 ACAATTTCCGAAAATTTTATATGTGTGGTTAA 15 65 0 AAATTTATAT 0.965614 -107 ATTTATATAGAAAACTTTATATTATCATAAAT 17 84 1 AAATTTATAT 0.965618 -64 TATGTACAGTAAAGTTTTAAATAGTTCTTTAA 24 42 1 AAATTTAAAT 0.781117 -86 AACTGAAGTCCAATATTAATATGGGGCTATTG 26 99 0 CAATTAATAT 0.76944 -36 *** ******* Masking position 3 Map Score: 12.5762 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 16 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 5 TAATTTTCGCGAGGTTGACCTGAGTGCTCC 1 29 1 GAGGTTGACC 0.979009 -272 CTTATACTTTGGGGTTAACCCTTTATAGTT 1 236 0 GGGGTTAACC 0.924194 -65 AATGCGTGATGTTGATGTCCT 8 13 1 GTTGATGTCC 0.749741 -11 GCTGAGGCCTGATGTTGATCCCGTGAACCG 10 51 1 GATGTTGATC 0.884768 -80 GTGTTGCCGTGATTATGACCGCAAGACATG 11 135 1 GATTATGACC 0.74525 -129 GGAAATACGTGAGGATATCCATTATAACTG 12 32 1 GAGGATATCC 0.851713 -108 GTTCAACAAGGAGGATGACCCTGTCCCCGG 19 21 0 GAGGATGACC 0.975074 -37 TGAACCCGACGATGTTGTCCTG 19 46 1 GATGTTGTCC 0.952074 -12 GGGCCCGGGGGGTGTTAATCTCAG 25 5 0 GGTGTTAATC 0.66619 -97 ATTATTTTTAAGTGATGACCCACAACCTAT 25 39 1 AGTGATGACC 0.701735 -63 GGAACTCCAAGATGTTAACCGGGTGATGCA 25 82 1 GATGTTAACC 0.948004 -20 ********** Masking position 6 Map Score: 9.53506 Number of sites scoring better than the average of aligned sites = 629 Number in coding regions = 613 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 6 TGTTATGGCTCTGTTTGCGGGAACTGCCTCAT 1 123 0 CGTTTCGGGA 0.993447 -178 TGTTATGGCTCTGTTTGCGGGAACTGCCTCAT 1 167 0 CGTTTCGGGA 0.993447 -134 ATCCACTTACCGGTTTCTGTGAATATAATCAC 2 52 1 CGTTTTGTGA 0.883236 -198 ATTTTCATAGTCGTTTTCGTGATTATATTCAC 2 70 0 TGTTTCGTGA 0.938247 -180 TCAGCACACCCAGATTCCCGGATCCAGCACAT 10 24 0 CGATTCCGGA 0.90978 -107 AATTTTTTTCCGGTTCACGGGATCAACATCAG 10 59 0 CGTTCCGGGA 0.972542 -72 CTTGAGGTTGTGGTTTCCCTGAATCCAGTACC 11 95 1 TGTTTCCTGA 0.865069 -169 TAAAACAGTACTGTTTTCATGAGGTCCATTAA 12 83 1 CGTTTCATGA 0.954646 -57 GTGTATATTCCGGTTTTCAGGTTTTCCGGGGC 13 54 0 CGTTTCAGGT 0.867007 -176 * **** ***** Masking position 5 Map Score: 8.59893 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 71 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 7 GCTCTGATTCGGGACCGGCATCAGCTACTG 1 74 0 GGGACCGGCA 0.949612 -227 AGGATGAGGCAGTTCCCGCAAACAGAGCCA 1 120 1 AGTTCCCGCA 0.872638 -181 AGGATGAGGCAGTTCCCGCAAACAGAGCCA 1 164 1 AGTTCCCGCA 0.872638 -137 TTAATGTGCTGGATCCGGGAATCTGGGTGT 10 21 1 GGATCCGGGA 0.929003 -110 GGCAGCTGAGGACCCCCGCAGTTATAATGG 12 50 0 GACCCCCGCA 0.778631 -90 TGATTTACATAGGCCCCGGAAAACCTGAAA 13 42 1 AGGCCCCGGA 0.94666 -188 ATGCCCTGTCAGTCCCGGGGTAAAGATGTG 13 83 0 AGTCCCGGGG 0.94768 -147 GGATGACCCTGTCCCCGGCGGATACATC 19 9 0 GTCCCCGGCG 0.849502 -49 AAAGATATAAAGAACCGGCGCCATAGGTTC 20 21 1 AGAACCGGCG 0.804411 -24 GTTTCTGGATGGCTCCGGGAGAAAAAAATC 23 36 0 GGCTCCGGGA 0.967194 -21 AATAATTAATGGGCCCGGGGGGTGTTAATC 25 15 0 GGGCCCGGGG 0.981874 -87 ********** Masking position 5 Map Score: 6.99018 Number of sites scoring better than the average of aligned sites = 689 Number in coding regions = 632 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 8 ATTACTAAATCTTCTGTAGAGGGACCCTTC 2 113 1 CTTCTGTAGA 0.84242 -137 TAAAAAAAAGTTTCTGTAGAGAAACCTCCA 2 152 1 TTTCTGTAGA 0.805913 -98 ATATAGATGATTACTGGTGA 3 15 1 TTACTGGTGA 0.967787 -10 CATTCCGGTGTTAATGGTGATGAG 5 28 1 TTAATGGTGA 0.747102 -14 TTGCTGAAAACCTCTGGTGAAGGGAACACC 13 114 1 CCTCTGGTGA 0.944961 -116 TTTACCACCTTTCTGGTGAAA 14 3 0 TTTCTGGTGA 0.98286 -19 TCATAGGAGCCTTCTGGTGGAAGGGGAGTG 15 14 1 CTTCTGGTGG 0.945291 -158 CAACTCTTTATTTCTGGTGATTCA 22 17 1 TTTCTGGTGA 0.98286 -14 GAACTGGTCCCTACTGATGAAATCATCATT 24 93 0 CTACTGATGA 0.834235 -35 ********** Masking position 5 Map Score: 7.80891 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 94 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 9 TCCTATCAAGGCAGTAGCTGATGCCGGTCCCG 1 63 1 GCAAGCTGAT 0.913836 -238 CTTTTATCATGGGGTTGCTTATACTTTGGGGT 1 251 0 GGGTGCTTAT 0.884942 -50 GGAACCTCCAGGACATGATGGGGTGGGAAT 2 9 0 GGATGATGGG 0.857297 -241 TCAATAAAGAGCAAATGCTGAGGTAAAGAA 7 21 1 GCATGCTGAG 0.959833 -20 CCGGGAATCTGGGTGTGCTGAGGCCTGATGTT 10 35 1 GGGTGCTGAG 0.984782 -96 CCGCAGTTTTGGGCATGCTGATCTGGCCTTGA 11 68 1 GGGTGCTGAT 0.987414 -196 ATAAAATAGGGGATCCGATGATTAAACACTTG 17 48 0 GGACGATGAT 0.905588 -100 CTTACTGCATGGAAATGATGATTTCATCAGTA 24 80 1 GGATGATGAT 0.968918 -48 GGTGATGGATGGAGCAGCTGATGGTTGTGAGG 26 55 0 GGAAGCTGAT 0.972083 -80 *** ******* Masking position 9 Map Score: 5.40536 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 231 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 10 AAATTTTAAGGATTTTCATAGTCGTTTTCG 2 83 0 GATTTTCATA 0.844492 -167 GACTCAAATAAATTTATATAGAAGTAAACC 11 165 1 AATTTATATA 0.702764 -99 CATTAAGAAAGATTTATATATGGACCTGTG 12 109 1 GATTTATATA 0.947914 -31 TCAGGTATCTGATTTACATAGGCCCCGGAA 13 33 1 GATTTACATA 0.955462 -197 CCGGGGTAAAGATGTGTATATTCCGGTTTT 13 69 0 GATGTGTATA 0.817674 -161 ATTTTATTACGATTTATATAGAAAACTTTA 17 73 1 GATTTATATA 0.947914 -75 CATTCCCTTTGATGTACATATATGTACAGT 24 22 1 GATGTACATA 0.919402 -106 ********** Masking position 8 Map Score: 3.69263 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 14 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 11 CTTCAGATCATGAATCTTTTATCATGGGGTTGC 1 265 0 TGAATCTATC 0.956015 -36 AACACCGGAATGATTCTATTATCATAAAC 5 7 0 TGATTCTATC 0.818588 -35 GTTTAAATCTTATACCGGTTGACCCA 11 4 1 TAAATCTACC 0.974732 -260 GTGGTTTCCCTGAATCCAGTACCTCAGCGGCGT 11 104 1 TGAATCTACC 0.987603 -160 AACTCCTCCTTGAATCATGAACCAGATCAGAAT 11 237 0 TGAATCAACC 0.94299 -27 GGGGCCTATGTAAATCAGATACCTGAGATTCTC 13 26 0 TAAATCTACC 0.97469 -204 TTACCACTCCTAAACCATATACCAAGTACAATT 15 117 1 TAAACCTACC 0.922299 -55 ****** **** Masking position 3 Map Score: 3.60653 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 13 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 12 TAAGAGGTCTTTTTTAGGTCTAACTCACCTTTTTTA 2 211 1 TTTTTAGATC 0.940228 -39 AAATCCCCTCTTTTCTGATTAAATCCCTTCCATTTT 6 29 0 TTTTCTGACC 0.874677 -27 TCACCAGAGGTTTTCAGCAAAATGCCCTGTCAGTCC 13 98 0 TTTTCAGACC 0.974966 -132 ATTTTTATTATTTTTAATACCACTCCCCTTCCACCA 15 28 0 TTTTTAAACC 0.94023 -144 CCATTAATTATTTTTAAGTGATGACCCACAACCTAT 25 33 1 TTTTTAATCC 0.738157 -69 TCATCAGGTATTTTTAGCAACAAACCGCGGCTCATT 26 17 1 TTTTTAGACC 0.985668 -118 TCACCAACTATTTTTAGCAATAGCCCCATATTAATA 26 82 1 TTTTTAGACC 0.985669 -53 TGGACTTCAGTTTTTAGGGTGACATC 26 119 1 TTTTTAGATC 0.94023 -16 ******* * ** Masking position 4 Map Score: 3.87153 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 21 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 13 CTTTGGGGTTAACCCTTTATAGTTCCTAAT 1 230 0 AACCCTTTAT 0.947833 -71 ATATAAATCTTTTTAAAAAAGGTG 2 236 0 AAATCTTTTT 0.757542 -14 GAGTTAACACAACCCTTTATTACCTTTTAA 10 104 0 AACCCTTTAT 0.947833 -27 GAACACTTCGATACCTTTATGGGTCAACCG 11 26 0 ATACCTTTAT 0.876423 -238 GTCCATATATAAATCTTTCTTAATGGACCT 12 104 0 AAATCTTTCT 0.822413 -36 TGTGTGGTTAAAATTTTTATTATTTTTAAT 15 46 0 AAATTTTTAT 0.633926 -126 GTTTCATAAGTAACCTTTATACTTACCACT 15 95 1 TAACCTTTAT 0.782167 -77 ATTTATATAGAAAACTTTATATTATCATAA 17 84 1 AAAACTTTAT 0.830108 -64 CCGGTTCTTTATATCTTTATGCCATCAA 20 9 0 ATATCTTTAT 0.846364 -36 ATCCGTCAACTCTTTATTTCTGGTGAT 22 8 1 AACTCTTTAT 0.93383 -23 ********** Masking position 6 Map Score: 5.53192 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 22 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 14 TGCCTTGATAGGAGATGGGAGCACTCAGGT 1 46 0 GGAGATGGGA 0.911552 -255 TGGAATGAAAATGGAAGGGATTTAATCAGA 6 22 1 ATGGAAGGGA 0.892745 -34 GAAAACCTCTGGTGAAGGGAACACCCTGAT 13 119 1 GGTGAAGGGA 0.980254 -111 GAGCCTTCTGGTGGAAGGGGAGTGGTATTA 15 20 1 GTGGAAGGGG 0.973577 -152 AACACTTGAAGGGGAAGAGGCTGCCGTAAT 17 26 0 GGGGAAGAGG 0.946004 -122 TTGGTACTAAAGAGAAGGGAGCTATAAA 17 130 1 AGAGAAGGGA 0.931234 -18 GGGGTGAGGTGGTGGAGGGGT 23 2 0 GGTGGAGGGG 0.948575 -55 ********** Masking position 4 Map Score: 3.10064 Number of sites scoring better than the average of aligned sites = 372 Number in coding regions = 342 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 15 ATTTATAATTTTCGCGAGGTTGACCTGAGT 1 24 1 TTCGCGAGGT 0.752352 -277 TGAATCTTTTATCATGGGGTTGCTTATACT 1 258 0 ATCATGGGGT 0.982966 -43 CCTCCAGGACATGATGGGGTGGGAAT 2 7 0 ATGATGGGGT 0.882012 -243 TTTTTTCCGGTTCACGGGATCAACATCAGG 10 58 0 TTCACGGGAT 0.788275 -73 CAGTACTGTTTTCATGAGGTCCATTAAGAA 12 88 1 TTCATGAGGT 0.908468 -52 AGGACTCATGGGGTTATTACGGCA 17 5 1 CTCATGGGGT 0.946705 -143 CAAGTGTTTAATCATCGGATCCCCTATTTT 17 48 1 ATCATCGGAT 0.871045 -100 CAGGACAACATCGTCGGGTTCAACAAGGA 19 39 0 ATCGTCGGGT 0.943826 -19 TGCATCACCCGGTTAACATCTTG 25 89 0 ATCACCCGGT 0.842352 -13 GATCCATCATCAGGTATTTTTAGCA 26 6 1 ATCATCAGGT 0.927575 -129 ********** Masking position 2 Map Score: 6.45907 Number of sites scoring better than the average of aligned sites = 339 Number in coding regions = 312 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185