AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00640_mjan_reg_100.orf -o00640_mjan_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: MJ0266 27 pyruvate ferredoxin oxidoreductase, subunit beta (porB) MJ0267 21 pyruvate ferredoxin oxidoreductase, subunit alpha (porA) Input sequences: #1 MJ0210 86 succinyl-CoA synthetase, beta subunit #2 MJ0269 283 pyruvate ferredoxin oxidoreductase, subunit gamma (porG) #3 MJ0276 119 2-ketoglutarate ferredoxin oxidoreductase, subunit alpha (korA) #4 MJ0487 282 phenylalanyl-tRNA synthetase, subunit alpha (pheS) #5 MJ0490 47 L-lactate dehydrogenase EGAD|7256|705 #6 MJ0537 276 2-ketoglutarate ferredoxin oxidoreductase, subunit beta (korB) #7 MJ1230 22 M. jannaschii predicted coding region MJ1230 #8 MJ1231 255 oxaloacetate decarboxylase alpha chain (oadA) #9 MJ1246 300 succinyl-CoA synthetase, alpha subunit (sucD) Motif number 1 CAAAATTTTAAAATTATCATATAAAAAATTTGGTGAT 1 26 0 AAATAAAAAA 0.937278 -61 TGATAATTTTAAAATTTTGCATTAAAAAGAAATTTAT 1 44 1 AAATATAAAA 0.895068 -43 ATGAAAGCTGGGAGATTAAGATTTATGACAG 2 5 1 AAGTATAAGA 0.791146 -279 TATTATATTGAAGGAGTTAAAAAAGGAACTGCTATAG 2 79 1 AAGAAAAGGA 0.701929 -205 AGAAAAAATAAAATTAATTTACATGGATTACATAGTC 2 157 0 AAATAATGGA 0.624615 -127 ACAATTATTAAAAGTAATATATAAAGTTTTGGAGATT 2 224 0 AAATAAAAGT 0.881433 -60 AGAAAATAACAATTTAAAAAAATAGAAGCATGGGCTA 3 17 0 AATTATAGAA 0.762624 -103 TAACGACTATAATATAATAGAGAAGAAAATAACAATT 3 40 0 AATTAAAGAA 0.849132 -80 TATAGTCGTTAAATATTAACACAAGGTTATATTATAT 3 66 1 AAAAAAAGGT 0.725111 -54 ATATTATATAAAAGTAGCTTAGAAGGAGGGGGTTTA 3 94 1 AAATAAAGGA 0.96863 -26 ATTAAATATTAACTACTAAAATAAATTTTTA 4 5 1 AATTATAAAA 0.747377 -278 GAACTTTAATAATCTCAATTAATAAAAATTTATTTTA 4 27 0 AATTATAAAA 0.747377 -256 AGTCCTATTCAAAGATTGCCATTAAAATTTCTAATAT 4 88 1 AAAAATAAAA 0.735965 -195 TCTATTTGTAAAACTTTGATATTAGAAATTTTAATGG 4 106 0 AAATATAGAA 0.902563 -177 AAAGTTTTACAAATAGAAAAAGAAGGACGAAAATTTT 4 126 1 AAAAAAAGGA 0.90983 -157 AGAAGGACGAAAATTTTTAAAATAAGAATATGGACGA 4 146 1 AAATATAAGA 0.941964 -137 TTATTAAAGAAAATAATACTATAAAAAGAATAAAATT 4 233 1 AAAAAAAAAA 0.830023 -50 AGAGATTTTAAAATTAAATTAAAAAGAGGAA 5 5 0 AAATAAAAGA 0.966026 -43 GGTTGATCAAAACTTAGTTAAATAGGTATCCCAATAG 6 82 0 AACTATAGGT 0.610372 -195 TTACTCGAACAACCTTTTAGAAAAGGTTGATCAAAAC 6 106 0 AACTAAAGGT 0.73292 -171 AATATCACAAAAAAAGAGAAGT 7 6 0 AATTAAAAGA 0.907935 -17 CCCTCATCAAAAATTGATTAAGAAAATTTAAGATTTA 8 117 0 AAATAAAAAT 0.796207 -139 AAAATAAATCAGAAAGATTTAAGTTAT 9 1 1 AAATAAAAGA 0.966026 -300 TTTAGGCATCAAAGTGCCTTATAAATATATAAATTGT 9 211 1 AAATAAAATA 0.633814 -90 AAAGTTCTACAACGACACATATAAAAAGTAAAAGGGG 9 249 1 AACAAAAAAA 0.624068 -52 *** * * ***** Masking position 11 Map Score: 22.0991 Number of sites scoring better than the average of aligned sites = 1656 Number in coding regions = 1337 Number in noncoding regions = 319 Number of orfs with sites within 600 bp upstream = 268 Fraction of orfs with sites within 600 bp upstream = 0.0430453 Motif number 2 AATTTTGCATTAAAAAGAAATTTATCATTTAA 1 56 1 TAAAAGAATT 0.798698 -31 TAAAGCTGTTTAAAAATCAAATCGGCTATTAT 2 53 1 TAAAATAAAT 0.942705 -231 AGTCTTTCTCTAAAAATGATGTTGTATTTATT 2 129 0 TAAAATATGT 0.738533 -155 TAAGAAAAAATAAAATTAATTTACATGGATTA 2 164 0 TAAAATATTT 0.885385 -120 GTTAATTGCTTAAATCTCCAAAACTTTATATA 2 212 1 TAAATTCAAA 0.54271 -72 TAACAATTATTAAAAGTAATATATAAAGTTTT 2 231 0 TAAAATATAT 0.942705 -53 AGATTGCCATTAAAATTTCTAATATCAAAGTT 4 100 1 TAAAATCTAA 0.785638 -183 AACCCATGTTTAAATCTACAATTCATCAGTTT 4 182 0 TAAATTCAAT 0.785639 -101 AATAATACTATAAAAAGAATAAAATTTAGCAG 4 244 1 TAAAAGATAA 0.732368 -39 AAAGAGATTTTAAAATTAAATTAAAAAGAGGA 5 12 0 TAAAATAATT 0.885385 -36 CATTATAAATTAAAAATTATTTGAGGTGGTAA 6 254 1 TAAAATATTT 0.885367 -23 ATTTAGGAGATAAAATTGAGTTTAAATTAATT 8 90 0 TAAAATAGTT 0.643477 -166 TTTTATCTCCTAAATCTTAAATTTTCTTAATC 8 107 1 TAAATTAAAT 0.841971 -149 CACAGCCAAATAAAACGGCAATGCAGTTCCGT 8 195 0 TAAAAGCAAT 0.853228 -61 TTCACAGGAATAAATCTACTATTGGAATGACG 9 173 1 TAAATTCTAT 0.785639 -128 ACGACACATATAAAAAGTAAAAGGGGATATAT 9 260 1 TAAAAGAAAA 0.732373 -41 TATTAAACCGTAAAATTTATATATCCCCTTTT 9 278 0 TAAAATATAT 0.942705 -23 ***** * **** Masking position 4 Map Score: 12.1072 Number of sites scoring better than the average of aligned sites = 1147 Number in coding regions = 741 Number in noncoding regions = 406 Number of orfs with sites within 600 bp upstream = 350 Fraction of orfs with sites within 600 bp upstream = 0.0562159 Motif number 3 TAAACCTATAAATTTATCACCAAATTTTT 1 10 1 AAATTTATCA 0.666563 -77 ATTTATCACCAAATTTTTTATATGATAATT 1 22 1 AAATTTTTTA 0.757086 -65 TTTTTAATGCAAAATTTTAAAATTATCATA 1 42 0 AAAATTTTAA 0.507895 -45 CATTAAAAAGAAATTTATCATTTAAGGTGA 1 63 1 AAATTTATCA 0.666563 -24 CAATTAACGAAAATAGTTTAGGCATAAGAA 2 190 0 AAATAGTTTA 0.537831 -94 TTATTAAAAGTAATATATAAAGTTTTGGAG 2 227 0 TAATATATAA 0.66295 -57 TTACTTTTAATAATTGTTAATGATTGATAA 2 244 1 TAATTGTTAA 0.734558 -40 CTATTTTTTTAAATTGTTATTTTCTTCTCT 3 29 1 AAATTGTTAT 0.678295 -91 AACCTTGTGTTAATATTTAACGACTATAAT 3 64 0 TAATATTTAA 0.771196 -56 TTTTAGTAGTTAATATTTAAT 4 2 0 TAATATTTAA 0.771196 -281 CTACTAAAATAAATTTTTATTAATTGAGAT 4 23 1 AAATTTTTAT 0.792183 -260 ATTGCCATTAAAATTTCTAATATCAAAGTT 4 102 1 AAATTTCTAA 0.69468 -181 AGAAGGACGAAAATTTTTAAAATAAGAATA 4 146 1 AAATTTTTAA 0.935171 -137 TTTCTTTAATAAATAGATAACTATGTTTAT 4 215 0 AAATAGATAA 0.761767 -68 CCACCTCAAATAATTTTTAATTTATAATGG 6 253 0 TAATTTTTAA 0.833417 -24 CCCTCATCAAAAATTGATTAAGAAAATTTA 8 124 0 AAATTGATTA 0.505971 -132 TATCCCTCACAAATATTTATTTTGATTTAA 8 233 0 AAATATTTAT 0.719893 -23 AATAAATCAGAAAGATTTAAGTTATTTAAA 9 13 1 AAAGATTTAA 0.508011 -288 AGTGCCTTATAAATATATAAATTGTGAAAG 9 223 1 AAATATATAA 0.851083 -78 TTAAACCGTAAAATTTATATATCCCCTTTT 9 278 0 AAATTTATAT 0.693529 -23 ********** Masking position 8 Map Score: 15.4053 Number of sites scoring better than the average of aligned sites = 1791 Number in coding regions = 1190 Number in noncoding regions = 601 Number of orfs with sites within 600 bp upstream = 460 Fraction of orfs with sites within 600 bp upstream = 0.0738837 Motif number 4 TATATATTACTTTTAATAATTGTTAATGAT 2 238 1 TTTTAATAAT 0.366788 -46 AAACTGTCATTATCAATCATTAACAATTAT 2 253 0 TATCAATCAT 0.679273 -31 ACTTTAATAATCTCAATTAATAAAAATTTA 4 32 0 TCTCAATTAA 0.692554 -251 TCAACCCATGTTTAAATCTACAATTCATCA 4 186 0 TTTAAATCTA 0.640775 -97 AATGCATCTGTTTTGATCAACGCACCATAG 6 45 1 TTTTGATCAA 0.867098 -232 TTTAACTAAGTTTTGATCAACCTTTTCTAA 6 97 1 TTTTGATCAA 0.867098 -180 TTAAGCCCTATTTTAATCAAACGAACTCAT 6 202 0 TTTTAATCAA 0.953813 -75 GGGTATCCATTATAAATTAAAAATTATTTG 6 247 1 TATAAATTAA 0.478655 -30 ATATATATCATTTCAATCAATACTACACTA 8 28 1 TTTCAATCAA 0.963751 -228 TAAAATTGAGTTTAAATTAATTAATACAAA 8 82 0 TTTAAATTAA 0.787231 -174 TCTTAAATTTTCTTAATCAATTTTTGATGA 8 121 1 TCTTAATCAA 0.887967 -135 AGTCTTATAATTTCAATCATAGTTACCCCT 8 150 0 TTTCAATCAT 0.895133 -106 CTGTGCCTTTTTTAAATCAAAATAAATATT 8 222 1 TTTAAATCAA 0.94368 -34 ********** Masking position 6 Map Score: 8.87685 Number of sites scoring better than the average of aligned sites = 392 Number in coding regions = 328 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 5 AATTTCCCCTCACAAAAGAGATTTT 5 33 0 CCCCTCACAA 0.991735 -15 ACGAACTCATCTCCTCATAACTACCGCATG 6 182 0 CTCCTCATAA 0.921909 -95 ATCATAGTTACCCCTCATCAAAAATTGATT 8 135 0 CCCCTCATCA 0.991735 -121 AGCTATCCCTCACAAATATTTATTT 8 241 0 TCCCTCACAA 0.958322 -15 AAATCCCAGCACCCCCACCATTTTTTAAAT 9 36 0 ACCCCCACCA 0.942155 -265 TACACCACACCCCCGCATCAATGTAGAATC 9 143 1 CCCCGCATCA 0.981836 -158 ********** Masking position 7 Map Score: 4.50431 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 29 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 ATGATAATTTTAAAATTTTGCATTAAAAAG 1 43 1 TAAAATTTTG 0.729153 -44 TCTCAATTAATAAAAATTTATTTTAGTAGT 4 22 0 TAAAAATTTA 0.459097 -261 GAAGTCCTATTCAAAGATTGCCATTAAAAT 4 86 1 TCAAAGATTG 0.929379 -197 TTTCTATTTGTAAAACTTTGATATTAGAAA 4 115 0 TAAAACTTTG 0.885917 -168 CAACCTTTTAGAAAAGGTTGATCAAAACTT 6 104 0 GAAAAGGTTG 0.888407 -173 CAACCTTTTCTAAAAGGTTGTTCGAGTAAC 6 114 1 TAAAAGGTTG 0.974459 -163 AACCTTTTAGTAAAAGGTTACTCGAACAAC 6 130 0 TAAAAGGTTA 0.868021 -147 AACCTTTTACTAAAAGGTTGGGAGCAATGT 6 141 1 TAAAAGGTTG 0.974459 -136 ATGGCTAAGCTCAAACATTGCTCCCAACCT 6 155 0 TCAAACATTG 0.847401 -122 TTACCCCTCATCAAAAATTGATTAAGAAAA 8 128 0 TCAAAAATTG 0.782137 -128 ********** Masking position 5 Map Score: 6.78532 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 196 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 7 TTTGAGAATGACACTATAGCAGTTCCTTTT 2 99 0 ACACTATAGC 0.960006 -185 TTTGATCAACGCACCATAGCTTCGCCCTAT 6 56 1 GCACCATAGC 0.969025 -221 AATCAATACTACACTACGGCTATAAACAAG 8 42 1 ACACTACGGC 0.983425 -214 TGAAATTATAAGACTATGGCTAACCAAATA 8 165 1 AGACTATGGC 0.951763 -91 ATAGGGCGCTGGACCACGGCAGGAGAAATC 9 81 0 GGACCACGGC 0.97587 -220 AGACCTGGCTACACCACACCCCCGCATCAA 9 134 1 ACACCACACC 0.931557 -167 ********** Masking position 6 Map Score: 2.40167 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 10 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 GGAGTTAAAAAAGGAACTGCTATAGTGTCA 2 91 1 AAGGAACTGC 0.987338 -193 AAGAATATGGACGAAACTGATGAATTGTAG 4 169 1 ACGAAACTGA 0.865808 -114 ATCCCACCATACAGAACTGCTAAATTTTAT 4 262 0 ACAGAACTGC 0.970794 -21 TAACCAAATAACGGAACTGCATTGCCGTTT 8 185 1 ACGGAACTGC 0.994314 -71 TGATTTAAAAAAGGCACAGCCAAATAAAAC 8 211 0 AAGGCACAGC 0.914368 -45 ********** Masking position 6 Map Score: 1.8793 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 28 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 9 ********** No masking Map Score: 9.97192e-13 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 10 GAAAGACTATGTAATCCATGTAAATTAATT 2 153 1 GTAATCCATG 0.936583 -131 GCTACGCTCGGTAATGCCTCTTAGCATAG 6 10 0 GTAATGCCTC 0.977632 -267 GCGTAGCGAGGTAATGCATCTGTTTTGATC 6 33 1 GTAATGCATC 0.936582 -244 TTCAATCATAGTTACCCCTCATCAAAAATT 8 139 0 GTTACCCCTC 0.942486 -117 AGCTATCCCTCACAAATATTT 8 245 0 GCTATCCCTC 0.952807 -11 CACGGCAGGAGAAATCCCTGGACCTGGGTT 9 67 0 GAAATCCCTG 0.929994 -234 ********** Masking position 4 Map Score: 0.371515 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 48 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 11 ********** No masking Map Score: 9.97192e-13 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 12 ********** No masking Map Score: 9.97192e-13 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: 9.97192e-13 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