AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -iarcA_aquae_opreg_100.orf -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 aq_194 53 putative protein #2 frdB1 35 fumarate reductase iron-sulfur subunit #3 frdA 295 fumarate reductase flavoprotein subunit #4 lpdA 85 dihydrolipoamide dehydrogenase #5 cydA 116 cytochrome oxidase d subunit I #6 icd 113 isocitrate dehydrogenase #7 leuS' 300 leucyl-tRNA synthetase beta subunit Motif number 1 ATAATAGCCTTTAAAAAGTAAGCTTGTAGA 1 19 1 TTAAAAAGTA 0.881387 -35 CTTATTAATAATATTTCTACAAGC 1 40 0 TTAATAATAT 0.780419 -14 AATTCCGTTTGAAAAATTTATCCCCCAGA 2 10 1 TGAAAAATTT 0.692358 -26 GCTCTACGGATTAATAATTTCTTTGATACT 3 82 1 TTAATAATTT 0.910328 -214 AGGTGGTAAATTAAAAAGAGATGAGTGAAG 3 142 1 TTAAAAAGAG 0.843098 -154 ATAATTTGCCTTAAAAGGAGGAAGCGA 4 8 0 TTAAAAGGAG 0.677545 -78 TTTTGATATACTAATAATTTGCCTTAAAAG 4 21 0 CTAATAATTT 0.849346 -65 AAGTGTTGGGTTAATGATTATTAACTTTTA 5 78 1 TTAATGATTA 0.474022 -39 CTCCGGAAGGTTAAAAGTTAATAATCATTA 5 89 0 TTAAAAGTTA 0.697524 -28 ACTTAAAGATTTTACCTCTAGA 6 3 1 TTAAAGATTT 0.805513 -111 ATAACAAAAATCAAAAAGTGTTTTAAATTA 6 38 1 TCAAAAAGTG 0.675568 -76 GGTTAGGTGTCTAATAAGTTATTGATAAAG 7 26 0 CTAATAAGTT 0.876602 -275 TGCAACATAGCTAAAAAGATTGAAAATCAA 7 131 0 CTAAAAAGAT 0.802523 -170 TAGGTGGGTCCTAATAAGTGATGTTTCGAT 7 184 0 CTAATAAGTG 0.839133 -117 AGCCCTCCAATTAAAAGTTTACTAAAGTAA 7 251 1 TTAAAAGTTT 0.866421 -50 AATTAAAAATTTTATATTGACC 7 289 0 TTAAAAATTT 0.94314 -12 ********** Masking position 4 Map Score: 11.1857 Number of sites scoring better than the average of aligned sites = 769 Number in coding regions = 653 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 2 GTAGCAAAAAGTATTTTCCTAATTCTGTGA 3 28 0 GTATTTTCCT 0.950291 -268 CATCTCTTTTTAATTTACCACCTAAGTTGA 3 135 0 TAATTTACCA 0.721006 -161 ACTTATCCTTGTTTTTTCCTTAATCGTGGG 3 200 1 GTTTTTTCCT 0.896441 -96 GGAGGCACGATTATATACCTTGTAAACAGG 3 228 1 TTATATACCT 0.850909 -68 CTGCTGTTCTTTATTTGCCTGTTTACAAGG 3 245 0 TTATTTGCCT 0.975464 -51 GATATACTAATAATTTGCCTTAAAAGGAGG 4 17 0 TAATTTGCCT 0.947375 -69 AAAAGGGGTTTTAATTGCCTTTAATTTTAG 4 53 0 TTAATTGCCT 0.848351 -33 CAGAGAGTTTTTATTTACTTACCAA 5 6 0 TTATTTACTT 0.875185 -111 ACTTAAAGATTTTACCTCTAGAGATTT 6 8 1 GATTTTACCT 0.9001 -106 TTGACCCGAAGTTTTTACTTTAGTAAACTT 7 265 0 GTTTTTACTT 0.774765 -36 ********** Masking position 6 Map Score: 7.30134 Number of sites scoring better than the average of aligned sites = 477 Number in coding regions = 442 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 3 AGAGTTCAATATTATCAACTTAGGTGGTAAA 3 121 1 ATTATAACTT 0.949259 -175 TAAAGAGAGCTTTGTCAACTTCACTCATCTC 3 159 0 TTTGTAACTT 0.951226 -137 TCAGAGAGTTTTTATTTACTTACCAA 5 6 0 TTTATTACTT 0.793994 -111 ATCTTTGTTGTAAATTAATTTCTATGATGTA 5 39 0 TAAATAATTT 0.659564 -78 TGGGTTAATGATTATTAACTTTTAACCTTCC 5 84 1 ATTATAACTT 0.949259 -33 AAAAGTGTTTTAAATTAACTTGACACACTTC 6 51 1 TAAATAACTT 0.894419 -63 TCACGAAACGAATGTTAATTTCCGCTAACCC 7 57 1 AATGTAATTT 0.674312 -244 TGAGTATACCTTTATAAAATTTCCATCCTTG 7 103 1 TTTATAAATT 0.862353 -198 AGTTTTTACTTTAGTAAACTTTTAATTGGAG 7 255 0 TTAGTAACTT 0.89828 -46 ACTTCGGGTCAATATAAAATTTTTAATT 7 283 1 AATATAAATT 0.742338 -18 ***** ***** Masking position 5 Map Score: 4.68893 Number of sites scoring better than the average of aligned sites = 314 Number in coding regions = 281 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 GATGCTCTCACAGAATTAGGAAAATACTTT 3 21 1 CAGAATTAGG 0.944172 -275 AGCATCAAACCAAAATTGGGTTTATTCGTA 3 55 0 CAAAATTGGG 0.974659 -241 GAAGCTCCTCCTGAAAAGGGGTTTTAATTG 4 66 0 CTGAAAAGGG 0.964572 -20 TCCTTGGCAACTGAATAGGGTAGGTGGGTC 7 204 0 CTGAATAGGG 0.988913 -97 TGCCAAGGAGCAAAGTAGGGCTCTGTAGCC 7 225 1 CAAAGTAGGG 0.962495 -76 ********** Masking position 4 Map Score: 1.88051 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 83 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 5 AGAAGTAGTAGTATCAAAGAAATTATTAAT 3 91 0 GTATCAAAGA 0.85554 -205 CTTAGGTGGTAAATTAAAAAGAGATGAGTG 3 139 1 AAATTAAAAA 0.495676 -157 AAGTGTAAATACAATAAAGAGAGCTTTGTC 3 174 0 ACAATAAAGA 0.86432 -122 GATTAAGGAAAAAACAAGGATAAGTGTAAA 3 195 0 AAAACAAGGA 0.909557 -101 TCTATGATGTATATCAGAGAGTTTTTATTT 5 20 0 ATATCAGAGA 0.870676 -97 TCTCTGATATACATCATAGAAATTAATTTA 5 30 1 ACATCATAGA 0.877191 -87 AAATTAATTTACAACAAAGATCAAACTTTA 5 49 1 ACAACAAAGA 0.970016 -68 CTAGAGATTTATAACAAAAATCAAAAAGTG 6 28 1 ATAACAAAAA 0.802032 -86 AAAAGATTGAAAATCAAGGATGGAAATTTT 7 118 0 AAATCAAGGA 0.925318 -183 ********** Masking position 6 Map Score: 2.53499 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 229 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 CAATATTATCAACTTAGGTGGTAAATTAAA 3 127 1 AACTTAGGTG 0.937588 -169 GGAAAAAACAAGGATAAGTGTAAATACAAT 3 189 0 AGGATAAGTG 0.959132 -107 CGTTTCGTGAAGGTTAGGTGTCTAATAAGT 7 37 0 AGGTTAGGTG 0.993951 -264 GCAACTGAATAGGGTAGGTGGGTCCTAATA 7 198 0 AGGGTAGGTG 0.992817 -103 ********** Masking position 5 Map Score: 1.11208 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 15 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 7 TTTTAACCTTCCGGAGGTTCGAAA 5 103 1 CCGGAGGTTC 0.993966 -14 TTTCCGCTAACCCGAGGTTCTGCAAACTTG 7 75 1 CCCGAGGTTC 0.996712 -226 TTTATATTGACCCGAAGTTTTTACTTTAGT 7 271 0 CCCGAAGTTT 0.976045 -30 ********** Masking position 5 Map Score: 0.873131 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 8 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 8 ********** No masking Map Score: -2.7829e-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 9 ********** No masking Map Score: -2.7829e-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 10 ********** No masking Map Score: -2.7829e-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