AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -inarL_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 MTH170 141 phosphoribosylaminoimidazolesuccinocarboxamide synthase #2 MTH420 300 conserved protein #3 MTH1354 124 NADH oxidase #4 MTH1502 189 succinate dehydrogenase, flavoprotein subunit #5 MTH1552 139 formate dehydrogenase, alpha subunit homolog #6 MTH1553 71 tungsten formylmethanofuran dehydrogenase, subunit H #7 MTH1560 107 nitrogenase NifH subunit #8 MTH1563 37 nitrogenase NifD subunit #9 MTH1567 235 catalytic subunit of nitrate reductase (flp) #10 MTH1850 105 fumarate reductase Motif number 1 CCGGGCTGCAGACTGACAGATAAATCCATGATAC 2 82 1 GACACATAAA 0.707964 -219 TGTGAGCATAGATTTTTGGTTAAATGCTGCATAT 2 128 0 GATTTTTAAA 0.929376 -173 GTTTGATGCTCCCTTATAACTACCACAC 3 5 1 GATTCTTATA 0.714065 -120 TATAAATTTGGATACATCAATAGATCTGTGTGGT 3 32 0 GATATATAGA 0.733216 -93 AAATAATTCAGATATATTTATAAATTTGGATACA 3 50 0 GATATATAAA 0.952954 -75 AAATATATCTGAATTATTTATAAAATGAAGAAGA 3 65 1 GAAATATAAA 0.867712 -60 ATCTGAGGGTGATGTATGGATTTAAGCCTTCAAT 4 59 0 GATATATTTA 0.503222 -131 ACTTTATCATGATGCACAGATAAAGGTTATGAGT 5 30 0 GATACATAAA 0.943242 -110 AAATCAAATAGAAAAATATATATATAGGTGTGTG 6 12 0 GAAATATATA 0.602647 -60 TTTTCTATTTGATTTTTGTAGAAAATTATTATAT 6 31 1 GATTTAGAAA 0.646804 -41 TAAATTTTTTGGTAAATGGTTAAAATAAAGAACA 7 79 0 GGTATTTAAA 0.847337 -29 GGACTTACTTGAAGGATGATTTAAA 8 23 1 GAAATTTTAA 0.533367 -15 TGTAGATGGGGATACTCTTATAAAAATTGAATTT 9 32 1 GATTCATAAA 0.930531 -204 AATTTAATAAGGATATTCCTTAAATAAGGAAATT 9 61 1 GGATTTTAAA 0.591612 -175 CCGATCTGAAGATAGTTCAATTAATTTAACTAAA 9 195 1 GATTTATTAA 0.779241 -41 TTTACATCCAGGTATTTAGTTAAATTAATTGAAC 9 209 0 GGTTTTTAAA 0.817308 -27 GATTTTAACTGATAATCTTTTAAACAATACAGAC 10 13 0 GATTCTTAAA 0.915229 -93 AATATGTGTTGATAAACAATTAAAATTCAGTTCA 10 56 1 GATACTTAAA 0.930521 -50 *** ** ***** Masking position 14 Map Score: 12.3227 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 87 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 2 TATAAGTATTGGAGAGTTGATCAGGATTTCATA 1 95 1 GGAGTTATCA 0.96387 -47 CATATTTCGGTGTCCCTGTATCATGGATTTATC 2 100 0 TGTCTGATCA 0.763008 -201 TGATACTGAAGGACAGATAATCACATCCTTACC 2 237 0 GGAGATATCA 0.923545 -64 GTGGTAGTTATAAGGGAGCATCAAAC 3 4 0 TAAGAGATCA 0.910261 -121 GAGGACCGGGTGATGGTTCATCACCTGAGCTTG 4 106 1 TGAGTTATCA 0.958367 -84 TTATTCTCGGTTATGGTTCATCACCTTAACTAT 4 142 1 TTAGTTATCA 0.905238 -48 TCATAACCTTTATCTGTGCATCATGATAAAGTT 5 32 1 TATGTGATCA 0.862151 -108 CTTTTTATGGTGAAACTTTATCATGATGCACAG 5 45 0 TGACTTATCA 0.930387 -95 CTGTATTGTTTAAAAGATTATCAGTTAAAATCA 10 15 1 TAAGATATCA 0.934648 -91 AACTGAATTTTAATTGTTTATCAACACATATTA 10 55 0 TAAGTTATCA 0.968827 -51 *** *** **** Masking position 10 Map Score: 7.57619 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 97 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 3 GTAAATTCTATTATGAGTTATATTGCGATTCAGTT 1 55 0 TTTGATTATG 0.774462 -87 ATTTACACCTATATAAGTATTGGAGAGTTGATCAG 1 84 1 ATTAATATTG 0.848863 -58 TCTATTTAAGTTTTTGTGGTTGATTTCT 2 4 1 ATTAATTTTG 0.957692 -297 GTATCCAAATTTATAAATATATCTGAATTATTTAT 3 51 1 TTTAATATAG 0.744443 -74 CTTCCATCTATTCTAAATTTAACAGTCCCCTTCAT 5 93 0 TTTAATTTAG 0.921498 -47 ATATTTTTCTATTTGATTTTTGTAGAAAATTATTA 6 27 1 ATTGATTTTG 0.949037 -45 AATGGGAAAAATAGAATTTATTTAGGATCGGAC 7 9 0 ATGAATTATG 0.736091 -99 CTATTTAAATTTTTTGGTAAATGGTTA 7 91 0 ATTAATTTTG 0.957692 -17 TCTTATAAAAATTGAATTTAATAAGGATATTCCTT 9 47 1 ATGAATTAAG 0.736091 -189 AGTCAGATTCATCTAATTTTATGAGTTGCACCACA 9 125 0 ATTAATTTAG 0.957692 -111 AATTAGATGAATCTGACTGTATATGTGGCAAGGTA 9 142 1 ATTGATGTAG 0.795232 -94 ATATTAAGGTTTGTGATTTTAACTGATAATCTTTT 10 26 0 TTTGATTTAG 0.906177 -80 ** *** **** * Masking position 6 Map Score: 6.30583 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 50 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 4 ATTCATGCTTCTTAGGGTGAAATA 1 5 0 CTTAGGGTGA 0.954747 -137 ATTTAAGTTTTTGTGGTTGATTTCTCCGGG 2 14 1 TTGTGGTTGA 0.743909 -287 AATCCATTCCCTGATACTGAAGGACAGATA 2 251 0 CTGATACTGA 0.879416 -50 AATCAGGCGACTGATCCTGATTGAAGGCTT 4 40 1 CTGATCCTGA 0.918573 -150 ACGTTCTAATCTGAGGGTGATGTATGGATT 4 71 0 CTGAGGGTGA 0.990753 -119 GGTTCATCACCTGAGCTTGACTTTATTCTC 4 120 1 CTGAGCTTGA 0.938562 -70 AGGTTATGAGTAGAGAGTGAGGTGAAGAGG 5 11 0 TAGAGAGTGA 0.70106 -129 CAGTGTCCTTTTTATGGTGAAACTTTATCA 5 55 0 TTTATGGTGA 0.778732 -85 GGAAGGGAACTTGAGGCTGAACCTGGA 5 123 1 TTGAGGCTGA 0.976481 -17 ********** Masking position 8 Map Score: 5.16923 Number of sites scoring better than the average of aligned sites = 849 Number in coding regions = 813 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 5 AAATTCTTTAAAAGTGATAGT 1 131 1 AAAGTGATAG 0.698294 -11 CCCCTCTGATACGGGGATTGCCGGTGCTGC 2 45 0 ACGGGGATTG 0.928886 -256 CCCCGTATCAGAGGGGACACACTCCGGGCT 2 59 1 GAGGGGACAC 0.957151 -242 AATCCATGATACAGGGACACCGAAATATGC 2 104 1 ACAGGGACAC 0.956751 -197 CTCCTAGGAGAAGGGGATAG 3 115 1 AAGGGGATAG 0.98149 -10 TTTCACCATAAAAAGGACACTGAAGATAAC 5 63 1 AAAAGGACAC 0.785919 -77 AGATAACATGAAGGGGACTGTTAAATTTAG 5 86 1 AAGGGGACTG 0.968543 -54 ATACCTGTAGATGGGGATACTCTTATAAAA 9 27 1 ATGGGGATAC 0.928983 -209 ********** Masking position 7 Map Score: 3.72518 Number of sites scoring better than the average of aligned sites = 402 Number in coding regions = 373 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 6 ATATTGCGATTCAGTTATATAATCTTGCGA 1 41 0 TCAGTTATAT 0.960938 -101 AATTCTATTATGAGTTATATTGCGATTCAG 1 57 0 TGAGTTATAT 0.825457 -85 GCATAGATTTTTGGTTAAATGCTGCATATT 2 127 0 TTGGTTAAAT 0.854646 -174 TATAAATAATTCAGATATATTTATAAATTT 3 57 0 TCAGATATAT 0.794997 -68 CTAGGAGTTATCGGTTATAGGTCTCTTCTT 3 92 0 TCGGTTATAG 0.968792 -33 GACTTTATTCTCGGTTATGGTTCATCACCT 4 138 1 TCGGTTATGG 0.878833 -52 TATCTTCAGATCGGTTAAAGATTTCAGTAC 9 179 0 TCGGTTAAAG 0.961828 -57 ATCCAGGTATTTAGTTAAATTAATTGAACT 9 208 0 TTAGTTAAAT 0.820371 -28 TAAAAGATTATCAGTTAAAATCACAAACCT 10 25 1 TCAGTTAAAA 0.831253 -81 ********** Masking position 6 Map Score: 5.73358 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 33 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 ATCTATGGTAAAGGGAAGGTAAGGATGTGATTAT 2 220 1 AAGGAATAAG 0.967657 -81 AACTACCACACAGATCTATTGATGTATCCAAATT 3 28 1 CAGACTTGAG 0.818176 -97 AAGGACACTGAAGATAACATGAAGGGGACTGTTA 5 75 1 AAGAAATGAG 0.967657 -65 GAATAGATGGAAGGGAACTTGAGGCTGAACCTGG 5 115 1 AAGGAATGAG 0.979362 -25 TCCCCATCTACAGGTATTTTAACGTATTTCAAA 9 10 0 CAGGATTAAG 0.944265 -226 TTCCTTAAATAAGGAAATTTGATGGGATAAGACT 9 76 1 AAGGAATGAG 0.979361 -160 TAAGACTGAAAAGAAATGATAATGTGGTGCAACT 9 103 1 AAGAATTAAG 0.949653 -133 ATTGTTTATCAACACATATTAAGGTTTGTGATTT 10 42 0 AACAATTAAG 0.757391 -64 **** ** *** * Masking position 12 Map Score: 2.5246 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 137 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 TTGCCTTTACTCATATCAGTGCTGCAGTGT 2 164 0 TCATATCAGT 0.963711 -137 TCTCATGAAAACTGTTCAGTTTTTGCTTTT 7 48 1 ACTGTTCAGT 0.588755 -60 CATTATCATTTCTTTTCAGTCTTATCCCAT 9 97 0 TCTTTTCAGT 0.93692 -139 GTTAAAGATTTCAGTACAGTACCTTGCCAC 9 166 0 TCAGTACAGT 0.934716 -70 TGAACTATCTTCAGATCGGTTAAAGATTTC 9 184 0 TCAGATCGGT 0.943211 -52 CAATTAAAATTCAGTTCATTCTGAAGTTTT 10 72 1 TCAGTTCATT 0.903294 -34 CTGAAGTTTTTCATATGAGTCAGC 10 92 1 TCATATGAGT 0.837406 -14 ********** Masking position 10 Map Score: 1.22305 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 123 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 9 TGGTTAAATGCTGCATATTTCGGTGTCCCTG 2 115 0 CTGCATATTC 0.892408 -186 CATATCAGTGCTGCAGTGTTCTGTGAGCATA 2 152 0 CTGCAGTTTC 0.949453 -149 ATAAATATATCTGAATTATTTATAAAATGAA 3 63 1 CTGAATTTTT 0.971712 -62 GATCAGTCGCCTGATTTATTCGATAATGATC 4 25 0 CTGATTTTTC 0.857831 -165 AAAGCAAAAACTGAACAGTTTTCATGAGAAG 7 46 0 CTGAACATTT 0.849962 -62 AGGTACTGTACTGAAATCTTTAACCGATCTG 9 172 1 CTGAAATTTT 0.912593 -64 ATGTCTGTATTGTTTAAAAGATTAT 10 5 1 CTGTATTTTT 0.894454 -101 TCAGTTCATTCTGAAGTTTTTCATATGAGTC 10 82 1 CTGAAGTTTT 0.966077 -24 ******* *** Masking position 9 Map Score: 2.78564 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 99 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 10 TATTTCGGTGTCCCTGTATCATGGATTTAT 2 101 0 TCCCTGTATC 0.786283 -200 ATCCTTACCTTCCCTTTACCATAGATCTCT 2 216 0 TCCCTTTACC 0.939152 -85 CGGTTATAGGTCTCTTCTTCATTTTATAAA 3 81 0 TCTCTTCTTC 0.85171 -44 CTATCCCCTTCTCCTAGGAGTTAT 3 111 0 CCCCTTCTCC 0.97974 -14 CCTCTTCACCTCACTCTCTA 5 1 1 CCTCTTCACC 0.931633 -139 ATTTAACAGTCCCCTTCATGTTATCTTCAG 5 82 0 CCCCTTCATG 0.898289 -58 ATTCTATTTTTCCCATTTTCTTCTCATGAA 7 27 1 TCCCATTTTC 0.870206 -81 ATAAGAGTATCCCCATCTACAGGTATTTTA 9 23 0 CCCCATCTAC 0.864585 -213 ATGAGTTGCACCACATTATCATTTCTTTTC 9 110 0 CCACATTATC 0.677941 -126 ********** Masking position 4 Map Score: 2.22265 Number of sites scoring better than the average of aligned sites = 1069 Number in coding regions = 994 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 11 GTTGATTTCTCCGGGTGCAGCACCGGCAAT 2 29 1 CCGGGTGCAG 0.996489 -272 GGACACACTCCGGGCTGCAGACTGACAGAT 2 73 1 CGGGCTGCAG 0.971599 -228 GCATATTAACCCGGGACCAGAGATCTATGG 2 198 1 CCGGGACCAG 0.962644 -103 AATGATCACTGGGGGTTCTGT 4 2 0 GGGGGTTCTG 0.890639 -188 CCGTAGAGGACCGGGTGATGGTTCATCACC 4 101 1 CCGGGTGATG 0.959493 -89 TCCAGGTTCAGCCTCAAGTTC 5 129 0 CCAGGTTCAG 0.951492 -11 ********** Masking position 4 Map Score: 1.93908 Number of sites scoring better than the average of aligned sites = 321 Number in coding regions = 302 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 12 ********** No masking Map Score: -2.3921e-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 13 TAAATTCTATTATGAGTTATATTGCGATTC 1 59 0 TATGAGTTAT 0.936178 -83 AATACTTATATAGGTGTAAATTCTATTATG 1 75 0 TAGGTGTAAA 0.813335 -67 GCAGCACTGATATGAGTAAAGGCAATAAAG 2 169 1 TATGAGTAAA 0.954583 -132 CCCCTTCTCCTAGGAGTTATCGGTTATAGG 3 101 0 TAGGAGTTAT 0.892546 -24 AGATAAAGGTTATGAGTAGAGAGTGAGGTG 5 17 0 TATGAGTAGA 0.953707 -123 CATCTAATTTTATGAGTTGCACCACATTAT 9 121 0 TATGAGTTGC 0.923574 -115 TTTAAAAGATTATCAGTTAAAATCACAAAC 10 23 1 TATCAGTTAA 0.848039 -83 CAAACCTTAATATGTGTTGATAAACAATTA 10 48 1 TATGTGTTGA 0.923659 -58 ********** Masking position 2 Map Score: 3.96489 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 30 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 14 ********** No masking Map Score: -2.3921e-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 15 ********** No masking Map Score: -2.3921e-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