AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -ifhlA_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 MTH384 249 unknown #2 MTH387 24 conserved protein #3 MTH388 35 unknown #4 MTH393 41 NADH dehydrogenase (ubiquinone), subunit 1 related protein #5 MTH394 55 unknown #6 MTH397 40 formate hydrogenlyase, subunit 7 #7 MTH783 83 hydrogenase expression/formation protein HypA #8 MTH1072 67 hydrogenase expression/formation protein HypD #9 MTH1246 30 NADH dehydrogenase I, subunit N #10 MTH1251 147 conserved protein #11 MTH1252 143 conserved protein #12 MTH1253 135 unknown #13 MTH1552 139 formate dehydrogenase, alpha subunit homolog #14 MTH1553 71 tungsten formylmethanofuran dehydrogenase, subunit H #15 MTH1649 110 hydrogenase expression/formation protein HypC Motif number 1 ACTTACCGGTTTCTGTGAATATAATCACGAAAACG 1 56 1 TTCTTGAAAT 0.825786 -194 TTACTAAATCTTCTGTAGAGGGACCCTTCAGATAT 1 114 1 TTCTTAAGAC 0.852856 -136 ACAGAAACTTTTTTTTACTGATATCTGAAGGGTCC 1 134 0 TTTTTATAAC 0.977621 -116 AAAAAAAAGTTTCTGTAGAGAAACCTCCAGATATT 1 153 1 TTCTTAAAAC 0.97545 -97 AATTATGGCCTTTTTTACTAATATCTGGAGGTTTC 1 172 0 TTTTTATAAC 0.977612 -78 CTAACTCACCTTTTTTAAAAAGATTTATAT 1 230 1 TTTTTAAAAT 0.918861 -20 AAATCCCCTCTTTTCTGATTAAATCCCTTCCATTT 5 30 0 TTTTTGTAAC 0.952614 -26 AATTAACAATTTTTATATAGATAACTCTATTAATT 7 29 1 TTTTTAAAAC 0.977621 -55 TCTGACAAAATTTTATAATTAGAATTAATAGAGTT 7 51 0 TTTTTATAAT 0.918861 -33 TAATATAAAGTTTTCTATATAAATCGTAATAAAAT 10 73 0 TTTTTAAAAC 0.977621 -75 ATATCTATAGTGCTGTAATAAAAACATGAGCGTAT 12 32 0 TGCTTATAAC 0.852847 -104 CTTCACCTCACTCTCTACTCATAACCTTTATCTGT 13 14 1 CTCTTATAAC 0.852855 -126 TCAGTGTCCTTTTTATGGTGAAACTTTATCATGAT 13 51 0 TTTTTGTAAT 0.839007 -89 CATATAATAATTTTCTACAAAAATCAAATAGAAAA 14 31 0 TTTTTAAAAC 0.977619 -41 **** ** * * * * Masking position 13 Map Score: 19.9152 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 48 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 2 AACCTCCAGGACATGATGGGGTGGGAAT 1 8 0 AATGATGGGG 0.986089 -242 AAGACATGATGTGGAATGAAAATG 5 4 1 AATGATGTGG 0.901908 -52 TGTGGAATGAAAATGGAAGGGATTTAATCAG 5 20 1 AATGGAAGGG 0.972099 -36 AATAAAGAGCAAATGCTGAGGTAAAGAA 6 23 1 AATGCTGAGG 0.894678 -18 GATCATATATATATGGAGGAGGCCAAAGGAT 8 12 0 AATGGAGGAG 0.946261 -56 ATGATTAAACACTTGAAGGGGAAGAGGCTGC 10 32 0 ATTGAAGGGG 0.980186 -116 GTAGAGAGTGAGGTGAAGAGG 13 1 0 AGTGAAGAGG 0.931635 -139 ACTGAAGATAACATGAAGGGGACTGTTAAAT 13 81 1 AATGAAGGGG 0.993653 -59 AATTTAGAATAGATGGAAGGGAACTTGAGGC 13 109 1 AATGGAAGGG 0.972099 -31 AATCCTATTAATTTGGAGAGGGTTATTGA 15 92 1 ATTGGAGAGG 0.954283 -19 * ********* Masking position 4 Map Score: 14.8874 Number of sites scoring better than the average of aligned sites = 321 Number in coding regions = 291 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 3 CTCACCTTTTTTAAAAAGATTTATAT 1 234 1 TTAAAAAGAT 0.82695 -16 GAATATATAGATGATTACTGGT 2 3 1 ATATATAGAT 0.927405 -22 TTAACAATTTTTATATAGATAACTCTATTA 7 31 1 TTATATAGAT 0.919867 -53 GGCCTCCTCCATATATATATGATCGTGATA 8 19 1 ATATATATAT 0.437485 -49 TATGATCGTGATAAATAGATCTTTAAGTGT 8 36 1 ATAAATAGAT 0.898208 -32 TTATTACGATTTATATAGAAAACTTTATAT 10 76 1 TTATATAGAA 0.721197 -72 ATTTATGATAATATAAAGTTTTCTATATAA 10 86 0 ATATAAAGTT 0.899348 -62 CATGATGCACAGATAAAGGTTATGAGTAGA 13 27 0 AGATAAAGGT 0.910444 -113 CTGTGCATCATGATAAAGTTTCACCATAAA 13 45 1 TGATAAAGTT 0.676252 -95 AAGTTTCACCATAAAAAGGACACTGAAGAT 13 60 1 ATAAAAAGGA 0.569059 -80 AGAAAAATATATATATAGGTGTGTGG 14 7 0 ATATATAGGT 0.944396 -65 GATCCGTCACATATAAAGATTTGTGGGAAA 15 32 0 ATATAAAGAT 0.968877 -79 ACTAATGTTTAGATAAAGATCCGTCACATA 15 49 0 AGATAAAGAT 0.941933 -62 ********** Masking position 5 Map Score: 12.4735 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 78 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 4 ACAGAAGATTTAGTAATAAATTTTAAGGAT 1 100 0 TAGTAATAAA 0.931435 -150 CTTCAGATATCAGTAAAAAAAAGTTTCTGT 1 139 1 CAGTAAAAAA 0.878956 -111 CTCCAGATATTAGTAAAAAAGGCCATAATT 1 177 1 TAGTAAAAAA 0.844019 -73 AAAAAAGACCTCTTAATAAAATTATGGCCT 1 196 0 TCTTAATAAA 0.732502 -54 CCCCGTAAATAATCCTGAATGA 3 24 0 CCGTAAATAA 0.821725 -12 AATCACCTTCCGGTAATTAACAATTTTTAT 7 15 1 CGGTAATTAA 0.830018 -69 ATATATATGATCGTGATAAATAGATCTTTA 8 31 1 TCGTGATAAA 0.867458 -37 GAAGAGGCTGCCGTAATAACCCCATGAGTC 10 13 0 CCGTAATAAC 0.897782 -135 TCTATATAAATCGTAATAAAATAGGGGATC 10 65 0 TCGTAATAAA 0.972031 -83 TGTTAATTATTGGTACTAAAGAGAAGGGAG 10 121 1 TGGTACTAAA 0.734161 -27 ATCTATAGTGCTGTAATAAAAACATGAGCG 12 35 0 CTGTAATAAA 0.878273 -101 ********** Masking position 9 Map Score: 7.01934 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 47 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 AATCCTTTGGCCTCCTCCATATATATAT 8 9 1 GGCCTCCTCC 0.979622 -59 TTATTACGGCAGCCTCTTCCCCTTCAAGTG 10 24 1 AGCCTCTTCC 0.846481 -124 TTTATAGCTCCCTTCTCTTTAGTAC 10 133 0 AGCTCCCTTC 0.971509 -15 TCACCAGTAAGGCCGGCGCCAATGACTTTG 11 46 1 GGCCGGCGCC 0.839291 -98 CTGAATTGCTGGCCCACTTCCGGAAAAATC 12 116 0 GGCCCACTTC 0.949883 -20 TAAATTTAACAGTCCCCTTCATGTTATCTT 13 85 0 AGTCCCCTTC 0.97151 -55 TTCAGCCTCAAGTTCCCTTCCATCTATTCT 13 114 0 AGTTCCCTTC 0.886356 -26 ACATTTAGCCGCCGTCCATATAATAA 14 56 0 AGCCGCCGTC 0.977821 -16 ********** Masking position 2 Map Score: 4.92901 Number of sites scoring better than the average of aligned sites = 852 Number in coding regions = 811 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 6 TAGGTCTAACTCACCTTTTTTAAAAAGATT 1 225 1 TCACCTTTTT 0.783624 -25 TCACCAGTAATCATCTATAT 2 15 0 TCACCAGTAA 0.987322 -10 CTCATCACCATTAACACCGGAATG 4 28 0 TCACCATTAA 0.980796 -14 AATTCCTCACCTGTTAGATTCCTCAT 9 15 0 TCACCTGTTA 0.958102 -16 GCGATGTTGCTCACCAGTAAGGCCGGCGCC 11 36 1 TCACCAGTAA 0.987322 -108 TGATAAAGTTTCACCATAAAAAGGACACTG 13 55 1 TCACCATAAA 0.926511 -85 ********** Masking position 3 Map Score: 6.60833 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 18 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 CAGAAACTTTTTTTTACTGATATCTGAAGG 1 138 0 TTTTTACTGA 0.807243 -112 TAAATCCCCTCTTTTCTGATTAAATCCCT 5 37 0 TCTTTTCTGA 0.963311 -19 CTCTTTAGTCTGACAAAATTTTA 7 71 0 TTTAGTCTGA 0.920518 -13 GTTTTGATGCTGTATTCTGACTTGAGGTTA 11 100 1 TGTATTCTGA 0.979998 -44 TTCCCTTCCATCTATTCTAAATTTAACAGT 13 102 0 TCTATTCTAA 0.883441 -38 TAAACATTAGTGTATTCTGACTTTAATCCT 15 68 1 TGTATTCTGA 0.979998 -43 ********** Masking position 3 Map Score: 2.50387 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 57 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 8 TGACTCCATAGGAACCTCCAGGACATGATG 1 21 0 GGAACCTCCA 0.946404 -229 TTTCTGTAGAGAAACCTCCAGATATTAGTA 1 162 1 GAAACCTCCA 0.919459 -88 TGAACTTCAATCAATAAAGA 6 1 1 TGAACTTCAA 0.879158 -40 TTCTTTACCTCAGCATTTGCTCT 6 28 0 TTTACCTCAG 0.870814 -13 TCCCAGAAATTTAACCTCAAAGTCATTGGC 11 63 0 TTAACCTCAA 0.974577 -81 CAGGCATCAATTAACCTCAAGTCAGAATAC 11 111 0 TTAACCTCAA 0.974577 -33 TTATAAACCTCCGCAGGCATCAA 11 131 0 TAAACCTCCG 0.951832 -13 CCCCTTCATGTTATCTTCAGTGTCCTTTTT 13 72 0 TTATCTTCAG 0.606577 -68 ********** Masking position 7 Map Score: 4.29132 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 344 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 9 TTCCTCACCTGTTAGATTCCTCATTTTA 9 9 0 GTTAGATTCC 0.951203 -22 GGTTAAATTTCTCTGAGTCGC 11 2 1 GTTAAATTTC 0.982647 -142 TGACTTTGAGGTTAAATTTCTGGGATTCCA 11 68 1 GTTAAATTTC 0.982647 -76 GAAGGGGACTGTTAAATTTAGAATAGATGG 13 95 1 GTTAAATTTA 0.934483 -45 ********** Masking position 6 Map Score: 1.42391 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 5 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 10 GATGTGACTCCATAGGAACCTCCAGGACAT 1 25 0 CATAGGAACC 0.972711 -225 TGATTATATTCACAGAAACCGGTAAGTGGA 1 53 0 CACAGAAACC 0.900818 -197 TGAATGAGAACATGGAAGCC 3 1 0 CATGGAAGCC 0.953636 -35 CTCATCACCATTAACACCGGAATGATTC 4 24 0 CATTAACACC 0.844199 -18 AGTGTTTAATCATCGGATCCCCTATTTTAT 10 50 1 CATCGGATCC 0.943689 -98 ACCTCAAAGTCATTGGCGCCGGCCTTACTG 11 50 0 CATTGGCGCC 0.95212 -94 CAGAATACAGCATCAAAACCCTGGAATCCC 11 89 0 CATCAAAACC 0.92568 -55 ********** Masking position 2 Map Score: 0.961611 Number of sites scoring better than the average of aligned sites = 321 Number in coding regions = 300 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 11 GGAGTCACATCCACTTACCGGTTTCTGTGAA 1 44 1 CCACTTCCGG 0.974051 -206 GAAAAATCACCTTCCGGTAATTAACAA 7 7 1 TCACCTCCGG 0.993563 -77 GGCAGCCTCTTCCCCTTCAAGTGTTTAATCA 10 31 1 TCCCCTCAAG 0.940178 -117 AGTGTATGTCCCACCTGCCGCAGGTATACGG 12 86 1 CCACCTCCGC 0.982345 -50 GAATTGCTGGCCCACTTCCGGAAAAATCCGT 12 113 0 CCCACTCCGG 0.983344 -23 AATTTAACAGTCCCCTTCATGTTATCTTCAG 13 82 0 TCCCCTCATG 0.940178 -58 ****** **** Masking position 6 Map Score: 2.22644 Number of sites scoring better than the average of aligned sites = 335 Number in coding regions = 315 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 12 ********** No masking Map Score: 2.51122e-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: 2.51122e-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 14 ********** No masking Map Score: 2.51122e-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