AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -iarcA_mthe_opreg_100.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 MTH155 228 rubredoxin #2 MTH184 125 isocitrate dehydrogenase #3 MTH978 95 NADP-dependent glyceraldehyde-3-phosphate dehydrogenase #4 MTH980 74 conserved protein #5 MTH981 21 aminopeptidase P #6 MTH982 104 unknown #7 MTH1386 300 3-isopropylmalate dehydratase, LeuD subunit #8 MTH1502 189 succinate dehydrogenase, flavoprotein subunit #9 MTH1648 110 dihydrolipoamide dehydrogenase #10 MTH1707 300 cobalamin biosynthesis protein M #11 MTH1726 117 citrate synthase I Motif number 1 ACATCATAAAAACCCCCAGCTTCCAAACTA 2 29 1 AACCCCCAGC 0.983637 -97 TTGAATCTATAATCCAGAGCAGGGCTACGT 3 42 1 AATCCAGAGC 0.769583 -54 TCTATATTTTCACCCGGCCCTATAAATACT 7 113 0 CACCCGGCCC 0.942915 -188 ACAGAACCCCCAGTGATCATTATC 8 5 1 AACCCCCAGT 0.840048 -185 ATCCATACATCACCCTCAGATTAGAACGTC 8 72 1 CACCCTCAGA 0.947286 -118 GATGAACCATCACCCGGTCCTCTACGGACG 8 98 0 CACCCGGTCC 0.938655 -92 TCAATAACCCTCTCCAAATTAATAG 9 6 1 AACCCTCTCC 0.944079 -105 CTATCTGGCACATCCCCACCATTTATTAAA 10 99 0 CATCCCCACC 0.915726 -202 TAATGGTAATAATCCTCCGCCTATCTGGCA 10 119 0 AATCCTCCGC 0.887182 -182 TACCATTATACACCCTGAGACCCCCGGCAA 10 141 1 CACCCTGAGA 0.947286 -160 GGTAATATCGCACCCTGAGCGGAGGGATGA 10 174 0 CACCCTGAGC 0.9915 -127 TTGTGAACTAAACCCTGTGCGCAGAGGAAT 11 84 1 AACCCTGTGC 0.970588 -34 ********** Masking position 2 Map Score: 12.4563 Number of sites scoring better than the average of aligned sites = 752 Number in coding regions = 717 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 2 GCGAAAGCTTTATAGTGTTGAGAGACCCGGC 1 157 0 TTAGTGTTGA 0.861043 -72 ATTTTAAGGCTGTAATGATAAAAATAGTTTG 2 52 0 TTAATGATAA 0.794862 -74 TGTGGTAATTATAAATAATAG 4 1 1 TTGGTAATTA 0.829828 -74 TACACTGGAATGTGGTGTTGAG 4 63 1 TTGGTGTTGA 0.92919 -12 CTCTCTGTCCTCTGGTGATGA 5 11 1 TTGGTGATGA 0.985901 -11 GATTTAAATATATAGTAATAACTTATTAGTT 7 72 0 TTAGTAATAA 0.841099 -229 CTATAAATACTTTGATAATAAGATTTAAATA 7 93 0 TTGATAATAA 0.743976 -208 AAAGTCAAGCTCAGGTGATGAACCATCACCC 8 113 0 TAGGTGATGA 0.966923 -77 AGTCAATAGTTAAGGTGATGAACCATAACCG 8 149 0 TAGGTGATGA 0.966924 -41 TGCCAAACCTTATAATAATGA 8 179 1 TTAATAATGA 0.751954 -11 TTAATGATTTATAATGATGTTTTTAATTTT 10 10 1 TTAATGATGT 0.616322 -291 TCCCTTATATTGTGGTAATATCGCACCCTGA 10 186 0 TTGGTAATAT 0.67778 -115 ATATAAAGGTTGAAGTGATTATTACTAATCT 10 223 0 TAAGTGATTA 0.731055 -78 AGGTAAAGGTTGAGGTGATAAA 11 2 0 TAGGTGATAA 0.929737 -116 * ********* Masking position 6 Map Score: 11.4287 Number of sites scoring better than the average of aligned sites = 357 Number in coding regions = 306 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 3 ATTCACTGCGAAAGCTTTATAGTGTTGAGAG 1 164 0 AAGCTTTATA 0.87191 -65 TAAAATTTAAAATTATCTATAAAATTCACTG 1 187 0 AATATCTATA 0.855189 -42 CCAGCTTCCAAACTATTTTTATCATTACAGC 2 44 1 AATATTTTTA 0.782517 -82 ACCGGCTTTGATTGATTTATAATTTTGAATC 3 18 1 ATGATTTATA 0.875999 -78 ATCTGGCGCCTATTATTTATAATTACCACA 4 10 0 TATATTTATA 0.782438 -65 AGTTATTACTATATATTTAAATCTTATTATC 7 80 1 ATTATTTAAA 0.736747 -221 CTTATTATCAAAGTATTTATAGGGCCGGGTG 7 102 1 AATATTTATA 0.965891 -199 TGTTTCCCACAAATCTTTATATGTGACGGAT 9 71 0 AATCTTTATA 0.915741 -40 TTAATGATTTATAATGATGTTTT 10 3 1 AAGATTTATA 0.946624 -298 ATTTTATGGAATCTATATATAAACTTTGTGC 10 36 1 ATTATATATA 0.613467 -265 CTTATCCTAGAACTATTTAAAATTTACTATT 11 31 1 AATATTTAAA 0.875408 -87 ** ******** Masking position 11 Map Score: 5.64223 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 14 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 4 TCTCAACACTATAAAGCTTTCGCAGTGAATTTT 1 165 1 ATAAAGCTTC 0.852883 -64 TAGGAGAGTAATAAAGATATAGC 1 216 1 ATAAAGATAC 0.766988 -13 TGAAGGGTTCATAAAGGTTCCAGCAAGTGGTCC 7 252 0 ATAAAGGTTG 0.978727 -49 GATTTATTCGATAATGATCACTGGGGGTTCTGT 8 11 0 ATAATGATCG 0.805735 -179 TAATGTTTAGATAAAGATCCGTCACATATAAAG 9 55 1 ATAAAGATCC 0.928967 -56 TCCGTCACATATAAAGATTTGTGGGAAACAATG 9 72 1 ATAAAGATTG 0.972779 -39 ACCATTTATTAAAAAGGTCCATGTCTTTATGTG 10 79 0 AAAAAGGTCG 0.913413 -222 TTCATATAATATAAAGGTTGAAGTGATTATTAC 10 229 0 ATAAAGGTTG 0.978727 -72 TTGGAATTAAAAAAAGATTAAGGAGGCGAATAG 10 277 1 AAAAAGATTG 0.908541 -24 CTAGGATAAGGTAAAGGTTGAGGTGATAAA 11 8 0 GTAAAGGTTG 0.905615 -110 ********* * Masking position 8 Map Score: 5.93454 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 70 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 GTCCTGCAGATATTATTTTTTTGAGATTAATCT 1 34 1 TATTATTTTG 0.969511 -195 TCTGGACGTATATTATTCTTTGCTTCAGATCTT 1 64 1 TATTATCTTC 0.792147 -165 TTATAGATAATTTTAAATTTTAGGAGAGTAATA 1 196 1 TTTTAATTTG 0.724485 -33 AGTAATAACTTATTAGTTTTCAGGAGCTCACCA 7 57 0 TATTATTTTG 0.969511 -244 TCTACGGACGTTCTAATCTGAGGGTGATGTATG 8 75 0 TTCTATCTGG 0.847267 -115 ACTTTAATCCTATTAATTTGGAGAGGGTTATTG 9 12 0 TATTATTTGG 0.939551 -99 ATAATGATGTTTTTAATTTTATGGAATCTATAT 10 21 1 TTTTATTTTG 0.943436 -280 AAGTGATTATTACTAATCTTCGGTTTCCCTTAT 10 209 0 TACTATCTTG 0.95582 -92 ATTTAAAATTTACTATTTTTGTGTACTTAATTA 11 45 1 TACTATTTTG 0.963275 -73 ***** **** * Masking position 5 Map Score: 3.59661 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 17 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 6 AATAATATCTGCAGGACCCGGAGGTCCTTAA 1 20 0 GCAGACCCGG 0.861305 -209 AATCTATAATCCAGAGCAGGGCTACGTCTCT 3 45 1 CCAGGCAGGG 0.974283 -51 GTGGGCTGATCCTTTACGGGGTGTTTCCAG 3 76 1 CCTTACGGGG 0.931633 -20 TCATCACCAGAGGACAGAGAG 5 5 0 CCAGGGACAG 0.864348 -17 AGCAAGTGGTCCATGGGGCAGTCTGTGAAAA 7 233 0 CCATGGGCAG 0.922025 -68 AGGTGATGAACCATCACCCGGTCCTCTACGG 8 101 0 CCATACCCGG 0.967372 -89 AGGTGATGAACCATAACCGAGAATAAAGTCA 8 137 0 CCATACCGAG 0.949677 -53 GGAGGGATGACCATTGCCGGGGGTCTCAGGG 10 153 0 CCATGCCGGG 0.985977 -148 AATATCGCACCCTGAGCGGAGGGATGACCAT 10 170 0 CCTGGCGGAG 0.969634 -131 TGAACTAAACCCTGTGCGCAGAGGAATTTAA 11 87 1 CCTGGCGCAG 0.969634 -31 **** ****** Masking position 2 Map Score: 8.92062 Number of sites scoring better than the average of aligned sites = 575 Number in coding regions = 549 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 TTTAAGGACCTCCGGGTCCTGCAGATATTA 1 19 1 TCCGGGTCCT 0.944103 -210 TCAGCAGGTACCCTGCTCCTATGGCAGCCC 1 104 1 CCCTGCTCCT 0.929022 -125 TTACTAACTATCTGGCGCCTATTATTTATA 4 20 0 TCTGGCGCCT 0.983952 -55 TGGATAACTGTCTTTCGCCTTCATACTGAA 7 163 0 TCTTTCGCCT 0.929457 -138 TCAATCAGGATCAGTCGCCTGATTTATTCG 8 34 0 TCAGTCGCCT 0.939144 -156 ATGGTAATAATCCTCCGCCTATCTGGCACA 10 117 0 TCCTCCGCCT 0.983691 -184 GCTATTCGCCTCCTTAATCTTTTT 10 287 0 TTCGCCTCCT 0.886666 -14 ********** Masking position 10 Map Score: 2.11938 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 213 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 AAAGGGAATATGAAGACATCATAAAAACCCC 2 14 1 TGAAGCATCA 0.567484 -112 CAGCTTCATGAGAACACTTCAAGAGGAATTT 2 103 1 AGAACCTTCA 0.875737 -23 GGAACCTTTATGAACCCTTCAATTATTCTGC 7 264 1 TGAACCTTCA 0.609452 -37 TGATCCTGATTGAAGGCTTAAATCCATACAT 8 51 1 TGAAGCTTAA 0.593984 -139 GCATTGTCGCTGAACACATAAAGACATGGAC 10 65 1 TGAACCATAA 0.949676 -236 ***** ***** Masking position 4 Map Score: 0.583951 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 73 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 ATCTGATAATTTGTTTAATGGGCTGCCATAG 1 122 0 TTGTTAATGG 0.908732 -107 TTAATAAGGTTTAATTAAGAGTATACCTCCT 6 79 0 TTAATAAGAG 0.748193 -26 TAATTAAACCTTATTAAATGGT 6 93 1 TTATTAATGG 0.973782 -12 CGTGATATTATTAATCAAGTGAGGGACC 7 8 0 TTAATAAGTG 0.748195 -293 TTTAGCAGAATAATTGAAGGGTTCATAAAGG 7 268 0 TAATTAAGGG 0.958163 -33 GGTATTAATTCAATGGCATTGTTTCC 9 95 0 TAATTAATGG 0.958732 -16 ATGATGTTTTTAATTTTATGGAATCTATATA 10 24 1 TAATTTATGG 0.80725 -277 ATGGACCTTTTTAATAAATGGTGGGGATGTG 10 90 1 TTAATAATGG 0.958959 -211 ***** ***** Masking position 8 Map Score: 1.96314 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 71 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 10 ATTTATAATTTTGAATCTATAATCCAGAGCA 3 32 1 TTAATCTATA 0.968066 -64 GGTGCCATGATGAAATCTGTACTGAACCAGG 6 32 0 TGAATCTGTA 0.862578 -73 GCACCCCATGTTCTATATATAAGGAGGTATA 6 58 1 TTTATATATA 0.671074 -47 ATAATAAGATTTAAATATATAGTAATAACTT 7 79 0 TTAATATATA 0.892123 -222 CGTCTGAATTTTACATCTATATTTTCACCCG 7 127 0 TTCATCTATA 0.91725 -174 GATTGAAGGCTTAAATCCATACATCACCCTC 8 58 1 TTAATCCATA 0.903175 -132 TTTAATTTTATGGAATCTATATATAAACTTT 10 32 1 TGAATCTATA 0.953269 -269 ** ******** Masking position 5 Map Score: 0.68053 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 15 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 11 ACATTCCAGTGTAACATCATGCTCTGTTACTA 4 44 0 GTAAATCAGC 0.904638 -31 CACTTGATTAATAATATCACGCCCCGTCTATA 7 18 1 ATAAATCAGC 0.968585 -283 ATAACCGAGAATAAAGTCAAGCTCAGGTGATG 8 124 0 ATAAGTCAGC 0.973844 -66 CGCTGAACACATAAAGACATGGACCTTTTTAA 10 72 1 ATAAGACAGG 0.910337 -229 CGATATTACCACAATATAAGGGAAACCGAAGA 10 194 1 ACAAATAAGG 0.857818 -107 AAACATTCATATAATATAAAGGTTGAAGTGAT 10 235 0 ATAAATAAGG 0.951475 -66 TAGTTCTAGGATAAGGTAAAGGTTGAGGTGAT 11 14 0 ATAAGTAAGG 0.959479 -104 **** **** ** Masking position 4 Map Score: 0.445466 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 59 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 12 GCAGGACCCGGAGGTCCTTAAAAAAGAGTT 1 10 0 GAGGTCTTAA 0.969381 -219 CTGATAAAAAGAAGATCTGAAGCAAAGAATA 1 77 0 GAAGACTGAA 0.858793 -152 AACACTTCAAGAGGAATTTAA 2 115 1 GAGGATTTAA 0.95229 -11 ACCAGGCACTGAAGAACATAACATCCC 6 7 0 GAAGACATAA 0.662323 -98 AAGACTTGGTGAGCTCCTGAAAACTAATAAG 7 51 1 GAGCTCTGAA 0.888582 -250 GATTTATAATGATGTTTTTAATTTTATGGAA 10 16 1 GATGTTTTAA 0.824938 -285 TAAAGACATGGACCTTTTTAATAAATGGTGG 10 83 1 GACCTTTTAA 0.782574 -218 CCTTATCCTAGAACTATTTAAAATTTACTAT 11 30 1 GAACTTTTAA 0.859866 -88 CCTGTGCGCAGAGGAATTTAATTCACAATAA 11 97 1 GAGGATTTAA 0.95229 -21 ***** ***** Masking position 2 Map Score: 1.65411 Number of sites scoring better than the average of aligned sites = 226 Number in coding regions = 202 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 13 TTAAAGTCAGAATACACTAATGTTTAGATA 9 38 1 AATACACTAA 0.884872 -73 GTTCAGCGACAATGCACAAAGTTTATATAT 10 50 0 AATGCACAAA 0.955061 -251 TAGGTAATTAAGTACACAAAAATAGTAAAT 11 52 0 AGTACACAAA 0.964662 -66 CACAGGGTTTAGTTCACAAAATAGGTAATT 11 73 0 AGTTCACAAA 0.964662 -45 AGAGGAATTTAATTCACAATAA 11 106 1 AATTCACAAT 0.88487 -12 ********** Masking position 6 Map Score: 0.0048262 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 5 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 14 ********** No masking Map Score: 3.55515e-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: 3.55515e-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