AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00020_mthe_reg_100.orf -o00020_mthe_100.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: MTH1735 22 fumarate hydratase, class I Input sequences: #1 MTH139 269 heterodisulfide reductase HdrD related protein #2 MTH184 125 isocitrate dehydrogenase #3 MTH563 140 succinyl-CoA synthetase, alpha subunit #4 MTH964 103 unknown #5 MTH1032 229 ferredoxin (putative 2-oxoglutarate oxidoreductase, delat subunit) #6 MTH1115 21 fumarate hydratase, class I #7 MTH1116 146 glutamate decarboxylase #8 MTH1202 236 proteasome, beta subunit #9 MTH1203 69 cleavage and polyadenylation specificity factor #10 MTH1204 46 phosphoribosylformylglycinamidine cyclo-ligase #11 MTH1502 189 succinate dehydrogenase, flavoprotein subunit #12 MTH1648 110 dihydrolipoamide dehydrogenase #13 MTH1726 117 citrate synthase I #14 MTH1740 86 pyruvate oxidoreductase, gamma subunit #15 MTH1850 105 fumarate reductase #16 MTH1910 209 fumarate hydratase, class I related protein Motif number 1 CTCAGAGCCGCAGGACTGGAATACAGAGTC 1 163 1 CAGGACTGGA 0.954621 -107 CGGTCCTTCTGAGGACAGGGTTCCTTGAAG 1 218 1 GAGGACAGGG 0.991897 -52 TTCAGATAAGCAGGACAGGAAGC 1 257 1 CAGGACAGGA 0.978929 -13 TCAGTTCCAGCATCACCGGGCAGATCCCAC 4 38 0 CATCACCGGG 0.929775 -66 TTACCCCGGGACTGACAGGGCATTTTGCTG 5 90 1 ACTGACAGGG 0.848868 -140 CTCCTCAAGGCCGCACAGGAACTCCTCTAA 7 43 1 CCGCACAGGA 0.914479 -104 CGTAAAAATGGATGAAAGGGTCTACCCGAG 7 85 1 GATGAAAGGG 0.76213 -62 CATTCCTTTTAATGACCGGATAACCGTTCT 8 22 1 AATGACCGGA 0.781934 -215 CAATGGGATCCAGGACTGGTTTTTTATTAT 8 198 1 CAGGACTGGT 0.838444 -39 ATTCGATAATGATCACTGGGGGTTCTGT 11 9 0 GATCACTGGG 0.90944 -181 AACGTCCGTAGAGGACCGGGTGATGGTTCA 11 96 1 GAGGACCGGG 0.988657 -94 AAATTCCTCTGCGCACAGGGTTTAGTTCAC 13 86 0 GCGCACAGGG 0.965724 -32 CTTATCTACTGAGGGCAGGAG 16 199 1 GAGGGCAGGA 0.897325 -11 ********** Masking position 8 Map Score: 14.2956 Number of sites scoring better than the average of aligned sites = 772 Number in coding regions = 739 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 2 GTTGTCAGCAGCCCTGAGAAAAAGAACCAC 1 31 0 GCCCTGAGAA 0.88892 -239 CACAGCATGACTCTTCATCAAGGACTCTGT 1 185 0 CTCTTCATCA 0.687029 -85 AAGGAACCCTGTCCTCAGAAGGACCGAACC 1 214 0 GTCCTCAGAA 0.942024 -56 TTCTGAAGAGCCCTTCACAATTAAGGATAA 3 45 0 CCCTTCACAA 0.937849 -96 TTGTGAAGGGCTCTTCAGAACTCTATCATA 3 55 1 CTCTTCAGAA 0.961773 -86 TCATGAAGAGCCGTTCAGGAGAAGTGTTTA 3 87 0 CCGTTCAGGA 0.87008 -54 TCCTGAACGGCTCTTCATGAGCATAATTAA 3 97 1 CTCTTCATGA 0.807689 -44 TCAGGGTGTTCCCTTCACCAGAGGTTTTCA 5 118 0 CCCTTCACCA 0.895232 -112 TCTTAGCTTTGCCTTCAGAATTTAAATAAT 5 192 0 GCCTTCAGAA 0.97568 -38 TTCCTGTGCGGCCTTGAGGAGGAGTCTCTG 7 34 0 GCCTTGAGGA 0.894817 -113 GTCCCTCCTCTGAAATTCGGCGAG 7 133 0 CTCCTCTGAA 0.731806 -14 CGTTCTTCAACCCCTCAGGAAGCCCCATCT 8 46 1 CCCCTCAGGA 0.985897 -191 CTCCTGCCCTCAGTAGATAAGGCTG 16 195 0 GCCCTCAGTA 0.894615 -15 ********** Masking position 10 Map Score: 11.1225 Number of sites scoring better than the average of aligned sites = 1358 Number in coding regions = 1285 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 3 ACAGAGTCCTTGATGAAGAGTCATGCTGTGGTT 1 185 1 TGATGAGTCA 0.776783 -85 TATTATCCCATGCAGATCATTCAGCTTCATGAG 2 82 1 TGCAGACTCA 0.939799 -44 GATAGAGTTCTGAAGAGCCCTTCACAATTAAGG 3 49 0 TGAAGACTTC 0.943486 -92 ATTATGCTCATGAAGAGCCGTTCAGGAGAAGTG 3 91 0 TGAAGACTTC 0.943486 -50 CCTGAGGGGTTGAAGAACGGTTATCCGGTCATT 8 32 0 TGAAGACTTA 0.979662 -205 TATATATTGGTACAGAACTTTTATGTCCATGGG 8 115 1 TACAGACTTA 0.698756 -122 CAGGGTTAAATGAAAACCCTTTATATACCATAA 8 160 1 TGAAAACTTA 0.911615 -77 CAAGCTCAGGTGATGAACCATCACCCGGTCCTC 11 106 0 TGATGACTCA 0.957146 -84 ATAGTTAAGGTGATGAACCATAACCGAGAATAA 11 142 0 TGATGACTAA 0.862243 -48 AATGTTTAGATAAAGATCCGTCACATATAAAGA 12 56 1 TAAAGACTCA 0.861498 -55 TGATTTTAACTGATAATCTTTTAAACAATACAG 15 15 0 TGATAACTTA 0.884862 -91 TAATATGTGTTGATAAACAATTAAAATTCAGTT 15 55 1 TGATAACTTA 0.885349 -51 ****** * *** Masking position 6 Map Score: 9.96669 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 150 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 4 GTGCAGTCTCTCCCTTGCAAGACATCCTCTGA 1 104 0 TCCTTGCAGA 0.982611 -166 TCCGTTGCGTGGAATTGTGATG 4 1 1 TCCTTGCGGG 0.98068 -103 GTTTAACTTTACGCTTGCGGGATTTCCGGTCG 4 69 0 ACGTTGCGGA 0.93298 -35 CCTGAGATTCTCCATTTCATGGTTTAC 5 6 0 TCCTTTCAGG 0.909171 -224 GGAAGACGGTTGCAAGGGCCGAGCAGA 7 6 1 ACGTTGCAGG 0.974997 -141 ATGGGGACAGCCCTTTGCAGGGTTAAATGAAA 8 143 1 CCCTTGCAGG 0.970357 -94 TTAAATTTATTCGATGGCACGAACTCATGATT 16 87 1 TCGTGGCAGA 0.969695 -123 CTTGTAATATTCGATGGCACGAACTCGTGATT 16 141 1 TCGTGGCAGA 0.969695 -69 *** ***** ** Masking position 5 Map Score: 6.13837 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 174 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 AACACTTCAAGAGGAATTTAA 2 115 1 GAGAATTTAA 0.928962 -11 CCGTTCAGGAGAAGTGTTTAATTATGATAGA 3 76 0 GAATGTTTAA 0.961952 -65 TTTGTGGTCTGAAATATTTAATTATGCTCAT 3 113 0 GAATATTTAA 0.927893 -28 GAAATTCGGCGAGAAGTTCAAGTACTTTTTC 7 115 0 GAGAGTTCAA 0.8572 -32 TAAAAAAATCGCAAAGTTTAATAAGGACCTC 8 80 1 GCAAGTTTAA 0.892158 -157 CACCACTAAAGAATAGTTTAAGGTTATCTAA 10 21 0 GAAAGTTTAA 0.968894 -26 CCTTATCCTAGAACTATTTAAAATTTACTAT 13 30 1 GAATATTTAA 0.927893 -88 CCTGTGCGCAGAGGAATTTAATTCACAATAA 13 97 1 GAGAATTTAA 0.928962 -21 ATGTCTGTATTGTTTAAAAGATTATCA 15 7 1 GTATGTTTAA 0.819193 -99 *** ******* Masking position 7 Map Score: 5.80641 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 17 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 TTCCCCCCATGGGTGTATTC 1 1 1 TTCCCCCCAT 0.885318 -269 TTTTTTCAGTGACCTCCACCGATGTGGAG 3 10 1 TGACCTCCAC 0.943665 -131 TTTTTCACCTCCAGTTTAACTTTA 4 90 0 TCACCTCCAG 0.978215 -14 TATCAGGGTGTTCCCTTCACCAGAGGTTTT 5 120 0 TTCCCTTCAC 0.905271 -110 TATCTTAGCTTTGCCTTCAGAATTTAAATA 5 194 0 TTGCCTTCAG 0.798119 -36 AATCCATACATCACCCTCAGATTAGAACGT 11 71 1 TCACCCTCAG 0.931713 -119 TTATGGTTCATCACCTTAACTATTGACTGC 11 152 1 TCACCTTAAC 0.813125 -38 TTTATCACCTCAACCTTTACCTTA 13 5 1 TCACCTCAAC 0.910682 -113 TTCGTTACCCCCATTAATTTTAGT 14 5 1 TTACCCCCAT 0.940452 -82 AGTTTACCTCCATTTCTCATTGT 14 74 0 TTACCTCCAT 0.956862 -13 ********** Masking position 9 Map Score: 5.86538 Number of sites scoring better than the average of aligned sites = 547 Number in coding regions = 500 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 7 ATTAAATATTTCAGACCACAAAAGAAAGG 3 122 1 TAGACACAAA 0.968717 -19 GATCCCACCATCACATCACAATTCCACGCAAC 4 14 0 TACACACAAT 0.898705 -90 TTATATACCATAAAAACACAATGGGATCCAGG 8 180 1 TAAACACAAT 0.937986 -57 AATAGGTAATTAAGTACACAAAAATAGTAAAT 13 52 0 TAGTCACAAA 0.959604 -66 CGCACAGGGTTTAGTTCACAAAATAGGTAATT 13 73 0 TAGTCACAAA 0.958568 -45 GCAGAGGAATTTAATTCACAATAA 13 104 1 TAATCACAAT 0.920734 -14 GATTATCAGTTAAAATCACAAACCTTAATATG 15 30 1 TAAACACAAA 0.951679 -76 * *** ****** Masking position 8 Map Score: 4.49014 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 8 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 CCTTGCAAGACATCCTCTGAAGTAGATAAC 1 94 0 CATCCTCTGA 0.974587 -176 CAGATCCCACCATCACATCACAATTCCACG 4 18 0 CATCACATCA 0.853776 -86 GGTATCAACCTCTGACCCGGG 6 7 0 CAACCTCTGA 0.923774 -15 GTCCCTCCTCTGAAATTCGGCGA 7 134 0 CCTCCTCTGA 0.949357 -13 AACCGTTCTTCAACCCCTCAGGAAGCCCCA 8 43 1 CAACCCCTCA 0.973669 -194 GGTGATGGTTCATCACCTGAGCTTGACTTT 11 114 1 CATCACCTGA 0.983487 -76 GGTTATGGTTCATCACCTTAACTATTGACT 11 150 1 CATCACCTTA 0.919439 -40 TTTATCACCTCAACCTTTACCT 13 3 1 TATCACCTCA 0.853776 -115 CTCCTGCCCTCAGTAGATAAGG 16 198 0 CCTGCCCTCA 0.892598 -12 ********** Masking position 8 Map Score: 5.32793 Number of sites scoring better than the average of aligned sites = 633 Number in coding regions = 600 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 9 GGCTGCTGACAACTATTAATAGTCAGGGAA 1 48 1 AACTATTAAT 0.793755 -222 CCAGCTTCCAAACTATTTTTATCATTACAG 2 44 1 AACTATTTTT 0.946883 -82 AACTCCTCTAAACTATTTTTGGGCGTAAAA 7 62 1 AACTATTTTT 0.946883 -85 TTTTTCTCCTATTTTTAATTGCAGTA 9 7 1 TCCTATTTTT 0.851819 -63 GGCTAACTATTTAGATAACCTTAA 10 5 1 AACTATTTAG 0.85618 -42 GATAACCTTAAACTATTCTTTAGTGGTGAT 10 24 1 AACTATTCTT 0.825648 -23 CTGACTTTAATCCTATTAATTTGGAGAGGG 12 18 0 TCCTATTAAT 0.553728 -93 CTTATCCTAGAACTATTTAAAATTTACTAT 13 31 1 AACTATTTAA 0.685787 -87 ATTTAAAATTTACTATTTTTGTGTACTTAA 13 45 1 TACTATTTTT 0.88979 -73 GTACTTAATTACCTATTTTGTGAACTAAAC 13 67 1 ACCTATTTTG 0.861218 -51 ********** Masking position 5 Map Score: 4.76575 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 19 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 10 GCCCTGAGAAAAAGAACCACGAATACACCC 1 21 0 AAAGAACCAC 0.971191 -249 CCTCAGAAGGACCGAACCACAGCATGACTC 1 202 0 ACCGAACCAC 0.987951 -68 AAAGCTAAGATAAGAACCACGATGGAAG 5 212 1 TAAGAACCAC 0.911083 -18 ACAGAACCCCCAGTGATCAT 11 1 1 ACAGAACCCC 0.971605 -189 GCACAAGGACACCGAATCACGAGTTCGTGC 16 157 0 ACCGAATCAC 0.940164 -53 ********** Masking position 5 Map Score: 1.86253 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 29 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 11 AAGCTGGGGGTTTTTATGATGTCTTCATAT 2 21 0 TTTTTATGAT 0.939842 -105 TTCCAAACTATTTTTATCATTACAGCCTTA 2 49 1 TTTTTATCAT 0.816078 -77 GAGAAGTGTTTAATTATGATAGAGTTCTGA 3 69 0 TAATTATGAT 0.600245 -72 CCCTGATAATTTATTATAATCTGAGTTCTG 5 142 1 TTATTATAAT 0.837837 -88 CTTTGCGATTTTTTTATAATAGATGGGGCT 8 66 0 TTTTTATAAT 0.883231 -171 TCCCATTGTGTTTTTATGGTATATAAAGGG 8 176 0 TTTTTATGGT 0.870426 -61 CAGGACTGGTTTTTTATTATTTTTATTAGA 8 208 1 TTTTTATTAT 0.840736 -29 CTGCCAAACCTTATAATAATGA 11 178 1 TTATAATAAT 0.700557 -12 TATTAAAAATTTATAATGATTAACAATGAG 14 52 1 TTATAATGAT 0.828531 -35 ATGAACTGAATTTTAATTGTTTATCAACAC 15 61 0 TTTTAATTGT 0.506859 -45 ********** Masking position 6 Map Score: 2.23644 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 96 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 12 AGAGACTGCACGGGATATCCAGGGCCACAG 1 125 1 CGGGATATCC 0.94705 -145 TTTACGCTTGCGGGATTTCCGGTCGATCAG 4 64 0 CGGGATTTCC 0.986394 -40 TTCCGGTTTTCAGGTTTTCCGGGGCCTATG 5 49 0 CAGGTTTTCC 0.956071 -181 ATAAATTATCAGGGTGTTCCCTTCACCAGA 5 126 0 AGGGTGTTCC 0.963535 -104 AAATAGTTTAGAGGAGTTCCTGTGCGGCCT 7 50 0 GAGGAGTTCC 0.887502 -97 CAATATATAACAGGAGGTCCTTATTAAACT 8 94 0 CAGGAGGTCC 0.949217 -143 AACCCTGCAAAGGGCTGTCCCCATGGACAT 8 137 0 AGGGCTGTCC 0.914095 -100 TGGTATATAAAGGGTTTTCATTTAACCCTG 8 160 0 AGGGTTTTCA 0.750649 -77 ********** Masking position 8 Map Score: 3.03326 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 364 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 13 ATAGTTGTCAGCAGCCCTGAGAAAAAGAAC 1 34 0 GCAGCCCTGA 0.979235 -236 TATCTTCTCTGTGGCCCTGGATATCCCGTG 1 133 0 GTGGCCCTGG 0.982111 -137 TTCCAGTCCTGCGGCTCTGAGTATCTTCTC 1 154 0 GCGGCTCTGA 0.98063 -116 GAGTCTCTGCTCGGCCCTTGCAACCGTCTT 7 13 0 TCGGCCCTTG 0.913189 -134 GAGTTCCTGTGCGGCCTTGAGGAGGAGTCT 7 37 0 GCGGCCTTGA 0.980714 -110 ********** Masking position 8 Map Score: 1.36341 Number of sites scoring better than the average of aligned sites = 415 Number in coding regions = 392 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 14 TAGATAACCATAATATCAGTTATGTTCCCTG 1 71 0 TAATATCGTT 0.773344 -199 GATGTCTTCATATTCCCTTTTAT 2 3 0 TATTCCCTTT 0.864843 -123 AAGATGTGTATATTCCGGTTTTCAGGTTTTC 5 60 0 TATTCCGTTT 0.864842 -170 TAATTTATTATAATCTGAGTTCTGAATAATA 5 148 1 TAATCTGGTT 0.937146 -82 TGTTTACTGATATTCCCTGTTTTTTAGAAGT 9 43 1 TATTCCCGTT 0.959111 -27 AGCTTGACTTTATTCTCGGTTATGGTTCATC 11 133 1 TATTCTCGTT 0.959889 -57 AACATTAGTGTATTCTGACTTTAATCCTATT 12 31 0 TATTCTGCTT 0.845843 -80 TCACAAACCTTAATATGTGTTGATAAACAAT 15 45 1 TAATATGGTT 0.773344 -61 ******* *** Masking position 2 Map Score: 0.849375 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 51 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 15 GATCTGCATGGGATAATATTTTAAGGCTGT 2 70 0 GGATAATATT 0.964821 -56 TCACAATTAAGGATAATATGACTCCACATC 3 31 0 GGATAATATG 0.925122 -110 AATTAATCAAGAATAATATTATTCAGAACT 5 165 0 GAATAATATT 0.840141 -65 AATTTAATAGGGATCAGATTTTTAAATATC 16 64 0 GGATCAGATT 0.969661 -146 ATTACAAGATGGATCAGATTTTTGGCACTT 16 119 0 GGATCAGATT 0.969661 -91 ********** Masking position 6 Map Score: 0.57123 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 21 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701