AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00380_mthe_reg_300.orf -o00380_mthe_300.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: MTH147 23 phenylacrylic acid decarboxylase Input sequences: #1 MTH125 126 unknown #2 MTH126 88 inosine-5'-monophosphate dehydrogenase related protein VII #3 MTH127 199 deoxyhypusine synthase #4 MTH148 47 conserved protein #5 MTH150 75 conserved protein #6 MTH243 231 conserved protein #7 MTH248 195 conserved protein #8 MTH249 64 conserved protein #9 MTH250 23 tRNA intron endonuclease #10 MTH251 54 tryptophanyl-tRNA synthetase #11 MTH1014 127 conserved protein #12 MTH1015 63 methyl coenzyme M reductase system, component A2 #13 MTH1016 65 conserved protein #14 MTH1018 31 conserved protein #15 MTH1020 109 conserved protein #16 MTH1022 172 biopolymer transport protein #17 MTH1023 35 ribonuclease HII #18 MTH1025 222 unknown #19 MTH1348 139 precorrin-2 methyltransferase #20 MTH1496 194 amidase #21 MTH1514 125 precorrin-6Y methylase Motif number 1 GATCTCCTGTGAAAATGATAAAT 1 114 0 CTCCTGTGAA 0.87656 -13 TATGTACTGGATCCTGTTAAGCTGGTGCAA 3 115 0 ATCCTGTTAA 0.427835 -85 ACAGTTATCAATCCAGGGAA 3 190 1 ATCCAGGGAA 0.96884 -10 GAGAGGCTGTGCCCAGGGGATGGCCCATGA 6 18 1 GCCCAGGGGA 0.913922 -214 GTTACCTATAATCCAGGGGAGAGTGTGAC 6 213 1 ATCCAGGGGA 0.986173 -19 GAGTGTTGAGTTCCTGAGGAATATTATACC 7 23 1 TTCCTGAGGA 0.81982 -173 GCCTTCCGTGTTCCTGGGGAATATTCCGCT 7 86 1 TTCCTGGGGA 0.966142 -110 ACCAGCACCCCTCCAGCGGAATATTCCCCA 7 100 0 CTCCAGCGGA 0.944022 -96 GGTGCTGGTTTTCCAGGGAACTCTATCTGG 7 121 1 TTCCAGGGAA 0.8771 -75 AACCCTGACCCTCCAGGGGAAATCCTTCAG 7 163 0 CTCCAGGGGA 0.992289 -33 CGCTGCAGTCATCCATGGAAGACCCCTTTA 8 12 1 ATCCATGGAA 0.767344 -53 TTACCCATGGTCCCTGTGGAATCTCATAAG 15 45 1 TCCCTGTGGA 0.768465 -65 TTTAAATATCCACCAGGTGAGGCAGAAAA 16 154 1 CACCAGGTGA 0.740056 -19 TCACCGTGAACTCCATGTGAGAAGAAACCT 18 63 0 CTCCATGTGA 0.80498 -160 TCGCTGTGAACTCCATGTGAAATGTTCATG 18 93 0 CTCCATGTGA 0.80498 -130 GTCTGGATATTTCCAGAGAAGGATGACCAG 19 82 1 TTCCAGAGAA 0.821575 -58 GATTGCTGAGACCCAGTGAATATCTGCCTC 21 75 1 ACCCAGTGAA 0.77189 -51 ********** Masking position 10 Map Score: 20.5768 Number of sites scoring better than the average of aligned sites = 1081 Number in coding regions = 1021 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 2 ATCTTTACAGTTATCAATCCAGGGAA 3 184 1 TTTCCAGGGA 0.716166 -16 AGATTCTTTGCCTGTAATGCCGGGGTGATAAACTG 6 76 0 CGTGCCGGGG 0.986507 -156 CCATAGGTTACCTATAATCCAGGGGAGAGTGTGAC 6 207 1 CATCCAGGGG 0.983079 -25 GGAAGGCCTCCCGGGCATCACGGGACCCGGGGCCC 7 58 0 CGTCACGGGA 0.960724 -138 CGGGAGGCCTTCCGTGTTCCTGGGGAATATTCCGC 7 80 1 TGTCCTGGGG 0.923989 -116 TGGAGGGGTGCTGGTTTTCCAGGGAACTCTATCTG 7 115 1 CGTCCAGGGA 0.988653 -81 ATCTCAAACCCTGACCCTCCAGGGGAAATCCTTCA 7 164 0 CATCCAGGGG 0.983079 -32 TCGCTGCAGTCATCCATGGAAGACCCCTTT 8 6 1 GGTCCATGGA 0.802912 -59 CTCAACCAGCACTCACGGGAGGT 9 6 1 CGTCACGGGA 0.960724 -18 CAGGAACTTACCCATGGTCCCTGTGGAATCTCATA 15 38 1 CATCCCTGTG 0.655988 -72 TGGTGGATATTTAAAAATCAATGGGTATTTAAGAA 16 134 0 TATCAATGGG 0.716196 -39 TCATTCTTTTTTTGATTTGAAGGGGCCTCCAGCAG 17 11 1 TGTGAAGGGG 0.874542 -25 TTCATGTCACCGTGAACTCCATGTGAGAAGAAACC 18 64 0 CGTCCATGTG 0.941927 -159 TTCATATCGCTGTGAACTCCATGTGAAATGTTCAT 18 94 0 TGTCCATGTG 0.87702 -129 AACCTCAGAATGTGATATGCCGGTGAAAGATATAT 18 141 1 TGTGCCGGTG 0.85682 -82 CATGGCTGTCCCGGCGGTCCATGGACCGGAAACTC 20 98 1 CGTCCATGGA 0.972131 -97 ATTAATAAGTAGTGCCGGGATATTATAATA 21 6 1 TGTGCCGGGA 0.927905 -120 AGCACGGAGGCAGATATTCACTGGGTCTCAGCAAT 21 76 0 CATCACTGGG 0.867209 -50 * * ******** Masking position 8 Map Score: 21.7901 Number of sites scoring better than the average of aligned sites = 1618 Number in coding regions = 1539 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 3 GCACCAGCTTTCATATCACCCCTCCACGAA 3 52 1 TCATATCACC 0.961488 -148 ATTTTTTTTCTCATGGTACTTACAATATTT 6 150 1 TCATGGTACT 0.673992 -82 GCTTAAGCCGTCATAGTAGCCAAA 10 5 0 TCATAGTAGC 0.882428 -50 TCATATCACCGTTATTAAGT 10 45 0 TCATATCACC 0.961488 -10 ATATACAGATTCATGTTTACTGACA 12 49 1 TCATGTTTAC 0.715397 -15 AGGATATTCATATTAACCTGGCTAACA 14 15 0 TCATATTAAC 0.815407 -17 ACCTATCAGATCATATTACCGGTAATGGGA 18 37 0 TCATATTACC 0.918704 -186 TGTGAAATGTTCATGTCACCGTGAACTCCA 18 78 0 TCATGTCACC 0.975586 -145 CAGACCATCATCATGTCTACAGAGTTATTA 19 109 1 TCATGTCTAC 0.847405 -31 ATGAGTACTGTCATGGCTGTCCCGGCGGTC 20 87 1 TCATGGCTGT 0.567282 -108 CTCGAGGCAGTCATGGCAGCTATTAAGGTT 20 137 1 TCATGGCAGC 0.963688 -58 CCCTATTCCATCAAATCAGCACGGAGGCAG 21 98 0 TCAAATCAGC 0.70011 -28 ********** Masking position 3 Map Score: 10.2455 Number of sites scoring better than the average of aligned sites = 430 Number in coding regions = 402 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 4 CTCCAAATAGTATTTAAGATGAAACCAAGAT 1 78 1 TATTTAAGAG 0.865968 -49 TAATTATTTTTAATTAATATGTCTTTTTATT 2 47 0 TAATTAATAG 0.620519 -42 TGGCTGCATCTGTTAAAGGGGTCTTCCATGG 8 24 0 TGTTAAAGGG 0.935127 -41 AGAAATGACTTAATAACGGTGATATGA 10 38 1 TAATAACGGG 0.910997 -17 GTGGTTCCCCTGATTAAGAGGGGTCTAT 11 8 0 TGATTAAGAG 0.802653 -120 TAAATATAGTTAATAAAGGAGGACTTTGT 11 109 1 TAATAAAGGG 0.980032 -19 GGACCTATTTAAGGGGGTGGAACTAT 19 6 1 TATTTAAGGG 0.958156 -134 AAAATAATGATAATAAAGGCGGGTCTGGATA 19 60 1 TAATAAAGGG 0.980032 -80 TCTACAGAGTTATTAAAGGTGTTCTA 19 124 1 TATTAAAGGG 0.971035 -16 TTTCCAACACTAATAAATGTGAGATGTTCAA 20 39 0 TAATAAATGG 0.894565 -156 ********* * Masking position 6 Map Score: 9.28606 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 78 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 AAAGATTTTAGGAGTCCTGGACAAGGATAT 3 81 1 GGAGTCCTGG 0.964576 -119 ACAGAGTGTTGAGTTCCTGAGGAATATTAT 7 20 1 GAGTTCCTGA 0.831347 -176 TATACCTTGAGGGGCCCCGGGTCCCGTGAT 7 47 1 GGGGCCCCGG 0.90759 -149 GAGGCCTTCCGTGTTCCTGGGGAATATTCC 7 83 1 GTGTTCCTGG 0.87554 -113 TTCCGCTGGAGGGGTGCTGGTTTTCCAGGG 7 109 1 GGGGTGCTGG 0.987368 -87 CCCCAGATAGAGTTCCCTGGAAAACCAGCA 7 123 0 AGTTCCCTGG 0.711001 -73 GAAATCCTTCAGGGCGCTGACACCCCAGAT 7 145 0 AGGGCGCTGA 0.907375 -51 ACCTCCCGTGAGTGCTGGTTGAG 9 6 0 TGAGTGCTGG 0.691181 -18 TAAAAAATCAGGGTTGCTGATAGCATAAGG 13 34 1 GGGTTGCTGA 0.957415 -32 TGATAGCATAAGGGTCCTGGCCCCC 13 51 1 AGGGTCCTGG 0.98719 -15 GGCAATTATGAGGTTCCTCAGTGAATGA 15 9 0 AGGTTCCTCA 0.683932 -101 GACCATGGGTAAGTTCCTGGCAATTATGAG 15 27 0 AAGTTCCTGG 0.885718 -83 TTTAATGGAGAGATTGCTGAGACCCAGTGA 21 64 1 AGATTGCTGA 0.756147 -62 ********** Masking position 7 Map Score: 9.8179 Number of sites scoring better than the average of aligned sites = 1611 Number in coding regions = 1535 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 6 AGATGAAACCAAGATAAGAGATTTATCATTTTC 1 94 1 AAAAGAGATT 0.878646 -33 GTTTGATGTTAAAAATAAAGAGT 3 1 0 AATAAAGAGT 0.925325 -199 TATCACCCCTCCACGAAAAGATTTTAGGAGTCC 3 65 1 CCAAAAGATT 0.785182 -135 CTGGATTGATAACTGTAAAGATTTAATTAAATA 3 173 0 AATAAAGATT 0.899688 -27 ACAGAAACCTCCTGGAACAGATTAACGGGGCAA 4 22 1 CCAACAGATT 0.641144 -26 CAGCATCTAAACCCGAAGAGATTCTTTGCCTGT 6 96 0 ACAAGAGATT 0.871319 -136 ATTAATGGAACACTAAAGATTTTGGTGACCT 16 9 1 AATAAAGATT 0.899688 -164 ATCCGGCTACACGGTTAAAGAGTATCATGGTCT 16 90 0 ACTAAAGAGT 0.92048 -83 AATGTAATCCAAGTTAAAAGAGTAGCTTCCCTT 18 197 1 AAAAAAGAGT 0.914501 -26 GGAACTATATAAGTTTAGAGAGTGCCACAGAAA 19 29 1 AATAGAGAGT 0.92056 -111 GACCATCATCATGTCTACAGAGTTATTAAAGGT 19 111 1 ATTACAGAGT 0.656836 -29 GAGATGTTCAATATTTAAAGATTGGTAGATTGA 20 17 0 ATTAAAGATT 0.739191 -178 GCAATCTCTCCATTAAAGAGAGTGTCCCATACC 21 48 0 CAAAGAGAGT 0.834708 -78 ** ******** Masking position 7 Map Score: 6.74404 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 34 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 TAACATCAAACACCTGAGGGATATTAATTG 3 23 1 CACCTGAGGG 0.877171 -177 GGACCCGGGGCCCCTCAAGGTATAATATTC 7 41 0 CCCCTCAAGG 0.972526 -155 GTCCCGTGATGCCCGGGAGGCCTTCCGTGT 7 67 1 GCCCGGGAGG 0.966811 -129 GGGGAATATTCCGCTGGAGGGGTGCTGGTT 7 101 1 CCGCTGGAGG 0.99054 -95 GGGTGTCAGCGCCCTGAAGGATTTCCCCTG 7 150 1 GCCCTGAAGG 0.976527 -46 TGAAGGATTTCCCCTGGAGGGTCAGGGTTT 7 164 1 CCCCTGGAGG 0.994757 -32 TTTTCTGCCTCACCTGGTGGATATTTAAAA 16 153 0 CACCTGGTGG 0.936284 -20 CTGCTGGAGGCCCCTTCAAA 17 26 0 CTGCTGGAGG 0.934096 -10 CGGAAACTCCACCCTCGAGGCAGTCATGGC 20 124 1 ACCCTCGAGG 0.933803 -71 ********** Masking position 4 Map Score: 12.1111 Number of sites scoring better than the average of aligned sites = 542 Number in coding regions = 527 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 ACATGTAACCGGAATCATGGGCCATCCCCTG 6 31 0 GGATCATGGG 0.966442 -201 AGGCCTCCCGGGCATCACGGGACCCGGGGCC 7 59 0 GGATCACGGG 0.898595 -137 TTTCCCCTGGAGGGTCAGGGTTTGAGATAAT 7 171 1 AGGTCAGGGT 0.909351 -25 CTATTAATAAAACATCATGGTTAACAGATAC 11 78 0 AAATCATGGT 0.923707 -50 TTCTCCATAAAAAATCAGGGTTGCTGATAGC 13 27 1 AAATCAGGGT 0.929552 -39 GGTTGCTGATAGCATAAGGGTCCTGGCCCCC 13 45 1 AGATAAGGGT 0.92954 -21 AGATTCCACAGGGACCATGGGTAAGTTCCTG 15 38 0 GGACCATGGG 0.844321 -72 CATGGCGATTAAGATCATGGTGTTCCTTTAA 16 50 1 AAATCATGGT 0.924115 -123 ACGGTTAAAGAGTATCATGGTCTCAATCACA 16 82 0 AGATCATGGT 0.980059 -91 TGGGTATTTAAGAATAGTGGTTTTAATCCGG 16 117 0 AGATAGTGGT 0.823765 -56 CTGATTTGATGGAATAGGGGTAATTTT 21 109 1 GGATAGGGGT 0.825663 -17 ** ******** Masking position 9 Map Score: 7.49865 Number of sites scoring better than the average of aligned sites = 425 Number in coding regions = 395 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 9 GGAATGCAGTTGTAGGGAGGTTTACAGAGA 1 21 0 TGTAGGGAGG 0.510906 -106 AAATACTATTTGGAGGGGGCTTGATGCGAA 1 63 0 TGGAGGGGGC 0.986627 -64 AATCTTTTCGTGGAGGGGTGATATGAAAGC 3 58 0 TGGAGGGGTG 0.993082 -142 TTGCCTGTAATGCCGGGGTGATAAACTGAT 6 74 0 TGCCGGGGTG 0.838633 -158 ATATTATACCTTGAGGGGCCCCGGGTCCCG 7 43 1 TTGAGGGGCC 0.849761 -153 AATATTCCGCTGGAGGGGTGCTGGTTTTCC 7 105 1 TGGAGGGGTG 0.993082 -91 CTGCATCTGTTAAAGGGGTCTTCCATGGAT 8 22 0 TAAAGGGGTC 0.9258 -43 TCCCCTGATTAAGAGGGGTCTAT 11 4 0 AAGAGGGGTC 0.772025 -124 TAAAAAAGTTTGAAGTGGTGGTTTT 15 95 1 TGAAGTGGTG 0.814663 -15 TTTTTTGATTTGAAGGGGCCTCCAGCAG 17 18 1 TGAAGGGGCC 0.955782 -18 GGACCTATTTAAGGGGGTGGAACTATATA 19 10 1 TAAGGGGGTG 0.764991 -130 CATGACTGCCTCGAGGGTGGAGTTTCCGGT 20 122 0 TCGAGGGTGG 0.571347 -73 ********** Masking position 5 Map Score: 6.62033 Number of sites scoring better than the average of aligned sites = 667 Number in coding regions = 623 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 10 GGGATATTAATTGCACCAGCTTTCATATCA 3 40 1 TTGCACCAGC 0.978538 -160 GGATATATAATTGCACCAGCTTAACAGGAT 3 105 1 TTGCACCAGC 0.978538 -95 GTCTTGCCCCGTTAATCTGTTCC 4 35 0 TTGCCCCGTT 0.853966 -13 GGTTTAGATGCTGCACCGGTCAGTATAGAA 6 116 1 CTGCACCGGT 0.974227 -116 TATATATATCTTTCACCGGCATATCACATT 18 149 0 TTTCACCGGC 0.954285 -74 ACTGTCATGGCTGTCCCGGCGGTCCATGGA 20 93 1 CTGTCCCGGC 0.934842 -102 ********** Masking position 2 Map Score: 2.16381 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 174 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 11 CTCATCAAGATCTCTGTAAACCTCCCTACA 1 11 1 TCTCTGTAAA 0.814188 -116 GTCTTGCCCCGTTAATCTGTTCCAG 4 33 0 GCCCCGTTAA 0.838811 -15 TCGCCACCGGCTCCATGAATATATACTAG 5 10 1 GCTCCATGAA 0.954959 -66 AGCGGAATATTCCCCAGGAACACGGAAGGC 7 86 0 TCCCCAGGAA 0.895921 -110 TGGGGTGTCAGCGCCCTGAAGGATTTCCCC 7 148 1 GCGCCCTGAA 0.883705 -48 TCAGATTGATTCTCCATAAAAAATCAGGGT 13 18 1 TCTCCATAAA 0.917306 -48 ATGATCTTAATCGCCATGAAATGCTGAGGT 16 38 0 TCGCCATGAA 0.970743 -135 AATGTTCATGTCACCGTGAACTCCATGTGA 18 73 0 TCACCGTGAA 0.930135 -150 GGTGTTCATATCGCTGTGAACTCCATGTGA 18 103 0 TCGCTGTGAA 0.929111 -120 TGGTCATCCTTCTCTGGAAATATCCAGACC 19 81 0 TCTCTGGAAA 0.625911 -59 CTCAGCAATCTCTCCATTAAAGAGAGTGTC 21 55 0 TCTCCATTAA 0.885617 -71 ********** Masking position 9 Map Score: 4.33489 Number of sites scoring better than the average of aligned sites = 409 Number in coding regions = 383 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 12 TGCATTCCTGTCCATTACAGTTCGCATCAAGC 1 43 1 TATTACAGTT 0.970644 -84 AGATGCTATGTGGATAACATTTATATCTTGCT 2 12 1 TATAACATTT 0.89562 -77 AAGATTTAATTAAATAACAGATCTCGAGTGCA 3 157 0 TATAACAGAT 0.786285 -43 TTTAATGGCTTTAATTACAGTTTAATAAATAA 11 46 0 TATTACAGTT 0.970644 -82 TATCATGGTCTCAATCACAGTTAAAGGAACAC 16 69 0 TATCACAGTT 0.937088 -104 TCTTTTAACTTGGATTACATTTAATCTTCAGT 18 186 0 TATTACATTT 0.941209 -37 ATCCGTGGTTTTAATTTCATTTCCAACACTAA 20 57 0 TATTTCATTT 0.768714 -138 * ********* Masking position 4 Map Score: 1.19741 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 10 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 13 ********** No masking Map Score: 5.73651e-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 14 ********** No masking Map Score: 5.73651e-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: 5.73651e-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