AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00360_mthe_reg_100.orf -o00360_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 Input sequences: #1 MTH52 189 aspartate aminotransferase related protein #2 MTH147 23 phenylacrylic acid decarboxylase #3 MTH148 47 conserved protein #4 MTH150 75 conserved protein #5 MTH234 93 gamma-carboxymuconolactone decarboxylase #6 MTH1014 127 conserved protein #7 MTH1496 194 amidase #8 MTH1506 189 ATP phosphoribosyltransferase #9 MTH1587 31 histidinol-phosphate aminotransferase #10 MTH1591 30 phosphonopyruvate decarboxylase #11 MTH1592 21 conserved protein #12 MTH1593 205 ribosomal protein S3a #13 MTH1601 246 aspartate aminotransferase #14 MTH1694 207 aspartate aminotransferase related protein #15 MTH1894 34 aspartate aminotransferase homolog #16 MTH1895 170 conserved protein Motif number 1 CCCCGTTAATCTGTTCCAGGAGGTTTCTGTC 3 21 0 CGTTCCAGGA 0.88262 -27 TCGCCACCGGCTCCATGAATATATACTA 4 8 1 CGCTCCATGA 0.989969 -68 GGTGGAGTTTCCGGTCCATGGACCGCCGGGA 7 106 0 CGGTCCATGG 0.994564 -89 GGTTTGGAGTCCGGTCCCTGACCGATTATAA 8 41 0 CGGTCCCTGA 0.995216 -149 TCGGTTAACTCAGGTCACTGGAGAG 9 5 0 CGGTCACTGG 0.924693 -27 GGACCTGAATCAGGCTCCTGAGCTCCAGCTC 13 63 0 CGGCTCCTGA 0.940882 -184 GAGCCTGATTCAGGTCCCTGAAGCCGCGATC 13 77 1 CGGTCCCTGA 0.995216 -170 CACCTCTTCAGGGCCCCATGACTGGCTGATT 13 119 1 GGCCCCATGA 0.890719 -128 GGCACTTAAACTGCTCCATGGGGCAATACCA 16 80 0 CGCTCCATGG 0.987833 -91 AGATTATATTTAGGTTCATGGCACTTAAACT 16 99 0 TGGTTCATGG 0.779214 -72 TGTATTCCCGGAGTTCCATGAGATTATATTT 16 119 0 GGTTCCATGA 0.912572 -52 TCAACCTTCTCGGGTTCTTGATGATGACATT 16 149 0 CGGTTCTTGA 0.897957 -22 * ********* Masking position 3 Map Score: 16.3029 Number of sites scoring better than the average of aligned sites = 784 Number in coding regions = 745 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 2 AAAAGGAATTATAAACCCCAGAAAACAGAAA 1 13 0 ATAACCCCAG 0.881124 -177 ATTGCTGTGCTGAATCCCCAGCCTGTGAAGA 1 97 0 TGAACCCCAG 0.912305 -93 AGCAATTTTTATTAACTCCAGTGGACTACAT 1 122 1 ATTACTCCAG 0.8159 -68 GATTTATCCTCCAGAAGTTAATTC 1 176 0 TTATCTCCAG 0.94517 -14 AATCAGGACAGAAACCTCCTGGAACAGATTA 3 15 1 GAAACTCCTG 0.881848 -33 GGTTCAACCTCCACTGGTTTCATC 5 80 0 TCAACTCCAC 0.871952 -14 TCCATGGACCGGAAACTCCACCCTCGAGGCA 7 115 1 GGAACTCCAC 0.937567 -80 GAGATATAAGTTAATCTCCAGTGAAGAATGA 8 93 1 TTAACTCCAG 0.984641 -97 TTATTTTACATTAAGCTCCTGCAGGGTTTAT 8 144 0 TTAACTCCTG 0.97338 -46 CATTCTTTGGGTTTTCTCCTGGTGGGAGCTG 13 38 1 GTTTCTCCTG 0.583985 -209 GATCCATCAGTTAATCACCTCTTCAGGGCCC 13 104 1 TTAACACCTC 0.664639 -143 AAAACCTCCAGATTAAAGTGG 13 236 0 AAAACTCCAG 0.863685 -11 TGAACCTCAATTAAACTCCACTTTAGGGTTT 14 122 0 TTAACTCCAC 0.970284 -86 TCTTTCGCATGGATACTCCTGTGCTGATGTG 14 182 1 GGATCTCCTG 0.818898 -26 TGAAGGTTCATTAATCTCCGCTGTCTAGCAT 16 41 0 TTAACTCCGC 0.871952 -130 **** ****** Masking position 6 Map Score: 14.1019 Number of sites scoring better than the average of aligned sites = 481 Number in coding regions = 429 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 3 GAGTACTGTCATGGCTGTCCCGGCGGTCCA 7 89 1 ATGGCTGTCC 0.925938 -106 AATAGCTGCCATGACTGCCTCGAGGGTGGA 7 131 0 ATGACTGCCT 0.945797 -64 AAATCCCTCGATGACTGGTTAAATTTATTT 8 169 0 ATGACTGGTT 0.931857 -21 CCCGCATAACTGGCTGTTCATATTC 12 6 1 ATAACTGGCT 0.971873 -200 CACCGTAAAAACAGCTGGATTTAACATAAA 12 166 0 ACAGCTGGAT 0.832593 -40 TCAGGGCCCCATGACTGGCTGATTTTCAGG 13 126 1 ATGACTGGCT 0.990604 -121 GGATTTACTGATGGCTGGCCGGGACTCATG 13 158 1 ATGGCTGGCC 0.991147 -89 ACCATGACTGGACTGTTTTTAGC 14 4 1 ATGACTGGAC 0.95213 -204 ACATTATCCTACAGCTGGCTAAAAACAGTC 14 21 0 ACAGCTGGCT 0.956033 -187 ********** Masking position 6 Map Score: 10.852 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 117 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 4 ACATGATAATATCATTCTTCTCGTGTTGAA 1 149 1 ATCATTCTTC 0.981511 -41 CACTGGTTTCATCATTCTTCGACTTAAAAT 5 63 0 ATCATTCTTC 0.981511 -31 GGGTCAATCTACCAATCTTTAAATATTGAA 7 14 1 ACCAATCTTT 0.836327 -181 TATAAGTCTGATCAACCTTAATAGCTGCCA 7 150 0 ATCAACCTTA 0.865278 -45 TGCAGGATCTATCATTCTTCACTGGAGATT 8 105 0 ATCATTCTTC 0.981511 -85 GATTAACCCACCTTCCTAGATTTAT 10 16 0 ACCCACCTTC 0.923596 -15 ACATTTATATATCATTCTTTGGGTTTTCTC 13 26 1 ATCATTCTTT 0.912691 -221 AGGTAAGAGAAGCCTTCTTCTCTTTCGCAT 14 162 1 AGCCTTCTTC 0.858415 -46 GCGGAGATTAATGAACCTTCAACCTCACAT 16 51 1 ATGAACCTTC 0.881623 -120 ATCAACCTTCTCGGGTTCTT 16 161 0 ATCAACCTTC 0.98291 -10 ********** Masking position 8 Map Score: 10.5112 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 190 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 GGGATACCCTGTTAAAAAAGGAATTATAAACCCCA 1 24 0 GTTAAAGGTT 0.926589 -166 TAAAGTATCTGTTAACCATGATGTTTTATTAATAG 6 74 1 GTTAATGATT 0.984809 -54 ATTTATTAGTGTTGGAAATGAAATTAAAACCACGG 7 52 1 GTTGATGATT 0.931129 -143 TATTTAACTGGTTAACCATGATTTAGAGTTACATA 12 118 0 GTTAATGATA 0.977916 -88 TGGTTAACCAGTTAAATATGAATTTTTTGAATTTA 12 135 1 GTTAATGATT 0.984809 -71 TAATCTGTCCATTTAAAAAGATTTACATGAGTCCC 13 178 0 ATTAAAGATA 0.662805 -69 GGTAAACAAAGTTTATTAAGAGGTTTGTTTAATAT 14 79 1 GTTAAAGATT 0.967056 -129 TAAGAGGTTTGTTTAATATGGTATAAGAAACCCTA 14 95 1 GTTAATGGTA 0.9501 -113 AATCTCCGCTGTCTAGCATGATTTATAAATTCAGC 16 25 0 GTCAATGATA 0.902293 -146 TTCTCGGGTTCTTGATGATGACATTGTATTCCCGG 16 139 0 CTTAATGATT 0.904026 -32 *** * **** ** Masking position 8 Map Score: 6.5747 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 69 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 GAGAAGAATGATATTATCATGTAGTCCACTG 1 140 0 ATATATCATG 0.625806 -50 AAAAAATCAGGACAGAAACCT 3 1 1 AAAAATCAGG 0.719054 -47 TGCTTCTAGTATATATTCATGGAGCCGGTGG 4 14 0 ATAATTCATG 0.935732 -62 ATGTCATCCTATAAATTAATGTGGAATTTTA 5 38 1 ATAATTAATG 0.913332 -56 TGGTTAACAGATACTTTAATGGCTTTAATTA 6 61 0 ATATTTAATG 0.723358 -67 TGAAAGAGATATAAGTTAATCTCCAGTGAAG 8 88 1 ATAGTTAATC 0.44183 -102 ATACTCTATAATAGGATAAGGGAGTATTTAA 12 72 0 ATAGATAAGG 0.776838 -134 TTACGGTGTTAAAGATTAAGGTGATATA 12 188 1 AAAATTAAGG 0.800062 -18 CCAAAGAATGATATATAAATGTGGATAAAGT 13 17 0 ATAATAAATG 0.771862 -230 CAGATTAAAAATAGATACAGGTTATGAAATC 13 206 1 ATAATACAGG 0.896803 -41 AGCCTCTGTAATAAAATCAGGCCACATTATC 14 43 0 ATAAATCAGG 0.926096 -165 GAGATCAAAAATAAATAAAGGCG 15 22 1 ATAATAAAGG 0.862825 -13 AGCATGATTTATAAATTCAGCTGATCTAACT 16 15 0 ATAATTCAGC 0.841208 -156 *** ******* Masking position 3 Map Score: 6.5776 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 227 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 7 GTCTTGCCCCGTTAATCTGTTCCAGGA 3 31 0 CCCCTTAATC 0.974279 -17 ACTTAAAATTCCACATTAATTTATAGGATGA 5 41 0 CCACTTAATT 0.970049 -53 ATAGACCCCTCTTAATCAGGGGAACCA 6 7 1 CCCTTTAATC 0.787843 -121 ACAAAGTCCTCCTTTATTAACTATATTT 6 110 0 CCTCTTTATT 0.779112 -18 ATTGAACATCTCACATTTATTAGTGTTGGAA 7 38 1 TCACTTTATT 0.769877 -157 TAAGTCTGATCAACCTTAATAGCTGCCATGA 7 147 0 CAACTTAATA 0.689045 -48 TATATCACCTTAATCTTTAACACCG 12 191 0 TCACTTAATC 0.929439 -15 ATAACTTTATCCACATTTATATATCATTCTT 13 14 1 CCACTTTATA 0.92222 -233 GTTATGAAATCCACTTTAATCTGGAGGTTTT 13 226 1 CCACTTAATC 0.985271 -21 **** ****** Masking position 6 Map Score: 4.86372 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 123 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 ATCAGGACAGAAACCTCCTGGAACAGATTA 3 16 1 AAACCTCCTG 0.885827 -32 ATATATACTAGAAGCACCATAGTTCTAATA 4 29 1 GAAGCACCAT 0.914106 -47 TTAATCAGGGGAACCACAATTTATTTATTT 6 22 1 GAACCACAAT 0.960008 -106 GGAACCACCTTATAACTTATA 8 2 1 GAACCACCTT 0.974633 -188 GATTAACCCACCTTCCTAGATTTA 10 17 0 AACCCACCTT 0.820435 -14 ACAGCACCCCAAACCACCATGTCAAGATTT 12 44 1 AAACCACCAT 0.973876 -162 AAAACCTCCAGATTAAAGTGG 13 236 0 AAACCTCCAG 0.936672 -11 ACCCGAGGCTGAACCTCAATTAAACTCCAC 14 132 0 GAACCTCAAT 0.951182 -76 TAAGTGCCATGAACCTAAATATAATCTCAT 16 103 1 GAACCTAAAT 0.656371 -68 ********** Masking position 2 Map Score: 6.39027 Number of sites scoring better than the average of aligned sites = 373 Number in coding regions = 327 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 9 CCGGATCACTGCTGGAAAACAAAAAATTCT 1 65 0 GCTGGAAAAC 0.692475 -125 AGTTATTATGTCAGTAAAACTATTAGAACT 4 49 0 TCAGTAAAAC 0.957034 -27 CATTAAAGTATCTGTTAACCATGATGTTTT 6 71 1 TCTGTTAACC 0.945604 -57 TATATCTCTTTCAGGAAACCTATATAATAG 8 71 0 TCAGGAAACC 0.956872 -119 TCCAGTGACCTGAGTTAACCGAGATTGT 9 14 1 TGAGTTAACC 0.828033 -18 CCGCGATCCATCAGTTAATCACCTCTTCAG 13 100 1 TCAGTTAATC 0.936338 -147 CGGCCAGCCATCAGTAAATCCGACCTGAAA 13 149 0 TCAGTAAATC 0.922709 -98 CAGAGGCTCCTCTGGTAAACAAAGTTTATT 14 66 1 TCTGGTAAAC 0.922322 -142 AGGCTGAACCTCAATTAAACTCCACTTTAG 14 127 0 TCAATTAAAC 0.729018 -81 ********** Masking position 7 Map Score: 5.15106 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 172 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 10 GAAGCCGGATCACTGCTGGAAAACAAAAAA 1 69 0 CACTGCTGGA 0.979957 -121 GTGTTGAATTAACTTCTGGAGGATAAATC 1 171 1 AACTTCTGGA 0.903415 -19 CAGGACAGAAACCTCCTGGAACAGATTAAC 3 18 1 ACCTCCTGGA 0.977709 -30 TTATCCGTTCATCTGCAGGATCTATCATTC 8 118 0 ATCTGCAGGA 0.943263 -72 AACGGATAAACCCTGCAGGAGCTTAATGTA 8 139 1 CCCTGCAGGA 0.915427 -51 ACACCGTAAAAACAGCTGGATTTAACATAA 12 167 0 AACAGCTGGA 0.949563 -39 AGCTCCAGCTCCCACCAGGAGAAAACCCAA 13 44 0 CCCACCAGGA 0.857269 -203 AGAGGTGATTAACTGATGGATCGCGGCTTC 13 96 0 AACTGATGGA 0.922516 -151 CCTAAATATAATCTCATGGAACTCCGGGAA 16 116 1 ATCTCATGGA 0.796966 -55 ********** Masking position 10 Map Score: 8.83707 Number of sites scoring better than the average of aligned sites = 505 Number in coding regions = 467 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 11 GTGATCCGGCTTCTTCACAGGCTGGGGATT 1 86 1 TTCTTCACAG 0.958342 -104 AGGCTGGGGATTCAGCACAGCAATTTTTAT 1 104 1 TTCAGCACAG 0.986705 -86 AAAAAATCAGGACAGAAACCTCCTG 3 6 1 ATCAGGACAG 0.936406 -42 GGATCTATCATTCTTCACTGGAGATTAACT 8 101 0 TTCTTCACTG 0.874906 -89 TTTATCACATCAGCACAGGAGTATCCAT 14 190 0 ATCAGCACAG 0.981064 -18 ********** Masking position 7 Map Score: 1.38901 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 51 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 12 ********** No masking Map Score: 5.50914e-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 ********** No masking Map Score: 5.50914e-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: 5.50914e-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