AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00680_mthe_reg_300.orf -o00680_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 Input sequences: #1 MTH310 178 conserved protein #2 MTH312 50 ATP-dependent helicase #3 MTH313 79 transcriptional regulator #4 MTH384 249 unknown #5 MTH387 24 conserved protein #6 MTH388 35 unknown #7 MTH393 41 NADH dehydrogenase (ubiquinone), subunit 1 related protein #8 MTH394 55 unknown #9 MTH397 40 formate hydrogenlyase, subunit 7 #10 MTH611 84 prolyl-tRNA synthetase #11 MTH612 50 unknown #12 MTH709 300 GMP synthetase, subunit A #13 MTH710 102 GMP synthetase, subunit B #14 MTH711 166 transcriptional regulator #15 MTH783 83 hydrogenase expression/formation protein HypA #16 MTH890 145 conserved protein #17 MTH891 59 conserved protein #18 MTH892 21 ATP-dependent protease LA related protein #19 MTH893 60 integrase-recombinase protein #20 MTH894 179 conserved protein #21 MTH895 51 conserved protein #22 MTH898 22 conserved protein #23 MTH1063 134 transcriptional regulator related protein #24 MTH1072 67 hydrogenase expression/formation protein HypD #25 MTH1141 300 conserved protein (FlpE) #26 MTH1192 76 conserved protein #27 MTH1193 146 transcriptional regulator #28 MTH1246 30 NADH dehydrogenase I, subunit N #29 MTH1251 147 conserved protein #30 MTH1252 143 conserved protein #31 MTH1253 135 unknown #32 MTH1287 177 transcriptional regulator HypF homolog #33 MTH1380 167 serine hydroxymethyltransferase #34 MTH1381 151 heterodisulfide reductase, subunit A #35 MTH1383 52 DNA repair protein RadA #36 MTH1385 300 replication factor A related protein #37 MTH1396 28 thiamine monphosphate kinase #38 MTH1398 269 conserved protein #39 MTH1522 116 nitrogenase alpha chain (NifD) related protein #40 MTH1547 118 nitrate assimilation protein, narQ #41 MTH1552 139 formate dehydrogenase, alpha subunit homolog #42 MTH1627 220 TATA-binding transcription initiation factor #43 MTH1634 151 transcriptional control factor (enhancer-binding protein) #44 MTH1636 101 S-adenosylhomocysteine hydrolase #45 MTH1649 110 hydrogenase expression/formation protein HypC #46 MTH1708 300 carbon monoxide dehydrogenase, alpha subunit #47 MTH1710 21 carbon monoxide dehydrogenase, alpha subunit #48 MTH1722 264 transcriptional regulator Icc related protein #49 MTH1740 86 pyruvate oxidoreductase, gamma subunit #50 MTH1795 72 transcriptional regulator Motif number 1 GAGGATTGATAGATAAATTTTTTTATAACCCTAT 1 58 0 AGATAAATTT 0.862417 -121 TATTAAACACATTTAAAGATTTCTGAGGATTGAT 1 82 0 ATTTAAATTT 0.723616 -97 GGGAAAACATATATAAATGTTGTCATTGCAACTG 3 41 0 ATATAAATTC 0.714 -39 ATATAAATCTTTTTAAAAAAGGTG 4 236 0 ATATAAATTT 0.966281 -14 TGCATACATCATATACATCTTCCTGCGGGGAAGG 12 119 0 ATATACATTT 0.795747 -182 AGAGTTATCTATATAAAAATTGTTAATTACCGGA 15 23 0 ATATAAATTT 0.966315 -61 TTAATTCTAATTATAAAATTTTGTCAGACTAAAG 15 58 1 TTATAAATTT 0.789543 -26 AAATTTATGGATATAAAGGTAAATTGGGATTGCC 20 145 0 ATATAAATAT 0.731335 -35 AGTTAATGACATATAAATCTTCCGGTGCAAAATG 23 60 1 ATATAAATTG 0.897857 -75 GTATTACATATATAAATGTTCCTAAAATTTAAA 25 278 0 ATATAAATTT 0.966304 -23 ATATAAAACTGCCTAATCTGTTTA 26 63 0 ATATAAATGT 0.808298 -14 TCCCATCTTCAGATAAACATTTATAAGGGAACAT 27 33 1 AGATAAATTT 0.864956 -114 ATCCCCTATCTTATAAAAGTTGATGACTTCTTCT 27 65 1 TTATAAATTT 0.789543 -82 GAAAGTTATATTATAAAGTTTTTTAAGTGAATAT 27 105 0 TTATAAATTT 0.789541 -42 AAAGTTTTCTATATAAATCGTAATAAAATAGGGG 29 68 0 ATATAAAGTT 0.670991 -80 ATTTATGATAATATAAAGTTTTCTATATAAATCG 29 82 0 ATATAAATTT 0.966244 -66 TGCAATGACAATATAAAATTGGTGTTAACTTCCA 33 132 0 ATATAAATGG 0.563702 -36 CAGGTATATTAAATAAATGTTTATTCTGTGTGTA 34 26 0 AAATAAATTT 0.736802 -126 GTGTAATAGTATATAAACCTTACTTAAAGTTTTT 34 76 1 ATATAAATTT 0.966314 -76 CCACAGTGCTAAATAAATATTTCTATCAAAAACT 34 103 0 AAATAAATTT 0.739715 -49 ATTACTATATATTTAAATCTTATTATCAAAGTAT 36 201 0 ATTTAAATTT 0.723614 -100 CATGATGCACAGATAAAGGTTATGAGTAGAGAGT 41 23 0 AGATAAATTG 0.662471 -117 TTAAACCTACATATAAATTTAAATGCACCTATAT 42 177 0 ATATAAATAT 0.617049 -44 GATCCGTCACATATAAAGATTTGTGGGAAACAAT 45 28 0 ATATAAATTT 0.966315 -83 ACGGATCTTTATCTAAACATTAGTGTATTCTGAC 45 55 1 ATCTAAATTT 0.687558 -56 CATTCATATAATATAAAGGTTGAAGTGATTATTA 46 29 1 ATATAAATTA 0.627479 -272 TGGAATCTATATATAAACTTTGTGCATTGTCGCT 46 217 0 ATATAAATTG 0.897857 -84 TTTTTAATATATATACATGTTGGTCAACTAAAAT 49 27 0 ATATACATTT 0.795744 -60 ******* ** * Masking position 7 Map Score: 30.1328 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 10 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 2 ATCTTTAAATGTGTTTAATACCGGGAAGGGGGTTTTCAAAT 1 96 1 GTATGAGGGG 0.978421 -83 ACTCCATAGGAACCTCCAGGACATGATGGGGTGGGAAT 4 8 0 ATAGGAGGGG 0.97649 -242 AATATAAATAGCTTTTCAGAATCAGAAGAGGAGA 12 277 1 GTAGGAGAGG 0.656681 -24 TCACTTTCATAATCTCCATCTCTTGAAGGGGAACTGCTGGT 14 92 0 ATATGAGGGG 0.989951 -75 CTATATAAAAATTGTTAATTACCGGAAGGTGATTTTTC 15 8 0 ATATGAGGTG 0.938097 -76 ATTTATCACGATCATATATATATGGAGGAGGCCAAAGGATT 24 11 0 ATATGAGAGG 0.907669 -57 TTCCCTTATAAATGTTTATCTGAAGATGGGAAAATAAAAAA 27 23 0 ATATGAGGGA 0.938097 -124 AGGGGATCCGATGATTAAACACTTGAAGGGGAAGAGGCTGC 29 32 0 ATAAGAGGGG 0.91293 -116 AGTTAGAAAAAGGATAAAGGATTTGATGGGGTTAACCCAT 33 10 0 ATAGGAGGGG 0.976558 -158 TTTATCAAAAATAGTTGGATGGGAACAG 37 5 0 AAATGAGGGA 0.902674 -24 TAAAAAGGACACTGAAGATAACATGAAGGGGACTGTTAAAT 41 71 1 AAATGAGGGG 0.983687 -69 GGACTGTTAAATTTAGAATAGATGGAAGGGAACTTGAGGCT 41 100 1 AAATGAGGGA 0.902674 -40 ATAATTTAACATACTTAATGAATAGAGGGGGATGAA 42 6 0 ATATGAGGGG 0.989953 -215 ATTAAGTATGTTAAATTATTTAAGGATGGTGCTTAAAATAT 42 28 1 TAATGAGGTG 0.654496 -193 TAGACTCTCAGAAGATCATATGCTGAAGGGGGTACCATGTC 43 49 0 GAATGAGGGG 0.965217 -103 TCTGAGAGTCTATAAAGATCCGGAGAGGGTGAGAGAATCAG 43 78 1 TAATGAGGTG 0.654496 -74 * * ** ** **** Masking position 8 Map Score: 19.5241 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 90 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 3 GTGTTTAATACCGGGAAGGGGGTTTTCAAAT 1 106 1 CCGGAAGGGG 0.979549 -73 ACGGCCAGATACTGGATGGGGGGA 2 4 0 ACGGATGGGG 0.980703 -47 AACCTCCAGGACATGATGGGGTGGGAAT 4 8 0 ACTGATGGGG 0.98407 -242 AAGACATGATGTGGAATGAAAATG 8 4 1 ACTGATGTGG 0.895652 -52 AATCTCCATCTCTTGAAGGGGAACTGCTGGT 14 92 0 TCTGAAGGGG 0.981796 -75 ATTGTTAATTACCGGAAGGTGATTTTTC 15 8 0 ACGGAAGGTG 0.875479 -76 ATGATTAAACACTTGAAGGGGAAGAGGCTGC 29 32 0 ACTGAAGGGG 0.991674 -116 TACGGATTTTTCCGGAAGTGGGCCAGCAATT 31 112 1 TCGGAAGTGG 0.860426 -24 AGGATAAAGGATTTGATGGGGTTAACCCAT 33 10 0 ATTGATGGGG 0.829572 -158 ACTGAAGATAACATGAAGGGGACTGTTAAAT 41 81 1 ACTGAAGGGG 0.991674 -59 GAAGATCATATGCTGAAGGGGGTACCATGTC 43 49 0 TGTGAAGGGG 0.862984 -103 TAATCAATTACCATGCAGGGGTGCCCGAGCG 48 45 1 CCTGCAGGGG 0.909048 -220 ** ******** Masking position 5 Map Score: 15.1188 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 192 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 4 ACGACTATGAAAATCCTTAAAATTTATTACTAAATCTTC 4 88 1 AATTAATATA 0.950199 -162 CCCCGTAAATAATCCTGAATGAGAACATGGAAGCC 6 11 0 AATTGATAGA 0.819778 -25 AAGACATGATGTGGAATGAAAATGGAAGGGAT 8 4 1 AATTGATAAA 0.625134 -52 AAAGCTATTTATATTTTACCGAATAATTAAATATTATGG 12 253 0 AATTGATATA 0.940004 -48 GAATCTGTTAAAATGATATAGTATTATGATAACATAGAT 16 22 1 AATTGTTATA 0.588835 -124 TATAAGATATAGATATTATCAAGTTATTAAAGGGCCAGA 16 116 1 AATTAATATA 0.9502 -30 AAACCACGTTAAATATTAAAAAATAATCATCTATTATGA 25 94 1 AATTAATATA 0.950199 -207 AGAAAACTTTATATTATCATAAATAATCATGTTAATTAT 29 92 1 AATTAATATA 0.950195 -56 AGATTTAAATATATAGTAATAACTTATTAGTTTTCAGGA 36 215 1 AATTAATATA 0.9502 -86 AATATTACCTAAATATTAATAAAGTATTATTAATTCTTT 38 49 1 AATTAAGATA 0.721356 -221 GAACCAAGATAGATAATGAAAAGTGATTACTGTATGGAG 38 236 1 AATTAATATA 0.9502 -34 ATGAACTCAAATATATTATAGATTAAGGACAAAAGATCT 40 35 1 AATTGATAGA 0.819781 -84 CGGGCCCATTAATTATTTTTAAGTGATGACCCACAACCT 44 28 1 ATTTAATATA 0.635926 -74 AAAATTAAAAACATCATTATAAATCATTAATAATTGTCA 46 252 1 AATTAATATA 0.949977 -49 CAACATGTATATATATTAAAAATTTATAATGATTAACAA 49 39 1 AATTAATATA 0.9502 -48 * ** * ** * ** * Masking position 16 Map Score: 12.3402 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 8 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 TTTCAAATAAAACAGAAGAGACTGGTTCCCA 1 129 1 AAAGAAGAGA 0.836579 -50 GTGGAATGAAAATGGAAGGGATTTAATCAGA 8 21 1 AAGGAAGGGA 0.964145 -35 ATTTAATCAGAAAAGAGGGGATTTA 8 41 1 AAAGAGGGGA 0.976475 -15 TTTCAGAATCAGAAGAGGAGA 12 290 1 AGAGAGGAGA 0.866949 -11 AATTAACAGAAGGCATCAAAA 18 5 1 AAAGAAGGCA 0.635021 -17 GGAAAATAAAAAAGGAGGGTAATTA 27 5 0 AAGGAGGGTA 0.842959 -142 CAACTTTTATAAGATAGGGGATGTTCCCTTA 27 56 0 AAATAGGGGA 0.885416 -91 AAACACTTGAAGGGGAAGAGGCTGCCGTAAT 29 26 0 AGGGAAGAGG 0.480454 -122 AAATCGTAATAAAATAGGGGATCCGATGATT 29 57 0 AAATAGGGGA 0.885416 -91 ATTGGTACTAAAGAGAAGGGAGCTATAAA 29 129 1 AAAGAAGGGA 0.954017 -19 ATATAATCTTAGCATAGGAGAACTCATGCAA 32 33 1 AGATAGGAGA 0.548126 -145 CCCATCTCACAGTGGAGGGAATAGTCCAGGG 32 91 1 AGGGAGGGAA 0.659475 -87 TTATTCTGCTAAAGGAGGATAG 36 2 0 AAGGAGGATA 0.56979 -299 ATTTAGAATAGATGGAAGGGAACTTGAGGCT 41 110 1 GAGGAAGGGA 0.751003 -30 ATACTTAATGAATAGAGGGGGATGAA 42 6 0 AAAGAGGGGG 0.900927 -215 ATATTACCACAATATAAGGGAAACCGAAGAT 46 66 0 AAATAAGGGA 0.794335 -235 CTTTTTAATAAATGGTGGGGATGTGCCAGAT 46 166 0 AAGGTGGGGA 0.802816 -135 TTCTTAGTGCAGGGGAAGGGATTCGAACCCT 48 118 0 AGGGAAGGGA 0.944774 -147 ** ******** Masking position 8 Map Score: 12.0203 Number of sites scoring better than the average of aligned sites = 545 Number in coding regions = 495 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 6 CAATTTAATGTTTTTTCATGTACTTAAAGTATTCACAT 1 18 1 TTTTTCATAA 0.960084 -161 CAGAAACTTTTTTTTACTGATATCTGAAGGGTCCCTCT 4 130 0 TTTTTCATAA 0.960085 -120 ATTATGGCCTTTTTTACTAATATCTGGAGGTTTCTCTA 4 168 0 TTTTTCATGA 0.805037 -82 AAAAATTATTTTATTACTCCTACTTAAAATATACTCCA 10 24 0 TTATTCATAA 0.843485 -61 AAATATATTTTTCCCTGGAGATAAACACTAATCAA 10 60 0 TTTTTCATAA 0.960079 -25 GCTATTTATATTTTACCGAATAATTAAATATTATGGAG 12 251 0 TTTTACATAA 0.843485 -50 ACTGCTGGTGTTTTTTCAAGCATCTTAAGAAAAAAAGG 14 63 0 TTTTTCATAA 0.960085 -104 TTAATTTATTTTTCATTTATTTCAATAAAATTCAG 20 8 1 ATTTTCATAA 0.843486 -172 ACAAGTTAAATTTTAACCGAAAGTTAAAAATTAACTGA 23 22 0 TTTTACATAA 0.843485 -113 TTTCCTCAGTTTTTTTCAGGTATATTAAATAAATGTTT 34 38 0 TTTTTCATAA 0.960084 -114 AGATATAAAAATATTACCTAAATATTAATAAAGTATTA 38 40 1 ATATTCATAA 0.546994 -230 AATAACTAGTTTTTTACGTCAATATTAATATAGGTGCA 42 150 1 TTTTTCATAA 0.960084 -71 ***** * * * ** Masking position 12 Map Score: 11.4254 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 6 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 ATGTGTTTAATACCGGGAAGGGGGTTTTCA 1 104 1 TACCGGGAAG 0.654014 -75 GACTGGTTCCCACCGGGAAGCCAGGATTCT 1 148 1 CACCGGGAAG 0.91908 -31 GCCAGGCACGCACCGGGAGCATTCTC 2 35 1 CACCGGGAGC 0.954582 -16 TCACCATTAACACCGGAATGATTCTATTAT 7 18 0 CACCGGAATG 0.730506 -24 AATTGTTAATTACCGGAAGGTGATTTTTC 15 10 0 TACCGGAAGG 0.872597 -74 CAGCACCCTAAGGAGGTATGAT 22 4 1 CACCCTAAGG 0.938133 -19 AAACATTTTGCACCGGAAGATTTATATGTC 23 67 0 CACCGGAAGA 0.891226 -68 CTATTCCCTCCACTGTGAGATGGGCACGGT 32 85 0 CACTGTGAGA 0.53342 -93 TTCTCACGTATCCCGTGAGGCTGAGTTCCT 32 157 0 TCCCGTGAGG 0.803814 -21 AAATCACTGCCTCCCTGAGGGAATAATAAA 38 173 0 CTCCCTGAGG 0.806693 -97 GGTTTAACTTCACCGGGAGGTATCTAG 42 204 1 CACCGGGAGG 0.989866 -17 GGTAATATCGCACCCTGAGCGGAGGGATGA 46 89 1 CACCCTGAGC 0.88564 -212 TACCATTATACACCCTGAGACCCCCGGCAA 46 122 0 CACCCTGAGA 0.877658 -179 GGGATTCGAACCCTCGAAGGCCTGCGCCAG 48 102 0 CCCTCGAAGG 0.577729 -163 GGTTCGAATCCCCCCTAAGGCTTTTCTACT 48 228 1 CCCCCTAAGG 0.874639 -37 ********** Masking position 8 Map Score: 9.97982 Number of sites scoring better than the average of aligned sites = 997 Number in coding regions = 949 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 8 TGAAAAGCTATTTATATTTTACCGAATAATT 12 264 0 TTTATATTTA 0.583349 -37 TTAATAGAGTTATCTATATAAAAATTGTTAA 15 31 0 TATCTATATA 0.720961 -53 TATATTTAAATATCTATGTTATCATAATACT 16 41 0 TATCTATGTA 0.784825 -105 CTCTGATTATTTTATATATCAGTATCGTCAT 16 86 1 TTTATATATA 0.834347 -60 TCATATAAGATATAGATATTATCAAGTTATT 16 113 1 TATAGATATA 0.784883 -33 CACCGGAAGATTTATATGTCATTAACTACAA 23 56 0 TTTATATGTA 0.876698 -79 GCCTCCTCCATATATATATGATCGTGATAAA 24 20 1 TATATATATA 0.8766 -48 TAGGAACATTTATATATGTAATAC 25 287 1 TATATATGTA 0.909323 -14 AATATAAAGTTTTCTATATAAATCGTAATAA 29 76 0 TTTCTATATA 0.646882 -72 ATTACAGCACTATAGATATTAATATGGGATA 31 48 1 TATAGATATA 0.784883 -88 CGGGTGAAAATATAGATGTAAAATTCAGACG 36 161 0 TATAGATGTA 0.837417 -140 AAGTTATTACTATATATTTAAATCTTATTAT 36 209 0 TATATATTTA 0.66383 -92 TATATATGTAAGCTTCTAAAT 39 1 1 TATATATGTA 0.909323 -116 GATATATGTTTTTAGATGTGAGGTGGTGGGT 40 96 1 TTTAGATGTA 0.785037 -23 TATGAGCCTCTTTATATATGATTTCAGCCTG 43 119 0 TTTATATATA 0.834347 -33 CCCACAAATCTTTATATGTGACGGATCTTTA 45 35 1 TTTATATGTA 0.876698 -76 GACCAACATGTATATATATTAAAAATTTATA 49 36 1 TATATATATA 0.8766 -51 ********* * Masking position 6 Map Score: 16.1652 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 12 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 9 CACCGGGAAGCCAGGATTCTGGCTTCACAG 1 158 1 CCAGGATTCT 0.69899 -21 CTATGAAAATCCTTAAAATTTATTACTAAA 4 92 1 CCTTAAAATT 0.652745 -158 GTAAAAAAGGCCATAATTTTATTAAGAGGT 4 189 1 CCATAATTTT 0.82569 -61 TCCACTGCCTCCATAATATTTAATTATTCG 12 243 1 CCATAATATT 0.709275 -58 CTTTCCTCCATGAATCTGTTAAAATGA 16 8 1 CCATGAATCT 0.651566 -138 TGGCTCCTGACCTGAATTTTATTGAAATAA 20 27 0 CCTGAATTTT 0.819241 -153 CAGAAGATTGCCTGAATTCTTCCTTCAAGG 20 55 1 CCTGAATTCT 0.788245 -125 ACCTTTATATCCATAAATTTGAATATATTG 20 159 1 CCATAAATTT 0.843381 -21 ACAGGTTCAACCTGGAATTTGAGGTGAA 21 34 1 CCTGGAATTT 0.685375 -18 TAATTTCCTGCCAGAATATTAACTCTGGAT 25 137 1 CCAGAATATT 0.774979 -164 GGCCGCATGGCCATAATTTTAGATTATTGT 25 174 1 CCATAATTTT 0.82569 -127 CCCTGGAATCCCAGAAATTTAACCTCAAAG 30 71 0 CCAGAAATTT 0.883745 -73 TTTAATCTCCCTTAAATCTTTAAATATTC 35 34 0 CCTTAAATCT 0.749851 -19 TTGGTGAGCTCCTGAAAACTAATAAGTTAT 36 233 0 CCTGAAAACT 0.685481 -68 TATATAGATTCCATAAAATTAAAAACATCA 46 238 1 CCATAAAATT 0.734988 -63 ********** Masking position 6 Map Score: 8.88441 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 96 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 10 CATCATGTCCTGGAGGTTCCTATGGAGTCA 4 21 1 TGGAGGTTCC 0.832942 -229 AACCGGTAAGTGGATGTGACTCCATAGGAA 4 37 0 TGGATGTGAC 0.683868 -213 TACTAATATCTGGAGGTTTCTCTACAGAAA 4 162 0 TGGAGGTTTC 0.770856 -88 AACCTGGAATTTGAGGTGAA 21 42 1 TTGAGGTGAA 0.930333 -10 GCCAATGACTTTGAGGTTAAATTTCTGGGA 30 63 1 TTGAGGTTAA 0.934552 -81 GTATTCTGACTTGAGGTTAATTGATGCCTG 30 111 1 TTGAGGTTAA 0.934552 -33 CAACTGGTAATGGAAGTTAACACCAATTTT 33 122 1 TGGAAGTTAA 0.778816 -46 GATTACTGTATGGAGGTTAC 38 260 1 TGGAGGTTAC 0.963604 -10 CCACAGACATTTGAGGTGACGTAAT 39 102 1 TTGAGGTGAC 0.939282 -15 TGAGTAGAGAGTGAGGTGAAGAGG 41 5 0 GTGAGGTGAA 0.822324 -135 ATACCTCCCGGTGAAGTTAAACCTACATAT 42 197 0 GTGAAGTTAA 0.432604 -24 CAATGAGAAATGGAGGTAAACT 49 75 1 TGGAGGTAAA 0.803763 -12 ********** Masking position 4 Map Score: 4.76546 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 253 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 11 AATTTATCTATCAATCCTCAGAAATCTTTA 1 73 1 TCAATCCTCA 0.397513 -106 TGTTTTATTTGAAAACCCCCTTCCCGGTAT 1 113 0 GAAAACCCCC 0.353341 -66 TTATGAAAGTGAATCCCTCATTAACTAAAT 14 121 1 GAATCCCTCA 0.904777 -46 TGATAACCAGTCATTCCTCAAAAGGAGGGT 17 36 1 TCATTCCTCA 0.740424 -24 GTAAACCCTCCTTTTGAGGAA 17 49 0 TAAACCCTCC 0.8881 -11 AAGATTGCCTGAATTCTTCCTTCAAGGGCG 20 58 1 GAATTCTTCC 0.401146 -122 ATCATACCTCCTTAGGGTGCT 22 12 0 TCATACCTCC 0.796386 -11 CGCCCTGGACTATTCCCTCCACTGTGAGAT 32 94 0 TATTCCCTCC 0.829341 -84 ATCGGATTCGGAATCCCCCCAGCTATCAAC 33 69 1 GAATCCCCCC 0.944451 -99 GGATCTTTATTATTCCCTCAGGGAGGCAGT 38 168 1 TATTCCCTCA 0.564732 -102 TTCATCCCCCTCTATTCATTA 42 2 1 TCATCCCCCT 0.469716 -219 TCAGCGTTTATCATTCCTCAATTGAAAAAT 42 97 0 TCATTCCTCA 0.740424 -124 CCGGCAATGGTCATCCCTCCGCTCAGGGTG 46 99 0 TCATCCCTCC 0.965695 -202 TGAATTCCTCCATTATCCTGA 47 11 0 GAATTCCTCC 0.931069 -11 CAGAGGATCTTAAGTCCTCCCCCTTTGGCC 48 75 0 TAAGTCCTCC 0.638582 -190 TCGAGGGTTCGAATCCCTTCCCCTGCACTA 48 115 1 GAATCCCTTC 0.624382 -150 TCGGGGGTTCGAATCCCCCCTAAGGCTTTT 48 223 1 GAATCCCCCC 0.944451 -42 TTTAATCCATCCGAATATTTCA 50 3 1 TAATCCATCC 0.629851 -70 ********** Masking position 6 Map Score: 6.00201 Number of sites scoring better than the average of aligned sites = 717 Number in coding regions = 665 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 12 TTACCGGTTTCTGTGAATATAATCACGAAA 4 58 1 CTGTGAATAT 0.681884 -192 CTCCATGAATCTGTTAAAATGATATAGTAT 16 16 1 CTGTTAAAAT 0.938391 -130 ATGCTGTTATCATCACACTTCAA 17 4 1 CTGTTATCAT 0.615125 -56 CAGGTTGAACCTGTTAACATGACATGTTGT 21 18 0 CTGTTAACAT 0.921023 -34 TTTTAACTTTCGGTTAAAATTTAACTTGTA 23 31 1 CGGTTAAAAT 0.92638 -104 ATGGGGCAGTCTGTGAAAATTAGAGCCTCT 36 67 1 CTGTGAAAAT 0.854124 -234 ATGAAGGGGACTGTTAAATTTAGAATAGAT 41 93 1 CTGTTAAATT 0.791025 -47 AATAATAACGCGGTTAATATTCAGCGTTTA 42 117 0 CGGTTAATAT 0.821641 -104 TGCATCACCCGGTTAACATCTTGGAGTTC 44 83 0 CGGTTAACAT 0.911946 -19 GCGACCGTTAAATTAATATACCAC 48 5 1 CCGTTAAATT 0.681885 -260 ATGATCAGAACCGTTAAAATTCTTAGTGCA 48 138 0 CCGTTAAAAT 0.896252 -127 ********** Masking position 6 Map Score: 4.93462 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 29 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 13 TCACTTACCTACTAATTCTTTTT 12 1 1 TCATACCACT 0.865243 -300 TTCGATGAAGTCACTGACCTTCTGAAAAATTAA 20 91 0 TCATACCTCT 0.972847 -89 CTCTTTAACCGTCAGTTAATTTTT 23 2 1 TCTTACCTCA 0.957144 -133 TCCGCAGGCATCAATTAACCTCAAGTCAGAATA 30 112 0 TCATAACTCA 0.713798 -32 AATTAGAGCCTCTTTAACCTTCTGATGTCCCCA 36 84 1 TCTTACCTCT 0.972847 -217 TGGATAACTGTCTTTCGCCTTCATACTGAAAAA 36 126 1 TCTTGCCTCA 0.855743 -175 GCCTGCTGATTCTCTCACCCTCTCCGGATCTTT 43 91 0 TCTTACCTCT 0.972847 -61 TCAATAACCCTCTCCAAATTAAT 45 98 0 TCATACCTCT 0.972847 -13 *** * *** *** Masking position 5 Map Score: 3.17729 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 47 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 14 TGGCTTCCCGGTGGGAACCAGTCTCTTCTGT 1 140 0 GGGGAACCAG 0.934067 -39 ATCTTCTGTAGAGGGACCCTTCAGATATCAG 4 121 1 GGGGACCCTT 0.926888 -129 CCGTGTTAGGGTGGGTACCTTCAGGTCCCAG 13 12 0 GGGGTACCTT 0.952129 -91 TGGACCACTTGCTGGAACCTTTATGAACCCT 36 37 0 GTGGAACCTT 0.957196 -264 ATGCAACATGGCTGGAACCATGATGCAAATC 39 69 0 GTGGAACCAT 0.957196 -48 ATATGCTGAAGGGGGTACCATGTCCATTCTG 43 42 0 GGGGTACCAT 0.952549 -110 ATACTTTATAGATGGAACCGTAGATAATAAT 50 49 0 GTGGAACCGT 0.929165 -24 * ********* Masking position 5 Map Score: 2.05663 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 40 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 15 AAGGGATTTAATCAGAAAAGAGGGGATTTA 8 36 1 ATCAGAAGAG 0.859802 -20 CCTAACACGGGTCAGAACACCGTCCATCCTTA 13 33 1 GTCAGAACCG 0.966276 -70 TTTTCTGAATATCAGACCACAGAAAAAAACAA 14 28 1 ATCAGAACAG 0.969605 -139 ATAAAATTTTGTCAGACTAAAGAG 15 70 1 GTCAGAAAAG 0.867781 -14 GTTCTTAGAGATCAGAGTACAAACCACGTTAA 25 74 1 ATCAGAACAA 0.805365 -227 TTAACCTCAAGTCAGAATACAGCATCAAAACC 30 99 0 GTCAGAACAG 0.98062 -45 TGATTTAAATATCAGATGACCGTATGATTTAA 38 197 1 ATCAGAACCG 0.947546 -73 TAGGATTAAAGTCAGAATACACTAATGTTTAG 45 67 0 GTCAGAACAC 0.906781 -44 ****** **** Masking position 6 Map Score: 2.63218 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 28 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432