AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00500_mthe_reg_100.orf -o00500_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 MTH122 127 mutator MutT related protein #2 MTH310 178 conserved protein #3 MTH312 50 ATP-dependent helicase #4 MTH409 258 unknown #5 MTH410 62 unknown #6 MTH436 129 unknown #7 MTH472 140 DNA helicase II #8 MTH511 240 DNA helicase II #9 MTH551 118 DNA helicase II related protein #10 MTH619 23 sensory transduction histidine kinase #11 MTH661 119 ammonium transporter #12 MTH662 61 nitrogen regulatory protein P-II #13 MTH663 205 ammonium transporter #14 MTH753 292 conserved protein #15 MTH977 300 endo-1,4-beta-glucanase related protein #16 MTH1073 67 cation antiporter #17 MTH1315 28 mutator MutT protein #18 MTH1318 231 conserved protein #19 MTH1336 73 mutator MutT protein homolog #20 MTH1355 124 arsenate reductase #21 MTH1383 52 DNA repair protein RadA #22 MTH1385 300 replication factor A related protein #23 MTH1493 78 cation transporting P-type ATPase related protein #24 MTH1494 266 conserved protein #25 MTH1511 109 arsenical pump-driving ATPase #26 MTH1516 152 cation-transporting P-ATPase PacL #27 MTH1534 40 aryldialkylphosphatase related protein #28 MTH1535 43 heavy-metal transporting CPx-type ATPase #29 MTH1639 163 cell division control protein Cdc48 #30 MTH1759 70 mannose-1-phosphate guanyltransferase #31 MTH1762 159 DNA mismatch recognition protein MutS #32 MTH1804 176 conserved protein #33 MTH1894 34 aspartate aminotransferase homolog #34 MTH1895 170 conserved protein Motif number 1 CTTAAAGTATTCACATTCATAGGGTTATAAAAA 2 40 1 TAATTATAGG 0.655461 -139 GAATACCTGAAAATATTGAGGGGTTATCAATCC 4 46 1 AAATTAGGGG 0.969623 -213 AAAAATGACGTCACTTTAAGGGGAGCTGTTGAA 4 97 1 TATTTAGGGG 0.95491 -162 TGCGAATAGATTTGATTGATGGGAATATTAATG 7 93 0 TTATTATGGG 0.889353 -48 CGCACTGATATATCATTCAGGGGTTCATC 7 122 1 TTATTAGGGG 0.954911 -19 CTGTGCATCTATAATTTCAGAGGTGATGTT 8 8 0 AATTTAGAGG 0.803094 -233 GTTATTATGAAGAATTTAATAGGCTGATGAATT 8 106 0 AATTTATAGG 0.607527 -135 TGTATTTTCAATAATCTCAGGGGAGGCTACCGG 8 156 1 AATCTAGGGG 0.713215 -85 AACCATAGAATAACATTTATGGG 8 228 1 TAATTATGGG 0.916244 -13 GAATTATTAAATGGGGAGTCACG 10 3 1 ATTTAATGGG 0.46603 -21 TCTATACACATGAATTTGATGGGACAGTTAATT 14 28 1 TATTTATGGG 0.889353 -265 CATGCCAGTTTTTCATTAAGGGGTCCATGCTAA 14 93 0 TTATTAGGGG 0.954911 -200 ATGGCGCTTTATTAATTGAGGGGTTGACTGTAC 14 242 0 ATATTAGGGG 0.959105 -51 ATGAATATTTAAAGATTTAAGGGAGATTAAA 21 32 1 AAATTAAGGG 0.864035 -21 CCTTTAGCAGAATAATTGAAGGGTTCATAAAGG 22 18 1 ATATTAAGGG 0.823608 -283 TATGGTATTAAGATTTTGAGAGGATACAGTGGC 23 37 0 AATTTAGAGG 0.803094 -42 TTCGATCTCTTCTCTTTTAAGGGACCTTGTCCG 24 178 0 TTTTTAAGGG 0.755974 -89 ATATACCTATATAGATTTAGGGGCTGATCTAC 27 10 0 AAATTAGGGG 0.969623 -31 CCCCTCAGGCTTTCATACAGGGGCCTTGGTGAA 32 118 1 TTATAAGGGG 0.738644 -59 * * *** ***** Masking position 9 Map Score: 17.7443 Number of sites scoring better than the average of aligned sites = 383 Number in coding regions = 314 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 2 TGAACCACTGATCCATTTATATGTCCTGAACC 1 89 1 ATATTTATAT 0.886914 -39 AGGGTTATAAAAAAATTTATCTATCAATCCTC 2 60 1 AAATTTATCT 0.816775 -119 CTCTTCAAGTAAGGTTTTATATCCACCTTGAA 6 82 1 AATTTTATAT 0.608441 -48 TAACCAAACAAAACATTAATATTCCCATCAAT 7 80 1 AAATTAATAT 0.60844 -61 AATTCAATAAAAAAATTTATATTCAATAATTT 8 78 0 AAATTTATAT 0.96007 -163 TATGGTTTCCATCCACTTTTATAGTTTTTCCA 8 203 0 ATACTTTTAT 0.42401 -38 TGGTTCACAGAAGTACTTATAAGAAATCCGGT 12 26 1 AAACTTATAA 0.705165 -36 GAAATTAAACAATTATTTTTATTTAACATATT 13 11 1 AAATTTTTAT 0.813257 -195 TTTACTCAGCATACATTTATCTGAAACTATAT 13 73 1 ATATTTATCT 0.592044 -133 ACTATATCCGAAAGATTTATATATCAGCATCA 13 98 1 AAATTTATAT 0.960138 -108 TTTTCTCTCCAACAATTTATATCATAGTCGGA 13 164 0 AAATTTATAT 0.960144 -42 AGTTAAACAAAAAAATTTTTATATTAAATATA 15 242 1 AAATTTTTAT 0.813199 -59 TCGCATGCAAAAGCATATATATAATCAGATCT 18 157 1 AAATATATAT 0.813258 -75 TTCACACCCTAAGGACTTATATTGTCATTTGG 19 49 0 AAACTTATAT 0.925969 -25 AATATATCTGAATTATTTATAAAATGAAGAAG 20 48 0 AAATTTATAA 0.821642 -77 AATAATTCAGATATATTTATAAATTTGGATAC 20 63 1 ATATTTATAA 0.599732 -62 CTTATTATCAAAGTATTTATAGGGCCGGGTGA 22 185 0 AAATTTATAG 0.72989 -116 TAATACCATAAAAAACATATATTGGTCCG 23 60 1 AAACATATAT 0.693088 -19 AAAGAGGTAGAAAAACTTATATCAGTGATGCT 25 50 1 AAACTTATAT 0.925962 -60 AACTTTACCGAAACATTTATATATGATTACCT 29 56 1 AAATTTATAT 0.960138 -108 CGCACTCTGAATCCATATATATCCAGGGAAAT 31 127 1 ATATATATAT 0.58621 -33 ** ******** Masking position 10 Map Score: 15.3973 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 19 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 3 ATACCGGGAAGGGGGTTTTCAAATAAAACAGAAGAG 2 113 1 GGGGTCAAAA 0.642285 -66 CTGGCTTCCCGGTGGGAACCAGTCTCTTCTGTTTTA 2 136 0 GGGGCCAGTC 0.891325 -43 AGAGAGATTAGGGGAATACCTGAAAATATTGAGGGG 4 33 1 GGGACCTGAA 0.888949 -226 AAAGATACCTGGAGGTTTCCATAGAATCCTGCCTTG 4 128 1 GGGGCCATAA 0.984788 -131 TCATATCACAGGAAAGGGCCAGAAAAACCAGAAACC 4 179 1 GGAACCAGAA 0.786996 -80 TATAAAAGTGGATGGAAACCATAGAATAACATTTAT 8 212 1 GAGGCCATAA 0.865937 -29 TCTGGTTAATGATGGCCACCATATTATAATGC 9 7 0 GAGGCCATAA 0.865937 -112 TCTCATTGTCGGAAGTTACCTTCCTATTTCCGACTA 13 136 1 GGAGCCTTCA 0.735786 -70 TGCTAATAGGGGAGGCGATCATAAAATTCGAATCCT 14 63 0 GGGGTCATAA 0.865937 -230 GACTGGATCTGGGGGGGGCCATAATCTGCTATTTCT 15 106 1 GGGGCCATAC 0.984467 -195 ATATATATATGGAGGAGGCCAAAGGATT 16 50 1 GGGGCCAAAA 0.947356 -18 TAAAAGACTTGGTGAGCTCCTGAAAACTAATAAGTT 22 235 0 GGGACCTGAA 0.888949 -66 CTGGAGGCACCCTGCCGCCGATAATCAT 24 3 1 GGGGCCTGCC 0.938647 -264 ACAGATGACTGGAAGGATCCTTATACTATGAGTGAT 24 40 1 GGAGCCTTAC 0.865808 -227 AACCATCCAAGGAGGCTTCCAGAAACAGTAAGCAGG 32 69 0 GGGGCCAGAC 0.987191 -108 TTGGTGAACCGGCAACCGCCATCACCGGATTCATAT 32 143 1 GGAACCATCC 0.557089 -34 ** ** ***** * Masking position 10 Map Score: 13.1837 Number of sites scoring better than the average of aligned sites = 479 Number in coding regions = 462 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 4 GCGGTCCGTTCACCTGAAGTGCTGGTC 1 6 1 CCGTCACCGA 0.737867 -122 TGGAAATAGACCACCTCCCAGAATTGAACCAC 1 65 1 CCACTCCCGA 0.978258 -63 GTTATCAATCCCATACCCTGGAAGATTTGAAA 4 68 1 CCATCCCTGA 0.971132 -191 GGTAAAACTCCTATTTCCCCGAGTATCTCTAT 4 227 0 CTATTCCCGA 0.924236 -32 AGTAGGAGGCCCACATCCTGGACTTAAATAAA 6 42 0 CCACTCCTGA 0.947032 -88 AATAAATTTACTGTTTCCCTGAACCAAAAGTC 9 41 0 CTGTTCCCGA 0.860302 -78 CCACTGATTACCATGCCTCTGATTACCATGCA 18 63 0 CCATCCTCGA 0.978511 -169 ATCGATTACTCCATGCCTCCGAATCTTACTAC 18 116 0 CCATCCTCGA 0.978511 -116 CAAGGATGGACCATGTCTTCGAGAGGATGAGG 24 137 1 CCATTCTTGA 0.929063 -130 AGGTGGTGGTCTATCTCTTCGATCTCTTCTCT 24 196 0 CTATTCTTGA 0.722796 -71 AGATAGACCACCACCTCTCAGAGATAATGAGG 24 212 1 CCACTCTCGA 0.96032 -55 TACTCTCATCCCATACCCTTGGGGTTGCACAG 26 87 0 CCATCCCTGG 0.913996 -66 CTACAGTGCACCGCCCCTCAGGCTTTCATACA 32 105 1 CCGCCCTCGG 0.842091 -72 **** **** ** Masking position 1 Map Score: 10.7748 Number of sites scoring better than the average of aligned sites = 554 Number in coding regions = 529 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 TCCTCATCCATGATTGGGGTTCAGGACATA 1 108 0 ATGATTGGGT 0.71168 -20 GTTTAATACCGGGAAGGGGGTTTTCAAATAA 2 108 1 GGGAAGGGGT 0.809635 -71 CCGGGAAGCCAGGATTCTGGCTTCACAGG 2 160 1 AGGATTCGGC 0.451704 -19 GTCACTTTAAGGGGAGCTGTTGAAAGATACC 4 106 1 GGGGAGCGTT 0.500768 -153 TGAATATACTGTGGTGGGGGTTTTCAT 9 102 1 GTGGTGGGGT 0.79111 -17 CACCAATATAAGGATGCCGGTAACCTACTTC 11 61 0 AGGATGCGGT 0.915674 -59 TGAGAGTAAGATGATGCTGATATATAAATCT 13 110 0 ATGATGCGAT 0.79256 -96 CATGCTAATAGGGGAGGCGATCATAAAATTC 14 70 0 GGGGAGGGAT 0.519713 -223 AGGTATTGTCATGAATCAGATCACTTCAAAC 15 73 0 ATGAATCGAT 0.664492 -228 TCATATATATATGGAGGAGGCCAAAGGATT 16 48 1 ATGGAGGGGC 0.650751 -20 TGCCTGCAGGAGGAGTCTGGT 17 18 1 AGGAGTCGGT 0.661112 -11 AGAAATTGATATGGAGCTGATAGCATGTACC 24 76 1 ATGGAGCGAT 0.837007 -191 ACTTATATCAGTGATGCTGATCTTGGATCGA 25 64 1 GTGATGCGAT 0.693334 -46 AGTCCCCTTGATGAAGCTGGTGGCTGTGCAA 26 64 1 ATGAAGCGGT 0.952794 -89 TAATTTAATAATGAGGGTGGTGTGTTTCAAG 26 125 1 ATGAGGGGGT 0.766505 -28 AGGTTGAATCATGGATCTGGTGGAATGTAA 28 24 1 ATGGATCGGT 0.876075 -20 GATTATTATTATGATTCCGGTTGATATTTAA 29 135 0 ATGATTCGGT 0.840249 -29 GGCTGGAAATATGAATCCGGTGATGGCGGTT 32 156 0 ATGAATCGGT 0.881211 -21 GTATTGCCCCATGGAGCAGTTTAAGTGCCAT 34 82 1 ATGGAGCGTT 0.690783 -89 ******* *** Masking position 3 Map Score: 11.5039 Number of sites scoring better than the average of aligned sites = 853 Number in coding regions = 782 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 6 ACAGTACAATTTAATGTTTTTTCATGTACT 2 12 1 TTAATGTTTT 0.899198 -167 TTTCATGTACTTAAAGTATTCACATTCATA 2 31 1 TTAAAGTATT 0.899198 -148 TTAAACACATTTAAAGATTTCTGAGGATTG 2 84 0 TTAAAGATTT 0.780372 -95 GTTAATGTATTGTACCAGATA 6 2 1 TTAATGTATT 0.899198 -128 GATGGGAATATTAATGTTTTGTTTGGTTAT 7 79 0 TTAATGTTTT 0.899198 -62 AACATTAAAATTAAAGTTATTATGAAGAAT 8 124 0 TTAAAGTTAT 0.712618 -117 AATTTTAATGTTAATGTATTTTCAATAATC 8 142 1 TTAATGTATT 0.899198 -99 GGACAGTTAATTAAAGGATTCGAATTTTAT 14 49 1 TTAAAGGATT 0.675768 -244 ATACCAATTTTTAATGTACTTGACTTGAAT 15 157 1 TTAATGTACT 0.793203 -144 ACCATTACACTTAAAGATCTATTTATCACG 16 17 1 TTAAAGATCT 0.604399 -51 TAATGAATATTTAAAGATTTAAGGGAGATT 21 30 1 TTAAAGATTT 0.780372 -23 CATTATTAAATTAATGTAATACTCTCATCC 26 108 0 TTAATGTAAT 0.712619 -45 ********** Masking position 4 Map Score: 5.55352 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 12 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 7 GCGGTCCGTTCACCTGAAGTGCTGGT 1 6 1 CCGTCACCTG 0.679079 -122 CATTATATCTCCAGGACTCTCTGGCTGTGGA 1 38 1 CCAGACTCTC 0.581259 -90 GCCAGAAAAACCAGAAACCTACAGAGAGGTA 4 196 1 CCAGAACCTA 0.921414 -63 ATTCTCATGGCCGGTAGCCTCCCCTGAGATT 8 168 0 CCGGAGCCTC 0.861999 -73 TATAAGGATGCCGGTAACCTACTTCCGAAAA 11 55 0 CCGGAACCTA 0.895934 -65 TAATAAAGCGCCATCAACATAAATAATGGTG 14 261 1 CCATAACATA 0.636238 -32 ACCAGACTCCTCCTGCAGGCAT 17 17 0 CCAGCTCCTC 0.791916 -12 CCATTCACCTCTTCAAGGTAA 18 221 0 CCATCACCTC 0.956998 -11 TAAGCGAGACCCATAAACATC 23 1 0 CCATAACATC 0.858853 -78 TATAACTGCCATACCCATCAGCAGCGACC 31 9 1 CCATCCCATC 0.692836 -151 ATAATTTACACCATAACCCTCCGGAATCCCT 32 31 1 CCATACCCTC 0.949401 -146 CCTTGGTGAACCGGCAACCGCCATCACCGGA 32 141 1 CCGGAACCGC 0.813715 -36 GATTAATGAACCTTCAACCTCACATGGTATT 34 56 1 CCTTAACCTC 0.825254 -115 AGTTTAAGTGCCATGAACCTAAATATAATCT 34 99 1 CCATAACCTA 0.906081 -72 **** ****** Masking position 2 Map Score: 5.82527 Number of sites scoring better than the average of aligned sites = 760 Number in coding regions = 715 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 8 GGTGGGAACCAGTCTCTTCTGTTTTATTTG 2 132 0 AGTCTCTTCT 0.865876 -47 AAAATGAGATCTCATCAAAATTAGAGA 4 8 1 GATCTCATCA 0.904826 -251 CTACTGATGTGATCTCTTCAAGTAAGGTTT 6 69 1 GATCTCTTCA 0.97863 -61 CGAGCTGCTTAATCTCTTCACTTCATTCAT 14 135 0 AATCTCTTCA 0.925884 -158 TCATGAATCAGATCACTTCAAACATGACTG 15 66 0 GATCACTTCA 0.904826 -235 ATCGGTTATAGGTCTCTTCTTCATTTTATA 20 33 1 GGTCTCTTCT 0.959457 -92 CTATCTCTTCGATCTCTTCTCTTTTAAGGG 24 188 0 GATCTCTTCT 0.972352 -79 ********** Masking position 3 Map Score: 4.5324 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 34 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 9 GCGGTCCGTTCACCTGAAGTGCTGGTCC 1 9 1 TTCACCTGAA 0.885429 -119 ATCAATCCCATACCCTGGAAGATTTGAAAA 4 71 1 TACCCTGGAA 0.844666 -188 GCCATGAGAATTCAATGGAAAAACTATAAA 8 188 1 TTCAATGGAA 0.46393 -53 TTAAATATCCTTAACCGGATTTCTTATAAG 12 41 0 TTAACCGGAT 0.752997 -21 ATTTTTTTGTTTAACTGGAATCATAAGACT 15 228 0 TTAACTGGAA 0.906766 -73 AGCATTGTTTTTACCTTGAAGAGGTGAATG 18 211 1 TTACCTTGAA 0.73067 -21 TCCCCATATGTTCACTGGATAACTGTCTTT 22 111 1 TTCACTGGAT 0.897968 -190 CAAGGGGACTTACACTTGAAATGCACCACT 26 44 0 TACACTTGAA 0.77567 -109 CAAGTGTAAGTCCCCTTGATGAAGCTGGTG 26 56 1 TCCCCTTGAT 0.579098 -97 ATTTACACTTGAAACACACCACC 26 140 0 TACACTTGAA 0.77567 -13 GATCCATGATTCAACCTGAACTTCAGCCAA 28 11 0 TCAACCTGAA 0.653025 -33 GATATTTAATTTAACCGGAATATTCTAGTA 29 114 0 TTAACCGGAA 0.888857 -50 AAATTAAATATCAACCGGAATCATAATAAT 29 132 1 TCAACCGGAA 0.81726 -32 TAATTGCATATTCGCTGGAAAAAAATACTT 30 28 1 TTCGCTGGAA 0.812947 -43 AACTATAAATTTCCCTGGATATATATGGAT 31 137 0 TTCCCTGGAT 0.853528 -23 ********** Masking position 9 Map Score: 6.70549 Number of sites scoring better than the average of aligned sites = 358 Number in coding regions = 323 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 10 ATTCATAGGGTTATAAAAAAATTTATCTATC 2 54 1 TTATAAAAAA 0.679302 -125 TTAAATAAACTTATTAAAGTATCTGGTACAA 6 20 0 TTATTAAATA 0.90045 -110 ACACAAGGAATTATTAAAGAATCTGTACATA 7 20 0 TTATTAAAAA 0.879039 -121 ATATACTTTTTTATTAAAAATTGTAGCT 15 8 0 TTATTAAAAT 0.491968 -293 TGACAATTTTTTATTAAAAAAATAATTACAT 15 37 0 TTATTAAAAA 0.879039 -264 TTAAGTTCTGTTATTAATTTAAATCTTGAGA 15 198 0 TTATTAATTA 0.782888 -103 GTATCCAAATTTATAAATATATCTGAATTAT 20 64 0 TTATAAATTA 0.500772 -61 TTAAATCTTATTATCAAAGTATTTATAGGGC 22 192 0 TTATCAAATA 0.679144 -109 GGGCGTGATATTATTAATCAAGTGAGGGACC 22 277 1 TTATTAATAA 0.752152 -24 ACCACTCATGTTATTAAATTAATGTGATATC 26 19 0 TTATTAAATA 0.895495 -134 ACCACCCTCATTATTAAATTAATGTAATACT 26 115 0 TTATTAAATA 0.895495 -38 ******** ** Masking position 6 Map Score: 4.59638 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 1 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 AGTGCTGGTCCATTATATCTCCAGGACTCTCTG 1 28 1 CATTATCCCA 0.687647 -100 AAAAATTTATCTATCAATCCTCAGAAATCTTTA 2 70 1 CTTAATCTCA 0.832989 -109 TTGATAACCCCTCAATATTTTCAGGTATTCCCC 4 43 0 CTATATTTCA 0.738985 -216 TCCTCCGGCTCTATTTATCTTCAAGGTGGATAT 6 100 0 CTTTATCTCA 0.93346 -30 AGAATCTGTACATAGAATCTTCA 7 1 0 CAAAATCTCA 0.863987 -140 TACCGAGCTGCTTAATCTCTTCACTTCATTCAT 14 135 0 CTATCTCTCA 0.871362 -158 TTGACTGTACCTTATTATCTTCAGTCACCTTCT 14 219 0 CTATATCTCA 0.975283 -74 TTTTCACCTCCACATTATCATCAGATATTAGAT 15 277 0 CAATATCTCA 0.946997 -24 CACCCTGCCGCCGATAATCATCACAGATGACTG 24 18 1 CCAAATCTCA 0.872729 -249 CCTTGTCCGGCTAACTATCCTCATCCTCTCGAA 24 154 0 CTATATCTCA 0.975283 -113 GTTGTATCTGTTCAGTATCCTCATTATCTCTGA 24 229 0 TTATATCTCA 0.738985 -38 AATTATTGCACCTAATATCCCCACTCTTTCTGA 31 49 1 CCATATCCCA 0.869867 -111 ** * **** *** Masking position 13 Map Score: 6.27639 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 145 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 ATTTATATGTCCTGAACCCCAATCATGGAT 1 103 1 CCTGAACCCC 0.860115 -25 GGAAAGCAGCCATGGCCCCTGTT 5 4 0 CATGGCCCCT 0.961824 -59 GATGAACCCCTGAATGATAT 7 131 0 GATGAACCCC 0.920329 -10 CCCCTATTAGCATGGACCCCTTAATGAAAA 14 87 1 CATGGACCCC 0.987098 -206 AATAGCAGATTATGGCCCCCCCCAGATCCA 15 109 0 TATGGCCCCC 0.940137 -192 TAAAAATTGGTATGAACCATATTTACCTAG 15 140 0 TATGAACCAT 0.582226 -161 CTGGAACCTTTATGAACCCTTCAATTATTC 22 27 0 TATGAACCCT 0.849084 -274 CAGACTGCCCCATGGACCACTTGCTGGAAC 22 50 0 CATGGACCAC 0.949879 -251 GAGCTGATAGCATGTACCCCACCAGGACGT 24 89 1 CATGTACCCC 0.908458 -178 TCCTCACAAGGATGGACCATGTCTTCGAGA 24 131 1 GATGGACCAT 0.77902 -136 GCCGGTTCACCAAGGCCCCTGTATGAAAGC 32 126 0 CAAGGCCCCT 0.761974 -51 ********** Masking position 7 Map Score: 7.93843 Number of sites scoring better than the average of aligned sites = 495 Number in coding regions = 469 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 13 AACATCACCTCTGAAATTATAGATGCACA 8 10 1 TCTGAAATTA 0.475554 -231 TGGTAGATTTTCGGAAGTAGGTTACCGGCA 11 48 1 TCGGAAGTAG 0.971335 -72 TATAAATCTTTCGGATATAGTTTCAGATAA 13 89 0 TCGGATATAG 0.844968 -117 ACTCTCATTGTCGGAAGTTACCTTCCTATT 13 134 1 TCGGAAGTTA 0.900471 -72 TATATCATAGTCGGAAATAGGAAGGTAACT 13 149 0 TCGGAAATAG 0.945198 -57 ATTAAGCAGCTCGGTAGTTGCTGTCTTCTT 14 152 1 TCGGTAGTTG 0.903142 -141 TCATCTGGATTCGGTAGTAAGAAGACAGCA 14 170 0 TCGGTAGTAA 0.900471 -123 CTAGGAGTTATCGGTTATAGGTCTCTTCTT 20 24 1 TCGGTTATAG 0.740866 -101 CCCCACTCTTTCTGAAGTAAAATCTGGGAG 31 67 1 TCTGAAGTAA 0.772533 -93 ********** Masking position 8 Map Score: 2.1394 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 = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 14 CAGGACTCTCTGGCTGTGGAAATAGACCAC 1 49 1 TGGCTGTGGA 0.973414 -79 ACCCCAATCATGGATGAGGA 1 118 1 TGGATGAGGA 0.907198 -10 ATCCAGTATCTGGCCGTGCCAGGCACGCAC 3 18 1 TGGCCGTGCC 0.919989 -33 CAGACTATAAGGGCTGTGCATCTATAATTT 8 24 0 GGGCTGTGCA 0.962518 -217 ACTCTCCTTTTGGATGTGCCTAACATATCT 11 97 0 TGGATGTGCC 0.950066 -23 CATATATATATGGAGGAGGCCAAAGGATT 16 49 1 TGGAGGAGGC 0.820338 -19 TGTCTTCGAGAGGATGAGGATAGTTAGCCG 24 150 1 AGGATGAGGA 0.669911 -117 ATGAAGCTGGTGGCTGTGCAACCCCAAGGG 26 74 1 TGGCTGTGCA 0.978423 -79 AAAGCCTGAGGGGCGGTGCACTGTAGAACC 32 101 0 GGGCGGTGCA 0.935658 -76 ********** Masking position 6 Map Score: 3.58833 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 179 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 15 AATCCTGGCTTCCCGGTGGGAACCAGTCTC 2 146 0 TCCCGGTGGG 0.994899 -33 GAGAATGCTCCCGGTGCGTGCCTGGCAC 3 33 0 TCCCGGTGCG 0.98646 -18 TTCATATACGTCCTGGTGGGGTACATGCTA 24 96 0 TCCTGGTGGG 0.980032 -171 TACTGAGGGATTCCGGAGGGTTATGGTGTA 32 37 0 TTCCGGAGGG 0.951109 -140 ********** Masking position 1 Map Score: 0.802386 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 34 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185