AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00500_mthe_reg_300.orf -o00500_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 MTH122 127 mutator MutT related protein #2 MTH123 91 sensory transduction histidine kinase #3 MTH124 126 conserved protein #4 MTH310 178 conserved protein #5 MTH312 50 ATP-dependent helicase #6 MTH409 258 unknown #7 MTH410 62 unknown #8 MTH436 129 unknown #9 MTH472 140 DNA helicase II #10 MTH511 240 DNA helicase II #11 MTH551 118 DNA helicase II related protein #12 MTH619 23 sensory transduction histidine kinase #13 MTH661 119 ammonium transporter #14 MTH662 61 nitrogen regulatory protein P-II #15 MTH663 205 ammonium transporter #16 MTH753 292 conserved protein #17 MTH977 300 endo-1,4-beta-glucanase related protein #18 MTH1073 67 cation antiporter #19 MTH1315 28 mutator MutT protein #20 MTH1318 231 conserved protein #21 MTH1320 184 adenine phosphoribosyltransferase #22 MTH1336 73 mutator MutT protein homolog #23 MTH1355 124 arsenate reductase #24 MTH1383 52 DNA repair protein RadA #25 MTH1385 300 replication factor A related protein #26 MTH1493 78 cation transporting P-type ATPase related protein #27 MTH1494 266 conserved protein #28 MTH1495 194 ornithine cyclodeaminase #29 MTH1511 109 arsenical pump-driving ATPase #30 MTH1515 125 GTP-binding protein #31 MTH1516 152 cation-transporting P-ATPase PacL #32 MTH1534 40 aryldialkylphosphatase related protein #33 MTH1535 43 heavy-metal transporting CPx-type ATPase #34 MTH1639 163 cell division control protein Cdc48 #35 MTH1759 70 mannose-1-phosphate guanyltransferase #36 MTH1762 159 DNA mismatch recognition protein MutS #37 MTH1763 28 collagenase #38 MTH1764 154 sensory transduction regulatory protein #39 MTH1804 176 conserved protein #40 MTH1805 149 unknown #41 MTH1894 34 aspartate aminotransferase homolog #42 MTH1895 170 conserved protein Motif number 1 GGATTGATAACCCCTCAATATTTTCAGGTATTC 6 46 0 CCCTAATTTT 0.913674 -213 CATTAATATTCCCATCAATCAAATCTATTCGCA 9 93 1 CCCTAATAAA 0.974795 -48 GATGAACCCCTGAATGATATATCAGTGCG 9 122 0 CCCTAATATA 0.965627 -19 CCCATAAATGTTATTCTATGGTT 10 228 0 CCCTAATTTA 0.935776 -13 TTAGCATGGACCCCTTAATGAAAAACTGGCATG 16 93 1 CCCTAATAAA 0.974795 -200 GTACAGTCAACCCCTCAATTAATAAAGCGCCAT 16 242 1 CCCTAATAAT 0.965627 -51 TTTAATCTCCCTTAAATCTTTAAATATTCAT 24 32 0 CCCTAATTTT 0.913674 -21 CCTTTATGAACCCTTCAATTATTCTGCTAAAGG 25 18 0 CCCTAATATT 0.953286 -283 AATATCACGCCCCGTCTATAAAAGACTTGGTGA 25 256 0 CCCTTATAAA 0.896535 -45 GTAGATCAGCCCCTAAATCTATATAGGTATAT 32 10 1 CCCTAATTAT 0.935776 -31 TTCACCAAGGCCCCTGTATGAAAGCCTGAGGGG 39 118 0 CCCTTATAAA 0.896535 -59 CGTGTTCAGCTCCATCAATGAAAATTAATTTAT 40 93 1 TCCTAATAAA 0.735095 -57 *** * *** *** Masking position 8 Map Score: 11.9036 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 32 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 2 GGCTGTGGAAATAGACCACCTCCCAGAATTGAACCACTGATCC 1 60 1 AACCCCTTAA 0.890029 -68 GTTCGCATCAAGCCCCCTCCAAATAGTATTTAAGATGAAACCA 3 43 0 ACCCCCTTAA 0.962584 -84 GATCTCTGTAAACCTCCCTACAACTGCATTCCTGTCCATTACA 3 86 0 ACCCTATTCT 0.40013 -41 TGTTTTATTTGAAAACCCCCTTCCCGGTATTAAACACATTTAA 4 100 0 GACCCCATAA 0.81839 -79 AGGATTCTATGGAAACCTCCAGGTATCTTTCAACAGCTCCCCT 6 115 0 GACCCCTTAA 0.928958 -144 TCTCAGGGGAGGCTACCGGCCATGAGAATTCAATGGAAAAACT 10 170 1 GCCCGCTTAA 0.891185 -71 AAAAGTGGATGGAAACCATAGAATAACATTTATGGG 10 215 1 GACCTATTAT 0.422995 -26 ATGAAAACCCCCACCACAGTATATTCATTTACATGATT 11 91 0 ACCCCCTTAT 0.976909 -28 AGCAGATTATGGCCCCCCCCAGATCCAGTCTCAGGTATTGTCA 17 93 0 GCCCCCTCCA 0.754827 -208 AATCCTTTGGCCTCCTCCATATATATATGATCGTGATAAAT 18 37 0 GCCCCCATAT 0.959277 -31 ACCAGACTCCTCCTGCAGGCATCTATTT 19 3 0 AACCCCTCAT 0.680674 -26 TTTATATGGCACAGCCCATCCACCACTCTTAATTATATAAGGT 21 56 0 AACCTCTTAT 0.727922 -129 AGGATCTGCCGCCCACCACCCTGTGACCTTTATATGGCACAGC 21 84 0 GCCCCCTTAT 0.985581 -101 GCTCCCTTATAACTACCACACAGATCTATTGATGTATCCAAAT 23 85 0 ACCCCATTAT 0.877675 -40 AATTTTCACAGACTGCCCCATGGACCACTTGCTGGAACCTTTA 25 45 0 GCCCCATTCT 0.842796 -256 CTGGAGGCACCCTGCCGCCGATAATCATCACAGATGAC 27 6 1 GCCCGCATAT 0.822737 -261 CGAAGAGATAGACCACCACCTCTCAGAGATAATGAGGATACTG 27 207 1 GCCCCCATAT 0.959277 -60 CCCAGTGAATATCTGCCTCCGTGCTGATTTGATGGAATAGGGG 30 18 0 ACCCCCTTAT 0.976909 -108 TTTTATTATAATATCCCGGCACTACTTATTAAT 30 103 1 AACCGCTTAT 0.723938 -23 CTTGAAACACACCACCCTCATTATTAAATTAATGTAATACTCT 31 113 0 ACCCCATTAT 0.877675 -40 TACTGTTTCTGGAAGCCTCCTTGGATGGTTCTACAGTGCACCG 39 75 1 GACCCCTTTA 0.483348 -102 TCTACAGTGCACCGCCCCTCAGGCTTTCATACAGGGGCCTTGG 39 104 1 ACCCTCATCA 0.451823 -73 TTGGTGAACCGGCAACCGCCATCACCGGATTCATATTTCCAGC 39 143 1 GCCCCCATCA 0.868841 -34 ATCAACCTTCTCGGGTTCTTGATGATGACATTG 42 148 0 ACCCTCTTAT 0.892463 -23 * * ** ** ** ** Masking position 7 Map Score: 19.8983 Number of sites scoring better than the average of aligned sites = 552 Number in coding regions = 518 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 3 TGAACCACTGATCCATTTATATGTCCTGAACC 1 89 1 ATATTTATAT 0.83886 -39 GAAAATGATAAATCTCTTATCTTGGTTTCATC 3 21 1 AATCTTATCT 0.492867 -106 AGGGTTATAAAAAAATTTATCTATCAATCCTC 4 60 1 AAATTTATCT 0.911932 -119 CTCTTCAAGTAAGGTTTTATATCCACCTTGAA 8 82 1 AATTTTATAT 0.695441 -48 TGAACCCCTGAATGATATATCAGTGCGAATAG 9 117 0 AAATATATCA 0.456344 -24 AATTCAATAAAAAAATTTATATTCAATAATTT 10 78 0 AAATTTATAT 0.92663 -163 TGGTTCACAGAAGTACTTATAAGAAATCCGGT 14 26 1 AAACTTATAA 0.620186 -36 TTTACTCAGCATACATTTATCTGAAACTATAT 15 73 1 ATATTTATCT 0.810148 -133 ACTATATCCGAAAGATTTATATATCAGCATCA 15 98 1 AAATTTATAT 0.92663 -108 TTTTCTCTCCAACAATTTATATCATAGTCGGA 15 164 0 AAATTTATAT 0.92664 -42 TTAAACAAAAAAATTTTTATATTAAATATATC 17 244 1 AATTTTATAT 0.695434 -57 ACACTTAAAGATCTATTTATCACGATCATATA 18 23 1 ATATTTATCA 0.515181 -45 TCGCATGCAAAAGCATATATATAATCAGATCT 20 157 1 AAATATATAT 0.804389 -75 TTCACACCCTAAGGACTTATATTGTCATTTGG 22 49 0 AAACTTATAT 0.86769 -25 AATATATCTGAATTATTTATAAAATGAAGAAG 23 48 0 AAATTTATAA 0.758749 -77 ATCCAAATTTATAAATATATCTGAATTATTTA 23 61 0 ATATATATCT 0.580791 -64 TAATACCATAAAAAACATATATTGGTCCG 26 60 1 AAACATATAT 0.681006 -19 AAAGAGGTAGAAAAACTTATATCAGTGATGCT 29 50 1 AAACTTATAT 0.867689 -60 AACTTTACCGAAACATTTATATATGATTACCT 34 56 1 AAATTTATAT 0.92663 -108 CGCACTCTGAATCCATATATATCCAGGGAAAT 36 127 1 ATATATATAT 0.628703 -33 ATCAATGAAAATTAATTTATCTCCCCGATGAT 40 106 1 ATATTTATCT 0.810166 -44 ** ******** Masking position 8 Map Score: 13.1536 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 36 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 4 AAGAGATTTATCATTTTCACAGGAGATC 3 5 0 TATTTACGGA 0.98287 -122 AAAAATGACGTCACTTTAAGGGGAGCTGTTGAAA 6 97 1 TATTTAGGGA 0.945165 -162 CTTAAATATCCTTAACCGGATTTCTTATAA 14 42 0 TTCTTACGGA 0.811484 -20 TCTATACACATGAATTTGATGGGACAGTTAATTA 16 28 1 TATTTATGGA 0.86502 -265 TAAAAATTTTTTTGTTTAACTGGAATCATAAGAC 17 229 0 TTTTTACGGA 0.958084 -72 TATGGTATTAAGATTTTGAGAGGATACAGTGGCA 26 36 0 AATTTAGGGA 0.689538 -43 TTCGATCTCTTCTCTTTTAAGGGACCTTGTCCGG 27 177 0 TTTTTAAGGA 0.718436 -90 GGATCGATGATTAATTTTACAGGAGGAGTATA 29 88 1 TATTTACGGA 0.982873 -22 CGGTTGATATTTAATTTAACCGGAATATTCTAGT 34 115 0 TATTTACGGA 0.982871 -49 CCCAACTATAAATTTCCCTGGATATATATGGA 36 138 0 TATTTCCGGA 0.915307 -22 ACCTGATTTTAACCGGAGGAAATTTCA 37 4 1 TATTTACGGA 0.982871 -25 * * *** ** *** Masking position 14 Map Score: 8.60068 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 10 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 5 TGAACACAAGGAATTATTAAAGAATCTGTACATAGAAT 9 16 0 GAATATACTG 0.934997 -125 GTACTTCTGTGAACCATGTTTAAATCTGTGT 14 4 0 GAACATACTG 0.971186 -58 CATAAAATTCGAATCCTTTAATTAACTGTCCCATCAAA 16 42 0 GAACCTACTG 0.887324 -251 GAAGTGATCTGATTCATGACAATACCTGAGACTGGATC 17 77 1 GATCATACTG 0.986744 -224 ACCTTACAGTGATCTATGGTTAGATCTGATTATATATA 20 172 0 GATTATACTG 0.969479 -60 AAATAATTCAGATATATTTATAAATTTGGATACATCAA 23 62 1 GATTATATTG 0.73511 -63 TATAAATTTGGATACATCAATAGATCTGTGTGGTAGTT 23 80 1 GATCATACTG 0.986744 -45 ATAGTATAAGGATCCTTCCAGTCATCTGTGATGATTAT 27 31 0 GATCTTACTG 0.921472 -236 CATTCCACCAGATCCATGATTCAACCTGAACTTCAGCC 33 13 0 GATCATACTG 0.986744 -31 TGTCTAGCATGATTTATAAATTCAGCTGATCTAACTGT 42 13 0 GATTATACTG 0.969481 -158 *** *** * *** Masking position 7 Map Score: 8.29222 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 18 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 CCTACTGATGTGATCTCTTCAAGTAAGGTTT 8 68 1 TGACTCTTCA 0.945312 -62 GATGAACCCCTGAATGATATATC 9 128 0 TGACCCCTGA 0.930196 -13 CCGAGCTGCTTAATCTCTTCACTTCATTCAT 16 135 0 TAACTCTTCA 0.727901 -158 TAAGGTACAGTCAACCCCTCAATTAATAAAG 16 238 1 TCACCCCTCA 0.972471 -55 GTTTTCACCTCCACATTATCATCAG 17 286 0 TCACTCCACA 0.821524 -15 CCATTCACCTCTTCAAGGTAAAAAC 20 217 0 TCACTCTTCA 0.933151 -15 GGAACCTTTATGAACCCTTCAATTATTCTGC 25 24 0 TGACCCTTCA 0.949047 -277 AAAGACTTGGTGAGCTCCTGAAAACTAATAA 25 238 0 TGACTCCTGA 0.924533 -63 CGTATATGAATGAACTCCTCACAAGGATGGA 27 116 1 TGACTCCTCA 0.975627 -151 GTAGATCAGCCCCTAAATCTATATAG 32 6 1 TCACCCCTAA 0.798288 -35 *** ******* Masking position 3 Map Score: 6.48398 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 207 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 7 TCCTCATCCATGATTGGGGTTCAGGACAT 1 109 0 TCCAGATGGG 0.975795 -19 CCACCGGGAAGCCAGGATTCTGGCTTCACAGG 4 157 1 GCCAGATTGG 0.96465 -22 CACGGCCAGATACTGGATGGGGGGA 5 3 0 TACTGATGGG 0.893657 -48 TTTCAAATCTTCCAGGGTATGGGATTGATAACC 6 67 0 TCCAGGTGGG 0.974151 -192 ATAGAATCCTGCCTTGATATTGGAGAAATGATC 6 148 1 GCCTGATTGG 0.958271 -111 TTTATTTAAGTCCAGGATGTGGGCCTCCTACTG 8 42 1 TCCAGATGGG 0.975785 -88 CAATACCTGAGACTGGATCTGGGGGGGGCCATA 17 96 1 GACTGATGGG 0.915391 -205 ATATAAAGGTCACAGGGTGGTGGGCGGCAGATC 21 92 1 CACAGGTTGG 0.767664 -93 TGCCATGACTGCCTCGAGGGTGGAGTTTCCGGT 28 61 1 GCCTGAGTGG 0.8981 -134 GCTGTGCAACCCCAAGGGTATGGGATGAGAGTA 31 86 1 CCCAGGGTGG 0.836579 -67 TTAACCACGATCCTCGGTAGGGGAAGATTTTTT 38 36 0 TCCTGGTGGG 0.969444 -119 **** *** *** Masking position 3 Map Score: 6.05235 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 262 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 TACAGTACAATTTAATGTTTTTTCATGT 4 9 1 AATTTAATGT 0.850745 -170 ATTGATGGGAATATTAATGTTTTGTTTGGT 9 82 0 ATATTAATGT 0.901732 -59 TGAGTATGACATAATAATGTACATTAAAAT 10 52 1 ATAATAATGT 0.852136 -189 ATATTCAATAATTTTAATGTACATTATTAT 10 62 0 ATTTTAATGT 0.934594 -179 AATAACTTTAATTTTAATGTTAATGTATTT 10 133 1 ATTTTAATGT 0.934594 -108 TCTCATGATATTTATAATGTTGGTAGATTT 13 28 1 TTTATAATGT 0.676986 -92 TTCATACCAATTTTTAATGTACTTGACTTG 17 154 1 TTTTTAATGT 0.780441 -147 CTAATATCTGATGATAATGTGGAGGTGAAA 17 279 1 ATGATAATGT 0.722149 -22 TCATGTTATTAAATTAATGTGATATCCTAT 31 15 0 AAATTAATGT 0.790959 -138 CCTCATTATTAAATTAATGTAATACTCTCA 31 111 0 AAATTAATGT 0.790959 -42 TTCTGGTTATTATAATGTAATTGCATAT 35 9 1 ATTATAATGT 0.894141 -62 ********** Masking position 6 Map Score: 5.66669 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 = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 GGTGGTCTATTTCCACAGCCAGAGAGTCCT 1 50 0 TTCCACAGCC 0.916918 -78 GGTGCGTGCCTGGCACGGCCAGATACTGGA 5 19 0 TGGCACGGCC 0.959836 -32 GAAATTATAGATGCACAGCCCTTATAGTCT 10 23 1 ATGCACAGCC 0.980847 -218 CAGATATGTTAGGCACATCCAAAAGGAGAG 13 96 1 AGGCACATCC 0.848605 -24 GACCTTTATATGGCACAGCCCATCCACCAC 21 73 0 TGGCACAGCC 0.984931 -112 TTTCCGGTCCATGGACCGCCGGGACAGCCA 28 86 1 ATGGACCGCC 0.850821 -109 ACCCTTGGGGTTGCACAGCCACCAGCTTCA 31 75 0 TTGCACAGCC 0.985225 -78 TGGTTCTACAGTGCACCGCCCCTCAGGCTT 39 100 1 GTGCACCGCC 0.95286 -77 ********** Masking position 5 Map Score: 5.19775 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 63 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 AACAGGGGCCATGGCTGCTTTCCT 7 5 1 GGGGCCATGG 0.976877 -58 TTTCATTAAGGGGTCCATGCTAATAGGGGA 16 86 0 GGGTCCATGC 0.985871 -207 TTTACCGACGATCCATGCTTAATGAATA 24 9 1 CGATCCATGC 0.80285 -44 TTCCAGCAAGTGGTCCATGGGGCAGTCTGT 25 51 1 TGGTCCATGG 0.976661 -250 CGTCCTGGTGGGGTACATGCTATCAGCTCC 27 88 0 GGGTACATGC 0.872456 -179 CTCGAAGACATGGTCCATCCTTGTGAGGAG 27 130 0 TGGTCCATCC 0.83076 -137 GTGGAGTTTCCGGTCCATGGACCGCCGGGA 28 80 1 CGGTCCATGG 0.978343 -115 CTTTCATACAGGGGCCTTGGTGAACCGGCA 39 127 1 GGGGCCTTGG 0.869449 -50 GCACTTAAACTGCTCCATGGGGCAATACCA 42 80 0 TGCTCCATGG 0.873833 -91 ********** Masking position 8 Map Score: 5.37634 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 246 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 GGGTTATCAATCCCATACCCTGGAAGATTT 6 66 1 TCCCATACCC 0.989371 -193 AAAGAGAGTGTCCCATACCAACATTTTATT 30 80 1 TCCCATACCA 0.959063 -46 AATACTCTCATCCCATACCCTTGGGGTTGC 31 91 0 TCCCATACCC 0.989371 -62 TATTTATGTCATACCGAACTAATAAG 35 55 0 TGTCATACCG 0.837846 -16 TATAACTGCCATACCCATCAGCAGCG 36 7 1 TGCCATACCC 0.979858 -153 AAAAAAATCTTCCCCTACCGAGGATCGTGG 38 35 1 TCCCCTACCG 0.958958 -120 ********** Masking position 6 Map Score: 3.65584 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 23 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 12 AATGATCATATCACAGGAAAGGGCCAGAAAAA 6 174 1 TCAGGAAAGG 0.821899 -85 TGCGGCTGGCTCTCATGCATGGTAATCAGAGG 20 48 1 TCATGCATGG 0.949253 -184 TGCATGGTAATCAGAGGCATGGTAATCAGTGG 20 63 1 TCAGGCATGG 0.993114 -169 GTAGTAAGATTCGGAGGCATGGAGTAATCGAT 20 116 1 TCAGGCATGG 0.993114 -116 GTGATGATTATCGGCGGCAGGGTGCCTCCAG 27 10 0 TCCGGCAGGG 0.941945 -257 CCTCATCCTCTCGAAGACATGGTCCATCCTTG 27 137 0 TCAGACATGG 0.949253 -130 GGAGCTGAACACGTAGGCATGGTCGGAAGTCA 40 74 0 ACAGGCATGG 0.967679 -76 ** ******** Masking position 9 Map Score: 2.87047 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 73 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 13 ATTTATATGTCCTGAACCCCAATCATGGATGA 1 103 1 CCGACCCCAA 0.727958 -25 GCCAGAAAAACCAGAAACCTACAGAGAGGTAA 6 196 1 CCGAACCTAC 0.971885 -63 ATTCTCATGGCCGGTAGCCTCCCCTGAGATTA 10 167 0 CCGAGCCTCC 0.855712 -74 TTTACTGTTTCCCTGAACCAAAAGTCTGGTTA 11 35 0 CCTAACCAAA 0.789684 -84 TATAAGGATGCCGGTAACCTACTTCCGAAAAT 13 54 0 CCGAACCTAC 0.971885 -66 TAATAAAGCGCCATCAACATAAATAATGGTGA 16 261 1 CCTAACATAA 0.492174 -32 TTGGTGAGCTCCTGAAAACTAATAAGTTATTA 25 231 0 CCGAAACTAA 0.681645 -70 ATAATTTACACCATAACCCTCCGGAATCCCTC 39 31 1 CCTACCCTCC 0.831658 -146 CCTTGGTGAACCGGCAACCGCCATCACCGGAT 39 141 1 CCGAACCGCC 0.869183 -36 CCGAACCTCTCCAGTAACCAAAGACAACTGAC 40 46 1 CCGAACCAAA 0.892417 -104 GATTAATGAACCTTCAACCTCACATGGTATTG 42 56 1 CCTAACCTCA 0.917437 -115 AGTTTAAGTGCCATGAACCTAAATATAATCTC 42 99 1 CCTAACCTAA 0.931069 -72 ** * ******* Masking position 6 Map Score: 4.43892 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 273 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 14 CTCATCAAGATCTCTGTAAACCTC 3 113 0 TCACAATCTC 0.911658 -14 TATATCAGCATCATCTTACTCTCATTGTCGGAA 15 117 1 TCACTCTCTC 0.832318 -89 CGGCTAACTATCCTCATCCTCTCGAAGACATGG 27 147 0 TCCCACTCTC 0.989699 -120 CTGTTCAGTATCCTCATTATCTCTGAGAGGTGG 27 222 0 TCCCAATCTC 0.969219 -45 TCACTGGGTCTCAGCAATCTCTCCATTAAAGAG 30 53 1 TCACACTCTC 0.969219 -73 GCACCTAATATCCCCACTCTTTCTGAAGTAAAA 36 56 1 TCCCACTTTC 0.969219 -104 GAGAATACTTTCCACACGCACTCTGAATCCATA 36 111 1 TCCCACACTC 0.968112 -49 AGTGCACCGCCCCTCAGGCTTTCATACAGGGGC 39 109 1 CCCCACTTTC 0.880336 -68 ATATAAATATTCCACAGTAATTCA 40 136 1 TCCCAAATTC 0.765316 -14 *** ** ***** Masking position 12 Map Score: 4.89265 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 127 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 15 GACCAGCACTTCAGGTGAACGGACCGC 1 8 0 TCAGGTGAAC 0.896433 -120 AGAGGTGAACCAATGGTAAC 2 1 1 AGAGGTGAAC 0.778237 -91 ACCTCCTTACTGGAGTGAACAATC 2 78 1 TGGAGTGAAC 0.734982 -14 GGCCTCCTACTGATGTGATCTCTTCAAGTA 8 63 1 TGATGTGATC 0.70129 -67 CTATAATTTCAGAGGTGATGTT 10 3 0 AGAGGTGATG 0.716713 -238 GTATAGATGATCGGGTGATCCACA 16 5 0 TCGGGTGATC 0.867116 -288 ATCAGATGAATGAAGTGAAGAGATTAAGCA 16 130 1 TGAAGTGAAG 0.726185 -163 CAGTCATGTTTGAAGTGATCTGATTCATGA 17 66 1 TGAAGTGATC 0.918755 -235 ATGCTTACCTTACAGTGATCTATGGTTAGA 20 186 0 TACAGTGATC 0.64688 -46 GGTTTCACCTGCAGTGATGGATAATCATT 21 10 1 TGCAGTGATG 0.792759 -175 CTTAATTATATAAGGTGATCCCAACAATAG 21 42 0 TAAGGTGATC 0.805443 -143 AAGACAGTTATCCAGTGAACATATGGGGAC 25 110 0 TCCAGTGAAC 0.792965 -191 GAAATATGAATCCGGTGATGGCGGTTGCCG 39 152 0 TCCGGTGATG 0.836961 -25 TCAGGAAAAAACAGGTGATCTT 40 3 0 ACAGGTGATC 0.816223 -147 ********** Masking position 8 Map Score: 4.9994 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 204 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035