AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00240_mthe_reg_100.orf -o00240_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 Purged sequences: MTH297 29 DNA-dependent RNA polymerase, subunit A' MTH418 21 phosphonopyruvate decarboxylase related protein Input sequences: #1 MTH21 109 ribosomal protein L19 #2 MTH34 236 ribosomal protein S18 (E.coli S13) #3 MTH40 58 DNA-dependent RNA polymerase, subunit N #4 MTH42 171 DNA-dependent RNA polymerase, subunit K #5 MTH129 171 orotidine 5' monophosphate decarboxylase #6 MTH255 269 ribosomal protein L7a #7 MTH256 49 ribosomal protein S28 #8 MTH261 24 translation initiation factor eIF-2, gamma subunit #9 MTH262 24 conserved protein #10 MTH296 300 unknown #11 MTH415 199 conserved protein #12 MTH419 51 CTP synthase #13 MTH550 118 DNA-dependent DNA polymerase family X #14 MTH650 300 conserved protein #15 MTH708 135 thioredoxin reductase #16 MTH777 48 conserved protein #17 MTH778 68 unknown #18 MTH779 300 conserved protein #19 MTH840 62 pseudouridylate synthase I #20 MTH848 103 protein-export membrane protein, SecF #21 MTH1048 300 DNA-dependent RNA polymerase, subunit H #22 MTH1049 40 DNA-dependent RNA polymerase, subunit B'' #23 MTH1050 22 DNA-dependent RNA polymerase, subunit B' #24 MTH1051 38 DNA-dependent RNA polymerase, subunit A' #25 MTH1127 90 dihydroorotase #26 MTH1208 220 DNA-dependent DNA polymerase family B (PolB1) #27 MTH1213 45 dihydroorotate oxidase #28 MTH1314 52 transcription elongation factor TFIIS #29 MTH1315 28 mutator MutT protein #30 MTH1318 231 conserved protein #31 MTH1405 82 DNA polymerase delta small subunit #32 MTH1413 42 aspartate carbamoyltransferase #33 MTH1415 175 ATP-dependent RNA helicase, eIF-4A family #34 MTH1492 51 5'-nucleotidase #35 MTH1493 78 cation transporting P-type ATPase related protein #36 MTH1494 266 conserved protein #37 MTH1539 246 anaerobic ribonucleoside-triphosphate reductase #38 MTH1765 154 thymidylate kinase #39 MTH1850 105 fumarate reductase Motif number 1 GGAGGACTGGAAGGGGCATATTTTCCAGT 1 7 1 CTGGAAGGGT 0.990636 -103 AGTTTTTTCGCTGGACTGGAAAATATGCCCCTT 1 21 0 CTGGACTGGA 0.754165 -89 TAACCGACGCCGGGACTGGGATTTGAACCCAGG 2 131 0 CGGGACTGGT 0.89325 -106 AGTGAATTCGCGGGACGGGGGTTTGCGAATTCT 2 196 0 CGGGACGGGT 0.956611 -41 GACTTTTCAACTGGAACGGGGATGGTCAGCACC 4 62 1 CTGGAACGGT 0.925117 -110 GCGGGGGCCTCTGAAAGGATAATATATGTAAGA 5 109 1 CTGAAAGGAT 0.812878 -63 AGGGCGGACCCTGGAATGGATTTGAAGAGGTAC 14 127 0 CTGGAATGGT 0.975699 -174 TCCCTGTGGCCTGGAATGATTTTTTTATTTTAA 18 56 1 CTGGAATGAT 0.914672 -245 TTTGAGTGGACTGGCCGGGATTTGAACCCGGGG 18 162 1 CTGGCCGGGT 0.973643 -139 GTTATGGCTGCTGGTATGGCTATGAGTGGCCTG 20 76 0 CTGGTATGGT 0.798049 -28 AGGAAACGCCCTGGCCGGGAATTGAACCCGAGT 21 160 0 CTGGCCGGGT 0.973643 -141 GTAGCTCAGTCTGGCAGAGCGCTTGGCTTTTAA 21 201 1 CTGGCAGAGT 0.672296 -100 ATATGAAAATCTGGAAGGGGTACTG 32 28 1 CTGGAAGGGC 0.930633 -15 ATTTTCAGCACTGAAAGGAACCTGAACCTTAAA 33 128 1 CTGAAAGGAT 0.812878 -48 GGTTAAAACCTGTAAGGGGGGTGTTTTATGGC 34 10 1 CTGTAAGGGT 0.865585 -42 TGTTTTATGGCTGAACTGAGCATAATCTAG 34 32 1 CTGAACTGAT 0.595511 -20 TCACAGATGACTGGAAGGATCCTTATACTATGA 36 38 1 CTGGAAGGAT 0.965805 -229 ********* * Masking position 3 Map Score: 19.5506 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 242 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 2 CGCCGGGACTGGGATTTGAACCCAGGAGGAG 2 126 0 GGGATTGAAC 0.988751 -111 TGGGACCGCCGAGATTTGAACTCGGGTCTCC 4 103 0 GAGATTGAAC 0.873828 -69 GCCTAATGAGGGATGGTGAACTTCGTAATAG 10 59 0 GGATGTGAAC 0.879071 -242 GTTCACTTCGGGGATCTGATCCCTGAGCCAG 10 209 1 GGGACTGATC 0.902076 -92 TGGACTGGCCGGGATTTGAACCCGGGGCCTC 18 168 1 GGGATTGAAC 0.988751 -133 CGCCCTGGCCGGGAATTGAACCCGAGTCGCG 21 156 0 GGGATTGAAC 0.988751 -145 CGGGCCCGACGGGAATTGAACCCGCGACCAC 21 238 0 GGGATTGAAC 0.988751 -63 GATTTCCTGGGGGTGTTGGACTTATAATAAG 26 84 0 GGGTTTGGAC 0.907059 -137 AGCACTGAAAGGAACCTGAACCTTAAATAAA 33 134 1 GGAACTGAAC 0.947254 -42 GAGATAATGAGGATACTGAACAGATACAACT 36 232 1 GGATCTGAAC 0.913708 -35 CCTTTAATATGGGTGGTGAACATAAAATTAC 37 202 1 GGGTGTGAAC 0.967047 -45 **** ****** Masking position 7 Map Score: 16.5585 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 65 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 3 GGGACCGTAGGGTAGCTTGGTC 4 1 1 GGGCCGTAGG 0.980496 -171 ATTTGAACTCGGGTCTCCAGCGTTCCGGTGCT 4 89 0 GGGCTCCAGG 0.93466 -83 TCGATTTGATGGGACCGCCGAGATTTGAACTC 4 111 0 GGGCCGCCGG 0.997264 -61 GTTTAACGGTGGGTCCTCCGGCTTAAGCCTCA 10 109 0 GGGCCTCCGC 0.946174 -192 TAAAGTCTATGGTGCTGCAGTGATATAAGGCT 11 138 0 GGTCTGCAGG 0.939386 -62 GATTTGAAGAGGTACTGCAGTGCAAGAAAACT 14 110 0 GGTCTGCAGG 0.939386 -191 ATCCATTCCAGGGTCCGCCCTGGGATCCCCCC 14 139 1 GGGCCGCCCG 0.972663 -162 ATTTTATGAATGGTCTGCAGTCTGTTCCTTAA 14 270 0 TGGCTGCAGC 0.736877 -31 TGGAGCTTTAGGGTCTGCTGAGCACCCTCAAT 15 35 0 GGGCTGCTGG 0.962164 -101 ATTTGAACCCGGGGCCTCCGCCATGCCAAGGC 18 181 1 GGGCCTCCGC 0.946173 -120 GCTATCATGCGGGCCTGTCGAGCCCGCGACTC 21 132 1 GGGCTGTCGG 0.977416 -169 CGTTTCCTGAGGGCCCGTAGCTCAGTCTGGCA 21 185 1 GGGCCGTAGT 0.814539 -116 ATTAGATAGCGGGCCCGACGGGAATTGAACCC 21 246 0 GGGCCGACGG 0.969553 -55 *** ****** * Masking position 5 Map Score: 16.319 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 227 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 CGAAAAAACTTTTTAAGGGGATACCTGAAA 1 44 1 TTTTAAGGGG 0.952741 -66 ACCGAGAACATATAAAGGTACTCACCCACT 6 180 1 TATAAAGGTA 0.663965 -90 ATTTCAATTTAATAAAGGTGATTTA 7 35 1 AATAAAGGTG 0.761125 -15 TAAAAGCGTTTATAGGTGTAATCT 8 9 1 TTTATAGGTG 0.597774 -16 CTGGAAAAGGTTTAACGGTGGGTCCTCCGG 10 120 0 TTTAACGGTG 0.813371 -181 GATTTTTAAGTTTAAAGGGAGTCACCGGGA 18 16 0 TTTAAAGGGA 0.879801 -285 TGGGAGAAACTTTAAAGGTGATCGTCTTGA 20 24 1 TTTAAAGGTG 0.941976 -80 CGCTATCTAATTTTACGGTGACTTTTTATC 21 267 1 TTTTACGGTG 0.793122 -34 TAATGGATTTAAGGGAATAACAAAAA 24 7 1 ATTTAAGGGA 0.768312 -32 GGTCTAAAAGATTTAAGGGAGG 33 3 0 ATTTAAGGGA 0.768312 -173 ATCTCTTCTCTTTTAAGGGACCTTGTCCGG 36 177 0 TTTTAAGGGA 0.865568 -90 TATAGAGGGAAATTAAGGGGCTCTGCATCA 37 60 0 AATTAAGGGG 0.798254 -187 TTTAAACCCTTATAAAGGTGTTATTAATCA 37 144 1 TATAAAGGTG 0.860851 -103 AGCCGATGATTTTTAAGGGGGGCGCGGCAC 37 173 1 TTTTAAGGGG 0.952741 -74 CACCACCCATATTAAAGGTGCCGCGCCCCC 37 190 0 ATTAAAGGTG 0.893176 -57 ********** Masking position 3 Map Score: 12.8037 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 103 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 5 CGAATTCACTCTTACTGGAGGTTAATGA 2 219 1 CTACTGGAGG 0.705754 -18 GGGTCTCCAGCGTTCCGGTGCTGACCATCCC 4 80 0 CTTCCGGTGC 0.872461 -92 CACCTTTAGGCTTCCCTGAGGCTTAAGCCGG 10 93 1 CTCCCTGAGG 0.982515 -208 TCGGGGATCTGATCCCTGAGCCAGGGGGGTT 10 216 1 GTCCCTGAGC 0.945835 -85 CAGGATCCATGTTCCCTCTGCTGAATCTGAG 11 40 1 GTCCCTCTGC 0.870984 -160 CTCTGTGACAGGTCTCTGTGGCAAGGTTTAT 11 85 1 GTCTCTGTGG 0.761993 -115 GGACATCCCGGTGACTCCCTTTAA 18 4 1 CTCCCGGTGA 0.948098 -297 TCATTGGGCACTTCCCTGTGGCCTGGAATGA 18 44 1 CTCCCTGTGG 0.988231 -257 CGGCCAGGGCGTTTCCTGAGGGCCCGTAGCT 21 176 1 GTTCCTGAGG 0.829122 -125 TTAACAGCCTCCCGGTGGAAAA 23 5 0 CTCCCGGTGG 0.965677 -18 TTAATAAAGTGTTCCCGCTGCGTTTATCTCT 26 178 0 GTCCCGCTGC 0.905034 -43 ACCAGACTCCTCCTGCAGGCATCTATTT 29 10 0 CTCCTGCAGG 0.814013 -19 TGAAAATCAGGTTACCTGAGGCTTTGGCCTT 33 104 0 GTACCTGAGG 0.829122 -72 CATTCATATACGTCCTGGTGGGGTACATGCT 36 97 0 CTCCTGGTGG 0.965178 -170 AGACATGGTCCATCCTTGTGAGGAGTTCATT 36 124 0 CTCCTTGTGA 0.753401 -143 * ********* Masking position 3 Map Score: 13.0189 Number of sites scoring better than the average of aligned sites = 1493 Number in coding regions = 1449 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 6 AGGCGCAAGACTGGAAATCTTGTGGAGCTT 2 94 1 CTGGAAATCT 0.925591 -143 ACGATTTCTCATGAAAATCTGTATCCAGCA 6 140 1 ATGAAAATCT 0.945796 -130 AACTAACGAGCTGAAAATCTTCCAATCAGA 14 50 1 CTGAAAATCT 0.981563 -251 ATAAGGAAACCTGAAAAACTTCATTTAATC 18 88 1 CTGAAAAACT 0.943896 -213 AGGGTTATATATGAAAATCTGGAAGGGGTA 32 20 1 ATGAAAATCT 0.945796 -23 CCTTTCAGTGCTGAAAATCAGGTTACCTGA 33 116 0 CTGAAAATCA 0.893536 -60 ACTGTATCCTCTCAAAATCTTAATACCATA 35 40 1 CTCAAAATCT 0.885528 -39 GTGATTTTAACTGATAATCTTTTAAACAAT 39 19 0 CTGATAATCT 0.893536 -87 GCTGACTCATATGAAAAACTTCAGAATGAA 39 86 0 ATGAAAAACT 0.846483 -20 ********** Masking position 6 Map Score: 7.78905 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 25 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 GGAGCTTAATCGTGATGGGGCAAACTACTG 10 275 1 CGTGATGGGG 0.909865 -26 ATGAATATACTGTGGTGGGGGTTTTCAT 13 9 0 TGTGGTGGGG 0.953868 -110 AGGATCACCTGGTGTGGAGATAAGAGA 19 46 0 CCTGGTGTGG 0.983139 -17 AGAGACTTGCCCTGGTGGTGTAGGGGCTAT 21 107 1 CCTGGTGGTG 0.983176 -194 CAGGAAACGCCCTGGCCGGGAATTGAACCC 21 164 0 CCTGGCCGGG 0.915214 -137 TTTAGGATTTCCTGGGGGTGTTGGACTTAT 26 90 0 CCTGGGGGTG 0.94732 -131 CCCTTTATCTGGTGTGGTATCTACAGA 30 8 1 TCTGGTGTGG 0.930396 -224 TCATATACGTCCTGGTGGGGTACATGCTAT 36 95 0 CCTGGTGGGG 0.996063 -172 ********** Masking position 3 Map Score: 7.72935 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 187 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 GGGCATATTTTCCAGTCCAGCGAAAAAACTTTT 1 24 1 TCCGTCCGGA 0.834171 -86 GAGAGAAAAAACATGGCCTCAGATTCAGCAGAG 11 55 0 ACAGGCCCGA 0.965991 -145 AATGATATAAACCTTGCCACAGAGACCTGTCAC 11 89 0 ACCTGCCCGA 0.989301 -111 CAGGGCAAAAATCCGGACCCTGAAACCAGAGAT 17 42 0 ATCGGACCGA 0.825499 -27 AAAAAATCATTCCAGGCCACAGGGAAGTGCCCA 18 48 0 TCCGGCCCGG 0.947904 -253 AATATTAATCTGTCCCGCGAGATAAATAAG 25 8 1 ATCGTCCGGA 0.757773 -83 TCCACTGATTACCATGCCTCTGATTACCATGCA 30 63 0 ACCTGCCCGA 0.989306 -169 CATACTGCACATCTGTCCACTGATTACCATGCC 30 78 0 ATCGTCCCGA 0.935717 -154 GATCGATTACTCCATGCCTCCGAATCTTACTAC 30 116 0 TCCTGCCCGA 0.979573 -116 CTGGAGGCACCCTGCCGCCGATAATCATCAC 36 9 1 ACCTGCCCGA 0.989304 -258 ACATAACTTTATAATGCTTCAGACACAGAATTA 38 33 0 ATATGCTCGA 0.365556 -122 GAAGATCTTTTCCCGGCTCCTGATGGATTAACC 38 80 1 TCCGGCTCGA 0.935397 -75 *** **** * ** Masking position 12 Map Score: 9.02933 Number of sites scoring better than the average of aligned sites = 367 Number in coding regions = 344 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 TCAGAGGCCCCCGCAACCATCAAGGAAACTTTAA 5 89 0 CCCACCATCG 0.928171 -83 CCTCATTAGGCCTCCACCTTTAGGCTTCCCTGAG 10 79 1 CCCACCTTTG 0.955685 -222 ATGAAAACCCCCACCACAGTATATTCATTTA 13 8 1 CCCACCACAA 0.828297 -111 CCCTAAAGCTCCACCTCCTTTTTAATATGAACCG 15 54 1 CCCTCCTTTA 0.823689 -82 CATGATAGCCCCTACACCACCAGGGCAAGTCTCT 21 107 0 CCAACCACCG 0.804315 -194 GGAATTGAACCCGCGACCACTTGGTTAAAAGCCA 21 224 0 CCCACCACTG 0.986486 -77 AGCATTCTGACACCGTCCACTCCATCCAGAACTA 25 43 0 CACTCCACTA 0.709735 -48 ACCCTCTACCTCCCCGTGTATTAATA 26 3 1 CCCACCTCCG 0.984125 -218 GGCTAACTATCCTCATCCTCTCGAAGACATGGTC 36 145 0 CCCTCCTCTA 0.949648 -122 AAGAGATAGACCACCACCTCTCAGAGATAATGAG 36 209 1 CCCACCTCTG 0.988645 -58 AGGGGCTCTGCATCATCCTCTCTGTTTTTGGCAG 37 41 0 CACTCCTCTG 0.887746 -206 ** * ****** * Masking position 7 Map Score: 6.40508 Number of sites scoring better than the average of aligned sites = 599 Number in coding regions = 575 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 10 CGGTTAAAGCAACCCTGTTGCACCTACGACTC 2 158 1 AACCTTTGCA 0.73436 -79 GATCCCATGCAGTCATTCTGCACACTGTACAA 10 169 0 AGTCTCTGCA 0.849888 -132 AGGCTTAGTCTATCGTGCTACAATGATATAAA 11 111 0 TATCTCTACA 0.831696 -89 ACATAAAGTCTATGGTGCTGCAGTGATATAAG 11 141 0 TATGTCTGCA 0.913916 -59 GACTCATTTAAACTCTTCTGCAAGTATATCTA 14 221 0 AACTTCTGCA 0.854986 -80 AAACTGTTTTTATTGTCCTGCATTTATTTTTA 18 120 0 TATTTCTGCA 0.870997 -181 TAGATGATGAAATGATCCTGCAGTGTTGATCT 22 17 0 AATGTCTGCA 0.933252 -24 TATCTCTGGTTACCGTTCTACAAGTAGCAGAA 26 153 0 TACCTCTACA 0.766173 -68 TCCACTAAAAAATCATTCTGCAGCATATC 28 34 1 AATCTCTGCA 0.972897 -19 ACCAGACTCCTCCTGCAGGCATCTATT 29 12 0 ACTCTCTGCA 0.849888 -17 CTTACTACAAAACCATACTGCACATCTGTCCA 30 92 0 AACCTCTGCA 0.959681 -140 CATGCCTCCGAATCTTACTACAAAACCATACT 30 105 0 AATCTCTACA 0.866807 -127 TGATTATATATATGCTTTTGCATGCGACGTTC 30 152 0 TATGTTTGCA 0.552185 -80 TAAAATATTTTACTGCACACACATTTT 31 6 1 TATTTCTGCA 0.870997 -77 **** * ***** Masking position 12 Map Score: 11.189 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 102 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 ATAACTTTATATATTTTTATTTTATAAACTA 3 19 1 ATTTTTTATT 0.945199 -40 CTCTATTTTAATGTTTTTCTTGGAGGCAT 4 153 1 ATTTTTTCTT 0.893965 -19 AATATTTTTATTAAATGGTGTA 10 2 1 ATTTTTTATT 0.945199 -299 CAGATACTTCATTTTTCTATTCTACTAATAT 14 76 1 ATTTTCTATT 0.801187 -225 AACCAGCCCCCTTTTTTTATTATTGAGGGTG 15 14 1 CTTTTTTATT 0.893965 -122 GCCTGGAATGATTTTTTTATTTTAATAAGGA 18 64 1 ATTTTTTATT 0.945199 -237 GTTTTTTAAACTGTTTTTATTGTCCTGCATT 18 128 0 CTTTTTTATT 0.893965 -173 TTCCCAATTAATTTTTTTCTTTCTGCCAAAA 37 19 1 ATTTTTTCTT 0.893965 -228 GTAGGGGAAGATTTTTTTACTCTTCCTGATA 38 123 1 ATTTTTTACT 0.801187 -32 ** ******** Masking position 6 Map Score: 5.04335 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 5 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 TCAAGAAACCTCCTTGTATTCAGCA 1 95 0 AAACCTCCTT 0.916752 -15 CGTCGGTTAAAGCAACCCTGTTGCACCTACGA 2 155 1 ACACCCTGTT 0.870599 -82 TCCGGTGCTGACCATCCCCGTTCCAGTTGAAA 4 66 0 ACACCCCGTT 0.959755 -106 TACGAAGTTCACCATCCCTCATTAGGCCTCCA 10 63 1 ACACCCTCAT 0.874922 -238 AAACCATAATATAACCCCCCTGGCTCAGGGAT 10 227 0 AAACCCCCTG 0.92103 -74 AAAAACCAGCCCCCTTTTTTTATTAT 15 5 1 ACACCCCCTT 0.988911 -131 TGGACTTATAATAAGCCTTCTTAGTTGCTGGC 26 67 0 AAACCTTCTT 0.756524 -154 ATTAGATGTTAAAAACCACCTTACAGGGCAGT 31 50 1 AAACCACCTT 0.861976 -33 ATCATCCCCAATAAACCCCCATTTATTCCTTC 33 45 1 AAACCCCCAT 0.939562 -131 TCAGCCATAAAACACCCCCCTTACAGGTTTTA 34 14 0 ACACCCCCTT 0.988911 -38 * ** ******* Masking position 4 Map Score: 7.04988 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 13 ACTGGGATTTGAACCCAGGAGGAGCAAAGC 2 120 0 GAACCCAGGA 0.960715 -117 GCCGAGATTTGAACTCGGGTCTCCAGCGTT 4 97 0 GAACTCGGGT 0.906355 -75 TGGATGGGGGGATCCCAGGGCGGACCCTGG 14 146 0 GATCCCAGGG 0.906231 -155 GCCGGGATTTGAACCCGGGGCCTCCGCCAT 18 175 1 GAACCCGGGG 0.985409 -126 GCCGGGAATTGAACCCGAGTCGCGGGCTCG 21 150 0 GAACCCGAGT 0.890291 -151 GACGGGAATTGAACCCGCGACCACTTGGTT 21 232 0 GAACCCGCGA 0.923239 -69 TATTAATACTGATCACAGGATTAAACTGTT 26 29 1 GATCACAGGA 0.709492 -192 TTTTTTAGTGGAACACGGGTGCATTCCTCA 28 16 0 GAACACGGGT 0.94465 -37 ********** Masking position 2 Map Score: 3.78801 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 102 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 14 GGAAAACAAGGATTAATAGAAATTAAAGCT 6 73 0 GATTAATAGA 0.869943 -197 CAATCCACACGATTAATAAATTTACTGTTT 13 53 1 GATTAATAAA 0.740565 -66 TTGCAGAAGAGTTTAAATGAGTCAATGATG 14 230 1 GTTTAAATGA 0.869943 -71 TATTTTTACTGATTAAATGAAGTTTTTCAG 18 98 0 GATTAAATGA 0.869943 -203 AATAAAAACAGTTTAAAAAACAGTTTTGAG 18 138 1 GTTTAAAAAA 0.863088 -163 TGTTATGTGAGATTAATAAAGTGTTCCCGC 26 191 0 GATTAATAAA 0.740565 -30 TGTTCAACCGGTCTAAAAGATTTAAGGGAG 33 12 0 GTCTAAAAGA 0.754945 -164 AGGTTTAAGAGATTAAAAGAAGGAATAAAT 33 65 0 GATTAAAAGA 0.936597 -111 CTTTATAAGGGTTTAAATAATTATTATTAT 37 131 0 GTTTAAATAA 0.740565 -116 TGTCTGTATTGTTTAAAAGATTATCAGTTA 39 12 1 GTTTAAAAGA 0.936597 -94 ********** Masking position 5 Map Score: 3.6032 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 16 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 15 ATCAATCGATAACTTTATATATTTTTATTT 3 10 1 TACTTTATAT 0.700874 -49 AATTTATAGAAAACATTATATACCTCAATTT 5 48 0 AACATTATAT 0.931658 -124 ATTGGCAGCAAAACTTTATATGTGATGAAGC 6 45 1 AACTTTATAT 0.91982 -225 AGTGGGTGAGTACCTTTATATGTTCTCGGTA 6 179 0 TACTTTATAT 0.700874 -91 CCCCGAAGTGAACCATTATATGATCCCATGC 10 191 0 AACATTATAT 0.931658 -110 CACGACAGTAAACCATAATATAACCCCCCTG 10 237 0 AACATAATAT 0.735752 -64 ACGATAGACTAAGCCTTATATCACTGCAGCA 11 127 1 AACCTTATAT 0.885316 -73 CTGAATGTGAAATCTTTATCTCCACCGGTGA 15 93 1 AACTTTATCT 0.783752 -43 ACCACCTTAATCATTATCTTGGTCACCGG 15 117 0 AACATTATCT 0.811565 -19 AGGAAATCCTAAACACTATATCTTAATAGTG 26 107 1 AACACTATAT 0.682554 -114 TAATTATTTAAACCCTTATAAAGGTGTTATT 37 138 1 AACCTTATAA 0.611904 -109 TCTGTGTCTGAAGCATTATAAAGTTATGTCC 38 37 1 AACATTATAA 0.735752 -118 TAAAATCACAAACCTTAATATGTGTTGATAA 39 40 1 AACTTAATAT 0.700874 -66 ** ******** Masking position 8 Map Score: 6.20043 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 10 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912