AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00240_mthe_reg_300.orf -o00240_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 Purged sequences: MTH5 22 ribosomal protein L8 (E.coli L2) MTH297 29 DNA-dependent RNA polymerase, subunit A' MTH418 21 phosphonopyruvate decarboxylase related protein Input sequences: #1 MTH1 170 conserved protein #2 MTH9 46 ribosomal protein L35 (E.coli L29) #3 MTH21 109 ribosomal protein L19 #4 MTH31 30 ribosomal protein L14 #5 MTH34 236 ribosomal protein S18 (E.coli S13) #6 MTH40 58 DNA-dependent RNA polymerase, subunit N #7 MTH42 171 DNA-dependent RNA polymerase, subunit K #8 MTH129 171 orotidine 5' monophosphate decarboxylase #9 MTH243 231 conserved protein #10 MTH248 195 conserved protein #11 MTH249 64 conserved protein #12 MTH250 23 tRNA intron endonuclease #13 MTH251 54 tryptophanyl-tRNA synthetase #14 MTH252 22 conserved protein #15 MTH253 75 threonine synthase #16 MTH254 206 histone HMtB #17 MTH255 269 ribosomal protein L7a #18 MTH256 49 ribosomal protein S28 #19 MTH261 24 translation initiation factor eIF-2, gamma subunit #20 MTH262 24 conserved protein #21 MTH296 300 unknown #22 MTH413 300 conserved protein #23 MTH415 199 conserved protein #24 MTH419 51 CTP synthase #25 MTH550 118 DNA-dependent DNA polymerase family X #26 MTH650 300 conserved protein #27 MTH700 110 conserved protein #28 MTH702 27 acetyl-CoA synthetase related protein #29 MTH708 135 thioredoxin reductase #30 MTH777 48 conserved protein #31 MTH778 68 unknown #32 MTH779 300 conserved protein #33 MTH840 62 pseudouridylate synthase I #34 MTH846 170 N-acetyl-gamma-glutamyl-phosphate reductase #35 MTH847 59 unknown #36 MTH848 103 protein-export membrane protein, SecF #37 MTH1048 300 DNA-dependent RNA polymerase, subunit H #38 MTH1049 40 DNA-dependent RNA polymerase, subunit B'' #39 MTH1050 22 DNA-dependent RNA polymerase, subunit B' #40 MTH1051 38 DNA-dependent RNA polymerase, subunit A' #41 MTH1127 90 dihydroorotase #42 MTH1208 220 DNA-dependent DNA polymerase family B (PolB1) #43 MTH1213 45 dihydroorotate oxidase #44 MTH1314 52 transcription elongation factor TFIIS #45 MTH1315 28 mutator MutT protein #46 MTH1318 231 conserved protein #47 MTH1320 184 adenine phosphoribosyltransferase #48 MTH1405 82 DNA polymerase delta small subunit #49 MTH1413 42 aspartate carbamoyltransferase #50 MTH1415 175 ATP-dependent RNA helicase, eIF-4A family #51 MTH1418 107 conserved protein #52 MTH1492 51 5'-nucleotidase #53 MTH1493 78 cation transporting P-type ATPase related protein #54 MTH1494 266 conserved protein #55 MTH1495 194 ornithine cyclodeaminase #56 MTH1537 300 adenylosuccinate lyase #57 MTH1538 96 unknown #58 MTH1539 246 anaerobic ribonucleoside-triphosphate reductase #59 MTH1765 154 thymidylate kinase #60 MTH1850 105 fumarate reductase Motif number 1 TTTAACCGACGCCGGGACTGGGATTTGAACCCAGGAGGAGCA 5 124 0 GCAGTTACCC 0.839535 -113 TCGATTTGATGGGACCGCCGAGATTTGAACTCGGGTCTCCAG 7 101 0 GGGGTTACTC 0.99025 -71 AGAGTGTTGAGTTCCTGAGGAATATTATACCTTGAGGGGCCC 10 22 1 GTGGTTACCT 0.839073 -174 CCATCGGTTGGTTCATGGGGCACCTTCAACCCAGCAGTATAT 16 108 0 GTGGTTACCC 0.98846 -99 GGCCCCTGTGGGTTCTGGAGGTCTTTATATCCCCTGAGAACC 22 80 0 GGGGTTATCC 0.977864 -221 CTATTACCGGGGAGGGGTAATAAATTTAACCCGGAATCAAGG 22 252 0 GGGATTACCC 0.963219 -49 AGTTTTGAGTGGACTGGCCGGGATTTGAACCCGGGGCCTCCG 32 159 1 GGGGTTACCC 0.997679 -142 AGTCTGCGAGGGTATGGTGGGGCCTCCCACCCATATAATGTC 34 92 0 GGGGTCACCC 0.982819 -79 CTCAGGAAACGCCCTGGCCGGGAATTGAACCCGAGTCGCGGG 37 154 0 GCGGTTACCC 0.989301 -147 ATTAGATAGCGGGCCCGACGGGAATTGAACCCGCGACCACTT 37 236 0 GGGGTTACCC 0.996722 -65 GCATCGGGATTGTTGAAAATTGAATTCATTATCTAGA 47 158 0 GGGGTTATTC 0.91598 -27 GGGGTTTATTGGGGATGATGCGTGTTCAACCGGTCTAAAAGA 50 22 0 GGGGTTACCG 0.974835 -154 TGGCAAAGAAGGATAAGAAGACACTTCCACCCAGCGGTGCAG 56 138 1 GGGGTTACCC 0.992637 -163 GCATAATACTGGCAGTGTTCTGCCTTGTACTCAGATTTTCGG 56 249 1 GGGCTTACTC 0.901606 -52 ACGATCCTCGGTAGGGGAAGATTTTTTTACTCTTCCTGATAG 59 113 1 GTGGTTACTC 0.952876 -42 ** * * ** **** Masking position 19 Map Score: 23.2216 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 76 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 2 TCTTGTGGAGCTTTGCTCCTCCTGGGTTCAAATCCC 5 111 1 CTTGCCCGGG 0.828127 -126 TGCTGACCATCCCCGTTCCAGTTGAAAAGTCCGGAA 7 57 0 CCCGCCGGAA 0.915403 -115 CTTGATGGTTGCGGGGGCCTCTGAAAGGATAATATA 8 99 1 GCGGCCCAAA 0.624463 -73 CATCACGGGACCCGGGGCCCCTCAAGGTATAATATT 10 42 0 CCGGCCCAAG 0.934983 -154 GCCCCGGGTCCCGTGATGCCCGGGAGGCCTTCCGTG 10 60 1 CCTGGCCGAG 0.843512 -136 GGGAGGCCTTCCGTGTTCCTGGGGAATATTCCGCTG 10 81 1 CCTGCCGGAA 0.959207 -115 TTATCTCAAACCCTGACCCTCCAGGGGAAATCCTTC 10 165 0 CCTGCCCGGG 0.99046 -31 GGGTCCTCCGGCTTAAGCCTCAGGGAAGCCTAAAGG 21 95 0 GCTACCCGGA 0.610148 -206 GGGATCTGATCCCTGAGCCAGGGGGGTTATATTATG 21 219 1 CCTGCCGGGG 0.980491 -82 ATAAAGACCTCCAGAACCCACAGGGGCCTCATCACA 22 94 1 CCGACCCGGG 0.923922 -207 AAAACCTGGGCCGGGATCCTGTCGAAAACTGGCCTT 22 143 0 CCGGCCGGAA 0.95454 -158 GGTGATCCCTGCATGAACCTGAGGAGAAAGACAGCG 22 214 0 GCTGCCGGAG 0.875569 -87 CAAATCCATTCCAGGGTCCGCCCTGGGATCCCCCCA 26 136 1 CCGGCCCTGG 0.905578 -165 GCATGATAGCCCCTACACCACCAGGGCAAGTCTCTA 37 106 0 CCTACCCGGG 0.904486 -195 AGGAATGCACCCGTGTTCCACTAAAAAATCATTCTG 44 18 1 CCTGCCCAAA 0.909376 -35 AGTTTCCGGTCCATGGACCGCCGGGACAGCCATGAC 55 84 1 CCTGCCCGGA 0.986164 -111 CTTAACACTCCTTGATCATCCCGAAAATCTGAGTA 56 276 0 CCTGCACGAA 0.692808 -25 ATTAAAGGTGCCGCGCCCCCCTTAAAAATCATCGGC 58 174 0 CCCGCCCAAA 0.821995 -73 AAGATCTTTTCCCGGCTCCTGATGGATTAACCACGA 59 81 1 CCGGCCGGGA 0.965322 -74 GATGGATTAACCACGATCCTCGGTAGGGGAAGATTT 59 101 1 CCCGCCCTAG 0.799645 -54 ** ** ** * *** Masking position 9 Map Score: 22.1429 Number of sites scoring better than the average of aligned sites = 816 Number in coding regions = 781 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 3 AAAAGTTTTTTCGCTGGACTGGAAAATATGCCCCTTCCA 3 18 0 TCCGACGGTT 0.915529 -92 GGCTAGGCTATCCCGGCACAGGATGTATCATATAACTGT 5 50 0 TCCGACGGAC 0.855679 -187 TGGGTTCAAATCCCAGTCCCGGCGTCGGTTAAAGCAACC 5 133 1 TCCGCCGGGT 0.944868 -104 AAGAGTGAATTCGCGGGACGGGGGTTTGCGAATTCTTCA 5 193 0 TCCGACGGTC 0.97156 -44 TGGGCGAGAGGCTGTGCCCAGGGGATGGCCCATGATTCC 9 13 1 GCGGCCGGGC 0.822572 -219 ATCTGGGGTGTCAGCGCCCTGAAGGATTTCCCCTGGAGG 10 145 1 TCGGCCGATT 0.821104 -51 TTCGACAGGATCCCGGCCCAGGTTTTTACAGGCGCATAT 22 153 1 TCCGCCGGTC 0.992828 -148 CTCTGCTGAATCTGAGGCCATGTTTTTTCTCTCTGTGAC 23 55 1 TCGGCCTGTC 0.834969 -145 GTGACAGGTCTCTGTGGCAAGGTTTATATCATTGTAGCA 23 89 1 TCGGCAGGTT 0.894511 -111 ATCTCTGGTTTCAGGGTCCGGATTTTTGCCCTGAAAC 31 42 1 TCGGCCGATC 0.935341 -27 ATAATGTCCATCACTGACCCGGTCGTGGCCACCAAAATT 34 61 0 TCCGCCGGGC 0.947813 -110 ATAATGTCCATCACTGACCTGGGTACTCTGGATAGTCTG 34 128 0 TCCGCCGGTT 0.977738 -43 CGGGTTCAATTCCCGGCCAGGGCGTTTCCTGAGGGCCCG 37 163 1 TCCGCAGGTC 0.97156 -138 CTTATTTATCTCGCGGGACAGATTAATATT 41 2 0 TCCGACGATT 0.591425 -89 GTAGTAAGATTCGGAGGCATGGAGTAATCGATCTGTGAA 46 116 1 TCGGCAGGAC 0.822654 -116 GTGATGATTATCGGCGGCAGGGTGCCTCCAG 54 3 0 TCGGCAGGTC 0.963935 -264 CCTCATCCTCTCGAAGACATGGTCCATCCTTGTGAGGAG 54 130 0 TCAGCAGGTC 0.840333 -137 GTCCCGGCGGTCCATGGACCGGAAACTCCACCCTCGAGG 55 72 0 TCAGACGGTC 0.840333 -123 ** * * ** ** * * Masking position 6 Map Score: 22.7436 Number of sites scoring better than the average of aligned sites = 330 Number in coding regions = 306 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 4 ATGGCTGGGAGGATGGACCAAGCTACCCTACG 7 16 0 GGATGACCAG 0.923268 -156 TTCAAATCTCGGCGGTCCCATCAAATCGAATC 7 114 1 GGCGGCCCAC 0.890318 -58 TTATCCTTTCAGAGGCCCCCGCAACCATCAAG 8 99 0 AGAGGCCCCC 0.662468 -73 ATGGGCGAGAGGCTGTGCCCAGGGGATGGCCC 9 12 1 GGCTGGCCCG 0.77191 -220 TGTGCCCAGGGGATGGCCCATGATTCCGGTTA 9 25 1 GGATGCCCAG 0.979899 -207 ATTATACCTTGAGGGGCCCCGGGTCCCGTGAT 10 45 1 GAGGGCCCCG 0.671932 -151 GCGCCCTGAAGGATTTCCCCTGGAGGGTCAGG 10 158 1 GGATTCCCCG 0.887537 -38 GCTGGGTTGAAGGTGCCCCATGAACCAACCGA 16 115 1 AGGTGCCCAG 0.669268 -92 GCGTCTTACTGGATGATCCGGGATAATTCAGA 17 106 1 GGATGTCCGG 0.877619 -164 GGCTTAAGCCGGAGGACCCACCGTTAAACCTT 21 112 1 GGAGGCCCAC 0.935776 -189 GAATCAAGGGGGGTGATCCCTGCATGAACCTG 22 229 0 GGGTGTCCCG 0.902561 -72 CTGTGTGACAGGATGACCACTGCAGACATGGG 23 11 0 GGATGCCACG 0.839913 -189 GGGATCCCAGGGCGGACCCTGGAATGGATTTG 26 136 0 GGCGGCCCTG 0.802687 -165 CTCATGGATGGGGGGATCCCAGGGCGGACCCT 26 148 0 GGGGGTCCCG 0.919267 -153 CCAGGCGGTGTCCCCTGTGTGGTAGTA 28 11 0 CGGTGCCCCG 0.731083 -17 AAGTTTAAAGGGAGTCACCGGGATGTCC 32 7 0 GGAGTACCGG 0.525837 -294 TTGGCATGGCGGAGGCCCCGGGTTCAAATCCC 32 178 0 GGAGGCCCGG 0.97808 -123 TATATGGGTGGGAGGCCCCACCATACCCTCGC 34 97 1 GGAGGCCCAC 0.941119 -74 CTGGAGGCACCCTGCCGCCGATAA 54 3 1 GGAGGACCCG 0.960061 -264 CTCCTCACAAGGATGGACCATGTCTTCGAGAG 54 130 1 GGATGACCAG 0.923263 -137 GTACTGTCATGGCTGTCCCGGCGGTCCATGGA 55 93 0 GGCTGCCCGC 0.829249 -102 CAGATTTTCGGGATGATCAAGGAGTGTTAAG 56 280 1 GGATGTCAAG 0.394877 -21 GGCTCCTGATGGATTAACCACGATCCTCGGTA 59 94 1 GGATTACCAG 0.547318 -61 ***** **** * Masking position 8 Map Score: 20.4943 Number of sites scoring better than the average of aligned sites = 849 Number in coding regions = 810 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 5 CCAGCGTTCCGGTGCTGACCATCCCCGTTC 7 75 0 GGTGCTGACC 0.619049 -97 GCACCGGAACGCTGGAGACCCGAGTTCAAA 7 90 1 GCTGGAGACC 0.899885 -82 GAAGCCTAAAGGTGGAGGCCTAATGAGGGA 21 77 0 GGTGGAGGCC 0.987675 -224 TGAGGCTTAAGCCGGAGGACCCACCGTTAA 21 109 1 GCCGGAGGAC 0.900919 -192 CCCTGTGGGTTCTGGAGGTCTTTATATCCC 22 89 0 TCTGGAGGTC 0.820638 -212 GCCTTGGCATGGCGGAGGCCCCGGGTTCAA 32 183 0 GGCGGAGGCC 0.955563 -118 TCACTGACCCGGTCGTGGCCACCAAAATTT 34 60 0 GGTCGTGGCC 0.819951 -111 TGACTTTTTATCTGGAGGACTGAATT 37 285 1 TCTGGAGGAC 0.849327 -16 ATTTCCTGGGGGTGTTGGACTTATAATAAG 42 84 0 GGTGTTGGAC 0.691818 -137 AAGGTCACAGGGTGGTGGGCGGCAGATCCT 47 97 1 GGTGGTGGGC 0.925716 -88 ATCTCTGAGAGGTGGTGGTCTATCTCTTCG 54 207 0 GGTGGTGGTC 0.965113 -60 CTCTCAGTAATCTGGAGGTCCTTCAGTTTC 56 31 1 TCTGGAGGTC 0.820638 -270 TCCACCCAGCGGTGCAGGTCTTGTAAGGTA 56 163 1 GGTGCAGGTC 0.879992 -138 CTTTAATATGGGTGGTGAACATAAAATTAC 58 203 1 GGTGGTGAAC 0.850122 -44 CTTCTCCTCCGCTGGAGGACATAACTTTAT 59 54 0 GCTGGAGGAC 0.971323 -101 ********** Masking position 7 Map Score: 13.0181 Number of sites scoring better than the average of aligned sites = 505 Number in coding regions = 475 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 6 TTAAAAAGTTTTTTCGCTGGACTGGAAAATATGC 3 26 0 TTTCGTGCTG 0.778602 -84 CCTGAAATTTTTCGGGTTTATCAGCAAATGCTGA 3 67 1 TTGGGTTCAG 0.780585 -43 GCTGGAGGGGTGCTGGTTTTCCAGGGAACTCTAT 10 113 1 TGTGGTTCAG 0.769823 -83 ATCGCTAATTTTAAGGTTTTTCTGAGCCATCGGT 16 142 0 TTAGGTTCTG 0.961358 -65 GGCCTCCACCTTTAGGCTTCCCTGAGGCTTAAGC 21 87 1 TTAGGTTCTG 0.961358 -214 GAACACAAATTTAAGGGTTCTCAGGGGATATAAA 22 65 1 TTAGGTTCAG 0.938372 -236 CCTGTTCATTTTATGAATGGTCTGCAGTCTGTTC 26 275 0 TTTGATGCTG 0.873489 -26 TTTTTTATTATTGAGGGTGCTCAGCAGACCCTAA 29 26 1 TTAGGTGCAG 0.968975 -110 TAAAAAACAGTTTTGAGTGGACTGGCCGGGATTT 32 151 1 TTTGATGCTG 0.873489 -150 ATAAGGATAGTTCTGGATGGAGTGGACGGTGTCA 41 36 1 TTTGGTGGTG 0.873866 -55 AGATATAGTGTTTAGGATTTCCTGGGGGTGTTGG 42 96 0 TTAGGTTCTG 0.961358 -125 TAATTAAGAGTGGTGGATGGGCTGTGCCATATAA 47 64 1 TGTGGTGCTG 0.918093 -121 CCTTCCTAGTTTGAGGTTTAAGAGATTAAAAGAA 50 74 0 TTAGGTTGAG 0.70149 -102 GGGGGGTGTTTTATGGCTGAACTGAGCATAATCT 52 26 1 TTTGGTGCTG 0.978209 -26 ATGGCAGCTATTAAGGTTGATCAGACTTATATCT 55 33 0 TTAGGTGCAG 0.968975 -162 TATGAAAAACTTCAGAATGAACTGAATTTTAATT 60 73 0 TTAGATGCTG 0.886992 -33 ** *** ** *** Masking position 8 Map Score: 13.7398 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 163 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 7 TCTTCCATGGATGACTGCAGCGA 11 4 0 ATGACTGCAG 0.975285 -61 GTACTTGTGTATGGCTGCATCTGTTAAAGG 11 36 0 ATGGCTGCAT 0.90332 -29 GGAAGGAATAATGGATGCAGATGAGAG 17 8 0 ATGGATGCAG 0.68185 -262 AGTGTGCAGAATGACTGCATGGGATCATAT 21 175 1 ATGACTGCAT 0.91886 -126 AAGGGGGGTGATCCCTGCATGAACCTGAGG 22 226 0 ATCCCTGCAT 0.802679 -75 CCCATGTCTGCAGTGGTCATCCT 23 4 1 ATGTCTGCAG 0.935263 -196 TAAGCCTTATATCACTGCAGCACCATAGAC 23 136 1 ATCACTGCAG 0.961553 -64 TTACAGTTATGGCTGCTGGTATGGCTAT 36 86 0 ATGGCTGCTG 0.790379 -18 TTTTAAGATCAACACTGCAGGATCATTTCA 38 12 1 AACACTGCAG 0.726884 -29 AAATAGATGCCTGCAGGAGGAGTCTG 45 7 1 ATGCCTGCAG 0.956951 -22 ATGATTATCCATCACTGCAGGTGAAACC 47 9 0 ATCACTGCAG 0.961553 -176 AATAGCTGCCATGACTGCCTCGAGGGTGGA 55 55 1 ATGACTGCCT 0.660722 -140 AGCTTATTATATCTCTGCAGATACCATATA 56 79 0 ATCTCTGCAG 0.901532 -222 ********** Masking position 1 Map Score: 13.7958 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 124 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 8 GCGGAAAGTTTAAATATGGATACCATACAATTTT 1 19 1 TAAATAGTCC 0.802623 -152 CCATCAGCGATAAATATTGTTGCCATAGGTTACC 9 185 1 TAAATAGTCC 0.802623 -47 CAGAAATGACTTAATAACGGTGATATGA 13 37 1 TTAATAGTAT 0.879764 -18 CAATTTCAATTTAATAAAGGTGATTTA 18 33 1 TTAATAGTAT 0.879764 -17 ATCCACACGATTAATAAATTTACTGTTTCCCTGA 25 55 1 TTAATATTCT 0.51025 -64 GTCTCTTCCCTTAATAAAGTTTCTCATCTTAAAT 27 34 0 TTAATAGTCT 0.948488 -77 TCAGGAAAAATTAATAATGATTATTAATGATAAA 27 69 0 TTAATAGTAT 0.879759 -42 TTTTTTTATTTTAATAAGGAAACCTGAAAAACTT 32 75 1 TTAATAGACC 0.580615 -226 CGTCGAAGATTTAATAAGGTTAACTTTAAATATT 32 267 0 TTAATAGTAC 0.857339 -34 TTCTGCCCATTTAATAACGGTCCTGTG 35 4 0 TTAATAGTCT 0.948488 -56 TCCCGCGAGATAAATAAGGATAGTTCTGGATGGA 41 23 1 TAAATAGTGT 0.56969 -68 TCCCCGTGTATTAATACTGATCACAGGATTAAAC 42 21 1 TTAATAGTAC 0.857339 -200 ACACTATATCTTAATAGTGCTACTTAAGTGTTTA 42 119 1 TTAATAGTCT 0.948488 -102 ATTGAGGATCTTAATATAGGTCCTCAAAGGATCT 47 120 0 TTAATAGTCT 0.948488 -65 CGCGGCACCTTTAATATGGGTGGTGAACATAAAA 58 195 1 TTAATAGTGT 0.831185 -52 ****** * * ** Masking position 6 Map Score: 11.7129 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 7 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 9 GGAGGACTGGAAGGGGCATATTTTCC 3 7 1 CTGGAAGGGG 0.948607 -103 TCTTCAATGGCTGGGAGGATGGACCAAGCT 7 24 0 CTGGGAGGAT 0.825982 -148 TCAACTGGAACGGGGATGGTCAGCACCGGA 7 68 1 CGGGGATGGT 0.741859 -104 GAATATTCCGCTGGAGGGGTGCTGGTTTTC 10 104 1 CTGGAGGGGT 0.969421 -92 TCCACGAGTGCTTGGAGGGTGAGAAATTAA 16 79 0 CTTGGAGGGT 0.625747 -128 TATCTATTACCGGGGAGGGGTAATAAATTT 22 267 0 CGGGGAGGGG 0.843228 -34 CCCATGTCTGCAGTGGTCATCCTGTCA 23 8 1 CTGCAGTGGT 0.626854 -192 AATGAATATACTGTGGTGGGGGTTTTCAT 25 10 0 CTGTGGTGGG 0.513295 -109 AGGGCGGACCCTGGAATGGATTTGAAGAGG 26 130 0 CTGGAATGGA 0.649204 -171 TCCCTGTGGCCTGGAATGATTTTTTTATTT 32 56 1 CTGGAATGAT 0.552731 -245 AGGATCACCTGGTGTGGAGATAAGAGAA 33 45 0 CTGGTGTGGA 0.531407 -18 TCTGGATAGTCTGCGAGGGTATGGTGGGGC 34 111 0 CTGCGAGGGT 0.84523 -60 GAGACTTGCCCTGGTGGTGTAGGGGCTATC 37 108 1 CTGGTGGTGT 0.575237 -193 TTAGGATTTCCTGGGGGTGTTGGACTTATA 42 89 0 CTGGGGGTGT 0.7866 -132 CCCTTTATCTGGTGTGGTATCTACAGAT 46 9 1 CTGGTGTGGT 0.858022 -223 ATATGAAAATCTGGAAGGGGTACTG 49 28 1 CTGGAAGGGG 0.948607 -15 GGTTAAAACCTGTAAGGGGGGTGTTTTAT 52 10 1 CTGTAAGGGG 0.632407 -42 TCACAGATGACTGGAAGGATCCTTATACTA 54 38 1 CTGGAAGGAT 0.770765 -229 CATATACGTCCTGGTGGGGTACATGCTATC 54 94 0 CTGGTGGGGT 0.942669 -173 ********** Masking position 1 Map Score: 13.2138 Number of sites scoring better than the average of aligned sites = 720 Number in coding regions = 664 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 10 AGCTTCATCACATATAAAGTTTTGCTGCCAA 17 46 0 CATTAAAGTT 0.759029 -224 ATACCGAGAACATATAAAGGTACTCACCCAC 17 178 1 CATTAAAGGT 0.975596 -92 TAAAAGCGTTTATAGGTGTAATCT 19 7 1 CGTTATAGGT 0.830953 -18 TGCATGGGATCATATAATGGTTCACTTCGGG 21 190 1 CATTAATGGT 0.908416 -111 TCCCCATGGACAGTTAAAGGTTGTCCATGAA 34 21 1 CAGTAAAGGT 0.882744 -150 AGGGGTACATCTATAGGTGACGGATATA 43 8 1 CATTATAGGT 0.9593 -38 TGGGCTGTGCCATATAAAGGTCACAGGGTGG 47 81 1 CATTAAAGGT 0.975596 -104 GTTATACTATCATGTATAGGTGGTTGT 51 91 1 CATTATAGGT 0.9593 -17 CCATAAAAAACATATATTGGTCCG 53 65 1 CATTATTGGT 0.853978 -14 TATTTAAACCCTTATAAAGGTGTTATTAATC 58 142 1 CTTTAAAGGT 0.849058 -105 TTTATCAACACATATTAAGGTTTGTGATTTT 60 41 0 CATTTAAGGT 0.835512 -65 *** ******* Masking position 5 Map Score: 8.79907 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 5 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 11 CATTGTGGAAATATTTATAAATAAATCCGGACAGATA 1 137 1 ATTTATAATC 0.663234 -34 CATAATATACAGTTATATGATACATCCTGTGCCGGGA 5 42 1 ATATATATCC 0.782166 -195 TATAAAATAAAAATATATAAAGTTATCGATTGAT 6 8 0 ATATATAATC 0.867354 -51 TTTAAAATTGAGGTATATAATGTTTTCTATAAATTCT 8 44 1 ATATATATTC 0.942496 -128 ATAAATTCTGATCTAAATTAAAGTTTCCTTGATGGTT 8 72 1 ATAAATATTC 0.815059 -100 TACATATCTTACATATATTATCCTTTCAGAGGCCCCC 8 111 0 ATATATATTC 0.942496 -61 ATGGTGGAGTTACATGAATAATTCAGAGTATCCA 22 8 1 ATACATATTC 0.826313 -293 ATTCCGGGTTAAATTTATTACCCCTCCCCGGTAATAG 22 257 1 ATTTATATCC 0.519574 -44 CAGTATATTCATTTACATGATTAATTCAATCCACACG 25 27 1 ATACATATTC 0.826312 -92 TTCCTTATTAAAATAAAAAAATCATTCCAGGCCACAG 32 59 0 ATAAAAATTC 0.384306 -242 CTGAGAAATTATATTACTTCTTCTAACTACAGG 33 7 1 ATATATATTC 0.942496 -56 GTGGCCACCAAAATTTATAAGTATTTCATGGACAACC 34 39 0 ATTTATATTC 0.831552 -132 ATGGGCAGAAATATATATGATGCCATCAAATCTCATC 35 28 1 ATATATAATC 0.867354 -32 GGGGTGTTGGACTTATAATAAGCCTTCTTAGTTGCTG 42 69 0 ATATAAATTC 0.698919 -152 CTGTTATGTGAGATTAATAAAGTGTTCCCGCTGCGTT 42 185 0 ATTAATATTC 0.570331 -36 ATGCAAAAGCATATATATAATCAGATCTAACCATAGA 46 161 1 ATATATAATC 0.867354 -71 CACCACTCTTAATTATATAAGGTGATCCCAACAATAG 47 42 0 ATATATAATC 0.867354 -143 CCTCAATCATATCTAGATAATGAATTCAATTTTCAAC 47 147 1 ATAGATATTC 0.72107 -38 * ***** * *** Masking position 4 Map Score: 9.9551 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 32 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 12 CCTCACCAGCGGAAAGTTTAAATATGGATACCA 1 11 1 GAATTTAAAT 0.919603 -160 CTGCATTGTGGAAATATTTATAAATAAATCCGG 1 134 1 GAATTTATAA 0.766722 -37 ACCGACGGCAGCAATACTTAAATAGATGTCATA 5 13 1 GAACTTAAAT 0.817279 -224 ATCAATCGATAACTTTATATATTTTTATTT 6 8 1 GTATTTATAT 0.710233 -51 TCCTTCTAAAGTAAACTTTAAAATTGAGGTATA 8 28 1 GAATTTAAAA 0.84302 -144 CAACCATCAAGGAAACTTTAATTTAGATCAGAA 8 77 0 GAATTTAATT 0.494623 -95 ATGAAAAATAGAAAAGCTTAAAAAAGAGAAAGG 16 32 0 GAACTTAAAA 0.677417 -175 TAAAATTAGCGATATATTTATATAGGATTATAT 16 163 1 GTATTTATAT 0.710233 -44 TCTGTATCCAGCAAGTTTTATATACCGAGAACA 17 157 1 GAATTTATAT 0.875009 -113 GGTCTCTGTGGCAAGGTTTATATCATTGTAGCA 23 95 1 GAATTTATAT 0.875009 -105 CAGCTCGTTAGTTAGATTTAAATATAATCCGGC 26 30 0 GTATTTAAAT 0.800192 -271 TATACTTGCAGAAGAGTTTAAATGAGTCAATGA 26 225 1 GAGTTTAAAT 0.591934 -76 ATTTAATAAGGTTAACTTTAAATATTAAAAGGC 32 260 0 GTATTTAAAT 0.800192 -41 GGTTGTCCATGAAATACTTATAAATTTTGGTGG 34 39 1 GAACTTATAA 0.56241 -132 ATCTAATTCAGAAAGTTTTAAAATGTGTGTGCA 48 24 0 GAATTTAAAA 0.84302 -59 TAACTTTAGAGAAAAATTTAAATATTGGGTTTT 51 42 1 GAATTTAAAT 0.919603 -66 * ** ******* Masking position 8 Map Score: 8.08732 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 23 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 13 CTATACTGACCGGTGCAGCATCTAAACCCGAA 9 112 0 CGTGCAGATC 0.960924 -120 GCACCTTCAACCCAGCAGTATATCCACGAGTG 16 99 0 CCAGCAGATA 0.725006 -108 CTCTCATCTGCATCCATTATTCCT 17 3 1 CCATCTGATC 0.533549 -267 GGGGGGTGATCCCTGCATGAACCTGAGGAGAA 22 222 0 CCTGCATAAC 0.711431 -79 TCCATGTTCCCTCTGCTGAATCTGAGGCCATG 23 45 1 CCTGCTGATC 0.940734 -155 AGCCTTATATCACTGCAGCACCATAGACTTTA 23 138 1 CCTGCAGACC 0.97796 -62 AGTTTTCTTGCACTGCAGTACCTCTTCAAATC 26 110 1 CCTGCAGACC 0.97796 -191 ATTGAGGGTGCTCAGCAGACCCTAAAGCTCCA 29 35 1 CCAGCAGCCC 0.798009 -101 TTAAGATCAACACTGCAGGATCATTTCATCAT 38 14 1 CCTGCAGATC 0.986081 -27 TATGGCTGAACTGAGCATAATCTAG 52 37 1 CGAGCATATC 0.737915 -15 TCAGTTGTATCTGTTCAGTATCCTCATTATCT 54 233 0 CGTTCAGATC 0.773589 -34 AATTAAGGGGCTCTGCATCATCCTCTCTGTTT 58 48 0 CCTGCATATC 0.939901 -199 * ****** *** Masking position 6 Map Score: 5.80583 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 219 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 14 TCAACTGGAACGGGGATGGTCAGCACCGGA 7 68 1 CGGGGATGGT 0.68017 -104 TCCGCTGGAGGGGTGCTGGTTTTCCAGGGA 10 110 1 GGGTGCTGGT 0.973647 -86 ACCTCCCGTGAGTGCTGGTTGAG 12 5 0 GAGTGCTGGT 0.860116 -19 GAGGCCTAATGAGGGATGGTGAACTTCGTA 21 63 0 GAGGGATGGT 0.768952 -238 TTTGTGTTCAGAGGGCTGTGGTTCCTTGAT 22 44 0 GAGGGCTGTG 0.572617 -257 CCGGAATCAAGGGGGGTGATCCCTGCATGA 22 234 0 GGGGGGTGAT 0.852422 -67 AATAAAAAAAGGGGGCTGGTTTTT 29 5 0 GGGGGCTGGT 0.99143 -131 TATACTTTGTTGGGGCTGGTAGCTCAGGTT 32 224 0 TGGGGCTGGT 0.936047 -77 TTACAGTTATGGCTGCTGGTATGGCTATGA 36 84 0 GGCTGCTGGT 0.782928 -20 TTTTCCACCGGGAGGCTGTTAA 39 11 1 GGAGGCTGTT 0.776936 -12 TAGGATTTCCTGGGGGTGTTGGACTTATAA 42 88 0 TGGGGGTGTT 0.706266 -133 GCCTGCAGGAGGAGTCTGGT 45 19 1 GGAGTCTGGT 0.431891 -10 AAAGGTCACAGGGTGGTGGGCGGCAGATCC 47 96 1 GGGTGGTGGG 0.862739 -89 AAACCTGTAAGGGGGGTGTTTTATGGCTGA 52 16 1 GGGGGGTGTT 0.950009 -36 TATCTCTGAGAGGTGGTGGTCTATCTCTTC 54 208 0 AGGTGGTGGT 0.626856 -59 ********** Masking position 7 Map Score: 8.69111 Number of sites scoring better than the average of aligned sites = 413 Number in coding regions = 371 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 15 CAGTCCAGCGAAAAAACTTTTTAAGGGGAT 3 36 1 AAAAAACTTT 0.558464 -74 ATGCCTCCAAGAAAAACATTAAAATAGAGG 7 152 0 GAAAAACATT 0.669945 -20 CTAACGAGCTGAAAATCTTCCAATCAGATA 26 52 1 GAAAATCTTC 0.867223 -249 ATTTATCATTAATAATCATTATTAATTTTT 27 68 1 AATAATCATT 0.589596 -43 CTTTAAACTTAAAAATCATTGGGCACTTCC 32 29 1 AAAAATCATT 0.790246 -272 ATTAAAATAAAAAAATCATTCCAGGCCACA 32 60 0 AAAAATCATT 0.790246 -241 AAGGAAACCTGAAAAACTTCATTTAATCAG 32 90 1 GAAAAACTTC 0.715939 -211 TGTTCCACTAAAAAATCATTCTGCAGCATA 44 31 1 AAAAATCATT 0.790246 -22 TGCAGTGATGGATAATCATTAACTATTGTT 47 20 1 GATAATCATT 0.669607 -165 CCCTGCCGCCGATAATCATCACAGATGACT 54 20 1 GATAATCATC 0.740764 -247 AATACCTCAAAAAAATCTTCTCATAAATTT 57 38 1 AAAAATCTTC 0.823142 -59 CGCCCCCCTTAAAAATCATCGGCTGATTAA 58 167 0 AAAAATCATC 0.841557 -80 GGAAGAGTAAAAAAATCTTCCCCTACCGAG 59 119 0 AAAAATCTTC 0.823142 -36 GATTTTAACTGATAATCTTTTAAACAATAC 60 17 0 GATAATCTTT 0.640148 -89 TGACTCATATGAAAAACTTCAGAATGAACT 60 84 0 GAAAAACTTC 0.715939 -22 ********** Masking position 5 Map Score: 8.15629 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 39 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357