AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00970_mthe_reg_300.orf -o00970_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: MTH44 27 ribosomal protein Sa (E.coli S2) MTH1680 41 ribosomal protein L10a (E.coli L1) Input sequences: #1 MTH1 170 conserved protein #2 MTH5 22 ribosomal protein L8 (E.coli L2) #3 MTH9 46 ribosomal protein L35 (E.coli L29) #4 MTH21 109 ribosomal protein L19 #5 MTH31 30 ribosomal protein L14 #6 MTH34 236 ribosomal protein S18 (E.coli S13) #7 MTH40 58 DNA-dependent RNA polymerase, subunit N #8 MTH42 171 DNA-dependent RNA polymerase, subunit K #9 MTH43 51 enolase #10 MTH47 21 conserved protein #11 MTH48 73 conserved protein #12 MTH225 300 histidinol dehydrogenase #13 MTH226 93 aspartyl-tRNA synthetase #14 MTH243 231 conserved protein #15 MTH248 195 conserved protein #16 MTH249 64 conserved protein #17 MTH250 23 tRNA intron endonuclease #18 MTH251 54 tryptophanyl-tRNA synthetase #19 MTH587 263 methionyl-tRNA synthetase #20 MTH611 84 prolyl-tRNA synthetase #21 MTH742 34 phenylalanyl-tRNA synthetase #22 MTH744 124 porphobilinogen synthase #23 MTH746 96 endonuclease III related protein (probably non-iron-sulfur homolog) #24 MTH767 83 valyl-tRNA synthetase #25 MTH770 32 phenylalanyl-tRNA synthetase #26 MTH1120 132 nifH / minD related protein #27 MTH1122 39 seryl-tRNA synthetase #28 MTH1375 22 isoleucyl-tRNA synthetase #29 MTH1376 65 conserved protein #30 MTH1449 135 dihydroxy-acid dehydratase #31 MTH1454 160 conserved protein #32 MTH1455 192 threonyl-tRNA synthetase #33 MTH1501 189 phenylalanyl-tRNA synthetase alpha subunit #34 MTH1510 109 NH(3)-dependent NAD+ synthetase #35 MTH1542 37 conserved protein #36 MTH1543 229 thiamine biosynthesis protein #37 MTH1544 219 ribokinase #38 MTH1545 63 conserved protein #39 MTH1675 151 conserved protein #40 MTH1676 235 cell division protein FtsZ #41 MTH1677 120 protein translocation complex sec61 gamma subunit related protein #42 MTH1678 26 transcription termination factor NusG #43 MTH1682 52 ribosomal protein Lp1 #44 MTH1683 89 alanyl-tRNA synthetase #45 MTH1768 26 conserved protein #46 MTH1769 37 translation initiation factor eIF-2, beta subunit #47 MTH1770 30 DNA replication initiator (Cdc21/Cdc54) #48 MTH1850 105 fumarate reductase Motif number 1 AAATAACCAGGAGGATATTCGG 2 3 1 ATACCGGAGG 0.78531 -20 ACTGGGATTTGAACCCAGGAGGAGCAAAGCTC 6 118 0 GACCCGGAGG 0.990191 -119 GCGAATTCACTCTTACTGGAGGTTAATGA 6 218 1 TCTACGGAGG 0.734264 -19 GTCAGCACCGGAACGCTGGAGACCCGAGTTCA 8 86 1 GACGCGGAGA 0.634536 -86 GCCCTAACTTTTTCACTGGAGG 12 289 1 TTCACGGAGG 0.979195 -12 GCGAGAGGCTGTGCCCAGGGGATGGCCCATGA 14 16 1 GTCCCGGGGA 0.662024 -216 TGAGGAATATTATACCTTGAGGGGCCCCGGGT 15 37 1 TAACCTGAGG 0.539211 -159 GGGTCCCGTGATGCCCGGGAGGCCTTCCGTGT 15 65 1 ATCCCGGAGG 0.971906 -131 TATTCCCCAGGAACACGGAAGGCCTCCCGGGC 15 77 0 GACACGAAGG 0.827109 -119 CTGGGGAATATTCCGCTGGAGGGGTGCTGGTT 15 99 1 TTCGCGGAGG 0.942237 -97 TGGGGTGTCAGCGCCCTGAAGGATTTCCCCTG 15 148 1 GCCCCGAAGG 0.87141 -48 CCTGAAGGATTTCCCCTGGAGGGTCAGGGTTT 15 162 1 TTCCCGGAGG 0.989105 -34 CTCAACCAGCACTCACGGGAGGT 17 11 1 ACCACGGAGG 0.901228 -13 AAATATATTTTTCCCTGGAGATAAACACTAA 20 64 0 TTCCCGGAGA 0.896584 -21 GCTTATTTGAGTAAACTGGAGGAGAATTATT 21 14 1 GTAACGGAGG 0.879727 -21 GTTATGTTTTTTACCCTTGAGGATGTAATAAG 22 74 1 TTCCCTGAGG 0.936045 -51 ATTCTCACAGGATCACAGGAGGATTATTT 26 8 0 GACACGGAGG 0.981248 -125 CAGGCCGCAGGCCCTCAGGAGGGATCG 30 6 0 GCCTCGGAGG 0.829995 -130 TCCCGGCCACATCCACCTGAGGGAACTTGCAG 30 97 1 ATCACTGAGG 0.743011 -39 TCACTCGTTATATCCCTGGAGTCCCCTCCCCA 31 136 0 TACCCGGAGT 0.722295 -25 AGGTTCAGGAGATCCCTTAAGGGTCATCATCT 32 76 1 GACCCTAAGG 0.598011 -117 ATTCGATAATGATCACTGGGGGTTCTGT 33 172 1 GACACGGGGG 0.88915 -18 CGATGATTAATTTTACAGGAGGAGTATA 34 7 0 TTTACGGAGG 0.832658 -103 GTTTGACCCTTAACCCGTGAGGGTATGATCTG 36 193 0 TACCCTGAGG 0.917137 -37 ATTTACACACTTTTACTGGAGGTATCAGTT 46 18 1 TTTACGGAGG 0.832658 -20 ** *** ***** Masking position 6 Map Score: 32.5035 Number of sites scoring better than the average of aligned sites = 1122 Number in coding regions = 1065 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 2 TAAATCACCTCAGTAACTTTT 5 20 0 AAATCACCTC 0.803511 -11 TAAAAATTTTCCATCACCCTATAAATTCCT 11 41 0 CCATCACCCT 0.965732 -33 TCAAATCACCTCTAACAGTTTA 13 82 0 AAATCACCTC 0.803511 -12 GAATCATGGGCCATCCCCTGGGCACAGCCT 14 21 0 CCATCCCCTG 0.799763 -211 AGTTATCAGTTTATCACCCCGGCATTACAG 14 70 1 TTATCACCCC 0.641126 -162 CCCTGGAAAACCAGCACCCCTCCAGCGGAA 15 109 0 CCAGCACCCC 0.791807 -87 TCGAAGTGTTCCATCACATCGAACCGCAGT 19 45 1 CCATCACATC 0.658693 -219 CTTATTTATATCATCACCCCAAAACCATAA 29 37 1 TCATCACCCC 0.9693 -29 TTTCTCGAAGTCATCATCTGTCAGGCCGCA 30 29 0 TCATCATCTG 0.709836 -107 CCCTTAAGGGTCATCATCTGAACATTACTA 32 89 1 TCATCATCTG 0.709836 -104 TATTTAAAAACCCTCACCTTAAAAACAATA 32 144 1 CCCTCACCTT 0.766704 -49 GCCATCACCTTGGTAAGAATA 32 182 0 CCATCACCTT 0.971733 -11 CGGTTATGGTTCATCACCTTAACTATTGAC 33 32 0 TCATCACCTT 0.964643 -158 GGGTGATGGTTCATCACCTGAGCTTGACTT 33 68 0 TCATCACCTG 0.970724 -122 AGGTGATGAACCATCACCCGGTCCTCTACG 33 79 1 CCATCACCCG 0.971632 -111 TTAAATCCATACATCACCCTCAGATTAGAA 33 113 0 ACATCACCCT 0.927307 -77 GTAATCACCCTTCTGGTTTGA 36 219 0 TAATCACCCT 0.806337 -11 CATTTTATAAAAATCACCTTAATCCGCCTC 37 73 1 AAATCACCTT 0.743379 -147 ATGATCACCTGAAAAATATGG 37 209 0 TGATCACCTG 0.836531 -11 AACATCACCTTCTGTTTGAGT 39 2 1 ACATCACCTT 0.939616 -150 ATGATCACCTCAAATTTTATT 43 42 0 TGATCACCTC 0.855992 -11 ********** Masking position 5 Map Score: 23.0976 Number of sites scoring better than the average of aligned sites = 497 Number in coding regions = 452 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 3 TGGAAATATTTATAAATAAATCCGGACAGATATTAATAG 1 142 1 TATAAACAAA 0.942123 -29 TATTCACTGATATGAATCTGTCCATATATA 3 1 0 TATGAACAAA 0.922734 -46 CTCCTTGAATCATGAACCAGATCAGAATAAGACGGGTCGA 19 225 0 CATGAACATA 0.839022 -39 GATCACAGAACATAAAAAGCAGCACAATCAGTAAACCAGC 23 54 0 CATAAACATA 0.876512 -43 AGACAATATTTATTAATGGTTACCGAGATACTCATTTCAT 26 44 0 TATTAACAAA 0.852664 -89 ACTATTTCAGTATAAAATGTAACAGATAGATGGGGAGGGG 31 106 1 TATAAACAAA 0.942123 -55 TTGATAGTTATATAAAATATACCCTACTTACTTTTAACCA 34 80 1 TATAAACATA 0.927436 -30 AATATATTAATCTTCTCTAAAAAAAGGAGTGGGT 35 14 0 TATTAACAAA 0.852667 -24 TCCTTAAGAGTATTAACGGGGACTGAAACAGTAGTTTTTA 36 100 1 TATTAACAAA 0.852667 -130 GCATGAAAACCCGCTGAAAAACCATTTATGG 37 2 1 CATGAACAAA 0.869076 -218 GACCACATTTTATAAAAATCACCTTAATCCGCCTCAAAGT 37 68 1 TATAAACATC 0.618448 -152 CGCCTCAAAGTATAAAGTCCCACCCAATAAAGGATGCTCA 37 97 1 TATAAACATA 0.927437 -123 CCAATCACATTATAAACCAACCCCAACAGAATTAACCCCA 37 172 1 TATAAACAAA 0.942123 -48 CTATACCTGCCATAAATATATCCAAATATAATTTGAGATC 39 95 1 CATAAACAAA 0.900398 -57 AAACAGTTTTTATAAATAGAATCAGAATTAAGAAAAATAA 44 57 0 TATAAACATA 0.927437 -33 GCTGACTCATATGAAAAACTTCAGAATGAACTGAATTTT 48 77 0 TATGAACATA 0.903709 -29 ****** * * * * Masking position 6 Map Score: 17.8507 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 16 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 4 GGAGGACTGGAAGGGGCATATTTTCCAG 4 9 1 GGAAGGGGCA 0.807937 -101 TTAATTTGGATTAGGGGGCATCTAATGGAC 12 67 0 TTAGGGGGCA 0.955619 -234 TTTTAAGAATTTAGGGGGCACACCGGATCA 12 231 0 TTAGGGGGCA 0.955619 -70 ATATTATACCTTGAGGGGCCCCGGGTCCCG 15 43 1 TTGAGGGGCC 0.980377 -153 GGATTTCCCCTGGAGGGTCAGGGTTTGAGA 15 168 1 TGGAGGGTCA 0.958371 -28 TTCGATACCTTTATGGGTCAACCGGTATAA 19 20 0 TTATGGGTCA 0.720505 -244 GTGGTGTTCATGAAGGGCCCCGGAATTTAT 22 27 1 TGAAGGGCCC 0.876297 -98 AGGAGATCCCTTAAGGGTCATCATCTGAAC 32 82 1 TTAAGGGTCA 0.942372 -111 TGTCAGAGTCTGGGGGGGCCCCA 36 4 0 TGGGGGGGCC 0.97668 -226 TCTCCCCTAGTTGAGGGGCCACGGCTTGCT 36 60 0 TTGAGGGGCC 0.980377 -170 CCCTCACGGGTTAAGGGTCAAACCAGAAGG 36 202 1 TTAAGGGTCA 0.942372 -28 CATGTCATGATGGGGGGTCCCGCCCAGATT 40 22 1 TGGGGGGTCC 0.96319 -214 AATAAAATTATTGATGGTCCACGTGGCCAT 40 62 0 TTGATGGTCC 0.672771 -174 ********** Masking position 9 Map Score: 15.0493 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 238 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 5 TGGATACCATACAATTTTTAGTACCTATTG 1 35 1 ACAATTTTTA 0.907691 -136 CTGCATTGTGGAAATATTTATAAATAAATC 1 134 1 GAAATATTTA 0.831073 -37 ACCGACGGCAGCAATACTTAAATAGATGTC 6 13 1 GCAATACTTA 0.747034 -224 AGGGTGATGGAAAATTTTTAAGGGCGTTAA 11 51 1 AAAATTTTTA 0.7602 -23 CTAATGGACCAAAATTTTTAAATAATAAGT 12 46 0 AAAATTTTTA 0.7602 -255 ACTACCATTTGCAATTTTTATATTAATCTG 12 107 0 GCAATTTTTA 0.919294 -194 CATGGTACTTACAATATTTATTTACCATCA 14 161 1 ACAATATTTA 0.931102 -71 ACCTATGGCAACAATATTTATCGCTGATGG 14 185 0 ACAATATTTA 0.931102 -47 GCTGTCCAAGACAATATTTATTAATGGTTA 26 62 0 ACAATATTTA 0.931102 -71 ATCCACCGGAGCAATATTTAAAAACCCTCA 32 130 1 GCAATATTTA 0.939943 -63 AGGTATAGGAAAAATTTTTATAAAGGTAGT 39 73 0 AAAATTTTTA 0.7602 -79 CACTTTACTGGCAATAGTTAACCCATAAAA 43 12 1 GCAATAGTTA 0.747034 -41 ********** Masking position 4 Map Score: 10.5518 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 9 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 ACTCTAATAAACCACTATTTTTCAGTCTAGAG 9 11 1 ACCTATTTTT 0.795505 -41 CATCTAATGGACCAAAATTTTTAAATAATAAG 12 47 0 ACCAATTTTT 0.555339 -254 TAACCATTCGCCCTAACTTTTTCACTGGAGG 12 280 1 CCCACTTTTT 0.909571 -21 CATGAAGGGCCCCGGAATTTATTTTCTGCGCG 22 35 1 CCCAATTTAT 0.838133 -90 GAACTTGCTTCCCCTTATTTCTCCTACAAGGT 24 28 1 CCCTATTTCT 0.970854 -56 TACCCAATCTTTATAAAGATGTTT 24 70 0 CCCTCTTTAT 0.942643 -14 GGAGTCCCCTCCCCATCTATCTGTTACATTTT 31 119 0 CCCTCTATCT 0.87394 -42 ACCACCCACTCCTTTTTTTAGAGAAG 35 5 1 CCCTCCTTTT 0.908241 -33 CAGAACCAGGCCCAATCCATCTATAACGAATA 37 138 1 CCCTCCATCT 0.686544 -82 ACAGAATTAACCCCATATTTTTCAGGTGATCA 37 197 1 CCCTATTTTT 0.9685 -23 TAATATGGATCCCGTTATTTCTGACTCAAACA 39 23 0 CCCTATTTCT 0.970854 -129 GGTTTATCCCCGCTATTTATATAGTTAAAA 41 101 0 CCCTATTTAT 0.941617 -20 ATCCCCCTTTATTTTTTTCCTCTGCC 44 5 1 CCCTATTTTT 0.9685 -85 *** ******* Masking position 10 Map Score: 10.0917 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 55 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 7 TGAGCGGATCCACCGCAGATTGCAATAGGTA 1 56 0 CACCCAGATT 0.963142 -115 TGCGGTGGATCCGCTCACATTGTATGCTCTG 1 70 1 CCGCCACATT 0.864523 -101 ATAAATAAATCCGGACAGATATTAATAG 1 153 1 CCGGCAGATA 0.669151 -18 TTTGATGGGACCGCCGAGATTTGAACTCGGG 8 108 0 CCGCGAGATT 0.92153 -64 ATTAAGGAATGACCACAGATTAATATAAAAA 12 92 1 GACCCAGATT 0.702163 -209 GCATCTAAACCCGAAGAGATTCTTTGCCTGT 14 96 0 CCGAGAGATT 0.680419 -136 AGGGCGCTGACACCCCAGATAGAGTTCCCTG 15 134 0 CACCCAGATA 0.87541 -62 AATCATGAACCAGATCAGAATAAGACGGGTC 19 227 0 CAGACAGAAT 0.692866 -37 TAACCATGTCCCGCGCAGAAAATAAATTCCG 22 47 0 CCGCCAGAAA 0.888275 -78 CCATTTCAATCAGCACAGAATGTACCTCATT 32 41 1 CAGCCAGAAT 0.925613 -152 TCCATACATCACCCTCAGATTAGAACGTCCG 33 107 0 ACCCCAGATT 0.790784 -83 TGGGGCCCCCCCAGACTCTGACAAACA 36 7 1 CCCCCAGACT 0.92122 -223 ATAAACCAACCCCAACAGAATTAACCCCATA 37 183 1 CCCACAGAAT 0.824749 -37 ATGGGGGGTCCCGCCCAGATTCATGATATTC 40 31 1 CCGCCAGATT 0.986059 -205 ATGATCACCTCAAATTTTATTTTTTA 43 37 0 CACCCAAATT 0.613997 -16 **** ****** Masking position 7 Map Score: 7.71519 Number of sites scoring better than the average of aligned sites = 274 Number in coding regions = 238 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 CTCCTGGGTTCAAATCCCAGTCCCGGCGTCGGTT 6 129 1 CAATCCGCCC 0.936757 -108 GAAGAATTCGCAAACCCCCGTCCCGCGAATTCAC 6 194 1 CAACCCGCCC 0.985315 -43 TAGCTTGGTCCATCCTCCCAGCCATTGAAGAAGT 8 23 1 CACCTCACCA 0.880233 -149 CGGAACGCTGGAGACCCGAGTTCAAATCTCGGCG 8 94 1 GAACCCGTCA 0.672057 -78 CCCCTGGGCACAGCCTCTCGCCCATA 14 3 0 CACCTCGCCA 0.971359 -229 CTGACCGGTGCAGCATCTAAACCCGAAGAGATTC 14 105 0 CACATCACCC 0.719693 -127 ATACCTTGAGGGGCCCCGGGTCCCGTGATGCCCG 15 48 1 GGCCCCGCCC 0.470367 -148 AAAATTATCTCAAACCCTGACCCTCCAGGGGAAA 15 171 0 CAACCCACCT 0.768827 -25 AGGGAAACCACAACCTCAAGGCCAGATCAGCATG 19 81 0 CACCTCGCCA 0.971359 -183 GGGTAAAAAACATAACCATGTCCCGCGCAGAAAA 22 56 0 CAAACCGCCC 0.950708 -69 CCGCCATCCTCATGATCACAGAACATAA 23 79 0 CACCTCGTCA 0.839135 -18 GGTGATGAACCATCACCCGGTCCTCTACGGACGT 33 80 1 CACACCGCCT 0.847529 -110 GGATGCTCAACAGAACCAGGCCCAATCCATCTAT 37 128 1 CAAACCGCCA 0.940722 -92 TCAACCGGACCATATTCCAGGCCCTTTACC 38 7 0 CAATTCGCCC 0.878364 -57 CCAGATTCATGATATTCATGGCCACGTGGACCAT 40 45 1 GAATTCGCCA 0.589661 -191 TATTCTTCCACACACCCCCACTCAAGGAAAACCT 41 11 1 CAACCCATCA 0.647907 -110 ** **** * *** Masking position 7 Map Score: 11.1261 Number of sites scoring better than the average of aligned sites = 698 Number in coding regions = 656 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 9 AAATAACCAGGAGGATATTCGG 2 9 1 AGGAGGATAT 0.892255 -14 GCTGAATACAAGGAGGTTTCTTGA 4 96 1 AGGAGGTTTT 0.948156 -14 TCACTCTTACTGGAGGTTAATGA 6 224 1 TGGAGGTTAT 0.789463 -13 AGAGTTTATTATGAGGTGTTTTA 9 39 1 ATGAGGTGTT 0.789213 -13 TCATGATTCAAGGAGGAGTTTGAG 19 250 1 AGGAGGAGTT 0.977198 -14 TTGAGTAAACTGGAGGAGAATTATT 21 20 1 TGGAGGAGAT 0.89782 -15 ACAGGATCACAGGAGGATTATTT 26 3 0 AGGAGGATTT 0.948156 -130 TTAATTTTACAGGAGGAGTATA 34 2 0 AGGAGGAGTT 0.977198 -108 ATATATAAGTAGGTGGTGTTTTC 39 139 1 AGGTGGTGTT 0.871063 -13 TTTCCTTGAGTGGGGGTGTGTGGAAGAATA 41 10 0 TGGGGGTGTT 0.819294 -111 ********* * Masking position 11 Map Score: 6.69126 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 223 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 10 AATTATTAAATGATCCGGTGTGCCCCCTAA 12 221 1 TGATCCGGTG 0.984144 -80 GAGGGGCCCCGGGTCCCGTGATGCCCGGGA 15 55 1 GGGTCCCGTG 0.84626 -141 CGTCTTATTCTGATCTGGTTCATGATTCAA 19 231 1 TGATCTGGTT 0.772745 -33 AATCCTCCTGTGATCCTGTGAGAATAACTA 26 15 1 TGATCCTGTG 0.944232 -118 ACTACATATATGATCCGGAG 31 1 0 TGATCCGGAG 0.96564 -160 TTTTAAATATTGCTCCGGTGGATCTTTAAA 32 123 0 TGCTCCGGTG 0.942809 -70 ATCAGGCGACTGATCCTGATTGAAGGCTTA 33 140 0 TGATCCTGAT 0.82781 -50 TCATTTCCGCTGATCCAGATCATACCCTCA 36 178 1 TGATCCAGAT 0.731641 -52 GCCTGGAATATGGTCCGGTTGATTATGAAA 38 19 1 TGGTCCGGTT 0.950061 -45 TAATTAATATGGATCCCGTTATTTCTGACT 39 29 0 GGATCCCGTT 0.875955 -123 ********** Masking position 4 Map Score: 4.89947 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 82 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 11 AAATAACCAGGAGGATATTCGG 2 9 1 AGGAGGATAT 0.791555 -14 ATTTGAACCCAGGAGGAGCAAAGCTCCACA 6 114 0 AGGAGGAGCA 0.955571 -123 TCATGATTCAAGGAGGAGTTTGAG 19 250 1 AGGAGGAGTT 0.948948 -14 GTATATTTTAAGTAGGAGTAATAAAATAAT 20 28 1 AGTAGGAGTA 0.920525 -57 TTGAGTAAACTGGAGGAGAATTATT 21 20 1 TGGAGGAGAA 0.920551 -15 ACTCTAACCTTGTAGGAGAAATAAGGGGAA 24 36 0 TGTAGGAGAA 0.695269 -48 ACAGGATCACAGGAGGATTATTT 26 4 0 AGGAGGATTA 0.950685 -129 TTAATTTTACAGGAGGAGTATA 34 3 0 AGGAGGAGTA 0.983283 -107 TTATACTTTGAGGCGGATTAAGGTGATTTT 37 82 0 AGGCGGATTA 0.81832 -138 ********** Masking position 7 Map Score: 5.60072 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 204 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 12 TTGGAATTCATCCCATGGATATGACTACCA 12 130 0 TCCCATGGAT 0.907444 -171 GTCACACTCTCCCCTGGATTATAGGTAAC 14 213 0 TCCCCTGGAT 0.985753 -19 AGCGGAATATTCCCCAGGAACACGGAAGGC 15 86 0 TCCCCAGGAA 0.816226 -110 CCAGATAGAGTTCCCTGGAAAACCAGCACC 15 121 0 TTCCCTGGAA 0.84569 -75 CTGAAGGATTTCCCCTGGAGGGTCAGGGTT 15 163 1 TCCCCTGGAG 0.986019 -33 TAAAGGGGTCTTCCATGGATGACTGCAGCG 16 12 0 TTCCATGGAT 0.657079 -53 AGGTTGTGGTTTCCCTGAATCCAGTACCTC 19 99 1 TTCCCTGAAT 0.867863 -165 AAATATATTTTTCCCTGGAGATAAACACTA 20 65 0 TTCCCTGGAG 0.97959 -20 CACTCGTTATATCCCTGGAGTCCCCTCCCC 31 137 0 ATCCCTGGAG 0.891316 -24 ATGGGATCAGTTCCCTGCATGAAATTTGAG 37 38 1 TTCCCTGCAT 0.906724 -182 ********** Masking position 9 Map Score: 11.9582 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 142 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 13 CAAATCTCGGCGGTCCCATCAAATCGAATCCA 8 116 1 CGGTCCATCA 0.882582 -56 TAAAAGGGAATGGCTCCATAAAACTAACCATT 12 256 1 TGGCTCATAA 0.803547 -45 CAGATTAATCTGCCTTCATCAA 13 1 0 TGCCTCATCA 0.841821 -93 TGATAATGCATGGTTTCATCAGAGACCTTAAA 13 41 1 TGGTTCATCG 0.959988 -53 CCCATGATTCCGGTTACATGTGTTTTTCCAGT 14 41 1 CGGTTCATGG 0.766172 -191 TACTTGTGTATGGCTGCATCTGTTAAAGGGGT 16 33 0 TGGCTCATCG 0.97849 -32 ACATAGTTCCCGGCCACATCCACCTGAGGGAA 30 90 1 CGGCCCATCA 0.936543 -46 TCATATTGATTGGTTCCATCCAGTTATAAAAA 36 134 0 TGGTTCATCA 0.948217 -96 ATGTGAGCCATGGCTCCATCGGTGCCAGATTA 40 150 1 TGGCTCATCG 0.979219 -86 ***** **** * Masking position 8 Map Score: 2.99358 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 140 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 14 AACTTTATATATTTTTATTTTATAAACTAA 7 21 1 ATTTTTATTT 0.752384 -38 AGTAATATAAACATTTATTTATATGCTTTC 12 180 0 ACATTTATTT 0.785433 -121 GGTACTTACAATATTTATTTACCATCAGCG 14 164 1 ATATTTATTT 0.752058 -68 ACTTCTATATAAATTTATTTGAGTCCATGT 19 160 0 AAATTTATTT 0.802263 -104 CTCCAGGGAAAAATATATTT 20 75 1 AAATATATTT 0.449909 -10 TTACTGTGTAACTTTTAATTAATATATCAT 23 15 1 ACTTTTAATT 0.676788 -82 ATATAAGGATACATATAATTAGCAGGG 26 116 1 ACATATAATT 0.448156 -17 GCAGTAAATTATATATAATTTTTGTCACTA 31 80 1 ATATATAATT 0.403688 -81 CCTGATCTCAAATTATATTTGGATATATTT 39 108 0 AATTATATTT 0.474789 -44 GACCATCAATAATTTTATTTTGCCCCAACC 40 73 1 AATTTTATTT 0.81669 -163 ACAGAAATTGATTTTTAATTTTGAATGTGA 40 126 1 ATTTTTAATT 0.634281 -110 GATCACCTCAAATTTTATTTTTTATGGGTT 43 31 0 AATTTTATTT 0.81669 -22 TAATGGCAAAAAATTTATTTTTCTTAATTC 44 43 1 AAATTTATTT 0.802263 -47 GAATGAACTGAATTTTAATTGTTTATCAAC 48 63 0 AATTTTAATT 0.727841 -43 ********** Masking position 7 Map Score: 5.30163 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 26 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 15 CCTCACCAGCGGAAAGTTTAAATATGG 1 6 1 CCAGCGAAGT 0.887392 -165 GGCATATTTTCCAGTCCAGCGAAAAAACTTTT 4 25 1 CCAGTCAGGA 0.859205 -85 CTAGGCTATCCCGGCACAGGATGTATCATATA 6 55 0 CCGGCCAGAT 0.945616 -182 CATCCCCGTTCCAGTTGAAAAGTCCGGAAACT 8 54 0 CCAGTGAAAG 0.516167 -118 TCTATACTGACCGGTGCAGCATCTAAACCCGA 14 113 0 CCGGTCAGAT 0.926391 -119 TACCTATAATCCAGGGGAGAGTGTGAC 14 215 1 CCAGGGAGGT 0.850173 -17 CAGCACCCCTCCAGCGGAATATTCCCCAGGAA 15 96 0 CCAGCGAAAT 0.845926 -100 AACCTCAAGGCCAGATCAGCATGCCCAAAACT 19 72 0 CCAGACAGAT 0.917322 -192 GAATCATGAACCAGATCAGAATAAGACGGGTC 19 227 0 CCAGACAGAT 0.917322 -37 AAAATATACTCCATTAGAGGGTTAAC 20 5 0 CCATTGAGGT 0.665692 -80 TATCCAGCTGAGGGAGAAACAC 28 4 1 CCAGCGAGGA 0.836672 -19 GTATATACATCCAGTTCAGGAGAAATT 29 6 0 CCAGTCAGAG 0.86804 -60 TCCATTTCAATCAGCACAGAATGTACCTCATT 32 40 1 TCAGCCAGAT 0.62671 -153 TAAAGATCCACCGGAGCAATATTTAAAAACCC 32 125 1 CCGGACAAAT 0.603404 -68 TCTGAAAATACCGGCTCAAGGTTGGGGCAAAA 40 90 0 CCGGCCAAGT 0.869503 -146 TTAACTATTGCCAGTAAAGTGT 43 1 0 CCAGTAAGGT 0.734825 -52 AAATTTTTTGCCATTACAGAGTGGCAGAGGAA 44 27 0 CCATTCAGGT 0.766246 -63 ***** *** ** Masking position 8 Map Score: 7.72484 Number of sites scoring better than the average of aligned sites = 535 Number in coding regions = 497 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822