AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -iaraC_bsub_opreg_300.orf -g0.435 -x5 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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 ydjK 300 similar to sugar transporter #2 glvA 300 6-phospho-alpha-glucosidase #3 yfiA 64 similar to hypothetical proteins #4 yfiB 105 similar to ABC transporter (ATP-binding protein) #5 yfiD 154 similar to hypothetical proteins #6 yfiF 93 similar to transcriptional regulator (AraC/XylS family) #7 yfiG 174 similar to metabolite transport protein #8 yfhG 88 yfhG #9 yfhI 142 similar to antibiotic resistance protein #10 yncC 300 similar to metabolite transport protein #11 araA 207 L-arabinose isomerase #12 abnA 196 arabinan-endo 1,5-alpha-L-arabinase #13 ysdC 183 similar to endo-1,4-beta-glucanase #14 ytbD 183 similar to antibiotic resistance protein #15 yufN 300 similar to ABC transporter (lipoprotein) #16 yufO 75 similar to ABC transporter (ATP-binding protein) #17 araE 137 permease #18 ywtG 300 similar to metabolite transport protein #19 rbsR 300 transcriptional regulator (LacI family) #20 iolR 300 transcriptional regulator (DeoR family) #21 iolS 53 alternate gene name: yxbF; myo-inositol catabolism #22 yxcE 261 yxcE #23 yxcC 238 similar to metabolite transport protein Motif number 1 GATCCCCCCATTTTCTTTCTATTATATACA 3 41 0 TTTTCTTTCT 0.780971 -24 TTTATAGTACTTTTATTTCATTTTCGTAAA 5 48 1 TTTTATTTCA 0.913443 -107 CAGGGGGATTTTTTATTTTTGTCCGCCTTG 6 37 1 TTTTATTTTT 0.841306 -57 CTGAAACGCGTTTTCTTTTATTACAATGAG 8 49 0 TTTTCTTTTA 0.913381 -40 TTCAATGATTTTTTCTTTAAGAATTCGTGT 9 60 0 TTTTCTTTAA 0.739268 -83 ACTGTCAATCTTTTCTTTTAAAAAAAGCCG 11 62 0 TTTTCTTTTA 0.913381 -146 GTACGAACAATTTTATTATAGTAATTGACT 11 97 0 TTTTATTATA 0.762058 -111 TTTGAAAGCGTTTTATTTTATGAGAAAGGG 11 179 1 TTTTATTTTA 0.927865 -29 GTTCAACCTCCTTTATTTTAGAAAGCGCTT 12 173 0 CTTTATTTTA 0.894573 -24 GTTTTTACAGCTTTCTTTTAGAAAAAGTGA 13 74 0 CTTTCTTTTA 0.874309 -110 AAGTACGTACTTTTATTTCTTAACGATATG 14 58 1 TTTTATTTCT 0.813065 -126 ATCTGCTCTTTTTTATTTATATAGCTTACT 14 118 1 TTTTATTTAT 0.587713 -66 TATCCCTTGTTTTTCTTTTATTTTGAAATA 16 40 1 TTTTCTTTTA 0.913381 -36 TTGACCGCTCCTTTATTTCAAAATAAAAGA 16 53 0 CTTTATTTCA 0.874396 -23 CATTAAACCTTTTTATTTTTCTGATCATAA 18 199 0 TTTTATTTTT 0.841306 -102 AAATATTAAGTTTTATTAAAATTGTTTCAA 19 101 0 TTTTATTAAA 0.462621 -200 TTTTCATTATTTTTATTATATTAATCTTTT 20 138 1 TTTTATTATA 0.762058 -163 AACTTTTGGTTTTTATTATATATTTATGTT 20 252 1 TTTTATTATA 0.762058 -49 GATAAACTACCTTTATTTTATCGGATTTAT 22 105 0 CTTTATTTTA 0.894573 -157 TTCTCAATCACTTTCTTTCTGAGATAAACT 22 127 0 CTTTCTTTCT 0.70168 -135 GCTGGGTCAGCTTTATTTCATATGAGCTAG 22 184 0 CTTTATTTCA 0.874396 -78 ********** Masking position 6 Map Score: 23.0092 Number of sites scoring better than the average of aligned sites = 855 Number in coding regions = 592 Number in noncoding regions = 263 Number of orfs with sites within 600 bp upstream = 283 Fraction of orfs with sites within 600 bp upstream = 0.0454545 Motif number 2 TCAATCCCTATGGAAGCGATTTCATTTCTCGTT 1 130 0 TGAACGTTTC 0.992579 -171 TAAATGGAATTGTAAACGTTATCAAGGAGGTCG 2 274 1 TGAACGTATC 0.949545 -27 TACCCCTTGTTGTAACCGCTTTCTAAAAAGATT 7 76 0 TGAACGTTTC 0.992579 -99 CCTCTGGATTTGTAACCGTTTACATTTTTAACC 10 193 0 TGAACGTTAC 0.973807 -108 CTTTTGTATTTGAAAGCGTTTTATTTTATGAGA 11 171 1 TGAACGTTTA 0.958537 -37 TAATCTAATTTGTAAGCGCTTTCTAAAATAAAG 12 160 1 TGAACGTTTC 0.992579 -37 TTAGAAAAAGTGAAACCTTTTTCTATGCTTTTC 13 54 0 TGAACTTTTC 0.92116 -130 CGGAAAACCGTGACATCGTTTTCTGAAGTAAGA 15 45 0 TGCACGTTTC 0.96539 -256 AAGGTTTAAATGAAAACGCTTTACTCAACATTC 17 101 1 TGAACGTTTA 0.958542 -37 TCCTTGTTTATGTAACCGTTTACATAGATAGAT 19 269 0 TGAACGTTAC 0.973807 -32 ** ** ** **** Masking position 5 Map Score: 18.1776 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 19 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 3 TTAAGATTACAAAAAAGGTAAAAAAACCAAAT 2 130 1 AAAAAAGGAA 0.469047 -171 TAAACGTTATCAAGGAGGTCGTCAT 2 286 1 CAAGGAGGGT 0.934626 -15 ACCCTCCCGAAAAGGAGGGCAGTCT 4 4 0 AAAGGAGGAG 0.905544 -102 TAACATTTATCAAGGAGGATAAA 5 142 1 CAAGGAGGAA 0.984398 -13 CTCATCATAACAAGGCGGACAAAAATAAAAAA 6 45 0 CAAGGCGGAA 0.932537 -49 GCCATTCTTGAAAGAAGGGGAAGAAAGCC 7 156 1 AAAGAAGGAA 0.860706 -19 TCTTTTATTACAATGAGGTAAAGTATATTTAT 8 34 0 CAATGAGGAA 0.781187 -55 AGCGTAACAGGAGGCTGATGATCAGCCT 9 7 1 ACAGGAGGGA 0.89177 -136 GCTGCAAACAAAAAGAGGCTGATCATCAGCCT 9 22 0 AAAAGAGGGA 0.90822 -121 TTTTAAAATCAAAGGAGGCGATGACG 9 127 1 AAAGGAGGAT 0.942343 -16 ATTTGACAGGAAGGGAGGATAAATAATCTAAT 12 137 1 AAGGGAGGAA 0.887961 -60 TTTCTAAAATAAAGGAGGTTGAACAAAA 12 179 1 AAAGGAGGGA 0.985758 -18 CACATCTTACAAAGGAGGAACATC 14 170 1 AAAGGAGGCA 0.960766 -14 ATTTCCTTCGAAAGGCGGGGAAGAGAAGGATG 15 94 0 AAAGGCGGAA 0.939319 -207 ATCGCAGGGATAAGGAGGTCGAGCCCTTATCC 16 13 1 TAAGGAGGGA 0.889099 -63 AATGGCCGGAAAAAGAGGCTAAAAGATTTCTA 18 225 1 AAAAGAGGAA 0.909925 -76 GTTACATAAACAAGGAGGAGCTGTT 19 286 1 CAAGGAGGCT 0.834931 -15 CCATTTTATTCTAGGAGGCAGATC 21 40 1 CTAGGAGGGA 0.832336 -14 ******** ** Masking position 7 Map Score: 18.545 Number of sites scoring better than the average of aligned sites = 505 Number in coding regions = 257 Number in noncoding regions = 248 Number of orfs with sites within 600 bp upstream = 291 Fraction of orfs with sites within 600 bp upstream = 0.0467395 Motif number 4 ATCAGATATAACAAAAATGTCACTATAACATCACTAC 1 20 1 AAAAATACAA 0.948615 -281 GAGGTTATGCACAAAGAAATGACCATTGTTCTTTTAA 1 95 1 AAAGATACAT 0.741001 -206 AGGTTATTGGATAAAAACATGAACAACTATTTTCTGA 1 189 1 AAAAATAAAC 0.569549 -112 TTTAAGATTACAAAAAAGGTAAAAAAACCAAATCTCT 2 129 1 CAAAATAAAA 0.534948 -172 TAAAAGTACTATAAAACTGTAACAAAAAAAGACCTCT 5 26 0 AAAACTACAA 0.904597 -129 ATTTCATTTTCGTAAAATGTAACAAAATTACTTGACG 5 62 1 CAAAATACAA 0.811623 -93 TAATCTTTTTAGAAAGCGGTTACAACAAGGGGTATTG 7 75 1 AAAGCTACAA 0.89437 -100 CAACGAGATGATCAAAACATCACCATCACATAGCGGA 10 30 1 AAAAATACAC 0.8321 -271 CAATAATGTGACAAAGACATTACTACAACATAACAAC 10 133 1 AAAGATACAA 0.942808 -168 CCTTTATTTTAGAAAGCGCTTACAAATTAGATTATTT 12 157 0 AAAGCTACAT 0.595057 -40 TTTTTCTAAAAGAAAGCTGTAAAAACATATACCCGAT 13 78 1 AAAGCTAAAA 0.693303 -106 CCTCACAGGCACCAAAAAGTGACTATAGCACTTCAAA 14 23 1 AAAAATACAA 0.948615 -161 ACGTACTTATATTAAAATTTAACGAAAATTACATTTA 17 57 0 AAAAATACAA 0.948615 -81 GAAGTTAGCAATAAAAATATCAAAAGAAATCTAATTG 19 217 0 AAAAATAAAA 0.831329 -84 TTAGAATATAACCAAGAAATGACCAAAAAGTAACCTG 20 63 0 AAAGATACAA 0.942808 -238 CTCTTACTTGATTAAAAGATTAATATAATAAAAATAA 20 144 0 AAAAATAAAA 0.831329 -157 CTGATTTTGAAGCAAAACCTTACAAAATGAGCCATAA 22 72 1 AAAAATACAA 0.948615 -190 * **** * ** * * Masking position 10 Map Score: 15.7335 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 104 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 5 GTTATGAGGTTATTGGATAAAAACATGAACAAC 1 183 1 TTTGTAAAAA 0.948063 -118 CTGAAAATAATATTGACTGAAAATGCTTTTAGA 10 78 1 TTTGTGAAAA 0.806069 -223 AGGTTTATTCTATTGGTTAAAAATGTAAACGGT 10 179 1 TTTGTAAAAA 0.948063 -122 TCAGTGTGGTTATTGAGTCAAAACTAAAGTCAT 10 244 0 TTTGTCAAAA 0.738378 -57 CTGGCCGTCCTATTGAATAAAAAGCCGGGCTCT 11 24 1 TTTGTAAAAA 0.943063 -184 TAGCGCCATGTTTTGTATAATAAGAATGCAGGA 13 139 1 TTTGTAATAA 0.660631 -45 CCCCAGAAAAATTTGGTTCAAAGCTGATCCGGC 15 242 0 ATTGTCAAAG 0.836206 -59 GGGGGTTATATCTTGAATAAACGAAAAATCGGA 15 272 1 TTTGTAAACG 0.679292 -29 GTTTTATTAAAATTGTTTCAAAGTCATGCGTTT 19 89 0 ATTGTCAAAG 0.836522 -212 TACTTCTCTTACTTGATTAAAAGATTAATATAA 20 153 0 ATTGTAAAAG 0.8615 -148 GTTAATCAATAGTTGCTTAAAAATGATAACATC 20 222 0 ATTGTAAAAA 0.894395 -79 TTTTGTAAGGTTTTGCTTCAAAATCAGTTATTT 22 66 0 TTTGTCAAAA 0.747063 -196 TGATCATCTCTTTTGGCTATAAAGTTTCCGTTT 23 109 1 TTTGTATAAA 0.660631 -130 * *** ****** Masking position 8 Map Score: 7.87453 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 127 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 6 TCATAACCTTCCCTTCTTCTTAGCATGTCA 1 160 0 CCCTTCTTCT 0.701169 -141 CAGGGCTGCTGCCTTCCTCACATTTCGTAA 1 233 0 GCCTTCCTCA 0.967158 -68 CAAACGAAAACCCTCCCGAAAAGGAGGGCA 4 15 0 CCCTCCCGAA 0.912855 -91 GCCAATGCATCCCTCCTTCAGCAATACCCC 7 103 0 CCCTCCTTCA 0.945265 -72 GTAAACTGCCCCTTTCTCATAAAATAAAA 11 189 0 CCCTTTCTCA 0.844018 -19 GTTCCAAACCCTCCTTCATCAGTCCTGC 13 166 0 CCCTCCTTCA 0.945265 -18 CGCCCGGAACGCCTTCCGCATCCTTCTCTT 15 76 1 GCCTTCCGCA 0.974302 -225 TCTCTTCCCCGCCTTTCGAAGGAAATACTC 15 100 1 GCCTTTCGAA 0.591308 -201 TTCCCTGCCCTCCCGAATGTTGAGTAA 17 121 0 CCCTCCCGAA 0.912855 -17 GAAGAAAACAGCCTTCTCCAATGGAGAAGG 22 11 1 GCCTTCTCCA 0.912425 -251 CAAAAAAACAGCCTTCTCCATTGGAGAAGG 22 22 0 GCCTTCTCCA 0.912425 -240 ********** Masking position 4 Map Score: 7.87687 Number of sites scoring better than the average of aligned sites = 470 Number in coding regions = 413 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 7 CATACGCATTTTGAAAAAGACTGGGGGAAA 1 277 1 TTGAAAAAGA 0.713172 -24 TTATAATCTTTTTAGAAAGCGGTTACAACA 7 72 1 TTTAGAAAGC 0.899045 -103 TTGAATTCACTTGAAAAATCTTTTAAGATG 9 85 1 TTGAAAAATC 0.745084 -58 CTCCTTTGATTTTAAAAAACAACGAGTTTC 9 114 0 TTTAAAAAAC 0.873295 -29 AATCTTTTCTTTTAAAAAAAGCCGGGGGCA 11 56 0 TTTAAAAAAA 0.66456 -152 CCTCCTTTATTTTAGAAAGCGCTTACAAAT 12 167 0 TTTAGAAAGC 0.899045 -30 ACAGCTTTCTTTTAGAAAAAGTGAAACCTT 13 68 0 TTTAGAAAAA 0.732417 -116 TAAGTCTTACTTCAGAAAACGATGTCACGG 15 41 1 TTCAGAAAAC 0.74555 -260 TTCGGCGACATTGAAAAAAATACAAGTAAA 18 157 1 TTGAAAAAAA 0.726678 -144 GTGGGATTTTTTTAGAAATCTTTTAGCCTC 18 239 0 TTTAGAAATC 0.75057 -62 AAGAAAGTGATTGAGAAAGCAAAAGTATGA 22 140 1 TTGAGAAAGC 0.922785 -122 AGAGAAACCATTAAAAAAACCTTACCCGCG 23 37 0 TTAAAAAAAC 0.58863 -202 AACATTTGTTTTGAAAAAACGGAAACTTTA 23 128 0 TTGAAAAAAC 0.902433 -111 ********** Masking position 6 Map Score: 6.67743 Number of sites scoring better than the average of aligned sites = 678 Number in coding regions = 579 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 8 AAAAGACCTCTGTGCAGGACAAAGGT 5 6 0 TGTGCAGACA 0.906922 -149 CACAACGAGATGATCAAAACATCACCATCAC 10 28 1 TGATCAAACA 0.767605 -273 TATATCGTCATGTTCAGGAAATTTTCGGTAT 12 93 0 TGTTCAGAAA 0.95923 -104 CCGGCAAATGTGATTATGAAACATATCGTTA 14 78 0 TGATTAGAAA 0.753408 -106 TTGGTTAGTTGATCCCGAAAAACTAAGTCA 15 10 1 TGATCCGAAA 0.788795 -291 TCTAAGAAATTGTTCAGGACAGCCCATCACA 15 205 1 TGTTCAGACA 0.958551 -96 GGAAAACTTATGATCAGAAAAATAAAAAGGT 18 192 1 TGATCAAAAA 0.753367 -109 ACTTAATATTTGTTCAAGAAATCTTCATCCA 19 120 1 TGTTCAGAAA 0.959285 -181 AACTTCGGATTGTTCATGATAATCTATCTAT 19 248 1 TGTTCAGATA 0.830295 -53 AGTAACCTGTTGTGCATGAAATGGTTGCTTG 20 41 0 TGTGCAGAAA 0.900446 -260 GAGTAAGGTTTGATTAAGACATTT 23 4 0 TGATTAGACA 0.767975 -235 ****** **** Masking position 9 Map Score: 6.85631 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 244 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 9 AACCCTCCCGAAAAGGAGGGCAGTCT 4 7 0 AAAAGGAGGG 0.675223 -99 TTGCCGAAATAACGGCAGGGGGATTTTTTA 6 22 1 AACGGCAGGG 0.945971 -72 TTCTTTCAAGAATGGCAGAGCACCCGACAC 7 142 0 AATGGCAGAG 0.753846 -33 AAGTATTCTTAAAGGCAGGGGAA 10 288 1 AAAGGCAGGG 0.98273 -13 CTATTGAATAAAAAGCCGGGCTCTGCCCCC 11 33 1 AAAAGCCGGG 0.945637 -175 TTCTTTTAAAAAAAGCCGGGGGCAGAGCCC 11 50 0 AAAAGCCGGG 0.945637 -158 AGTCGATTTGACAGGAAGGGAGGATAAATA 12 132 1 ACAGGAAGGG 0.656127 -65 ATTTCCTTCGAAAGGCGGGGAAGAGAAGGA 15 96 0 AAAGGCGGGG 0.945972 -205 CCATCACATGACTGGCCGGATCAGCTTTGA 15 228 1 ACTGGCCGGA 0.713404 -73 GAATCGCAGGGATAAGGAGGT 16 2 1 AATCGCAGGG 0.865463 -74 AAAAAGGTTTAATGGCCGGAAAAAGAGGCT 18 215 1 AATGGCCGGA 0.86644 -86 ********** Masking position 1 Map Score: 6.38325 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 322 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 10 ATGAAATTCCCCCATTTTCGAATCTGTAA 3 10 1 CCCCATTTTC 0.98897 -55 ATCAGATCCCCCCATTTTCTTTCTATTAT 3 46 0 CCCCATTTTC 0.98897 -19 AGACTGCCCTCCTTTTCGGGAGGGTTT 4 8 1 CCTCCTTTTC 0.865875 -98 AGCCTCCAAACCCCTTTTTACTCGATTGTC 4 81 0 CCCCTTTTTA 0.845662 -25 GTAAACTGCCCCTTTCTCATAAAATAAA 11 190 0 CCCCTTTCTC 0.928869 -18 AAAACATATACCCGATTTTCAAGTGAAATA 13 99 1 CCCGATTTTC 0.928713 -85 AATCTTTTAGCCTCTTTTTCCGGCCATTAA 18 223 0 CCTCTTTTTC 0.916706 -78 TTCTGTTTCTCCCCATTTACAGGTCTAAAC 19 63 1 CCCCATTTAC 0.941411 -238 ATAGATTAGTACCCATTTCCTATCTCATTT 23 160 0 ACCCATTTCC 0.700121 -79 ********** Masking position 6 Map Score: 6.2102 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 172 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 11 GATTCGAAAATGGGGGAATTTCAT 3 4 0 TGGGGGAATT 0.958655 -61 AGAAAGAAAATGGGGGGATCTGAT 3 51 1 TGGGGGGATT 0.939769 -14 AAATAACGGCAGGGGGATTTTTTATTTTTGT 6 28 1 AGGGGGATTT 0.976152 -66 CCACCTCAATAGGCGGATTCTTCCGTATCT 12 10 0 AGGCGGATTT 0.903711 -187 CCGCCTATTGAGGTGGATTCTATTTTTTTGT 12 25 1 AGGTGGATTT 0.863619 -172 CAAATTTTTCTGGGGGGTTATATCTTGAATA 15 260 1 TGGGGGGTTT 0.972875 -41 TGACATTGTCTGTGGGATTTTTTTAGAAATC 18 249 0 TGTGGGATTT 0.873633 -52 ********* * Masking position 9 Map Score: 1.88184 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 34 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 12 ACTGTTTCCCCCAGTCTTTTTC 1 289 0 TGTTTCCCCC 0.967264 -12 TCAACTTTAGTGTTTTTTCCCATAGAGCGG 2 192 0 TGTTTTTTCC 0.82348 -109 TTTACTCGATTGTCTCTTTCTTTACTTTAC 4 65 0 TGTCTCTTTC 0.818664 -41 GTGGTGTGAGTATTTCCTTCGAAAGGCGGG 15 107 0 TATTTCCTTC 0.694901 -194 TAGTCTTTTCTGTTTCTCCCCATTTACAGG 19 56 1 TGTTTCTCCC 0.920317 -245 TGGAGAAGGCTGTTTTCTTC 22 1 0 TGTTTTCTTC 0.82348 -261 TCTGTTTCCTCCATAGACCATC 22 250 0 TGTTTCCTCC 0.981196 -12 AAATGTCTCCTCCTCAGTTGTTG 23 226 0 TGTCTCCTCC 0.967264 -13 ********** Masking position 5 Map Score: 2.91144 Number of sites scoring better than the average of aligned sites = 455 Number in coding regions = 377 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 13 ATGAAAAGGTTCTTTTGTACGATTCGGATAC 2 50 0 TCTTTGTACG 0.971284 -251 ACTATGGCGGTCTTTTTGACGGCAAACGAAA 4 36 0 TCTTTTGACG 0.772696 -70 GTAATTTTGTTACATTTTACGAAAATGAAAT 5 62 0 TAATTTTACG 0.62642 -93 GGCTTTTTATTCAATAGGACGGCCAGCCCGA 11 19 0 TCATAGGACG 0.717336 -189 TATAAATAAATATTTTGTACGAACAATTTTA 11 112 0 TATTTGTACG 0.947898 -96 TATTTTCCTATCATTAGTACGTATCTTTTGT 11 147 1 TCTTAGTACG 0.915675 -61 CACTATGCTGTAATTTGTACAGACAAAAAAA 12 47 0 TATTTGTACA 0.545104 -150 ATAAATAATCTAATTTGTAAGCGCTTTCTAA 12 155 1 TATTTGTAAG 0.783646 -42 GATGTTCCTCCTTTGTAAGATGTGTTGTA 14 165 0 TCTTTGTAAG 0.870698 -19 AAATTACATTTAATTAGTACGTACAAATATA 17 38 0 TATTAGTACG 0.85382 -100 ATTTAAACCTTCAATTGTACGTACTTATATT 17 81 0 TCATTGTACG 0.93997 -57 TGAATCACCTTATATTGGACGCCGCAGCAGG 18 118 1 TAATTGGACG 0.80959 -183 ACCGATGTTATCATTTTTAAGCAACTATTGA 20 219 1 TCTTTTTAAG 0.572764 -82 ** ******** Masking position 9 Map Score: 8.0274 Number of sites scoring better than the average of aligned sites = 273 Number in coding regions = 231 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 14 TGTTATATCTGATATTATCATA 1 3 0 GATATTATCA 0.82671 -298 GCACTTAGGTCATTTGATCAACTTTAGTGT 2 209 0 CATTTGATCA 0.751606 -92 ACAATGTCTTCATATGATAAAGACGCGAGA 7 30 1 CATATGATAA 0.652631 -145 TAACAGGAGGCTGATGATCAGCCTCTTTTT 9 15 1 CTGATGATCA 0.913416 -128 ACTTCACAACGAGATGATCAAAACATCACC 10 24 1 GAGATGATCA 0.940371 -277 TGTCATTTCTCATATTATCATAATTCTAAA 10 105 0 CATATTATCA 0.875743 -196 CGTATTACATCAGATCATCACCATAAGGGA 13 25 0 CAGATCATCA 0.817484 -159 CATTCCATTTGTTATTATCAGAAAATTTTA 15 170 1 GTTATTATCA 0.683563 -131 GATTGGAAAACTTATGATCAGAAAAATAAA 18 188 1 CTTATGATCA 0.906867 -113 ATAGCCAAAAGAGATGATCACAGATCCGCT 23 99 0 GAGATGATCA 0.940371 -140 ********** Masking position 5 Map Score: 2.73168 Number of sites scoring better than the average of aligned sites = 356 Number in coding regions = 322 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 15 CCGCCTTGTTATGATGAGAGAACCAACTTGT 6 59 1 ATGATAGAGA 0.792648 -35 TATTAGAACGATGAGGAGAGATGTTC 8 6 0 ATGAGAGAGA 0.88758 -83 TTGACTGAAAATGCTTTTAGAATTATGATAA 10 90 1 ATGCTTTAGA 0.898319 -211 AACAAATGGAATGCGCTGAGACAGTTCTATT 15 152 0 ATGCGTGAGA 0.974151 -149 TTTCAAAGTCATGCGTTTAGACCTGTAAATG 19 76 0 ATGCGTTAGA 0.948043 -225 TATGGGTATTATGCGATTAGAATATAACCAA 20 85 0 ATGCGTTAGA 0.948043 -216 AAATAACTTTATGCTCAGAGAAACCATTAAA 23 52 0 ATGCTAGAGA 0.933391 -187 ***** ***** Masking position 9 Map Score: 2.36916 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 42 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555