AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i308_bsub_mtub_300.orf -o308_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 pgsA 300 phosphatidylglycerophosphate synthase #2 recA 172 multifunctional SOS repair regulator #3 pbpX 167 penicillin-binding protein #4 ymdA 276 similar to hypothetical proteins #5 ymdB 68 similar to hypothetical proteins #6 spoVS 199 spoVS #7 tdh 265 threonine 3-dehydrogenase #8 ymcB 147 similar to hypothetical proteins #9 cotE 261 morphogenic protein #10 mutS 132 mutS #11 miaA 98 tRNA isopentenylpyrophosphate transferase #12 ymaH 39 similar to host factor-1 protein #13 spoVK 300 alternate gene name: spoVJ; disruption leads to the production of immature spores (stage V sporulation) #14 ynbA 220 similar to GTP-binding protein protease modulator #15 dapF 24 dapF #16 Rv2728c 108 hypothetical protein Rv2728c #17 Rv2729c 66 hypothetical protein Rv2729c Motif number 1 ATAGGTTTCGTCTTTTTTCAGCGTTCCTTCTTTTAAAG 1 59 0 TTTTTTTTCT 0.753529 -242 ATCAGTTATGTCTTTTTTATAGGTTTCGTCTTTTTTCA 1 77 0 TTTTTTTTTG 0.896577 -224 TTTCTTCCTTTTTATTTACAATCTTTATGGTTTGTGCC 1 213 0 TTATTATTTT 0.870974 -88 TCTATTTTTTCCTCCTTTATGTTACCACTA 2 153 0 TTTTTTTTTT 0.966478 -20 AAAAAAGCAATATTTTTATCATTTTTTTGCAAAATACA 3 65 0 TTTTTATTTT 0.951131 -103 AAATATTGCTTTTTTTGACAACTTTTTTAGGGCTTTAT 3 88 1 TTTTTATTTT 0.951131 -80 TAACATTTGTTTTTTTAACATGATTGTTAAACCATTTA 4 123 1 TTTTTATTGT 0.673613 -154 TGTCGGCATGTACATTGTCTAGTTTTCTCAACATACTA 4 205 0 TCATTTTTTT 0.750417 -72 TTCCTGCTTTTCTTTTTAATATTTTTATAAAATAACCA 6 20 0 TTTTTATTTT 0.951131 -180 TTGTTTTTCATTTATTGTGATATTTTCTCCCGATAGTA 7 55 1 TTATTTTTTT 0.909088 -211 GGCGGAAATTTTTTTTGAAACGTTTTAGCTCATTTCTG 7 126 0 TTTTTATTTG 0.854059 -140 TTACTCTTCCTCTTTTGATTCCTTATTGATTATTATTC 8 24 1 TTTTTATATG 0.528087 -124 TACAGGCCCGTGTTTTTTTATCATTTGTGCGGTTAAAA 9 23 1 TTTTTTTTTT 0.966478 -239 ACAGAAACTTTGTATTTTTATATTTTATTTATAAAAAT 9 174 1 TTATTTTTTT 0.909088 -88 CCCAAGTCTCTTTTTTATATTGATATATCATTCTTTTA 10 36 1 TTTTTTTATT 0.846464 -97 GATATATCATTCTTTTATCACTTTTTGTTTATGTTATA 10 57 1 TTTTTTTTTT 0.966478 -76 CAACCACCTATCCATTTTGCCCTTTTTTTGCATCGGTA 11 20 0 TCATTTTTTT 0.750417 -79 TATAGTGAGCTTCTTTCTCATTATTTCTTTTTCATACA 13 71 0 TCTTTTTTTT 0.896577 -230 CATGAGATTTTGTTTTTAATCATTTTGTCAGAGTATTA 13 107 0 TTTTTATTTT 0.951131 -194 TTGAGAGGTCTGTTTTTTGCTCGTATTTCCGCCTTTTC 14 23 1 TTTTTTTATT 0.846464 -198 * **** * *** * Masking position 6 Map Score: 23.877 Number of sites scoring better than the average of aligned sites = 505 Number in coding regions = 334 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 176 Fraction of orfs with sites within 600 bp upstream = 0.0282686 Motif number 2 TTTTTCAGCGTTCCTTCTTTTAAAGAGCTG 1 54 0 TTCCTTCTTT 0.956435 -247 TTTTTATAGGTTTCGTCTTTTTTCAGCGTT 1 72 0 TTTCGTCTTT 0.673493 -229 AAGATGACTTTTCTTCCTTTTTATTTACAA 1 230 0 TTCTTCCTTT 0.873241 -71 CATATTCGGATTTTTTCTTGGCGTGATTCC 2 75 0 TTTTTTCTTG 0.716499 -98 ATGCGTTCGCTTTTTTCTTGGCAAATCCCT 2 102 1 TTTTTTCTTG 0.716499 -71 TCTATTTTTTCCTCCTTTATGTTACCAC 2 155 0 TTCCTCCTTT 0.975378 -18 TTGTAAATCCTTTCTTCTTGAAAATTCCTT 5 48 0 TTTCTTCTTG 0.93562 -21 AGTTGCTATATTCCTGCTTTTCTTTTTAAT 6 38 0 TTCCTGCTTT 0.904215 -162 AAACAGGTTGTTTTTCATTTATTGTGATAT 7 48 1 TTTTTCATTT 0.4362 -218 TTTTAGCTCATTTCTGATTTTGTATATTCG 7 112 0 TTTCTGATTT 0.514605 -154 GTACAATCCTCCTTGAAAAATTCTT 7 251 0 ATCCTCCTTG 0.813432 -15 GAGTTTACTCTTCCTCTTTTGATTCCTTAT 8 20 1 TTCCTCTTTT 0.706863 -128 CCTCTTTTGATTCCTTATTGATTATTATTC 8 32 1 TTCCTTATTG 0.887365 -116 GTCATATTTTCTCCTTTCAAACCAAAC 8 131 0 TTTCTCCTTT 0.947453 -17 TCCGGCATGCCTCCTTGTTCTTCTTCG 9 245 0 TGCCTCCTTG 0.859335 -17 GTTTCGTCCTCCTTGATTCTCTATA 12 25 0 GTCCTCCTTG 0.865988 -15 AAATACTTTATTTCTTATTGTATTCACGGA 13 161 0 TTTCTTATTG 0.781938 -140 AAGCGCAGGATTCCTTATTGTTCCCGAAAA 13 198 1 TTCCTTATTG 0.887365 -103 TTGCTCGTATTTCCGCCTTTTCAAAGCAAT 14 39 1 TTCCGCCTTT 0.891033 -182 ********** Masking position 8 Map Score: 19.6035 Number of sites scoring better than the average of aligned sites = 1407 Number in coding regions = 1006 Number in noncoding regions = 401 Number of orfs with sites within 600 bp upstream = 464 Fraction of orfs with sites within 600 bp upstream = 0.0745262 Motif number 3 CTGATCAGTTATGTCTTTTTTATAGGTTTCG 1 87 0 ATTCTTTTTT 0.7107 -214 GGTTTGTGCCATCACTTTTTTCGGATCGAGT 1 192 0 ATACTTTTTT 0.932011 -109 GGTAATTAAGATGACTTTTCTTCCTTTTTAT 1 236 0 ATACTTTTCT 0.84278 -65 TAATTACCAGATGACTTTTCTTCACGTCCGA 1 259 1 ATACTTTTCT 0.84278 -42 CGAATATGCGTTCGCTTTTTTCTTGGCAAAT 2 97 1 TTGCTTTTTT 0.938788 -76 AGTGAAAAACTCAGCTTTTTTGTATTTTGCA 3 45 1 TCGCTTTTTT 0.857086 -123 CAATATTTTTATCATTTTTTTGCAAAATACA 3 65 0 ATATTTTTTT 0.799477 -103 TGATAAAAATATTGCTTTTTTTGACAACTTT 3 82 1 ATGCTTTTTT 0.961625 -86 GCTTTTTTTGACAACTTTTTTAGGGCTTTAT 3 95 1 ACACTTTTTT 0.84278 -73 AGTTGTAACATTTGTTTTTTTAACATGATTG 4 118 1 TTGTTTTTTT 0.816868 -159 TAAGCATCACTTTATTTTTTTGACGGCAAGG 5 21 1 TTATTTTTTT 0.709313 -48 CATTGTGGGGATGGCTTTTTGGATAGCAACA 6 117 1 ATGCTTTTTG 0.907399 -83 AAATGTTCAATTGGTTTTTCTGTGCTCAGCC 9 84 1 TTGTTTTTCT 0.635601 -178 TCATTCTTTTATCACTTTTTGTTTATGTTAT 10 63 1 ATACTTTTTG 0.84278 -70 TGTCGAAACAATTGCTTTTTTCGGGAACAAT 13 214 0 ATGCTTTTTT 0.961625 -87 TTTTGAGAGGTCTGTTTTTTGCTCGTATTTC 14 21 1 TCGTTTTTTG 0.405494 -200 ** ******** Masking position 6 Map Score: 15.269 Number of sites scoring better than the average of aligned sites = 1493 Number in coding regions = 1197 Number in noncoding regions = 296 Number of orfs with sites within 600 bp upstream = 268 Fraction of orfs with sites within 600 bp upstream = 0.0430453 Motif number 4 CACCTAATCTGAAAATAAAAATCAACGGTAA 1 146 1 GAAAATAAAA 0.958386 -155 CATAAAGATTGTAAATAAAAAGGAAGAAAAG 1 222 1 GTAAATAAAA 0.710216 -79 CATTTTTTTGCAAAATACAAAAAAGCTGAGT 3 53 0 CAAAATAAAA 0.831923 -115 AGAAAAGCAGGAATATAGCAACTCCTTAGTG 6 45 1 GAATATACAA 0.932261 -155 ACTCCTTAGTGAATATAGTAAAAATGGAAGG 6 65 1 GAATATATAA 0.725067 -135 ACTATCGGGAGAAAATATCACAATAAATGAA 7 61 0 GAAAATACAC 0.871869 -205 ATAAATGAGCGAATATACAAAATCAGAAATG 7 103 1 GAATATAAAA 0.936372 -163 GGTACAATCCGAATATAACAAGAATTTTTCA 7 232 1 GAATATACAA 0.932261 -34 TTTGAAAGGAGAAAATATGAC 8 137 1 GAAAATAGAC 0.659 -11 TTTTTATAAATAAAATATAAAAATACAAAGT 9 180 0 TAAAATAAAA 0.644716 -82 AATGATATATCAATATAAAAAAGAGACTTGG 10 37 0 CAATATAAAA 0.759775 -96 ATGAAGGTTGGAAAATAGAAACGTTGATACA 10 95 1 GAAAATAAAA 0.958386 -38 TATTGTTCCCGAAAAAAGCAATTGTTTCGAC 13 213 1 GAAAAAACAA 0.696237 -88 ******* *** Masking position 5 Map Score: 7.72901 Number of sites scoring better than the average of aligned sites = 387 Number in coding regions = 297 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 5 GAACCTTACCGTTGATTTTTATTTTCAGAT 1 152 0 GTTGATTTTT 0.743447 -149 GAACGCATATTCGGATTTTTTCTTGGCGTG 2 80 0 TCGGATTTTT 0.78367 -93 GAATATGCGTTCGCTTTTTTCTTGGCAAAT 2 98 1 TCGCTTTTTT 0.81953 -75 ATACAAAAAAGCTGAGTTTTTCACTCAGCC 3 40 0 GCTGAGTTTT 0.562052 -128 GCAATATTTTTATCATTTTTTTGCAAAATA 3 67 0 TATCATTTTT 0.479257 -101 GATAAAAATATTGCTTTTTTTGACAACTTT 3 83 1 TTGCTTTTTT 0.654858 -85 AGTTGTAACATTTGTTTTTTTAACATGATT 4 118 1 TTTGTTTTTT 0.548595 -159 GCGGGCTACCTTCCATTTTTACTATATTCA 6 74 0 TTCCATTTTT 0.695396 -126 ACAGGTTGTTTTTCATTTATTGTGATATTT 7 50 1 TTTCATTTAT 0.424144 -216 TTGTATATTCGCTCATTTATGTGCTAAAAA 7 93 0 GCTCATTTAT 0.682258 -173 AAACGTTTTAGCTCATTTCTGATTTTGTAT 7 117 0 GCTCATTTCT 0.643463 -149 AAAAATTTCCGCCCATTTTTCAAGACAGAT 7 151 1 GCCCATTTTT 0.869373 -115 AGATTATTTAGTTCATTTTTAACCGCACAA 9 47 0 GTTCATTTTT 0.876713 -215 TTTGTCTAGTGTGCATTTTTATAAATAAAA 9 196 0 GTGCATTTTT 0.818977 -66 TACCCCCAAGTCTCTTTTTTATATTGATAT 10 32 1 TCTCTTTTTT 0.877116 -101 TATCCATTTTGCCCTTTTTTTGCATCGGTA 11 20 0 GCCCTTTTTT 0.772716 -79 CATACAACGGGCTGATTTTTGTACGAAACG 13 47 0 GCTGATTTTT 0.873986 -254 TGAGCTTCTTTCTCATTATTTCTTTTTCAT 13 74 0 TCTCATTATT 0.474031 -227 GTCGAAACAATTGCTTTTTTCGGGAACAAT 13 214 0 TTGCTTTTTT 0.654858 -87 ACCTCTCAGTTTTTGAGAGGTCT 14 4 1 TCTCAGTTTT 0.721104 -217 TTTTGAGAGGTCTGTTTTTTGCTCGTATTT 14 21 1 TCTGTTTTTT 0.744159 -200 ********** Masking position 7 Map Score: 15.4348 Number of sites scoring better than the average of aligned sites = 2042 Number in coding regions = 1630 Number in noncoding regions = 412 Number of orfs with sites within 600 bp upstream = 418 Fraction of orfs with sites within 600 bp upstream = 0.0671378 Motif number 6 GGATGAATTGCATTCGGCACGTGAAAAGAAG 4 27 1 CATCGGCACG 0.93592 -250 TGCTTAAAAAGTGTCGGCATGTACATTGTCT 4 223 0 GTTCGGCATG 0.956254 -54 GTTTCGTCCTCCTTGATTCTC 12 29 0 GTTCGTCCTC 0.885184 -11 GCGTTTGTCACAATCGGCATCCGCTTGAATA 13 253 1 CATCGGCATC 0.966059 -48 GCGCGGGACAGTGTCGGCCTCTCAGCACGGT 16 28 1 GTTCGGCCTC 0.983323 -81 TTGGCGGGCGGATTCGGCCTCGTGGAGCAAC 16 71 0 GATCGGCCTC 0.986151 -38 CTCCCACCGACATTCGGCCCGGAAGCTGACT 17 39 0 CATCGGCCCG 0.967891 -28 ** ******** Masking position 4 Map Score: 4.01425 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 124 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 7 AAGGCATCAGACAGCTCCTGGAT 1 2 1 AGGATCAGAA 0.871095 -299 GACGAAACCTATAAAAAAGACATAACTGATCA 1 85 1 ATAAAAAGAA 0.868603 -216 AAATATCATAATGTATCAGAGAAATCATGTTT 2 38 0 ATGATCAGAA 0.951216 -135 TTATAAAAATATTAAAAAGAAAAGCAGGAATA 6 28 1 ATTAAAAGAA 0.723471 -172 TAGTTTTACAATGGATAAGTGAGTGTTCATTA 6 165 0 ATGATAAGTA 0.796259 -35 TTTTGTCCTTCTGGAAAAGACAGTTCTGTTTA 7 183 1 CTGAAAAGAA 0.904404 -83 CCTGCATACAATGGAACAGAAACTTTGTATTT 9 159 1 ATGAACAGAA 0.968269 -103 GACAAATGCCCAGCATAAGATAACACGAAGAA 9 220 1 CAGATAAGAA 0.434427 -42 ATATATCAATATAAAAAAGAGACTTGGGGGTA 10 32 0 ATAAAAAGAA 0.868603 -101 AGCCCGTTGTATGAAAAAGAAATAATGAGAAA 13 64 1 ATGAAAAGAA 0.967685 -237 TATCATATAGAGAGAACAGAGAGGTGAAG 13 282 1 AGAAACAGAA 0.700111 -19 ACTGCCCAATATGCAAAAGAAAGGAACATCCA 14 111 1 ATGAAAAGAA 0.967685 -110 TTAAATCGAGATGTATCAGTCAGCTTCCGGGC 17 22 1 ATGATCAGTA 0.799296 -45 *** ****** * Masking position 5 Map Score: 8.31236 Number of sites scoring better than the average of aligned sites = 751 Number in coding regions = 641 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 8 TCTTAGGAGGATAATGTGCTGAAAATA 2 7 0 ATAAGTGCTG 0.851129 -166 TTCAAATGATACAAAAGGCTGAGTGAAAAAC 3 24 1 ACAAAGGCTG 0.81575 -144 CGTGAAAAGAAGACTGGCCTGCAAACGTTAA 4 46 1 AGACGGCCTG 0.979541 -231 CTTCTGGAAAAGACAGTTCTGTTTACGCTTA 7 190 1 AGACGTTCTG 0.837204 -76 TGATAAAAAAACACGGGCCTGTAAAGGCACC 9 15 0 ACACGGCCTG 0.979541 -247 GATAAAGTTTATACGCGGCTGAGCACAGAAA 9 100 0 ATACCGGCTG 0.90532 -162 TCTTTTTCATACAACGGGCTGATTTTTGTAC 13 53 0 ACAAGGGCTG 0.975398 -248 TGAGAGGCCGACACTGTCCCGCGCTCATTGG 16 21 0 ACACGTCCCG 0.809925 -88 GGCTGCAAAGAGACCGTGCTGAGAGGCCGAC 16 40 0 AGACGTGCTG 0.975398 -69 GGCCTCGTGGAGCAACGGCTGCAAAGAGACC 16 56 0 AGCACGGCTG 0.715785 -53 **** ****** Masking position 1 Map Score: 2.7875 Number of sites scoring better than the average of aligned sites = 449 Number in coding regions = 411 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 9 CAAATCCCTTCAAACAGGGTATAGTATATG 2 123 1 CAAACAGGGT 0.980499 -50 TTGCATTACGCAAACAGGTTGAGAATGCTT 7 20 0 CAAACAGGTT 0.978981 -246 TTGCGTAATGCAAACAGGTTGTTTTTCATT 7 37 1 CAAACAGGTT 0.978981 -229 TTCTCTATATCATACAGTTTCGA 12 4 0 CATACAGTTT 0.861661 -36 GTGGTATACACATGCAGGGTTTGGTATGAT 14 75 1 CATGCAGGGT 0.940501 -146 ********** Masking position 6 Map Score: 2.318 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 28 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 10 TGAGTGTTCATTAGAACAATCATTATTAGATGTTGC 6 142 0 TTACTCATAT 0.983967 -58 CAAACCAAACTTCCACCCTTCAGTATAAAGGTTATT 8 105 0 TTACTCATAT 0.983967 -43 CGTTTCTATTTTCCAACCTTCATTATAACATAAACA 10 82 0 TTACTCATAT 0.983967 -51 TGTTTAATCCCTCACTATGTATCAACGT 10 115 0 TTACTCATAT 0.983967 -18 TGCCCTTTTTTTGCATCGGTAAACATCCTT 11 5 0 TTACTAACAT 0.887274 -94 ATCTCCCCCATTATAGCATTCAACATGGACAACCAC 11 51 0 TTACTCACAT 0.980724 -48 ** * * *** *** Masking position 10 Map Score: 2.28795 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 42 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 11 TCATACTCGGACGTGAAGAAAAGTCATCTGG 1 265 0 ACGTGAGAAA 0.800947 -36 TAGGAGGATAATGTGCTGAAAATA 2 4 0 ATGTGCGAAA 0.980623 -169 TCTTCTTTTCACGTGCCGAATGCAATTCATC 4 28 0 ACGTGCGAAT 0.83526 -249 TTCATTGTAAATGTGTCGGAAATACTTGTCA 4 88 0 ATGTGTGGAA 0.675141 -189 TCGCTCATTTATGTGCTAAAAATACTATCGG 7 84 0 ATGTGCAAAA 0.955747 -182 TAGCACATAAATGAGCGAATATACAAAATCA 7 97 1 ATGAGCAATA 0.614511 -169 AAAATCAGAAATGAGCTAAAACGTTTCAAAA 7 121 1 ATGAGCAAAA 0.918891 -145 GTCTTGAAAAATGGGCGGAAATTTTTTTTGA 7 146 0 ATGGGCGAAA 0.939657 -120 AACGCCTATCATGTGTCGAAACAATTGCTTT 13 227 0 ATGTGTGAAA 0.908804 -74 AGGCGGAAATACGAGCAAAAAACAGACCTCT 14 26 0 ACGAGCAAAA 0.889702 -195 ****** **** Masking position 1 Map Score: 3.73032 Number of sites scoring better than the average of aligned sites = 498 Number in coding regions = 438 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 12 TGCATATCCGGTGCGGATATCAACTTGTTT 1 118 0 GTGCGGATAT 0.889988 -183 GGAGGATAATGTGCTGAAAATA 2 3 0 GTGCTGAAAA 0.823581 -170 AATTTATTTTGGGAGGAAAAAATGA 3 153 1 GGGAGGAAAA 0.898775 -15 AACTTGACAAGGGCGATGAACACACTCATT 4 161 1 GGGCGATGAA 0.718042 -116 AAATACTATCGGGAGAAAATATCACAATAA 7 66 0 GGGAGAAAAT 0.65793 -200 GCTCATTTATGTGCTAAAAATACTATCGGG 7 83 0 GTGCTAAAAA 0.631695 -183 CTTGAAAAATGGGCGGAAATTTTTTTTGAA 7 145 0 GGGCGGAAAT 0.971413 -121 TTTATCATTTGTGCGGTTAAAAATGAACTA 9 39 1 GTGCGGTTAA 0.861359 -223 TTACTTATAAGTGCGATAAAGTTTATACGC 9 115 0 GTGCGATAAA 0.834466 -147 AGGTATCTTAGGGCGGGTAATACGTTTCGT 13 25 1 GGGCGGGTAA 0.87392 -276 TGCTTTGAAAAGGCGGAAATACGAGCAAAA 14 37 0 AGGCGGAAAT 0.728074 -184 ********** Masking position 9 Map Score: 2.48159 Number of sites scoring better than the average of aligned sites = 881 Number in coding regions = 805 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 13 TAAGGTTCTTTCATATGAACTCGATCCGAA 1 174 1 TCATATGAAC 0.85596 -127 GCCTTTTGTATCATTTGAAACTTATTTTAT 3 13 0 TCATTTGAAA 0.761701 -155 GTCAAGCTTGCCATCTTAACGTTTGCAGGC 4 62 0 CCATCTTAAC 0.792141 -215 GATTGTTAAACCATTTAAACTTGACAAGGG 4 144 1 CCATTTAAAC 0.87537 -133 AAGTGAGTGTTCATTAGAACAATCATTATT 6 151 0 TCATTAGAAC 0.912883 -49 CACAGAAAAACCAATTGAACATTTGGTACA 9 78 0 CCAATTGAAC 0.890546 -184 TTTCCAACCTTCATTATAACATAAACAAAA 10 79 0 TCATTATAAC 0.740836 -54 AAAGGAACATCCATTTGAACGAACAAGAAA 14 130 1 CCATTTGAAC 0.978449 -91 ********** Masking position 3 Map Score: 0.975564 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 198 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 14 ACTCAAATCCAGGAGCTGTCTGATGCCTT 1 10 0 AGGAGCTGTC 0.882173 -291 TCATAGCAAGAGGAGGTGAAAGT 4 264 1 AGGAGGTGAA 0.910463 -13 AAAACTAAGGGGGAGCAGAA 6 190 1 GGGAGCAGAA 0.883502 -10 ATAATGAGAAAGAAGCTCACTATAATACTC 13 85 1 AGAAGCTCAC 0.803227 -216 AGAGAGAACAGAGAGGTGAAG 13 290 1 GAGAGGTGAA 0.74389 -11 CGTGATATGCGGCAGCTGACATCCGACTAA 14 180 0 GGCAGCTGAC 0.935972 -41 CATTCGGCCCGGAAGCTGACTGATACATCT 17 30 0 GGAAGCTGAC 0.966428 -37 GAATGTCGGTGGGAGGTCACCT 17 55 1 GGGAGGTCAC 0.958306 -12 ********** Masking position 4 Map Score: 0.505092 Number of sites scoring better than the average of aligned sites = 542 Number in coding regions = 443 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 15 CAATGATAGGTTGCCAGTTGTGCAGAGCTTC 8 74 1 TGCCAGTTGT 0.95335 -74 TATCTTATGCTGGGCATTTGTCTAGTGTGCA 9 211 0 TGGCATTTGT 0.967863 -51 GCAAAATGGATAGGTGGTTGTCCATGTTGAA 11 38 1 TGGTGGTTGT 0.919557 -61 CGACACATGATAGGCGTTTGTCACAATCGGC 13 240 1 TGGCGTTTGT 0.961491 -61 TTTTGCATATTGGGCAGTAGTATTATCATAC 14 98 0 TGGCAGTAGT 0.9565 -123 CATCTCGATTTAAGCAGTTGTTCA 17 4 0 TAGCAGTTGT 0.932379 -63 * ********* Masking position 8 Map Score: 0.118983 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 58 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493