AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -inagC_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 metS 300 methionyl-tRNA synthetase #2 yabD 78 similar to hypothetical proteins #3 yabE 155 similar to hypothetical proteins #4 yabF 144 similar to hypothetical proteins #5 yabG 161 yabG #6 veg 210 veg #7 sspF 159 small acid-soluble spore protein (alpha/beta-type SASP) #8 yabH 147 similar to hypothetical proteins #9 purR 55 transcriptional regulator #10 spoVG 193 spoVG #11 gcaD 192 UDP-N-acetylglucosamine pyrophosphorylase #12 glmS 300 L-glutamine-D-fructose-6-phosphate amidotransferase #13 ybfT 218 similar to glucosamine-6-phosphate isomerase #14 yflF 171 similar to phosphotransferase system enzyme II #15 ykvY 300 similar to Xaa-Pro dipeptidase #16 ykvZ 281 similar to transcriptional regulator (LacI family) #17 glcT 62 transcriptional antiterminator (BglG family) #18 ptsG 238 phosphotransferase system (PTS) glucose-specific enzyme IIABC component #19 xylR 300 transcriptional regulator #20 yqgQ 109 yqgQ #21 yqgP 89 similar to hypothetical proteins #22 yqgO 66 yqgO #23 yqgN 300 similar to 5-formyltetrahydrofolate cyclo-ligase #24 levD 189 phosphotransferase system (PTS) fructose-specific enzyme IIA component #25 levR 300 transcriptional regulator (NifA/NtrC family) #26 yutF 28 similar to N-acetyl-glucosamine catabolism #27 yutE 23 yutE #28 yutD 81 yutD #29 nagA 181 N-acetylglucosamine-6-phosphate deacetylase Motif number 1 TAATCAAATGAAATAAAAAACTTTGGTTCGA 1 55 0 AAAAAAAAAC 0.844843 -246 TCTTTAATGAAAATAAAAAAAGTCTGTTCGT 1 104 0 AAAAAAAAAA 0.896841 -197 TTTCTTGTCGAAACACAAAAGGTGTTCGACG 2 44 0 AAAACAAAAG 0.659225 -35 TGTCTATTATAACGAAAAAAACAGAGGGCGC 4 38 0 AACAAAAAAA 0.835319 -107 TGTGGTGCGCAAAACAAAAAGCCCTT 5 6 0 AAACAAAAAG 0.909899 -156 CATTCAATGATAAGAAAAAACTTGGACTCAG 5 72 1 TAAAAAAAAC 0.587391 -90 ACTTGGACTCAGCGAAAAAAGGCGCTTTCTC 5 91 1 AGCAAAAAAG 0.819284 -71 TCATTATGTAAAATAAAAAACCCGCATAGCT 6 33 0 AAAAAAAAAC 0.844843 -178 AAAAAAGGGCAAAACAAAAAGCAGTAAACAA 7 26 0 AAACAAAAAG 0.909899 -134 AATTATTGGAAACCAAAAAAGGGCAAAACAA 7 40 0 AACAAAAAAG 0.933914 -120 TTTATATCCAAAATAAAAAAACCAGGGAACA 8 33 0 AAAAAAAAAA 0.896841 -115 GGCATAAGGTAAATAAAAAAGTGATCCCGGC 10 33 0 AAAAAAAAAG 0.960351 -161 AAAATAACCAAAAAGCAAGGACTGC 11 5 1 TAACAAAAAG 0.725294 -188 GAAAAATCAGAATTAAAAAAGGACCGCCGGC 11 60 0 AATAAAAAAG 0.763722 -133 ATGGTATATTTGAAAAAAAAGGGTATGAGGG 14 143 1 TGAAAAAAAG 0.670132 -29 TAGAAATAAAAAAGGACTTTGTTC 16 4 1 AAAAAAAAAG 0.960351 -278 TATTTAATGCAGATAAAAAAGGACGATGTCG 16 36 0 AGAAAAAAAG 0.885978 -246 TATCTGCATTAAATAAAAAAATCATCAAATG 16 52 1 AAAAAAAAAA 0.896841 -230 TTCAGCTAAAAACACAAAAAGATATCTGGTA 16 199 1 AACCAAAAAG 0.854904 -83 GTTCATAAAAAACTAAAAAAAATATTGAAAA 19 97 0 AACAAAAAAA 0.835319 -204 AAGAAAACGCTGACAAAAAAGCCAGCTTCCT 20 26 0 TGAAAAAAAG 0.670132 -84 ACGCCTACTGAAAGCAAAAAATCCCGTTTTT 21 20 0 AAACAAAAAA 0.78377 -70 CAGCTGTTATAATGAAAAAAAACTATTGGAG 21 61 1 AATAAAAAAA 0.537074 -29 GTTTGAGGTGTAAGAAAAAAGCCAGAGCTTT 23 237 1 TAAAAAAAAG 0.863622 -64 AAACACTTAAAACGAAAAAAATAAACCTGTA 24 58 0 AACAAAAAAA 0.835319 -132 *** ******* Masking position 7 Map Score: 29.7494 Number of sites scoring better than the average of aligned sites = 1270 Number in coding regions = 873 Number in noncoding regions = 397 Number of orfs with sites within 600 bp upstream = 341 Fraction of orfs with sites within 600 bp upstream = 0.0547703 Motif number 2 TGCATCCACCTCACTACATTTA 6 199 0 CATCCACCTC 0.891783 -12 GGGAACAGCACGTCCCCCGGGTCACATCC 8 10 0 CGTCCCCCGG 0.900219 -138 TTCAAGGAGTCACCCCCTTGGTTTGAAGAA 12 170 0 CACCCCCTTG 0.927652 -131 GACTTTCAATCGTCCCCTCCTACATGTTTT 12 226 0 CGTCCCCTCC 0.952053 -75 GACGATTGAAAGTCCCCTTGAAATTTGACT 12 242 1 AGTCCCCTTG 0.922407 -59 ACCCATCCCCCTCATACCCTTTT 14 159 0 CATCCCCCTC 0.984879 -13 CAAACGGAACAACCCCCCTGCGATTGAACG 15 143 1 AACCCCCCTG 0.810227 -158 CTTCTTTCTAAATCCCCTTGATCTGGAATG 16 255 0 AATCCCCTTG 0.921049 -27 ATATCCACTTCATCCACTCCATTTGTTTAA 19 187 0 CATCCACTCC 0.711439 -114 CTCTCATCCCCCTCGGAATAGAAA 23 287 0 CATCCCCCTC 0.984879 -14 CTGGAGGGCCAGTCCCCTTCAAAAGTAATA 25 106 0 AGTCCCCTTC 0.942755 -195 GACAGCATCCCCTTTGTGTATAT 27 9 0 CATCCCCTTT 0.862612 -15 TTCATTGCCCCGTCCCCATCAATTGCTAAA 28 60 0 CGTCCCCATC 0.911249 -22 ********** Masking position 5 Map Score: 13.3424 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 202 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 3 AGAAAATGCACTTTGTCTATTATAACGAAA 4 52 0 CTTTGTCTAT 0.574112 -93 ATTCATGAAACTTTTTCTTATATCGAGCGT 4 91 0 CTTTTTCTTA 0.721103 -54 TGAGTCCAAGTTTTTTCTTATCATTGAATG 5 72 0 TTTTTTCTTA 0.745777 -90 AATCATAGAATTTTGTCAAAATAATTTTAT 6 101 1 TTTTGTCAAA 0.879001 -110 ACGAGCCCATTTTTGTCAAATAAAATTTAA 6 160 0 TTTTGTCAAA 0.879001 -51 CTATATCCTATTTTTTCAAAAAATATTTTA 10 96 1 TTTTTTCAAA 0.916753 -98 AATTCCACGATTTTTTCTGAAATCCTGCTC 10 131 0 TTTTTTCTGA 0.676239 -63 TTTAATTCTGATTTTTCAAACTTAGTTGCA 11 74 1 ATTTTTCAAA 0.520125 -119 GCAATCCGTTCTTTTTCATTGAGACCATAA 13 32 1 CTTTTTCATT 0.762167 -187 TCATACCCTTTTTTTTCAAATATACCATAT 14 141 0 TTTTTTCAAA 0.916753 -31 TGCTGATGAATTTTTTCAGACGAAAAGCAG 15 115 0 TTTTTTCAGA 0.835197 -186 ACGTCAAACCTTTTTTCAATGCATTCA 17 8 0 TTTTTTCAAT 0.849069 -55 CTGATCAAACCTTTGTCAAAAAAGTAAATC 19 219 1 CTTTGTCAAA 0.864916 -82 TCCAATAGTTTTTTTTCATTATAACAGCTG 21 61 0 TTTTTTCATT 0.784295 -29 AAGCTCTGGCTTTTTTCTTACACCTCAAAC 23 237 0 TTTTTTCTTA 0.745777 -64 AAGCCAGAACCTTTTTCAAAGCTCTGGCTT 23 255 0 CTTTTTCAAA 0.906595 -46 GGTTCTGGCTTTTTTTCTATTCCGAGGGGG 23 274 1 TTTTTTCTAT 0.698664 -27 AAACAGTTTTTTCATATGAACCTGTA 24 7 1 TTTTTTCATA 0.876813 -183 AAGATTCATTTTTTGTCATTGATTATTTTG 25 35 1 TTTTGTCATT 0.705754 -266 TAAAAGCCAGCTTTGTCAATCTGCTATAGA 25 197 1 CTTTGTCAAT 0.765849 -104 TTATTTTACTCTTTTTCAGACTAGTGATCT 29 130 0 CTTTTTCAGA 0.817072 -52 ********** Masking position 6 Map Score: 21.0315 Number of sites scoring better than the average of aligned sites = 1154 Number in coding regions = 952 Number in noncoding regions = 202 Number of orfs with sites within 600 bp upstream = 222 Fraction of orfs with sites within 600 bp upstream = 0.0356569 Motif number 4 TTCTACATGCTTTCTTCTCCTCATAGGATAGGTT 3 69 1 TTTCTCCCAT 0.791196 -87 GGCTTTTTGTTTTGCGCACCACATGGACTGCCGC 5 14 1 TTTGCCCCAT 0.985919 -148 CATAATACCATTTGCCCTCCCAATATGAAAGATT 13 57 1 TTTGCCCCAT 0.985918 -162 GTTTTGGGAATTTCCGCTCCTTTTATCGGGATGA 15 67 0 TTTCCCCCTT 0.93397 -234 AAAAAAGGACTTTGTTCTCGACATCGTCCTTTTT 16 18 1 TTTGTCCGAT 0.832692 -264 TTCTCGTTCTTTTGCGCACCCAATTTTGCTCATG 18 95 1 TTTGCCCCAT 0.985889 -144 CGCACCCAATTTTGCTCATGCCTTTTTGTTGTGT 18 109 1 TTTGCCTGTT 0.803971 -130 TTCAGATAATTTTGCTCTTGAAATAGGTGAATTT 19 277 0 TTTGCCTGAT 0.887733 -24 TTTCCTCACCATTTCTTGAACTTA 20 96 0 TTTCCCCCTT 0.93397 -14 TTTAAAAAATATTGCCCACGTGATAAAAAATCTA 23 170 1 ATTGCCCGAT 0.805788 -131 TGTTGAATCATTTGCACCTCATATTAGTATGATA 25 147 0 TTTGCCTCAT 0.939234 -154 AGCTGAGGTGTTTTCCCCCCTTTTATAAAATCTG 29 91 0 TTTTCCCCTT 0.780707 -91 ***** * ** ** Masking position 3 Map Score: 10.247 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 178 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 5 TGATAAACAAAAGGTGTTTCACGTGTAAC 2 7 1 AAAAAGGTGT 0.572853 -72 TATCACTTCTAAAAAAGGAGTTGTTTCGT 7 141 1 AAAAAGGAGG 0.970402 -19 TTTTATATAGGGAAAAGGTGGTGAACTACT 10 174 1 GAAAAGGTGG 0.967415 -20 TTTCTCAATAGGAAAAGAAGACGGGATTATTGC 12 17 1 GAAAAGAAGG 0.961364 -284 TCCTAAGATTGTAAAAGGAGACGAAGAAAGTCA 12 267 0 GAAAAGGAGG 0.987327 -34 AAAATTTGTTATAAAAGAAGGATACAAATCTTT 13 84 0 AAAAAGAAGT 0.529188 -135 CTTCATCCCGATAAAAGGAGCGGAAATTCCCAA 15 65 1 AAAAAGGAGG 0.970402 -236 TCAGTATACAGGAAGAGGAGCAGGAAATAAAAT 15 179 1 GAAGAGGAGG 0.913574 -122 AAATGCATTAGAAAATGAAGGCGTCGTGAAAGG 15 208 1 GAAATGAAGG 0.879259 -93 AATTGGGTGCGCAAAAGAACGAGAATGAACTTC 18 87 0 GAAAAGAACG 0.691826 -152 GGTCAGACTAGTAAAAAGAGGAGGTCAATTCTT 18 216 1 GAAAAAGAGG 0.815098 -23 TAAAGATTAAACAAATGGAGTGGATGAAGTGGA 19 181 1 AAAATGGAGG 0.905618 -120 GGTGGAATATGGAAAGGAAGCTGGCTTTTTTGT 20 12 1 GAAAGGAAGG 0.810304 -98 GTTAAGTTCAAGAAATGGTGAGGAAA 20 94 1 AAAATGGTGG 0.785249 -16 CCAGAGCTTTGAAAAAGGTTCTGGCTTTTTTTC 23 258 1 GAAAAGGTTG 0.64378 -43 * ******** * Masking position 4 Map Score: 10.5546 Number of sites scoring better than the average of aligned sites = 902 Number in coding regions = 752 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 6 TTAATTTTAATTATTCTTTTTCAGGGCGTATGTATATAT 1 138 1 TCTTTAGGGT 0.922206 -163 ATCGCCGCTCTCGTCCTTTGGGCGGGAGCTTTTTGACAT 1 252 1 TCTTGCGGGC 0.984061 -49 AGGGCTGACATAAGCCTTTTGCCGGCGGTCCTTTTTTAA 11 40 1 TCTTTCGGGT 0.981071 -153 CCTCGTCAACTAAGCCTTTTTCCGGGCGCTTAGTTCGGG 12 69 0 TCTTTCGGGC 0.989957 -232 GGTGCTTGTCTATCTCTTTGAGGGGGTGTCAC 13 197 1 TCTTGGGGGT 0.943595 -22 TAGTGATCTATACCAATTTTCCCGGGGGTATTTCTTTTT 14 94 0 TATTTCGGGT 0.888699 -78 CGAAAAGCAGTTATGCTCTTAACGGTTTTGGGAATTTCC 15 86 0 TCTTTCGGTT 0.819106 -215 TTGGGTTATGTCTCACTGTTCTCGGTGGCAGCTGTCTTG 16 128 0 TCTTTCGGGC 0.989957 -154 GTTTACTGATTATTACTTTTGAAGGGGACTGGCCCTCCA 25 96 1 TCTTTAGGAC 0.663282 -205 TATCAATCCCTCCTCATGTGTAGGGTAGCCAAATCGCAT 28 12 1 TATTGGGGGC 0.830561 -70 GATATGTTCCTCCTGTTCCGGGCTGCCCCGAGCTTG 29 8 1 TCTTTGGGGC 0.980695 -174 * ** ** *** ** Masking position 9 Map Score: 7.07818 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 117 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 CTTATCATTGAATGAAAGGTCCTTCTCTAGCCTA 5 52 0 AAGAAAGCCT 0.961656 -110 CCTCATCATGAAAGAAAGAGCCTTGAGAAAGCGC 5 112 0 AAGAAAGCCT 0.961616 -50 CAATAATTTTAACGAAAGTTCCATCTGATTTAAC 7 63 1 AAGAAAGCCT 0.961753 -97 TTATGCCCGAAATGAAAGCTTTATGACCTAATTG 10 57 1 AAGAAAGTTT 0.85275 -137 AAATAACCAAAAAGCAAGGACTGCTGAAAGGGCT 11 12 1 AAGCAAGCTC 0.724185 -181 GACTTCATGAAGTGCAAGAATTTTCTATTGAGTG 11 102 0 AGGCAAGTTT 0.75447 -91 GGAGGGGACGATTGAAAGTCCCCTTGAAATTTGA 12 236 1 ATGAAAGCCT 0.728039 -65 TGCATTAGAAAATGAAGGCGTCGTGAAAGGCAAA 15 211 1 AAGAAGGTCT 0.651221 -90 CGCTGACAAAAAAGCCAGCTTCCTTTCCATATTC 20 16 0 AAGCCAGTCT 0.953834 -94 GTGTAAGAAAAAAGCCAGAGCTTTGAAAAAGGTT 23 244 1 AAGCCAGCTT 0.940659 -57 GAATAGAAAAAAAGCCAGAACCTTTTTCAAAGCT 23 262 0 AAGCCAGCCT 0.974202 -39 ATCCATATATAATGCAAGGATCGTGCCAACACAG 24 139 0 AAGCAAGTCT 0.961767 -51 TCAGTTCTGGAGGGCCAGTCCCCTTCAAAAGTAA 25 108 0 AGGCCAGCCT 0.916331 -193 TATACGCATAAAAGCCAGCTTTGTCAATCTGCTA 25 189 1 AAGCCAGTTT 0.896852 -112 AAAGTGATAAAATGAAAGTATTGTGAGCAAGCTC 29 40 0 AAGAAAGTTT 0.85275 -142 ** ***** ** * Masking position 1 Map Score: 12.6499 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 209 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 AAGGATTTTTAGTAGGATAATAGCTTTATT 1 10 0 AGTAGGATAT 0.535501 -291 TCATAGATAAAGGATAAATATAAATAATATT 1 203 1 AGGATAAAAT 0.53004 -98 AATACATAATGGGCTGAATATGGATATGTTC 8 62 1 GGGCTGAAAT 0.848213 -86 TTTGAAGTACAGGATGAACATATCCATATTC 8 77 0 AGGATGAAAT 0.952226 -71 TCTAAACATAAGTATGAACATTGTATCACAT 8 107 0 AGTATGAAAT 0.824729 -41 TTACAATCTTAGGAGGAAGAAAAAT 12 286 1 AGGAGGAAAA 0.914698 -15 TCCTTTTATCGGGATGAAGATGGTGGGCTTT 15 53 0 GGGATGAAAT 0.893929 -248 GCAAATGGCAGGGAGGAACAAGAA 15 287 1 GGGAGGAAAA 0.819291 -14 GAGGTTATATAAGATGAAAATAAGTTAGTTT 19 59 0 AAGATGAAAT 0.530039 -242 AGGTGGAATATGGAAAGGAAG 20 1 1 AGGTGGAAAT 0.781436 -109 CCCTATTGGCAGGAGGGATATC 22 55 1 AGGAGGGAAT 0.792438 -12 ATTATATATAAGTCTGAATAAGTAAATGATT 23 27 1 AGTCTGAAAA 0.543171 -274 AGCCCGGAACAGGAGGAACATATC 29 4 0 AGGAGGAAAT 0.965681 -178 CTAGATCACTAGTCTGAAAAAGAGTAAAATA 29 128 1 AGTCTGAAAA 0.543171 -54 AATTCCAGAAAGGCGGATCATCT 29 169 1 AGGCGGATAT 0.764049 -13 ******** ** Masking position 10 Map Score: 5.25544 Number of sites scoring better than the average of aligned sites = 895 Number in coding regions = 700 Number in noncoding regions = 195 Number of orfs with sites within 600 bp upstream = 229 Fraction of orfs with sites within 600 bp upstream = 0.0367812 Motif number 9 CAAGTCTTTCTTCCGTTTCTCAGTGTATTTC 3 109 1 TTCCGTTTTC 0.691589 -47 AAAAAAGTGATCCCGGCTCTCCCAGAATCAC 10 19 0 TCCCGGCTTC 0.902935 -175 GCCTCCAATATCCCTTTTATCCATAGAAAAA 11 166 0 TCCCTTTTTC 0.804383 -27 AAAGCAATAATCCCGTCTTCTTTTCCTATTG 12 22 0 TCCCGTCTCT 0.94331 -279 CTGTATGCAATCCGTTCTTTTTCATTGAGAC 13 26 1 TCCGTTCTTT 0.559302 -193 CTGTCATTCCCGCTTTCTTTTTAAATAA 14 8 1 TCCCGCTTCT 0.8837 -164 AGGGGGGTTGTTCCGTTTGCTGATGAATTTT 15 131 0 TTCCGTTTCT 0.691589 -170 TGCATTTTATTTCCTGCTCCTCTTCCTGTAT 15 184 0 TTCCTGCTCT 0.444769 -117 AGATTCCCTTCTTTCTAAATCCCCT 16 267 0 TCCCTTCTTC 0.868632 -15 AGAATGAACTTCCCGTTTTTTTCCCTCAATC 18 68 0 TCCCGTTTTT 0.89145 -171 ATAGCGAATCTTCCCTTTATTAAATCTAATG 19 129 0 TTCCCTTTTT 0.409391 -172 AAGCAAAAAATCCCGTTTTTCACGGGATT 21 9 0 TCCCGTTTTC 0.911878 -81 GATATCCCTCCTGCCAATAGGGTTT 22 52 0 TCCCTCCTCC 0.85951 -15 TTCCTCCTGTTCCGGGCTGCCCCGAGCTTGC 29 17 1 TCCGGGCTCC 0.739232 -165 TGAGGTGTTTTCCCCCCTTTTATAAAATCTG 29 91 0 TCCCCCCTTT 0.790659 -91 AGATGATCCGCCTTTCTGGAATTTGAA 29 165 0 TCCGCCTTCT 0.417174 -17 ******** ** Masking position 8 Map Score: 3.84766 Number of sites scoring better than the average of aligned sites = 1397 Number in coding regions = 1134 Number in noncoding regions = 263 Number of orfs with sites within 600 bp upstream = 257 Fraction of orfs with sites within 600 bp upstream = 0.0412785 Motif number 10 GGTTCGAAAGTCTTGATTTAAAAGGATTTTTA 1 30 0 TCTGATTTAA 0.866786 -271 ATGTATATATTCTTGATCTTAAAGGCTAAGAT 1 167 1 TCTGATCTTA 0.964653 -134 TGTTAAGTTATATTGATCTTAAAATATTCGGA 9 18 1 TATGATCTTA 0.916184 -38 ATAAGATATCTAGTGATCTATACCAATTTTCC 14 111 0 TATGATCTAA 0.916491 -61 GAATTCGTTGTCATGATTTTTAGCTGTAAGGT 18 187 1 TCTGATTTTA 0.866504 -52 CCTCACCATTTCTTGAACTTAACTATCATAAG 20 85 0 TCTGAACTTA 0.836002 -25 GGGTAATTTGTCATGATCTATAAGATTCATTT 25 14 1 TCTGATCTAA 0.951553 -287 TTTTTCAGACTAGTGATCTAGACCAGCTGAGG 29 117 0 TATGATCTAA 0.914912 -65 ** ******* * Masking position 6 Map Score: 2.26162 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 68 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 11 TTTATTTTCATTAAAGATTTTTAATTTTAATT 1 118 1 TAAAGATTTT 0.778558 -183 TTCATGAATATACAAAAGTTTTTATTTTGTCT 4 112 1 TCAAAATTTT 0.795804 -33 TTTCGCTGAGTCCAAGTTTTTTCTTATCATTG 5 76 0 TCAAGTTTTT 0.741052 -86 TTTTTTGGTTTCCAATAATTTTAACGAAAGTT 7 51 1 TCAATATTTT 0.940467 -109 TGCTCGTTTTTAAAATATTTTTTGAAAAAATA 10 104 0 TAAATATTTT 0.729981 -90 GTGTATCAATTCCACGATTTTTTCTGAAATCC 10 136 0 TCACGATTTT 0.809215 -58 CTTCATGAAGTGCAAGAATTTTCTATTGAGTG 11 102 0 TCAAGATTTT 0.953136 -91 CGTCAGTATTTTCAATATTTTTTTTAGTTTTT 19 89 1 TCAATATTTT 0.940465 -212 GTTTACCGCTCCAATAGTTTTTTTTCATTAT 21 69 0 TCAATATTTT 0.940467 -21 TTATCACGTGGGCAATATTTTTTAAATTCAAC 23 164 0 GCAATATTTT 0.767144 -137 * ***** **** Masking position 4 Map Score: 3.07662 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 67 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 12 TCCTTTATCTATGATACCATCTTAGCCTTTAAG 1 184 0 ATGACCATCT 0.407219 -117 AGACTTGTCGACAAACCTATCCTATGAGGAGAA 3 83 0 ACAACTATCT 0.868533 -73 AGGTTTGTCGACAAGTCTTTCTTCCGTTTCTCA 3 98 1 ACAACTTTCT 0.953657 -58 TAGGCTAGAGAAGGACCTTTCATTCAATGATAA 5 52 1 AAGGCTTTCT 0.8335 -110 GCGCTTTCTCAAGGCTCTTTCTTTCATGATGAG 5 112 1 AAGGCTTTCT 0.833562 -50 GTTAAATCAGATGGAACTTTCGTTAAAATTATT 7 64 0 ATGGCTTTCT 0.86813 -96 CAATTAGGTCATAAAGCTTTCATTTCGGGCATA 10 58 0 ATAACTTTCT 0.835579 -136 AAAGAAGGATACAAATCTTTCATATTGGGAGGG 13 71 0 ACAACTTTCT 0.953616 -148 TTTTATTATTACAGCTCTATCATAGGCTGTGCA 15 23 0 ACAGCTATCT 0.870671 -278 TTTGCCTTTCACGACGCCTTCATTTTCTAATGC 15 212 0 ACGACCTTCT 0.898886 -89 AAACAGTTTTTTCATATGAACCTGT 24 3 1 ACAGTTTTCT 0.580038 -187 CTGTGTTGGCACGATCCTTGCATTATATATGGA 24 139 1 ACGACTTGCT 0.817631 -51 GAGCTTGCTCACAATACTTTCATTTTATCACTT 29 40 1 ACAACTTTCT 0.953174 -142 **** ***** * Masking position 1 Map Score: 4.33762 Number of sites scoring better than the average of aligned sites = 257 Number in coding regions = 224 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 13 AGCTCTTACAAAACCCGCTAGCGTTTTTTG 3 11 0 AAACCCGCTA 0.898653 -145 AGAGGGCGCAAAACCCTCTGAATACATAAG 4 17 0 AAACCCTCTG 0.83788 -128 GTAAAATAAAAAACCCGCATAGCTCTCCTA 6 27 0 AAACCCGCAT 0.800614 -184 AAGGAAACCCGCTGCACAGCCTAT 15 5 1 AAACCCGCTG 0.978831 -296 GTTTTACAGCAAGACAGCTGCCACCGAGAA 16 119 1 AAGACAGCTG 0.761481 -163 GCTGACAAAAAAGCCAGCTTCCTTTCCATA 20 19 0 AAGCCAGCTT 0.912085 -91 ATACGCATAAAAGCCAGCTTTGTCAATCTG 25 190 1 AAGCCAGCTT 0.912085 -111 CTAGTGATCTAGACCAGCTGAGGTGTTTTC 29 110 0 AGACCAGCTG 0.885715 -72 ********** Masking position 1 Map Score: 0.979759 Number of sites scoring better than the average of aligned sites = 492 Number in coding regions = 428 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 14 AGTGTGCAGATCACAGCCGTAAGAATTTCTTCA 12 144 1 TCAAGCGAAG 0.92255 -157 CCTTTTACAATCTTAGGAGGAAGAAAAAT 12 282 1 TCTAGGGAAG 0.972947 -19 CTTTTTGTGTTTTTAGCTGAAAGGAGAAGATCA 16 187 0 TTTAGCGAAG 0.957755 -95 GACAACGAATTCACAGGCGTAAGTCTTCCAGTT 18 166 0 TCAAGGGAAG 0.939924 -73 TTGTCATGATTTTTAGCTGTAAGGTCAGACTAG 18 194 1 TTTAGCGAAG 0.957755 -45 AGCTTTGCTGTTTGAGGTGTAAGAAAAAAGCCA 23 228 1 TTTAGGGAAG 0.96751 -73 ATAAAATCTGTTTTAGGTTCAAGCCCGAAAGTG 29 68 0 TTTAGGTAAG 0.794297 -114 *** *** * *** Masking position 5 Map Score: 1.60375 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 72 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 15 ATAGAAAAACGCTGTAAGGGACAAGCTCTT 3 34 0 GCTGTAAGGG 0.982829 -122 AGCAAGGACTGCTGAAAGGGCTGACATAAG 11 24 1 GCTGAAAGGG 0.982831 -169 TGTGTTTTTAGCTGAAAGGAGAAGATCACA 16 185 0 GCTGAAAGGA 0.954519 -97 ATGATTTTTAGCTGTAAGGTCAGACTAGTA 18 199 1 GCTGTAAGGT 0.954517 -40 ********** Masking position 6 Map Score: 0.481366 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 21 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234