AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i020_synecho_ctra_300.orf -o020_synecho_ctra_300.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RCY26206 300 Synechocystis #2 RCY07849 300 Synechocystis #3 RCY27056 300 Synechocystis #4 RCY16813 175 Synechocystis #5 RCY36770 293 Synechocystis #6 RCY48012 163 Synechocystis #7 RCY44500 158 Synechocystis #8 RCY37504 210 Synechocystis #9 RCT00053 300 Chlamydia_trachomatis #10 RCT00234 300 Chlamydia_trachomatis #11 RCT00380 245 Chlamydia_trachomatis #12 RCT00382 165 Chlamydia_trachomatis #13 RCT00385 300 Chlamydia_trachomatis #14 RCT00530 300 Chlamydia_trachomatis Motif number 1 TGGCTACCCGCGAAATACCCTCAACCGGGCGCTGT 3 62 0 CGAAACCCTC 0.856833 -239 CTAACGAGACGGGAATACCTTTGGAAAGTTTTATT 3 224 0 GGGAACCTTA 0.922342 -77 TGACTATTTCGGGAATTACCTCTGATTCTAACGAG 3 251 0 GGGAAACCTA 0.884531 -50 GGAAAAACCTTCAAAGAAGCAACAA 4 161 0 GGAAACCTTA 0.916307 -15 TTTTTTTGTCGAGAACCCCCTAGAATTGTGCCTAT 5 198 0 GAGAACCCTA 0.985027 -96 AGGAAATACCCTGGGAAAAGCAATAT 5 278 0 GGAAACCCTA 0.985027 -16 GGAAACCCCCTGAGAGCCAATTTAC 9 1 1 GGAAACCCTA 0.985027 -300 GATACTTTTAGAAAATTCCCATAGCAAAATTTTTA 9 252 0 GAAAACCCAC 0.857599 -49 GAACTCTCTAGAAAACCCCCTTATAAGGCCTTCTG 10 33 1 GAAAACCCTA 0.983777 -268 AAAACGAAGAGAGAAAACCCTCTTCGTTAAAAGAT 11 13 0 GAGAACCCTC 0.98599 -233 TGAAACCACAGAAAAGACGCTTAAACCTTAAAGAA 11 46 0 GAAAACGCTA 0.845471 -200 GTCTTGTGTTGAAAAGAACCTCTTCTTAGAAAGGT 13 119 1 GAAAAACCTC 0.874933 -182 ACCGCCCGTAGAGAAAACCTTTCTAAGAAGAGGTT 13 135 0 GAGAACCTTA 0.91618 -166 CTAGATACACGAAAAAGCCCTCTCCGGATCTGATC 13 217 0 GAAAACCCTC 0.981638 -84 GGCTTGGAAGGAGAATCCTCTTCCCTCAGATAATC 14 226 1 GAGAACTCTC 0.81161 -75 ***** **** * Masking position 5 Map Score: 19.2619 Number of sites scoring better than the average of aligned sites = 499 Number in coding regions = 439 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 2 CCCCCCTTGAGAAGGGGGGAACTGCCGTAAAA 1 129 0 GAAGGGGGAC 0.937144 -172 CCCCCCTTCTCAAGGGGGGCTAGGGGGGATTA 1 142 1 CAAGGGGGCA 0.875916 -159 AGTCAGGGGACAAGGGTGGATGTCGATTAGGG 2 127 0 CAAGGGGGAG 0.974831 -174 GCAAACCAAGCAAGGGCGATCGGGGCACAACA 2 204 0 CAAGGGGATG 0.738415 -97 ACCGGACCAACAAGGAGAGATGCGGCGGCGGT 2 240 1 CAAGGAAGAG 0.585831 -61 CCTTCATGGCCAAGGCTGGTTGGAAGTAATTT 3 13 0 CAAGGCGGTG 0.961696 -288 CAGCATTAGGGAAGGCAGGCCCCTAGGGATTG 4 126 1 GAAGGCGGCC 0.980032 -50 CTAAAATTCCCAAGGCGATCGCCCCTAAAATC 5 120 0 CAAGGCATCC 0.759659 -174 CTAAACCCACCAAGGCCGGACCATTTTCCTGC 6 50 1 CAAGGCGGAC 0.981073 -114 GATTCTATGCGAAGTCGGTCAGCCCCATCTAG 7 89 0 GAAGTCGTCG 0.491998 -70 TGCTTCCTACCAAGGGTAACTGCATCTTTTGC 9 37 1 CAAGGGAACG 0.771907 -264 GCTTTTGTAAGAAGTCAGGAGGCTAGGGTATT 9 179 1 GAAGTCGGAG 0.789447 -122 TTATATTTGCGAAGGCCGGACCTTTCCGGTTA 10 181 1 GAAGGCGGAC 0.963504 -120 TCTGGCTATGCAAGGCCGGCGCGGAAAAGTAA 10 210 0 CAAGGCGGCC 0.989729 -91 CGGATCTGATCAAGGCAAACAGCGGTTACTTA 13 196 0 CAAGGCAACG 0.856988 -105 ****** *** * Masking position 3 Map Score: 13.108 Number of sites scoring better than the average of aligned sites = 644 Number in coding regions = 572 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 3 AATTTTACGGCAGTTCCCCCCTTCTCAAGG 1 127 1 CAGTTCCCCC 0.882995 -174 ACCATAAATAGCCTTCGCCTTTGTGCCCTA 2 102 1 GCCTTCGCCT 0.898482 -199 TGCCCTAATCGACATCCACCCTTGTCCCCT 2 125 1 GACATCCACC 0.798046 -176 TTGTTGTGCCCCGATCGCCCTTGCTTGGTT 2 203 1 CCGATCGCCC 0.984334 -98 TTAACTAGCGGACAGCGCCCGGTTGAGGGT 3 51 1 GACAGCGCCC 0.928514 -250 AATTCCCAAGGCGATCGCCCCTAAAATCCA 5 118 0 GCGATCGCCC 0.991923 -176 TTTTTTTGTCGAGAACCCCCTAGAATTGTG 5 203 0 GAGAACCCCC 0.817634 -91 CTGTGAGGTAGCCTCCGCCCATATTGCTTT 5 258 1 GCCTCCGCCC 0.964776 -36 AAGTCCATTGCCCATCGACCCACATTTGGC 6 102 1 CCCATCGACC 0.897226 -62 GATATAAAACCCCTTCCCCTTTATCTACTG 7 128 1 CCCTTCCCCT 0.698473 -31 GACCATCTAGGCGATCGCCCAAAGGAAAAT 8 73 0 GCGATCGCCC 0.991923 -138 ATTATACTCCGAGACCGCCCGTAGAGAAAA 13 153 0 GAGACCGCCC 0.959845 -148 ********** Masking position 6 Map Score: 11.6016 Number of sites scoring better than the average of aligned sites = 3167 Number in coding regions = 2904 Number in noncoding regions = 263 Number of orfs with sites within 600 bp upstream = 277 Fraction of orfs with sites within 600 bp upstream = 0.0444908 Motif number 4 AGACTAGGTATTTATCCCCCTAAATCTCCTCACT 1 71 1 TTATCCTAAA 0.642066 -230 CTAGGGGGGATTAAACAGCCAAAACCCAACTTTC 1 161 1 TTAACCAAAA 0.935701 -140 AAGATTCAGATTAATACTCCAAAATTTAATTCAA 1 243 1 TTATCCAAAA 0.944004 -58 AAAAAAATTGATCAATCACCAAAAATGATTCAGC 4 96 1 ATAACCAAAA 0.870749 -80 GCAAAGAGATTTCATTTCTCAAAATTATTGCC 6 9 0 TTATTCAAAA 0.943001 -155 AGATCCATTGTTGATCAGTCAAGAAAATAGCAAA 8 16 0 TTATTCAAGA 0.722947 -195 GAATGAGTATTTTATTAGCCAAAATCTCTCCTGA 9 108 0 TTATCCAAAA 0.944003 -193 TAGCAAAATTTTTATTTTTCAAAAAAAGCAAACT 9 232 0 TTATTCAAAA 0.943 -69 AACAAGGAAAATGAAATTTCAAAACTTCAAACCA 10 68 1 ATAATCAAAA 0.868616 -233 TTTCATGTTATTAAACCCTCAAAAGGCATTTTTT 11 138 1 TTAATCAAAA 0.934559 -108 AACATTAAAAATCAAGTTTCAAAACTTGAA 12 7 0 ATAATCAAAA 0.868616 -159 AGGATCGCATATAAAACATTAAAAATCAAGTTTC 12 21 0 ATAATTAAAA 0.455481 -145 GACACAGGATTTTATCCATTAAAATAAAAACCGT 13 88 0 TTATTTAAAA 0.6767 -213 ** ** ****** Masking position 4 Map Score: 7.46186 Number of sites scoring better than the average of aligned sites = 250 Number in coding regions = 187 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 5 GGTGTAGGCAAACCAAGCAAGGGCGATCGG 2 213 0 AACCAAGCAA 0.773569 -88 AAAAACCTTCAAAGAAGCAACAATGACAAT 4 154 0 AAAGAAGCAA 0.874831 -22 AAGACTTGGGAAAATAGGCACAATTCTAGG 5 185 1 AAAATAGGCA 0.776644 -109 GTTCTCGACAAAAAAAGCCAGCAACGGGGT 5 217 1 AAAAAAGCCA 0.927863 -77 ATCAGTCAAGAAAATAGCAAACTGCC 8 7 0 AAAATAGCAA 0.932448 -204 GATACTTAAAAAAAAAGCAAAGTTTGCTTT 9 212 1 AAAAAAGCAA 0.963389 -89 TTATTTTTCAAAAAAAGCAAACTTTGCTTT 9 225 0 AAAAAAGCAA 0.963389 -76 GTTAAAATGCAACAAAGGAACTCTCTAGAA 10 16 1 AACAAAGGAA 0.868915 -285 CAGGAGAGAAAAAATAGGAACGTAAGAGTG 14 103 0 AAAATAGGAA 0.87675 -198 ********** Masking position 6 Map Score: 4.9201 Number of sites scoring better than the average of aligned sites = 243 Number in coding regions = 195 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 6 CGTGCCATGTTTTTGATAGGATA 2 4 0 TTTTGATAGG 0.509992 -297 CCCCGATCGCCCTTGCTTGGTTTGCCTACA 2 211 1 CCTTGCTTGG 0.774505 -90 TCCAACCAGCCTTGGCCATGAAGGTTAACT 3 21 1 CTTGGCCATG 0.550283 -280 ACCTTGCCCATCTGGCTAAGTATCTTTGCG 3 156 0 TCTGGCTAAG 0.8803 -145 TGGACTTTGCCTTTGCTCTGGATTAGGGCA 6 79 0 CTTTGCTCTG 0.896401 -85 TCGACCCACATTTGGCTCGGTAACCTAGAA 6 116 1 TTTGGCTCGG 0.906859 -48 ATGCAGTTACCCTTGGTAGGAAGCAAGTAA 9 32 0 CCTTGGTAGG 0.693996 -269 TAACTGCATCTTTTGCTCAGACAGAGCAAA 9 53 1 TTTTGCTCAG 0.864578 -248 CCTGCTCACTTTTTGCTCTGTCTGAGCAAA 9 64 0 TTTTGCTCTG 0.843078 -237 AAAATAAAAATTTTGCTATGGGAATTTTCT 9 248 1 TTTTGCTATG 0.825228 -53 ATTTCATTTTCCTTGTTCAGAAGGCCTTAT 10 55 0 CCTTGTTCAG 0.483741 -246 TGAATTTCACTCTGGCTATGCAAGGCCGGC 10 222 0 TCTGGCTATG 0.861833 -79 GGACGAAGAGTCTGTCTCAGCCCTTTAGGG 12 93 1 TCTGTCTCAG 0.52978 -73 GTAGAGAAAACCTTTCTAAGAAGAGGTTCT 13 133 0 CCTTTCTAAG 0.659774 -168 CCGCTGTTTGCCTTGATCAGATCCGGAGAG 13 203 1 CCTTGATCAG 0.622957 -98 AATTAAATACCTTTGCTAGGTCGTGACAAC 13 277 0 CTTTGCTAGG 0.93734 -24 TGAGCGATTCTTTGGCCAGG 14 1 0 TTTGGCCAGG 0.6355 -300 TCCTTCCAAGCCTTTCTAGGAAAGGAAAAG 14 208 0 CCTTTCTAGG 0.782247 -93 ********** Masking position 3 Map Score: 7.19552 Number of sites scoring better than the average of aligned sites = 1514 Number in coding regions = 1328 Number in noncoding regions = 186 Number of orfs with sites within 600 bp upstream = 197 Fraction of orfs with sites within 600 bp upstream = 0.0316415 Motif number 7 CCTTCTCAAGGGGGGCTAGGGGGGATTAAAC 1 146 1 GGGGCTAGGG 0.936886 -155 TCTCCGCTATGGTGGCCAGCCAGTGTGTCAA 2 163 1 GGGGCCAGCC 0.977949 -138 AACTTTAACTAGCGGACAGCGCCCGGTTGAG 3 47 1 AGGGACAGCG 0.813726 -254 GAGGGTATTTCGCGGGTAGCCAGGGATAGAT 3 75 1 CGGGGTAGCC 0.96012 -226 GACAATCCCTAGGGGCCTGCCTTCCCTAATG 4 129 0 AGGGCCTGCC 0.851513 -47 GTTAATGCCCAGGGGGCAGCGAATGATTTGG 5 52 0 AGGGGCAGCG 0.965082 -242 ATTGGATTTTAGGGGCGATCGCCTTGGGAAT 5 116 1 AGGGCGATCG 0.75819 -178 CAATATGGGCGGAGGCTACCTCACAGTTTAG 5 253 0 GGGGCTACCT 0.7898 -41 GGGGGCTACCGATTACCAATG 7 1 1 GGGGCTACCG 0.971093 -158 ATTGGCTCTCAGGGGGTTTCC 9 1 0 AGGGGTTTCC 0.588163 -300 TAAGAAGTCAGGAGGCTAGGGTATTCGATAC 9 186 1 GGGGCTAGGG 0.936887 -115 GCCTTCCAAACGAGGGTATCCCGAAGGATCG 12 48 0 CGGGGTATCC 0.872589 -118 GCTTGCTTATCGTGGGTACCGCTCTCTCCCT 14 57 1 CGGGGTACCG 0.937222 -244 ** ******** Masking position 5 Map Score: 6.70762 Number of sites scoring better than the average of aligned sites = 717 Number in coding regions = 672 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 8 TTGTAATTTTCAAACGCTTTCTTAGATAACGATG 1 38 0 CAAACTTTCA 0.955941 -263 GCCTATTTTCCCAAGTCTTTGACACCATTGAGCA 5 170 0 CCAACTTTGA 0.959194 -124 ATAAGGCTCTCCAATTCTAGGTTACCGAGCCAAA 6 126 0 CCAACTAGGA 0.90997 -38 GAAGACCGTTCAAATTCTATCAGATTTCTGCCGG 8 127 0 CAAACTATCA 0.955941 -84 ATCAGTTGAACAAATACTTTGGAATGAGTATTTT 9 129 0 CAAACTTTGA 0.955941 -172 TGACTTCTTACAAAAGCTAGCAGAGCTTGGCTTA 9 162 0 CAAACTAGCA 0.903187 -139 CTGCTGGGCGCCAAGTCTATGCTACAAAAAAAAA 10 141 0 CCAACTATGA 0.959194 -160 GAACAACCTGCAAAAACTATGACAACCCTAAAGG 12 114 0 CAAACTATGA 0.955941 -52 CGCCCGTAGAGAAAACCTTTCTAAGAAGAGGTTC 13 134 0 GAAACTTTCA 0.737496 -167 GATTCTCCTTCCAAGCCTTTCTAGGAAAGGAAAA 14 209 0 CCAACTTTCG 0.830572 -92 **** ***** * Masking position 8 Map Score: 4.35795 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 118 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 9 TCCTTTTTAAGCCGGAGCTTTAGTGAGGAGA 1 95 0 GCCGGAGCTT 0.992964 -206 ATTCGCTGCCCCCTGGGCATTAACCCATGGA 5 59 1 CCCTGGGCTT 0.953839 -235 ACCCACCAAGGCCGGACCATTTTCCTGCCCT 6 54 1 GCCGGACCTT 0.986624 -110 TCAGATTTCTGCCGGGGGGTTAGTTAAGGAG 8 111 0 GCCGGGGGTT 0.964062 -100 ATTTGCGAAGGCCGGACCTTTCCGGTTACTT 10 185 1 GCCGGACCTT 0.986624 -116 ACCGCTCTCTCCCTGAGCATTCGAAATAACA 14 74 1 CCCTGAGCTT 0.961426 -227 ******** ** Masking position 10 Map Score: 3.46807 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 90 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 10 CCTAGCCCCCCTTGAGAAGGGGGGAACTGCCG 1 134 0 CTGAAAGGGG 0.862581 -167 AAGGGTGGATGTCGATTAGGGCACAAAGGCGA 2 116 0 GTGATAGGGC 0.984533 -185 CGAGAACCCCCTAGAATTGTGCCTATTTTCCC 5 192 0 CTGATTGTGC 0.878869 -102 TGCCTTTGCTCTGGATTAGGGCAGGAAAATGG 6 70 0 CTGATAGGGC 0.99044 -94 CGCCTAGATGGTCGAAAAGTGCTCCTTAACTA 8 90 1 GTGAAAGTGC 0.901094 -121 TTGGAATACAGCGGATTAGGACTGCGGAAGAC 8 155 0 GCGATAGGAC 0.801054 -56 TTAGGAAGAACTTGAGTAGGGCGCCC 12 150 1 CTGATAGGGC 0.99044 -16 CAAGCAGAATCCCGACTAGTGCATAGATGTAT 14 30 0 CCGATAGTGC 0.958213 -271 ** ** ****** Masking position 5 Map Score: 3.46533 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 132 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 11 CACTAAAGCTCCGGCTTAAAAAGGAGAATTT 1 101 1 CCGGCTAAAA 0.663085 -200 AAGGGGGGAACTGCCGTAAAATTCTCCTTTT 1 119 0 CTGCCGAAAA 0.921114 -182 GATTTCTGGGGGAAAACTTAGTTTTT 2 285 0 CTGGGGAAAA 0.955363 -16 CTGGAGCACTGTGCCGCAAAGATACTTAGCC 3 142 1 GTGCCGAAAG 0.895523 -159 ATATACACAGGTGGGGCAAAAAAAATTGATC 4 78 1 GTGGGGAAAA 0.931333 -98 TGCTCTAGGACTGGGTGAAAAGTAGTCATGG 5 13 1 CTGGGTAAAA 0.860181 -281 GTGTCAAAGACTTGGGAAAATAGGCACAATT 5 179 1 CTTGGGAAAT 0.603827 -115 AGGAAATACCCTGGGAAAAGCAATATGGGC 5 274 0 CCTGGGAAAG 0.832597 -20 TTTCTGGGTAGTGCCGAAAAGTTTTTTTTTG 10 120 1 GTGCCGAAAG 0.895523 -181 TGCAAGGCCGGCGCGGAAAAGTAACCGGAAA 10 203 0 GCGCGGAAAG 0.872259 -98 TGGATAAAGGGTTCCTGAAAAATTCTAGAAT 10 271 0 GTTCCTAAAA 0.458051 -30 AGAAAACCCTCTTCGTTAAAAGATCT 11 6 0 CTTCGTAAAA 0.677907 -240 TGGAAGGCTACTTGGGTAAAGAGGACGAAGA 12 71 1 CTTGGGAAAG 0.90785 -95 ****** **** Masking position 8 Map Score: 4.65555 Number of sites scoring better than the average of aligned sites = 2070 Number in coding regions = 1852 Number in noncoding regions = 218 Number of orfs with sites within 600 bp upstream = 241 Fraction of orfs with sites within 600 bp upstream = 0.0387086 Motif number 12 CTTTAGTGAGGAGATTTAGGGGGATAAATA 1 79 0 GAGATTTAGG 0.95944 -222 TTTTAAGCCGGAGCTTTAGTGAGGAGATTT 1 92 0 GAGCTTTAGT 0.778965 -209 CACCATAGCGGAGATTTTAGTCAGGGGACA 2 147 0 GAGATTTTAG 0.951429 -154 ACACTGCAAAGAGATTTCATTTCTCAAAAT 6 18 0 GAGATTTCAT 0.847639 -146 GGATCTACAAGAGATTTAAGAGATAAAACC 8 188 1 GAGATTTAAG 0.951429 -23 TAGATCAGGAGAGATTTTGGCTAATAAAAT 9 104 1 GAGATTTTGG 0.95944 -197 TCTCCTCATTGAGATTTTATCCACCCAGAT 14 141 1 GAGATTTTAT 0.90462 -160 ********** Masking position 2 Map Score: 2.9577 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 47 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 13 TTCTAACTATTTTCAACTATGGATTAGCTA 4 46 0 TTTCAACTAT 0.626946 -130 AATTTTTATTTTTCAAAAAAAGCAAACTTT 9 230 0 TTTCAAAAAA 0.890181 -71 GAAAATGAAATTTCAAAACTTCAAACCAAC 10 74 1 TTTCAAAACT 0.90732 -227 CTAGAATGTCTTTCAAATAAATCTTTTGAA 10 248 0 TTTCAAATAA 0.747971 -53 TTTTCTGTGGTTTCAAAAAATGTTTAGTGT 11 66 1 TTTCAAAAAA 0.890181 -180 AAAAATCAAGTTTCAAAACTTGAA 12 5 0 TTTCAAAACT 0.90732 -161 GGTGATTTTTTTTCAAAAGTCGCCTAATAT 13 37 1 TTTCAAAAGT 0.785039 -264 AAGAGGTTCTTTTCAACACAAGACACAGGA 13 113 0 TTTCAACACA 0.84718 -188 ********** Masking position 5 Map Score: 1.78834 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 77 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 14 TAGATCCCTTGGAATACAGCGGATTAGGACTG 8 163 0 GGAACAGCGG 0.995235 -48 ATCTGATCAAGGCAAACAGCGGTTACTTATAA 13 193 0 GGAACAGCGG 0.995235 -108 CGAATGCTCAGGGAGAGAGCGGTACCCACGAT 14 65 0 GGAAGAGCGG 0.995235 -236 TTCTAGGAAAGGAAAAGAGAGGTCCTTCAGAC 14 193 0 GGAAGAGAGG 0.981334 -108 ** * ******* Masking position 6 Map Score: 1.31604 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 = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 15 CTAGTCTTGTAATTTTCAAACGCTTTCTTA 1 48 0 AATTTTCAAA 0.653074 -253 GCCAAAACCCAACTTTCCAAATATGCTCTA 1 178 1 AACTTTCCAA 0.922904 -123 GGCTCAATAAAACTTTCCAAAGGTATTCCC 3 219 1 AACTTTCCAA 0.922904 -82 GGAAAAACCTTCAAAGAAGCAACAA 4 161 0 AACCTTCAAA 0.966117 -15 TGAAATTTCAAAACTTCAAACCAACTTCAT 10 79 1 AAACTTCAAA 0.787165 -222 CATGTTATTAAACCCTCAAAAGGCATTTTT 11 141 1 AACCCTCAAA 0.869486 -105 ATTAAAAATCAAGTTTCAAAACTTGAA 12 8 0 AAGTTTCAAA 0.73615 -158 TTACCCAAGTAGCCTTCCAAACGAGGGTAT 12 60 0 AGCCTTCCAA 0.846038 -106 CTAAACGAACAACCTGCAAAAACTATGACA 12 124 0 AACCTGCAAA 0.869486 -42 ********** Masking position 9 Map Score: 2.54059 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 96 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529