AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i002_ecoli_bsub_300.orf -o002_ecoli_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 yohJ 238 orf, hypothetical protein #2 cdd 129 cytidine/deoxycytidine deaminase #3 yeiM 93 putative transport system permease protein #4 yeiC 300 putative kinase #5 deoC 257 2-deoxyribose-5-phosphate aldolase #6 deoA 83 thymidine phosphorylase #7 deoB 51 phosphopentomutase #8 deoD 56 purine-nucleoside phosphorylase #9 deoD 300 purine nucleoside phosphorylase #10 drm 160 phosphodeoxyribomutase #11 ripX 300 integrase/recombinase #12 cdd 118 cytidine/deoxycytidine deaminase #13 yqfF 78 yqfF #14 yqfC 56 yqfC #15 yqfB 24 yqfB #16 yqfA 21 yqfA #17 yqeZ 130 yqeZ #18 rpsU 163 ribosomal protein S21 #19 yutK 136 similar to Na+/nucleoside cotransporter #20 yuzB 262 yuzB #21 pdp 29 pyrimidine-nucleoside phosphorylase #22 nupC 115 pyrimidine-nucleoside transport protein #23 dra 105 deoxyribose-phosphate aldolase #24 deoR 90 transcriptional regulator #25 yxxB 72 yxxB #26 yxeR 69 similar to ethanolamine transporter #27 yxeN 22 similar to amino acid ABC transporter (permease) #28 yxeM 24 similar to amino acid ABC transporter (binding protein) #29 yxeK 185 similar to monooxygenase #30 yxeI 154 similar to penicillin amidase #31 yxeH 39 similar to hypothetical proteins #32 yxeF 87 yxeF Motif number 1 ATCACCCGCAAAAAAATGAGGCGCTATGTT 1 14 1 AAAAAATGAG 0.599397 -225 ACAGAACAATAAAAAAGGGCAGAAAATAAT 4 52 0 AAAAAAGGGC 0.921771 -249 CACCTTCGGCATAAAAGGAAAAGAAG 5 7 0 ATAAAAGGAA 0.770976 -251 GACGTATAGAAAAAAAGGAGGCTTTCAAG 10 142 1 AAAAAAGGAG 0.972797 -19 GGATCAGGATGAAAAAGGCGGATGGTTCGA 11 240 1 GAAAAAGGCG 0.712242 -61 TGTGTATGATTTGAAAGGAGGTTCTAACAC 14 12 0 TTGAAAGGAG 0.513102 -45 TACACATGAGATGAAAGGGGGTTCTTTTTG 14 36 1 ATGAAAGGGG 0.885289 -21 ATGGCAAAGAAAAGGACATCTTTCTAA 17 8 1 AGAAAAGGAC 0.882803 -123 GGCACTTATTATAAAAGGAAGGAGGGATAC 17 104 1 ATAAAAGGAA 0.770976 -27 TATATAATGAAAGAAAGGGGTTG 18 4 0 AAGAAAGGGG 0.926524 -160 AGAAAAGGGCCTGGACAGGC 19 1 1 AGAAAAGGGC 0.886532 -136 ACGGCAAAATAAAAAAGGGCCTGTCCAGGC 19 19 0 AAAAAAGGGC 0.921771 -118 TACTCTTCGGATTAAAGGGGAATTCAA 20 8 0 ATTAAAGGGG 0.774025 -255 AGCGAATACAAATAAAGGAGAAACACAT 22 98 1 AATAAAGGAG 0.843646 -18 ATATCTTAACAAAAAAGGAAGTGTGCGAAG 23 85 1 AAAAAAGGAA 0.846161 -21 TCATACGTTTGAAAAAGGAGAAAACC 26 54 1 GAAAAAGGAG 0.886807 -16 AAATAGAAAAGGCGGGAAAATCAA 28 5 1 AGAAAAGGCG 0.882234 -20 TAAAAACATGATAAAAGGAGTATCGCC 29 169 1 ATAAAAGGAG 0.956307 -17 TAATCTGAATTGAAAAGGGGACTGATCAA 30 136 1 TGAAAAGGGG 0.776957 -19 GCATTCGCCCAAAAAAGGAGGAAAGA 32 72 1 AAAAAAGGAG 0.972797 -16 ********** Masking position 5 Map Score: 22.6738 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 201 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 2 TGCAGACCTTTAATCCGCTGACCATAGGCGCT 1 44 0 TAATCCGCGC 0.891303 -195 TGACGGGCAGAAAGCCGTCGCCCGTACTCATC 3 15 1 AAAGCCGTGC 0.982601 -79 TCATGCCGGTAAACCCGGCGTCAGCGCCAGGT 3 59 0 AAACCCGGGC 0.959366 -35 GTAGGCCGGATAAGGCGTAGACGCATCCGGCA 6 26 1 TAAGGCGTGC 0.963115 -58 GTGACATAACAAAGGCGGAGTCAACGCTCCGC 8 20 0 AAAGGCGGGC 0.989836 -37 TCTAAACAAAAAAGCCGCAGCCACCTGCGG 10 9 0 AAAGCCGCGC 0.98386 -152 AAATTTTGAATCATCCGTTGTCTTTGACGAAT 20 198 1 TCATCCGTGC 0.765597 -65 AGAAAATGCATCAGGCGGAGACAACTATTAAG 22 15 1 TCAGGCGGGC 0.966355 -101 CAGGTGGATGAAAGCCGGCGCCAGCCTGTATA 24 15 1 AAAGCCGGGC 0.993107 -76 GAAACGGCGGTGACTCACCAGA 27 3 1 AACGGCGGGC 0.953251 -20 ******** * * Masking position 6 Map Score: 9.85144 Number of sites scoring better than the average of aligned sites = 304 Number in coding regions = 290 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 3 ACGGGCGACGGCTTTCTGCCCGTCAGAAA 3 10 0 GCTTTCTGCC 0.885431 -84 AGGGCAGATTATTTTCTGCCCTTTTTTATT 4 45 1 ATTTTCTGCC 0.843753 -256 AAACTTCAATATTTTCTGTCGCTCTAAACA 10 33 0 ATTTTCTGTC 0.552601 -128 AGTATAAACCGTTTTCATTCCCGTTGACAA 10 82 0 GTTTTCATTC 0.873824 -79 ATCGACAGCTGTTTTCAGGAATCTTCCCAT 11 77 0 GTTTTCAGGA 0.772579 -224 TGCATTGAAAGTTTTCATCCTGTTTACCGG 11 106 1 GTTTTCATCC 0.968029 -195 ACCGATGATAGTTTTCATACTCTTGATTCA 11 171 0 GTTTTCATAC 0.797052 -130 ACCATCCGCCTTTTTCATCCTGATCCATTT 11 236 0 TTTTTCATCC 0.725677 -65 AAATGTAAGAATTTTCAGCCA 12 2 0 ATTTTCAGCC 0.943884 -117 ACTAATTTGTGTTTTCAGGCTAAATTGTAG 20 133 0 GTTTTCAGGC 0.98098 -130 GCTGGCGCCGGCTTTCATCCACCTGATTT 24 10 0 GCTTTCATCC 0.905355 -81 CTTTTATCATGTTTTTAGGCTGAATAATGC 29 156 0 GTTTTTAGGC 0.772579 -30 CCTTCATGTCGTTTTCAGGCTATAGTCCCA 31 11 0 GTTTTCAGGC 0.98098 -29 ********** Masking position 5 Map Score: 10.1494 Number of sites scoring better than the average of aligned sites = 856 Number in coding regions = 780 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 4 TCCCTCTCTATGCTTGATGTATGCCTGAGTT 1 100 1 TCTTGATGTA 0.75508 -139 GCGTCGCGCATTTTTGATGTATGTTTCACGC 2 21 1 TTTTGATGTA 0.951325 -109 ATAACCTGAGTGTTTGATGAACGTTTG 4 7 0 TTTTGATGAA 0.862551 -294 ATAGTATGCATGTTTTACGTAAAGTAAATTA 4 180 0 TTTTTACGTA 0.93523 -121 TTTTATCCTTTTTGTGACATAACAAAGGCGG 8 34 0 TTGTGACATA 0.68428 -23 TATCACTTTATATTTTACATAATCGCGCGCT 12 64 0 TTTTTACATA 0.740897 -55 AAGGTTTCATTTTTTTATGTATAAAAAAAGA 17 46 0 TTTTTATGTA 0.885936 -85 CTTTGATACATTTGTTACGTATGAAGAGAAG 17 74 1 TTGTTACGTA 0.818026 -57 ACAATAATATTTTTTGATGTCTACACATTTT 19 63 0 TTTTGATGTC 0.755082 -74 TTCTAGATGTTATTTTACATAGTTCGTATTT 20 56 0 TTTTTACATA 0.740897 -207 TCATCCGTTGTCTTTGACGAATAGTGAAAAA 20 208 1 TTTTGACGAA 0.921048 -55 CTTTTCGTTTTATTTGATGTAATGTCAATTC 30 40 1 TTTTGATGTA 0.951312 -115 TAATGTCAATTCTTTGACGAATCGATTTGAC 30 59 1 TTTTGACGAA 0.921048 -96 * ********* Masking position 7 Map Score: 8.05472 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 241 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 5 AATTAATTGTATGATGAATCCATCTCATCT 1 207 1 ATGATGAATC 0.661713 -32 TTACATGATTATGAGGCAACGCC 2 117 1 ATGAGGCAAC 0.848922 -13 TGTCACAAAAAGGATAAAACA 8 46 1 AGGATAAAAC 0.928657 -11 AACGAATGTCATGATGAAACAAACTTCAGC 9 232 0 ATGATGAAAC 0.955292 -69 ACCGGTAAACAGGATGAAAACTTTCAATGC 11 107 0 AGGATGAAAA 0.708544 -194 TATCATCGGTATGATAAACCGGAAGCTCCG 11 191 1 ATGATAAACC 0.64323 -110 GAAATGGATCAGGATGAAAAAGGCGGATGG 11 235 1 AGGATGAAAA 0.708544 -66 ATGCATCAGGCGGAGACAACTATTAAGAGC 22 20 1 CGGAGACAAC 0.65529 -96 TTTCCGTTTTCTGAGGAAACAGTAATTGTA 22 68 1 CTGAGGAAAC 0.920786 -48 TGGATCAGTCCTGATAAAACTGCTTTTGAT 24 57 0 CTGATAAAAC 0.880661 -34 TTCAGATGATATGATAAAACCAATCATACG 26 31 1 ATGATAAAAC 0.930012 -39 CGTTTGAAAAAGGAGAAAACC 26 59 1 AGGAGAAAAC 0.927278 -11 TTGCGTGACCATGAGGGAACGGCATTGAT 29 10 0 ATGAGGGAAC 0.753288 -176 GCCTAAAAACATGATAAAAGGAGTATCGCC 29 166 1 ATGATAAAAG 0.704777 -20 TTTCGTTATGCTGATAAAACCAATTCGTTC 30 90 1 CTGATAAAAC 0.880661 -65 CGCCCAAAAAAGGAGGAAAGA 32 77 1 AGGAGGAAAG 0.786489 -11 ********** Masking position 4 Map Score: 11.0842 Number of sites scoring better than the average of aligned sites = 422 Number in coding regions = 361 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 6 AAAGGTCTGCAAAGAGGGATTGCTGCAAAC 1 65 1 AAAGAGGGAT 0.924404 -174 CATCAAGCATAGAGAGGGATTGCAGTTTGC 1 89 0 AGAGAGGGAT 0.780193 -150 TGACATAACAAAGGCGGAGTCAACGCTCCG 8 21 0 AAGGCGGAGT 0.759814 -36 TAACCGCAGGAAGGAGGGGTGGGACATGGG 9 105 0 AAGGAGGGGT 0.974165 -196 TATAGAAAAAAAGGAGGCTTTCAAG 10 146 1 AAGGAGGCTT 0.639783 -15 ACCATAGGGAAAGGATCGATTAGGACATGG 11 51 1 AAGGATCGAT 0.758504 -250 TTATAAAAGGAAGGAGGGATACACCGCCC 17 112 1 AAGGAGGGAT 0.98539 -19 GTGTATTCGGAGGGAGGGAAAGAGA 18 149 1 AGGGAGGGAA 0.851406 -15 CTTAATCGAAAAGGATCGGTGACCAAAC 21 12 1 AAGGATCGGT 0.637152 -18 GATTTCTGTGAAAGAGGGTTGGACAC 25 57 1 AAAGAGGGTT 0.752111 -16 AAATAGAAAAGGCGGGAAAATCAA 28 9 1 AAGGCGGGAA 0.929022 -16 CAGCCTTTAGAAGGCTGGATTTTTTA 30 7 0 AAGGCTGGAT 0.920596 -148 CAGCCTTCTAAAGGCTGGATCTTTTCGTTT 30 20 1 AAGGCTGGAT 0.920596 -135 TCGCCCAAAAAAGGAGGAAAGA 32 76 1 AAGGAGGAAA 0.714086 -12 ********** Masking position 1 Map Score: 11.3809 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 229 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 7 TAAGAAATCAGCGCTTATTTTTTCGCTCCCC 1 152 0 GCGTTATTTT 0.609272 -87 CAGCTGCAATGATATCTTTTTCAGGTATATG 9 31 1 GATTCTTTTT 0.923303 -270 GTATATGATTGTTCTTTTTTTGGCCGGTGAT 9 55 1 GTTTTTTTTT 0.650638 -246 ATCCGGTTACGATGTTTTTTACCCATGTCCC 9 84 1 GATTTTTTTA 0.712948 -217 TCGACCGGTTGATCTTTTTTTACCAAAACGG 11 266 1 GATTTTTTTT 0.929753 -35 ACATAATCGCGCGCTTTTTTTCACGCCCATT 12 48 0 GCGTTTTTTT 0.771077 -71 AGATGAAAGGGGGTTCTTTTTGT 14 44 1 GGGTCTTTTT 0.753914 -13 CTCTTAGAAAGATGTCCTTTTCTTTGCCAT 17 10 0 GATTCCTTTT 0.715147 -121 TTCTAAGAGAGATGTCTTTTTTTATACATAA 17 32 1 GATTCTTTTT 0.923303 -99 ATGTATCAAAGGTTTCATTTTTTTATGTATA 17 54 0 GGTTCATTTT 0.681421 -77 TCGTATAAAAGATATTTTTTTAAATAAAATT 19 96 1 GATTTTTTTT 0.929753 -41 TATAATTCTAGATGTTATTTTACATAGTTCG 20 61 0 GATTTATTTT 0.859695 -202 TTTTTGTTAAGATATTTTTTAGCATAACCGA 23 69 0 GATTTTTTTA 0.712948 -37 AGGAATATAGGAGTTTATTTTTCGCATTATT 29 133 1 GAGTTATTTT 0.802484 -53 *** ******* Masking position 5 Map Score: 7.75617 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 155 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 8 GCTGATTTCTTAATGTGATCGGTAGCACGTTTTACG 1 171 1 TATGTGACGC 0.962399 -68 AATTTGCGATGCGTCGCGCATTTTTGA 2 2 1 ATTGCGAGGC 0.961058 -128 TTGTGGCTTTATATGTGATCTGAATCTCATTAATTA 2 58 0 AATGTGACGC 0.985897 -72 AAAGCGAGGAATTTGTGACGGGATGCACAGAACAGA 4 77 0 ATTGTGAGGC 0.97757 -224 CAAAATGGGCAGATTTGAGCAGGCTCACAAAATGCG 4 132 0 AATTTGACGC 0.886461 -169 TGCATCACTGTAATGCGATCTGGTTCAAATAATTCA 5 115 0 TATGCGACGC 0.935458 -143 AGATTTCCTTAATTGTGATGTGTATCGAAGTGTGTT 5 162 1 ATTGTGAGGC 0.97757 -96 GATAATGGACATATGTGAGGTGAAACCGC 20 244 1 AATGTGAGGC 0.985899 -19 * ****** * * * Masking position 8 Map Score: 3.7811 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 15 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 ATCTACCCGTAGGCCGGATAAGGCGTAGACGC 6 18 1 AGGCGGATAG 0.964203 -66 TAAAATGGACGGGCTGGATGATAATTTAGATT 9 263 1 GGGCGGATAT 0.983307 -38 GATTGCTTATGGGCTTGATGTTTCAAGAGGAG 13 51 1 GGGCTGATTT 0.854392 -28 AAATAGAAAAGGCGGGAAAATCAA 28 10 1 AGGCGGAAAT 0.947844 -15 TCATGTTTTTAGGCTGAATAATGCGAAAAATA 29 148 0 AGGCGAATAT 0.919057 -38 AGCCTTTAGAAGGCTGGATTTTTTA 30 4 0 AGGCGGATTT 0.985343 -151 AGCCTTCTAAAGGCTGGATCTTTTCGTTTTAT 30 21 1 AGGCGGATTT 0.985343 -134 **** **** ** Masking position 8 Map Score: 3.09763 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 74 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 10 GCTTTTGTAATTCAGGCATTTAATCGCATTTTGTGA 4 108 1 TTCACTTATG 0.982862 -193 TGATATCTTTTTCAGGTATATGATTGTTCTTTTTTT 9 40 1 TTCATTTATG 0.908375 -261 TACTTGAGTTGTCAGACCTCTTAGCGATACAATAGA 10 108 1 GTCACTTAGG 0.923393 -53 ATACTCTTGATTCACCCATATCATAGCATAATAGAA 11 149 0 TTCACTTATG 0.982862 -152 GTACATTCCTCTCTTACCTATAATGGTACCGCTATC 12 91 0 CTCTCTTATG 0.873367 -28 CCGTTATCGGGTCATTTTTATGATTGCTTATGGGCT 13 30 1 GTCATTTATG 0.828943 -49 CAGCGTTCTCCCTTCTTAGAGAGA 15 4 0 TTCTCTTAGG 0.917802 -21 CAACCCCTTTCTTTCATTATATAGACAGGCAGTC 18 9 1 TTCTCTAATG 0.785126 -155 CACGTTCAAACCTTTCATTGAACAAAATTT 23 5 1 TTCACTTATG 0.982862 -101 TTTCTCCTTTTTCAAACGTATGATTGGTTTTATCAT 26 41 0 TTCACTTATG 0.982862 -29 **** * * * ** * Masking position 9 Map Score: 6.29763 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 36 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 11 CCGTCACAAATTCCTCGCTTTTGTAATTCA 4 92 1 TTCCTCGCTT 0.746818 -209 TTCATTCTCCTGGCTTGTCGCCAATA 5 242 0 CTCCTGGCTT 0.90162 -16 TACAGCGGAGCTTCCGGTTTATCATACCGA 11 196 0 CTTCCGGTTT 0.856947 -105 TCTTGATCTACTCCCCGTTTTGGTAAAAAA 11 281 0 CTCCCCGTTT 0.962007 -20 ATAACTTCTCCTCGTTTCTAT 16 5 0 CTCCTCGTTT 0.968452 -17 GTCACCGATCCTTTTCGATTAAGT 21 5 0 CTTTTCGATT 0.749624 -25 AGGCAGACTGCTTTCCGTTTTCTGAGGAAA 22 57 1 CTTTCCGTTT 0.909175 -59 ACGCAAGGGTCTTTTCGCTTGAATAGAAAA 29 34 1 CTTTTCGCTT 0.922453 -152 AAGGCTGGATCTTTTCGTTTTATTTGATGT 30 30 1 CTTTTCGTTT 0.923873 -125 ********** Masking position 2 Map Score: 3.65774 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 182 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 12 CGTAATGCCGGGGAGCGAAAAAATAAGCGC 1 143 1 GGGAGCGAAA 0.923099 -96 AAGCCACAACGGGTTCGTAAACTGTTATCC 2 85 1 GGGTTCGTAA 0.849187 -45 AATTTGTGACGGGATGCACAGAACAGAACA 4 74 0 GGGATGCACA 0.845414 -227 TGGATTGACAGGGTTGGTAATTTTTTACCA 4 270 1 GGGTTGGTAA 0.930285 -31 CAGGAAGGAGGGGTGGGACATGGGTAAAAA 9 99 0 GGGTGGGACA 0.978133 -202 TGTATTCGGAGGGAGGGAAAGAGA 18 150 1 GGGAGGGAAA 0.966041 -14 CTGTGAAAGAGGGTTGGACAC 25 62 1 GGGTTGGACA 0.973713 -11 ********** Masking position 10 Map Score: 2.52702 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 67 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 13 AAGGTCTGCAAAGAGGGATTGCTGCAAACTG 1 66 1 AAGAGGGTTG 0.979403 -173 ATCAAGCATAGAGAGGGATTGCAGTTTGCAG 1 87 0 GAGAGGGTTG 0.986802 -152 CTTGTGGATTGACAGGGTTGGTAATTTTTTA 4 266 1 GACAGGGTGG 0.970922 -35 AACCGCAGGAAGGAGGGGTGGGACATGGGTA 9 103 0 AGGAGGGTGG 0.964713 -198 TATAATGAAAGAAAGGGGTTG 18 1 0 GAAAGGGTTG 0.934758 -163 ATTTCTGTGAAAGAGGGTTGGACAC 25 58 1 AAGAGGGTGG 0.986802 -15 ******* *** Masking position 4 Map Score: 3.27799 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 10 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 14 CGTTGCCTCATAATCATGTAATGGGATAAC 2 108 0 TAATCATGTA 0.786335 -22 TGTTCATATTTAAACATGTGCTCATAGTAT 4 204 0 TAAACATGTG 0.955369 -97 AAAGACGGTTTAAACATGTGTTCATATTTA 4 222 0 TAAACATGTG 0.955369 -79 CGCCCATTTCTAAAAATGTAAAATAAATGT 12 26 0 TAAAAATGTA 0.895615 -93 GTTACACATATAAACATGTACTTTGACATT 18 102 0 TAAACATGTA 0.946565 -62 AAAAGAACTAAAAAAATGTGTAGACATCAA 19 51 1 AAAAAATGTG 0.682722 -86 TATGAATAAATCAAAATGTACCTTTGTCTT 29 93 0 TCAAAATGTA 0.725348 -93 ********** Masking position 6 Map Score: 1.10667 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 18 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 15 AAAGGAATATATCGAAAAAAGAAATGTTCG 9 193 0 ATCGAAAAAA 0.857673 -108 CAATAGACGTATAGAAAAAAAGGAGGCTTT 10 137 1 ATAGAAAAAA 0.911294 -24 TCATAGCATAATAGAACAAAGCGGTAAAAC 11 135 0 ATAGAACAAA 0.925405 -166 CTTAAATTTTATTTAAAAAAATATCTTTTA 19 101 0 ATTTAAAAAA 0.599003 -36 TGATAGATACATTGAAGAAAATACGAACTA 20 38 1 ATTGAAGAAA 0.857672 -225 CAAACCTTTCATTGAACAAAATTTCAATTA 23 17 1 ATTGAACAAA 0.941675 -89 AACATTCCCGATTGAACAAAGTTGAAACAG 25 19 0 ATTGAACAAA 0.941675 -54 TTTCGCTTGAATAGAAAAAATTAATCTTAA 29 46 1 ATAGAAAAAA 0.911294 -140 ********** Masking position 5 Map Score: 4.23156 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 66 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604