AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifis_ecoli_hinf_300.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 queA 92 synthesis of queuine in tRNA; probably S-adenosylmethionine:tRNA ribosyltransferase-isomerase #2 tgt 55 tRNA-guanine transglycosylase #3 yajC 22 orf, hypothetical protein #4 secD 27 protein secretion; membrane protein, part of the channel #5 nrdA 300 ribonucleoside diphosphate reductase 1, alpha subunit, B1 #6 nrdB 233 ribonucleoside-diphosphate reductase 1, beta subunit, B2 #7 yhdG 300 putative dehydrogenase #8 fis 25 site-specific DNA inversion stimulation factor; DNA-binding protein; a trans activator for transcription #9 HI0240 69 protein-export membrane protein (secD) #10 HI0241 107 conserved hypothetical protein #11 HI0243 64 H. influenzae predicted coding region HI0243 #12 HI0244 300 tRNA-guanine transglycosylase (tgt) #13 HI0245 123 queuosine biosynthesis protein (queA) #14 HI0246 300 H. influenzae predicted coding region HI0246 #15 HI0974.1 300 conserved hypothetical protein #16 HI0976 119 conserved hypothetical protein #17 HI0978 40 ribosomal protein L11 methyltransferase (prmA) #18 HI0979 148 nitrogen fixation protein (nifR3) #19 HI1655 71 antigen #20 HI1658 56 hemolysin, putative #21 HI1659 179 ribonucleoside-diphosphate reductase, alpha chain (nrdA) #22 HI1660 141 ribonucleoside diphosphate reductase, beta chain (nrdB) Motif number 1 GGGTCATTTTCACACTATCTTGCAGTGAATCCC 5 177 1 CACTATCTGC 0.873191 -124 AAGGCGTTTACGCCGCATCCGGCATCTCAATA 6 10 0 CGCCATCGGC 0.997964 -224 GCGGCGTAAACGCCTTATCCGGCCTACGGCTCG 6 27 1 CGCTATCGGC 0.997526 -207 GACGCTGGCGCGTCTTATCAGGCCTACAAACCG 6 58 0 CGTTATCGGC 0.994776 -176 GACGCGCCAGCGTCGCATCAGGCTCCGGGTGCC 6 77 1 CGTCATCGGC 0.995698 -157 AAGGCGTTCACGCTGCATCCGGCACCCGGAGCC 6 97 0 CGCCATCGGC 0.997964 -137 GCAGCGTGAACGCCTTATCCGGCCTACGGCTCG 6 114 1 CGCTATCGGC 0.997526 -120 GACGCTGGCGCGTCTTATCAGGCCTACAAATCC 6 146 0 CGTTATCGGC 0.994776 -88 GACGCGCCAGCGTCGCATCAGGCACAGGATGCG 6 165 1 CGTCATCGGC 0.995698 -69 AGGCATTTTACGCCGCATCCTGTGCCTGATGCG 6 178 0 CGCCATCTGT 0.885508 -56 CGGCGTAAAATGCCTTATCCGGCATTAAACTCC 6 196 1 TGCTATCGGC 0.979096 -38 AAATGATTGTTGCAACATCGTGCT 14 2 0 TGCCATCTGC 0.936536 -299 TGCATCAGTCCTTACTATCTGGCATAGAAACTT 15 49 1 CTTTATCGGC 0.926161 -252 TATCCTAATTCGTTATGTCGTGCTATCTTCCCC 22 38 0 CGTTGTCTGC 0.878069 -104 *** **** *** Masking position 8 Map Score: 37.6245 Number of sites scoring better than the average of aligned sites = 1191 Number in coding regions = 566 Number in noncoding regions = 625 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 2 TTTTCTCCACTACGTCAGAAAAACAGTCCAAC 2 33 0 TACGTAAAAA 0.679498 -23 ATGAAACTATTGCGGAAAGAATTCCAAAAACA 5 267 1 TGCGGAGAAT 0.828087 -34 AGATGCCGGATGCGGCGTAAACGCCTTATCCG 6 16 1 TGCGGGAAAC 0.952675 -218 AGGCACAGGATGCGGCGTAAAATGCCTTATCC 6 184 1 TGCGGGAAAA 0.969825 -50 CACGCAAATTTGCGTAAATAATCGGCAAATTT 7 43 0 TGCGTATAAT 0.640016 -258 TACGCAAATTTGCGTGCCAAAATTTTCATTCA 7 59 1 TGCGTCAAAA 0.923493 -242 GTGCAAAAAATGCGTAATATACGCCGCCTTGC 7 252 1 TGCGTAATAC 0.791053 -49 TGTGGCTCTGTGCGTTAGAAAAGAAAAGGAAA 9 45 1 TGCGTAAAAA 0.972089 -25 TTAAAAATTTTGCGTAAAATACCATAAATTGC 10 63 0 TGCGTAATAC 0.791053 -45 TTAATAAAAGTGCGGTAGAAAAATAAAACGTT 11 11 1 TGCGGAAAAA 0.984536 -54 TGTTAAAAAGTGCGGTCAAAAAACGTTTTATT 11 32 0 TGCGGCAAAA 0.956644 -33 CTTATCGGTATTCGTCAAAAAAATAAGGAATA 15 17 1 TTCGTAAAAA 0.679497 -284 AGTGCGGTAAAAATACGCAAAATT 17 3 1 TGCGGAAAAT 0.970606 -38 TCCTTCAAAGTGCGGTGAAAAATTCAACAAAT 21 11 1 TGCGGGAAAA 0.969825 -169 TAAGAAAAAGTGCGGTAAAAATTTGTTGAATT 21 31 0 TGCGGAAAAT 0.970606 -149 ***** * **** Masking position 11 Map Score: 19.2596 Number of sites scoring better than the average of aligned sites = 509 Number in coding regions = 387 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 3 CGTTTTATTTTTCTACCGCACTTTTATTAA 11 9 0 TTACCGCACT 0.995698 -56 TAAAACGTTTTTTGACCGCACTTTTTAACAAA 11 34 1 TTACCGCACT 0.995698 -31 AATTTCTGCCTTTAATCCCACTTCTTTTTGCC 14 45 0 TTATCCCACT 0.916812 -256 ATTTGGGGAATTACACCGAAATTATCTTGGTC 15 86 1 TTACCGAAAT 0.881459 -215 TTTTGCGTATTTTTACCGCACT 17 1 0 TTACCGCACT 0.995698 -40 TAAATCTAATTTATATCGAACTGCTCGACAAC 18 103 0 TTATCGAACT 0.961329 -46 TTGTTGAATTTTTCACCGCACTTTGAAGGA 21 9 0 TTACCGCACT 0.995698 -171 TTCAACAAATTTTTACCGCACTTTTTCTTATT 21 33 1 TTACCGCACT 0.995698 -147 TATTTATCCTTTAAATAGAACTTATCATTTAT 22 118 0 TTATAGAACT 0.709052 -24 ** ******** Masking position 5 Map Score: 15.7525 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 18 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 Motif number 4 GCAACCTTTACCCCCTTTTGGATAGAATAT 1 16 0 CCCCCTTTTG 0.845673 -77 CTAGACTACCCGCCTCTTATTTTAGTCTGA 1 64 1 CGCCTCTTAT 0.735276 -29 TAAATTTCCCTCATTATTAATA 3 6 0 CCCTCATTAT 0.555775 -17 GTGGCTTTCGCGCACCTTAGGTCAGACAAG 5 104 0 CGCACCTTAG 0.863947 -197 TATCGCACCACGCTCATTTTAAATGCAATT 7 176 1 CGCTCATTTT 0.855804 -125 GCGTATATTACGCATTTTTTGCACGAGATG 7 246 0 CGCATTTTTT 0.865286 -55 ATTTTTCTACCGCACTTTTATTAA 11 5 0 CGCACTTTTA 0.886328 -60 GTTTTTTGACCGCACTTTTTAACAAAGGAA 11 40 1 CGCACTTTTT 0.978226 -25 CTAGACTTACCGCCTATTTTATTTAACCTA 13 95 1 CGCCTATTTT 0.756717 -29 TGCCTTTAATCCCACTTCTTTTTGCCAATA 14 41 0 CCCACTTCTT 0.759136 -260 CAATTTCACGCCCACATTTTGCTGTTTGCC 14 128 0 CCCACATTTT 0.936115 -173 TGGGATCTGCCCCACCTTGTTTATCAATAA 14 194 0 CCCACCTTGT 0.915596 -107 TGGGGCAGATCCCACCTTTTTTATTTCAAT 14 210 1 CCCACCTTTT 0.9717 -91 ATGAAATATACGCCCCTTATACCATTCAAA 15 242 1 CGCCCCTTAT 0.951047 -59 AATTTTTCACCGCACTTTGAAGGA 21 5 0 CGCACTTTGA 0.711265 -175 AAATTTTTACCGCACTTTTTCTTATTTTTC 21 39 1 CGCACTTTTT 0.978226 -141 ACGCCCCTATTGTCTTCCCCA 22 2 1 CGCCCCTATT 0.813508 -140 ********** Masking position 7 Map Score: 13.4891 Number of sites scoring better than the average of aligned sites = 815 Number in coding regions = 672 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 5 GGAAGAGAAAAATTTGTTAAAAATAACTGTTCGGC 5 50 0 ATTTTAAAAA 0.375716 -251 TCTCAATTTTTCTTTATGAATGAAAATTTTGGCAC 7 72 0 TTTTTAATAA 0.952495 -229 TTTTAGTCACTATTTTCTAATATGATGATTTTTAT 7 134 1 TTTTCAATTA 0.692554 -167 AATATGATGATTTTTATGAGTAATTATCGCACCAC 7 152 1 TTTTTAGTAT 0.507037 -149 TGTGTTTTCCTTATTAATTTAAGTTAAAAATT 10 86 0 TCTTTAATTA 0.77757 -22 TAGCCAGTGCTACTTTTCAATAACAGGCAAAGTAG 12 51 1 TCTTTAATAA 0.870514 -250 GTAGATCCTGAGTTTGTTAATCATACTAAGGATAA 12 126 0 ATTTTAATAA 0.739665 -175 TTTCTGCTTTTATTTCTAAATCTCAAGGTTCGCAA 14 90 1 TTTTTAATTA 0.911364 -211 TGCCCCACCTTGTTTATCAATAAACGATACAATTA 14 182 0 TTTTTAATAC 0.717819 -119 GTAATCATCCTTTTTATGAATATGATAAAAATCGA 15 135 1 TTTTTAATTA 0.911344 -166 ACGTCCCTTGTGTTTGCTAATCTTACAACTTTTTT 15 207 0 TTTTCAATTA 0.692572 -94 TCCTTAAAATTTTTTATAAGTGAAAGTATATTTTT 15 270 0 TTTTTAGTAA 0.872098 -31 TGCTGTCACCTTCTTCTAAATGAGAGGAAGGTGAT 16 24 1 TCTTTAATAA 0.872111 -96 TTTCTTTTTGTCAATCAAAAAAAGTGTAT 18 5 1 TTTTTAATAA 0.952495 -144 AAAAAAAGTGTATTTTTTAAACAAATTTCACTTTG 18 27 1 TTTTTAAAAA 0.76136 -122 CTTTTTCTTATTTTTCTAAATAAAAAATTTTAATT 21 53 1 TTTTTAATAA 0.929898 -127 AAATAAACGGTTTTTGTGAGAATAAAAATTAAAAT 21 79 0 TTTTTAGATA 0.429694 -101 AAAAACCGTTTATTTTTAAATAAGTTATCTATTGT 21 99 1 TTTTTAATAT 0.744033 -81 * *** * *** * * Masking position 5 Map Score: 12.6076 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 90 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 6 AACGCCTTATCCGGCCTACGGCTCGGTTTGTAGG 6 35 1 CGGCCCGCTC 0.997425 -199 CGCGTCTTATCAGGCCTACAAACCGAGCCGTAGG 6 49 0 CGGCCCAACC 0.963915 -185 CCTGATAAGACGCGCCAGCGTCGCATCAGGCTCC 6 69 1 CCGCCCGCGC 0.994005 -165 CACGCTGCATCCGGCACCCGGAGCCTGATGCGAC 6 88 0 CGGCACGAGC 0.97669 -146 AACGCCTTATCCGGCCTACGGCTCGGATTTGTAG 6 122 1 CGGCCCGCTC 0.997425 -112 CGCGTCTTATCAGGCCTACAAATCCGAGCCGTAG 6 137 0 CGGCCCAATC 0.983415 -97 CCTGATAAGACGCGCCAGCGTCGCATCAGGCACA 6 157 1 CCGCCCGCGC 0.994005 -77 AATGCCTTATCCGGCATTAAACTCCCAACAGGAC 6 204 1 CGGCAAACTC 0.794854 -30 * **** ** *** Masking position 5 Map Score: 8.73251 Number of sites scoring better than the average of aligned sites = 365 Number in coding regions = 294 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 7 CGTTTTAAACCAGCGCCGCGGAA 2 4 0 CAGCGCCGCG 0.991006 -52 GGCCTACAAACCGAGCCGTAGGCCGGATAA 6 41 0 CCGAGCCGTA 0.962568 -193 TAAGACGCGCCAGCGTCGCATCAGGCTCCG 6 74 1 CAGCGTCGCA 0.977752 -160 GCCTACAAATCCGAGCCGTAGGCCGGATAA 6 128 0 CCGAGCCGTA 0.962568 -106 TAAGACGCGCCAGCGTCGCATCAGGCACAG 6 162 1 CAGCGTCGCA 0.977752 -72 AATTATTTTCCAGAGCCACGCATTGTGGCT 9 22 1 CAGAGCCACG 0.962562 -48 TTCTAACGCACAGAGCCACAATGCGTGGCT 9 35 0 CAGAGCCACA 0.963283 -35 TTGCTGTTTGCCGAGTTGCGAACCTTGAGA 14 110 0 CCGAGTTGCG 0.827892 -191 ********** Masking position 5 Map Score: 8.12328 Number of sites scoring better than the average of aligned sites = 998 Number in coding regions = 898 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 8 GTCGTACCTGTTTTTGGAATTCTTTCCGCA 5 277 0 TTTTTGGAAT 0.68284 -24 GGCACGTAAATTTGCCGATTATTTACGCAA 7 36 1 TTTGCCGATT 0.657467 -265 TTTAACAGGCTTTTTTGTTTAAAAAATCTT 12 255 1 TTTTTTGTTT 0.785144 -46 ACGCCCACATTTTGCTGTTTGCCGAGTTGC 14 121 0 TTTGCTGTTT 0.675507 -180 ACGATACAATTATGTTGATTTTTACCAACG 14 164 0 TATGTTGATT 0.659883 -137 TAATCATCCTTTTTATGAATATGATAAAAA 15 136 1 TTTTATGAAT 0.616663 -165 TTCAAAAGGTTTTGCTGATTTCTACGTAAA 15 171 0 TTTGCTGATT 0.910653 -130 ATCTTACAACTTTTTTGAATAATTCAAAAG 15 193 0 TTTTTTGAAT 0.919566 -108 TGAAAGTATATTTTTTGAATGGTATAAGGG 15 255 0 TTTTTTGAAT 0.919566 -46 AAAATACACTTTTTTTGATTGACAAAAAGA 18 13 0 TTTTTTGATT 0.947067 -136 AATTAACTCCTTTTTAGATTAAATTACTAT 20 37 0 TTTTTAGATT 0.694502 -20 GCGGTAAAAATTTGTTGAATTTTTCACCGC 21 22 0 TTTGTTGAAT 0.920948 -158 AAGTAATAAATTTTTTGATTTGATTCTTGA 21 133 0 TTTTTTGATT 0.947067 -47 ********** Masking position 3 Map Score: 8.21819 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 169 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 9 TCTCTTCCCATTGACTTTCCCGGACACCTTG 5 77 1 TTGCTTTCCC 0.955887 -224 TGGGCTTAGTTCGCCTTTCCCAATGAAGCAA 10 36 1 TCGCTTTCCC 0.903077 -72 GCTGGTTATTTTATCTTCCCCGAGGGGAGAT 13 36 1 TTACTTCCCC 0.986172 -88 AAATTAAATATCACCTTCCTCTCATTTAGAA 16 37 0 TCACTTCCTC 0.896397 -83 AAGGTGATATTTAATTTTCTCACTTTCAGCA 16 51 1 TTATTTTCTC 0.707855 -69 ACGCCCCTATTGTCTTCCCCAACTTATGGG 22 10 1 TTGCTTCCCC 0.980686 -132 TTATGTCGTGCTATCTTCCCCATAAGTTGGG 22 28 0 CTACTTCCCC 0.949854 -114 ACGAATTAGGATACTTTCCTCAGTCTTTGAT 22 58 1 ATATTTCCTC 0.642111 -84 TCAGTCTTTGATAGTTTCCCCTGATAAACAG 22 77 1 ATATTTCCCC 0.864107 -65 TATCATTTATTTAGCTTTCCCTGTTTATCAG 22 97 0 TTACTTTCCC 0.968188 -45 *** ******* Masking position 6 Map Score: 7.7226 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 164 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 10 TCCCTTAGGGAAAAATTTTAA 4 2 0 AAAAATTTTA 0.858349 -26 ATGGGAAGAGAAAAATTTGTTAAAAATAAC 5 58 0 AAAAATTTGT 0.752829 -243 TTACACTCAAAGAAATTTGAGTAAGTTCTC 7 103 0 AGAAATTTGA 0.886573 -198 TATTTTACGCAAAATTTTTAACTTAAATTA 10 74 1 AAAATTTTTA 0.780322 -34 TACTAAGGATAAAAATATGACTAAATTTAT 12 108 0 AAAAATATGA 0.7215 -193 GATTAAAGGCAGAAATTTTACATTTCCAAC 14 60 1 AGAAATTTTA 0.849367 -241 TTCACTTATAAAAAATTTTAAGGAAGAAAT 15 281 1 AAAAATTTTA 0.858349 -20 AAAAATACGCAAAATTTTGAAAGGAAAAAC 17 19 1 AAAATTTTGA 0.834637 -22 AAAGTGCGGTAAAAATTTGTTGAATTTTTC 21 27 0 AAAAATTTGT 0.752829 -153 TTTCTAAATAAAAAATTTTAATTTTTATTC 21 65 1 AAAAATTTTA 0.858349 -115 GAATCAAATCAAAAAATTTATTACTTGCGA 21 137 1 AAAAAATTTA 0.642963 -43 ********** Masking position 4 Map Score: 8.96975 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 34 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 11 TTAAAAATAACTGTTCGGCGATTTCTTGAACGGCATA 5 32 0 CGGGGATTTT 0.994104 -269 GAGTGTGTCCTGTTGGGAGTTTAATGCCGGATAAGG 6 208 0 CGGGGTTTTG 0.8892 -26 CTTGCAGTCACAGTATGGTCATTTCTTAACTC 7 279 1 CGGGCATTTT 0.970065 -22 CAATATCCTACGTTATGGCGATTAATT 10 1 0 CTGGGATTTT 0.974725 -107 CCAGTTGCCGCTGTCGGGCTATTTCGTAGATCCTGAG 12 149 0 CGGGTATTGT 0.853129 -152 AACGAATAAACAGTTCGAAGATTTTTTAAACAAAAAA 12 265 0 CGGAGATTTT 0.949566 -36 TTTATCTTCCCCGAGGGGAGATTTTTTCTTGAGATCA 13 45 1 CGGGGATTTT 0.994104 -79 AGTAGCACCCCATATAGGGGATTAATTAAGAGGATTT 14 270 1 CTGGGATTTT 0.974724 -31 * * ** **** ** Masking position 12 Map Score: 3.74666 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 164 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 12 TTTTAACAAATTTTTCTCTTCCCATTGACTT 5 63 1 TTTTCTCTTC 0.738492 -238 CGAAAGCCACTTTTTCCTTCCTGAGTTATCC 5 124 1 TTTTCCTTCC 0.957394 -177 TTGGTCAAAGTTTGGCCTTTCATCTCGTGCA 7 226 1 TTTGCCTTTC 0.888396 -75 AGTTTTCCTTTTCTTTTCTAACG 9 57 0 TTTTCTTTTC 0.947103 -13 TTGGGCTTAGTTCGCCTTTCCCAATGAAGCA 10 35 1 TTCGCTTTCC 0.701677 -73 TCAAAAAACGTTTTATTTTTCTACCGCACTT 11 18 0 TTTTTTTTTC 0.693756 -47 GTCATCATTATTCTACTTTGCCTGTTATTGA 12 67 0 TTCTCTTTGC 0.823502 -234 TTGCTGGTTATTTTATCTTCCCCGAGGGGAG 13 34 1 TTTTTCTTCC 0.739792 -90 AAGGCAGAAATTTTACATTTCCAACTTTCTG 14 65 1 TTTTCATTTC 0.762393 -236 TTGTTTTTCCTTTCAAAATTTTGC 17 27 0 TTTTCCTTTC 0.954003 -14 TTTAAACAAATTTCACTTTGCAAAGCAAGGC 18 42 1 TTTCCTTTGC 0.754897 -107 TAATACGGCATTTTGCCTTGCTTTGCAAAGT 18 56 0 TTTTCCTTGC 0.944775 -93 TTATCATTTATTTAGCTTTCCCTGTTTATCA 22 98 0 TTTACTTTCC 0.731866 -44 **** ****** Masking position 9 Map Score: 7.19396 Number of sites scoring better than the average of aligned sites = 445 Number in coding regions = 349 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 13 TCTGACGTAGTGGAGAAAAA 2 46 1 TGGAGAAAAA 0.911305 -10 TCCTCTGAGATGGATCAAAGAATTGCATTT 7 196 0 TGGATCAAAG 0.932982 -105 TCAATGCTCTTTGAGCAGAGGCGGATCTAC 12 198 0 TTGAGCAGAG 0.917478 -103 GTTTATTCGTTGGAGCAAAA 12 291 1 TGGAGCAAAA 0.968158 -10 CTGTTTATGATGGAGCAAAG 19 62 1 TGGAGCAAAG 0.989009 -10 GATAATGTGTTTGAGAAAAGATCGCAAGTA 21 158 0 TTGAGAAAAG 0.911305 -22 ********** Masking position 4 Map Score: 2.21343 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 165 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 14 AATTTGCGTAAATAATCGGCAAATTTACGT 7 39 0 AATAATCGGC 0.84736 -262 ACAGAAATAAAGAGCTGACAGAACT 8 6 1 AATAAAGAGC 0.737844 -20 ATCAACTACTAATAGCCAGTGCTACTTTTC 12 39 1 AATAGCCAGT 0.874495 -262 GCTACTTTTCAATAACAGGCAAAGTAGAAT 12 59 1 AATAACAGGC 0.800287 -242 TGCTCCAACGAATAAACAGTTCGAAGATTT 12 278 0 AATAAACAGT 0.84787 -23 TTAATCCCAAATGACCAGCATAATTGCTG 13 10 1 AATGACCAGC 0.910426 -114 GGGAAGATAAAATAACCAGCAATTATGCTG 13 26 0 AATAACCAGC 0.97753 -98 ATGCCGTATTAATAGCCAGCCTTGTCGGTT 18 76 1 AATAGCCAGC 0.955086 -73 CTTATTTAAAAATAAACGGTTTTTGTGAGA 21 93 0 AATAAACGGT 0.821337 -87 ********** Masking position 3 Map Score: 3.29149 Number of sites scoring better than the average of aligned sites = 623 Number in coding regions = 589 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 15 GAACAGTTATTTTTAACAAATTTTTCTCTT 5 53 1 TTTTAACAAA 0.765993 -248 CTTCCTGAGTTATCCACAAAGTTATGCACT 5 140 1 TATCCACAAA 0.576938 -161 TTTGGAATTCTTTCCGCAATAGTTTCATGC 5 265 0 TTTCCGCAAT 0.833541 -36 TTGCCGATTATTTACGCAAATTTGCGTGCC 7 47 1 TTTACGCAAA 0.801509 -254 TTTATGGTATTTTACGCAAAATTTTTAACT 10 67 1 TTTACGCAAA 0.801509 -41 TGACCGCACTTTTTAACAAAGGAAATCTT 11 46 1 TTTTAACAAA 0.765993 -19 TCGAAGATTTTTTAAACAAAAAAGCCTGTT 12 258 0 TTTAAACAAA 0.8593 -43 AGCACGATGTTGCAACAATCATTTGGGCG 14 10 1 TTGCAACAAT 0.720091 -291 ATTTTCTCACTTTCAGCAATTTCTACGCTA 16 64 1 TTTCAGCAAT 0.859264 -56 AAACATAGAATTGCAACAATTCACAGGGAT 16 94 1 TTGCAACAAT 0.720091 -26 AAGTGTATTTTTTAAACAAATTTCACTTTG 18 32 1 TTTAAACAAA 0.8593 -117 GCGGTGAAAAATTCAACAAATTTTTACCGC 21 22 1 ATTCAACAAA 0.623734 -158 ********** Masking position 8 Map Score: 4.38578 Number of sites scoring better than the average of aligned sites = 482 Number in coding regions = 414 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312