AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00251_ecoli_reg_100.orf -o00251_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 carA 300 carbamoyl-phosphate synthetase, glutamine (small) subunit #2 ylbE 266 orf, hypothetical protein #3 glnS 202 glutamine tRNA synthetase #4 aspC 184 aspartate aminotransferase #5 putA 300 proline dehydrogenase, P5C dehydrogenase #6 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #7 goaG 37 4-aminobutyrate aminotransferase #8 gadB 300 glutamate decarboxylase isozyme #9 nadE 201 NAD synthetase, prefers NH3 over glutamine #10 gdhA 235 NADP-specific glutamate dehydrogenase #11 purF 36 amidophosphoribosyltransferase = PRPP amidotransferase #12 cvpA 165 membrane protein required for colicin V production #13 gltX 258 glutamate tRNA synthetase, catalytic subunit #14 guaA 68 GMP synthetase (glutamine-hydrolyzing) #15 guaB 161 IMP dehydrogenase #16 b2659 230 orf, hypothetical protein #17 gabD 22 succinate-semialdehyde dehydrogenase, NADP-dependent activity #18 gshA 72 gamma-glutamate-cysteine ligase #19 yqaB 280 putative phosphatase #20 yqgB 120 orf, hypothetical protein #21 galP 300 galactose-proton symport of transport system #22 sprT 76 orf, hypothetical protein #23 endA 94 DNA-specific endonuclease I #24 yggJ 52 orf, hypothetical protein #25 gltB 300 glutamate synthase, large subunit #26 yhiR 202 orf, hypothetical protein #27 gor 71 glutathione oxidoreductase #28 gadA 210 glutamate decarboxylase isozyme #29 glmS 161 L-glutamine:D-fructose-6-phosphate aminotransferase #30 glnA 300 glutamine synthetase #31 btuB 300 outer membrane receptor for transport of vitamin B12, E colicins, and bacteriophage BF23 #32 adiA 195 biodegradative arginine decarboxylase Motif number 1 CAATGCGCTGGCAGGAGATGACCGGACCCAT 2 162 1 GCAGGAGTGA 0.778073 -105 TGGCAATACTGGAGCAGGGGAA 2 255 1 GGAGCAGGGA 0.833726 -12 GAAAAAAAAAGCGGCAGAGAAGATCTCCACC 3 63 0 GCGGCAGGAA 0.987055 -140 CTTTTTCTCTGCGGCAGTTAACATTTTTGAA 5 111 0 GCGGCAGTAA 0.976588 -190 TTGCATCAAGGCGGCAAGTGAGCGAATCCCG 6 76 1 GCGGCAATGA 0.863276 -199 TAAGTGATTCGGGGGAGCGAACGCAGCCAAG 6 122 1 GGGGGAGGAA 0.977884 -153 TTATTGATGCGCGGGAAGGAAATCCCTACGC 12 77 1 GCGGGAAGAA 0.916142 -89 GAGGAATCAGGCGGGAGTGATAGAATATCGC 13 178 1 GCGGGAGGAT 0.946384 -81 CCGTTTTATCGGGGCAGATATAACATTAAA 16 10 0 GGGGCAGTAT 0.883103 -221 CCGATAAAACGGGGCAGATAATATGTTTAGT 16 29 1 GGGGCAGTAA 0.965631 -202 CAACAGGTTAGGGGGAGTTAACATTAGAGAA 16 119 0 GGGGGAGTAA 0.960299 -112 ATTTTGACAGGCGGGAGGTCAAT 18 60 1 GCGGGAGTCA 0.882202 -13 AGCGGCAGAGGATAGAGCGAAG 22 65 0 GCGGCAGGGA 0.985786 -12 TTGTACGCGTGGGGTAGGGGTTAACAAAAAG 24 28 0 GGGGTAGGGT 0.712093 -25 CTGACGCGCAGCGGTAAGGAAAGGTGCGATG 31 114 1 GCGGTAAGAA 0.714187 -187 ******* *** Masking position 6 Map Score: 15.4556 Number of sites scoring better than the average of aligned sites = 988 Number in coding regions = 924 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 2 TTAGAATGCGCCCCGAACAGGATGACAGGGC 12 126 1 CCCCGAAAGG 0.989075 -40 TGCTTGCTATCCCCGAAGGGCGGGTTACTAT 15 52 0 CCCCGAAGGC 0.984772 -110 GCCAGCAACGGCCCGAAGGGCGAACGTCAGT 19 90 1 GCCCGAAGGC 0.980052 -191 GAGGCCGCCGCCGCGAAAGCGTAACGTTTCT 26 104 0 CCGCGAAGCG 0.849321 -99 CTTTTGTGCGCCCCGAATACGGGCCGATTTT 26 159 1 CCCCGAAACG 0.975715 -44 TAATTTGATCGCCCGAACAGCAATGTTTGGG 28 12 1 GCCCGAAAGC 0.983946 -199 TTTTAAATTGCCCCTAAAAGGCGTTATCATG 30 179 0 CCCCTAAAGG 0.887702 -122 GATGACTTCCCACCGAATGGCAGTGTCCGCA 31 154 0 CACCGAAGGC 0.895524 -147 ACCCCTCCAAGCCCGAAGACCTGCCGGCCAA 31 204 1 GCCCGAAACC 0.964533 -97 GCGCTTTACAGCCCGAAAAGGCCGGAAGATA 32 136 1 GCCCGAAAGG 0.983946 -60 ******* *** Masking position 6 Map Score: 12.5757 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 76 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 3 TCTGGAAAACGCTTGCGCAGCAAGAAGATTG 1 62 0 GCTTGCGCAC 0.944532 -239 CGCAGCATTGGCTTGCGCCACTGATGTAAAC 2 22 0 GCTTGCGCCC 0.965221 -245 TTCACGCCGGGCCGCCAATGCGCTGGCAGGA 2 147 1 GCCGCCAATC 0.680152 -120 TATTGCCAGCGCCTGCGCTTCATCTTTCGCC 2 232 0 GCCTGCGCTC 0.976687 -35 AAGCGCAGGCGCTGGCAATACTGGAGCAGGG 2 243 1 GCTGGCAATC 0.727353 -24 TCATTTTTAAGCTTGCTACGCATGTCACATT 5 196 1 GCTTGCTACC 0.862679 -105 CATCCTTCAAGCCGCCTCTGCCTTGGCTGCG 6 143 0 GCCGCCTCTC 0.932444 -132 TGCAAAAAATGCTTGCTATCCCCGAAGGGCG 15 61 0 GCTTGCTATC 0.870426 -101 TCGGGCCGTTGCTGGCGCAACGTTATCCTTC 19 75 0 GCTGGCGCAC 0.949911 -206 GCAAGAGGTGGCTTCCTCCGCGATGGGAGGA 22 23 0 GCTTCCTCCC 0.893895 -54 TACCAAAACAGCTTTCGCTACGTTGCTGGCT 23 53 1 GCTTTCGCTC 0.721659 -42 TGGATGAGCAGCCTGCTCATCATATTTATGC 25 205 1 GCCTGCTCAC 0.930003 -96 ACGCGCGCCTCCGATTCGCCCCCTTGT 25 284 0 GCCTCCGATC 0.908729 -17 CCGAAAAGAGGCCGCCGCCGCGAAAGCGTAA 26 111 0 GCCGCCGCCC 0.959659 -92 TTCTGGCCGGCTAACCCGGTCACATG 29 6 1 GCCGGCTAAC 0.858465 -156 ********* * Masking position 6 Map Score: 14.8078 Number of sites scoring better than the average of aligned sites = 1784 Number in coding regions = 1676 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 4 TAAGTTGACTTTTAGCGCCCATATCTCCAG 1 172 1 TTTAGCGCCC 0.831577 -129 CTTCGAACAGACATGCGCCCACGCACGCCC 2 198 0 ACATGCGCCC 0.936553 -69 CTGCGCTTCATCTTTCGCCCAACCTTCGAA 2 221 0 TCTTTCGCCC 0.76518 -46 CGGGTAAGCGCAATGCGCCCGGCAATCTAT 6 29 1 CAATGCGCCC 0.846653 -246 ACGGGCTTGAAAAAGCGCCCAATGTATTCC 9 49 0 AAAAGCGCCC 0.9594 -153 TTTTCTGTTAGAATGCGCCCCGAACAGGAT 12 119 1 GAATGCGCCC 0.846653 -47 GGAGTGATAGAATATCGCCCACTTAATTTT 13 191 1 AATATCGCCC 0.818277 -68 ACAGATAATATAAATCGCCCGACATGAAGT 14 24 0 TAAATCGCCC 0.920131 -45 TGACTCACTGACGTTCGCCCTTCGGGCCGT 19 97 0 ACGTTCGCCC 0.877989 -184 TTGTTTTTACAAGAGCGCCCTTGTTCAGTC 20 54 0 AAGAGCGCCC 0.964756 -67 ACACATTATGTAAAGCGCCTGTTGAGCGCT 26 41 0 TAAAGCGCCT 0.607685 -162 TGATACGCTTTTGTGCGCCCCGAATACGGG 26 152 1 TTGTGCGCCC 0.905583 -51 TTAATTTGATCGCCCGAACAGCAAT 28 6 1 TTGATCGCCC 0.841662 -205 TATCGTAATAAAAATCGCCCAAACATTGCT 28 30 0 AAAATCGCCC 0.90863 -181 GCCCGTTTTTTCGGGCGCCCCGAGCCTTGT 29 100 0 TCGGGCGCCC 0.859062 -62 ********** Masking position 6 Map Score: 11.7346 Number of sites scoring better than the average of aligned sites = 723 Number in coding regions = 657 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 5 TTCTTGCTGCGCAAGCGTTTTCCAGAACAGGTT 1 67 1 GAGCGTTTCC 0.885415 -234 TCTCCAGAATGCCGCCGTTTGCCAGAAATTCGT 1 195 1 GCCCGTTGCC 0.984259 -106 GATAAGTGAAGAAGCCGGTTGCACATCCAGCCA 2 86 0 GACCGTTGCA 0.978984 -181 TGCAAAAACAGCCTGCGTTTTCATCAGTAATAG 4 92 1 GCGCGTTTCA 0.950584 -93 TATGACTCCTGTTTCACGTCTATCAG 6 259 0 GCCCTTTTCA 0.9302 -16 TGAACGAAACGGCTCCGCTTTCAGAGGATTCCT 9 78 1 GCCCGTTTCA 0.986579 -124 TATACAGAGCGTAACCGATTGCATCTACCCCTT 15 94 0 GACCGTTGCA 0.978984 -68 CATCACAACTGAAACCGATTACACCAACCACAA 21 23 1 GACCGTTACA 0.947939 -278 AAATGTTAGTGTAAGCGATTACACTGATGTGAT 21 205 1 GAGCGTTACA 0.826538 -96 CGCGGAGGAAGCCACCTCTTGCAGTCATCTTTT 22 32 1 GCCCTTTGCA 0.939164 -45 CATTTGACCTGTATCAGCTTTCCCGATAAGTTG 25 152 1 GACAGTTTCC 0.830914 -149 AGCCATTGCTGGCACCTATTACGTCTCGCGCTA 27 15 1 GCCCTTTACG 0.698431 -57 TTTAAAAGTTGGCACAGATTTCGCTTTATCTTT 30 203 1 GCCAGTTTCG 0.824413 -98 ACAACCTGTAGCATCCACTTGCCGGTCCTGTGA 31 51 1 GACCATTGCC 0.710504 -250 GAAGAAGGATGCCGCAGGTTTCATCAATATTAC 31 260 0 GCCAGTTTCA 0.924434 -41 * * *** ***** Masking position 9 Map Score: 11.7897 Number of sites scoring better than the average of aligned sites = 682 Number in coding regions = 636 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 6 AAATAAAAACGAGCAGAAAAAAGTGGACCAA 1 27 0 GGCAGAAAAA 0.941561 -274 CATGCGTAGCAAGCTTAAAAATGAATGAAAT 5 189 0 AGCTTAAAAA 0.742623 -112 GACACAGAATGCGCATAAAAATAACAGCATA 8 93 1 GGCATAAAAA 0.962582 -208 TTTCGTTCACGGGCTTGAAAAAGCGCCCAAT 9 56 0 GGCTTGAAAA 0.91592 -146 GATGCCGCAAAGGCATAAAAAGTCGATGGCG 12 22 1 AGCATAAAAA 0.864355 -144 AATAAAAATGGCGCTGAAAAAATATTCAACG 12 51 0 GGCTGAAAAA 0.879454 -115 TATGATTTAAGTGCATGAAAATAATTGAGTT 21 166 0 GGCATGAAAA 0.960092 -135 ACAAAATCCTAAGCAGAAAAACGACTTTTTA 28 103 0 AGCAGAAAAA 0.799641 -108 CGCTTTCACGGAGCATAAAAAGGGTTATCCA 30 51 1 GGCATAAAAA 0.962582 -250 GCACGATGGTGCGCATGATAACGCCTTTTAG 30 166 1 GGCATGATAA 0.753501 -135 GGGCTGTAAAGCGCGTGAAAAACAAACATTT 32 119 0 GGCGTGAAAA 0.86468 -77 * ********* Masking position 8 Map Score: 8.49107 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 185 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 7 AAATAATATAAAAAATCCCGCCATTAAGTTG 1 148 1 AAAAATCCGC 0.928397 -153 CCCATATCTCCAGAATGCCGCCGTTTGCCAG 1 189 1 CAGAATGCGC 0.899784 -112 AGGTTGGGCGAAAGATGAAGCGCAGGCGCTG 2 226 1 AAAGATGAGC 0.77932 -41 AGTGTATATAAAGAATGTCGCCAGAAATAAA 6 175 1 AAGAATGCGC 0.958264 -100 CACGGGCTTGAAAAAGCGCCCAATGTATTCC 9 49 0 AAAAAGCCCC 0.550807 -153 TAAGCAAGAAAAAAATGACCCAGGAAAGCAA 10 120 0 AAAAATGCCC 0.87115 -116 GCGCATCAATAAAAATGGCGCTGAAAAAATA 12 58 0 AAAAATGCGC 0.965464 -108 TTACGTTTAGAAAGATGCCGACAACCGGCAA 13 229 0 AAAGATGCGA 0.548252 -30 CCTTTGAAAACAGGATGTAGCG 17 11 1 CAGGATGAGC 0.531441 -12 CCATCAGCGACAAAATCAAGCAATTACGCTA 19 225 1 CAAAATCAGC 0.438146 -56 GCAAGTCGAAAAATATGACGCTACTTTAGCG 19 251 0 AAATATGCGC 0.780317 -30 CTGAGGACTGAACAAGGGCGCTCTTGTAAAA 20 49 1 AACAAGGCGC 0.673057 -72 GGTTAACAAAAAGAATCCCGCTAGTGTAGG 24 10 0 AAGAATCCGC 0.914157 -43 AGTATACCGAAAAGAGGCCGCCGCCGCGAAA 26 117 0 AAAGAGGCGC 0.899784 -86 TTATCGTAATAAAAATCGCCCAAACATTGCT 28 30 0 AAAAATCCCC 0.758207 -181 ACAATAGAAGAAGGATGCCGCAGGTTTCATC 31 268 0 AAGGATGCGC 0.949642 -33 ******* *** Masking position 5 Map Score: 8.96976 Number of sites scoring better than the average of aligned sites = 1019 Number in coding regions = 889 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 8 GCGACGCTCAAGCGTCGCATCAGGCATAAAG 3 15 0 AGCGTCGCAC 0.91828 -188 GCGACGCTTGAGCGTCGCATCCAACAATGAC 3 28 1 AGCGTCGCAC 0.91828 -175 AACATTTTTGAAAGGTGCAACCGCAAAAAAT 5 92 0 AAAGGTGCAC 0.944101 -209 ATGGTTGCACAAAGTTGCAACATCATGGATA 5 231 1 AAAGTTGCAC 0.947533 -70 TGTTGTTCAGAAAGGTGCAACTTAACGTTAT 5 269 0 AAAGGTGCAC 0.944101 -32 CAAAATCATTCAAGTTGCATCAAGGCGGCAA 6 62 1 CAAGTTGCAC 0.885914 -213 CAGGAAGGATAACGTTGCGCCAGCAACGGCC 19 72 1 AACGTTGCGC 0.843615 -209 TTTTGGAGAAGATGGTGCATCCGGGAGGATG 19 125 0 GATGGTGCAC 0.751828 -156 CCACGATGTGAATGTTGCACCAATATAGTGC 30 123 0 AATGTTGCAC 0.932747 -178 ACATTCACATCGTGGTGCAGCCCTTTTGCAC 30 139 1 CGTGGTGCAC 0.777438 -162 CCTGCCGGCCAACGTCGCATCTGGTTCTCAT 31 223 1 AACGTCGCAC 0.947205 -78 ********* * Masking position 8 Map Score: 5.58656 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 208 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 AACAGCATAAAACACCTTACCACCACCCAA 8 115 1 AACACCTTAC 0.836801 -186 TTTAAACTCCTTAAAATGATTGGA 8 287 0 AACTCCTTAA 0.955944 -14 AGGGAACTCCTTAACGTTATTGTC 10 5 1 AACTCCTTAA 0.955944 -231 ATTTCTAAATAACTCCTTTATCCATTTCCT 19 177 1 AACTCCTTTA 0.943388 -104 TTAACACACCTTTATGACAGTCAG 25 5 1 CACACCTTTA 0.797481 -296 TACTTACCGGAACACCTTTACCC 26 190 1 AACACCTTTA 0.927524 -13 TTCGAACTCCTTAAATTTATTTGA 28 197 0 AACTCCTTAA 0.955944 -14 ********** Masking position 2 Map Score: 4.27812 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 33 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 10 TCGATAACCGCAGCATTGGCTTGCGCCACT 2 31 0 CAGCATTGGC 0.8248 -236 GGAGCGAACGCAGCCAAGGCAGAGGCGGCT 6 135 1 CAGCCAAGGC 0.842732 -140 TTGCCCGATGCCGCAAAGGCATAAAAAGTC 12 16 1 CCGCAAAGGC 0.965323 -150 CCGTAACCTTCAGCAATGAAGGTATCGAAG 19 17 1 CAGCAATGAA 0.73764 -264 AACGTTGCGCCAGCAACGGCCCGAAGGGCG 19 82 1 CAGCAACGGC 0.975847 -199 TAAAACGAGCCAGCAACGTAGCGAAAGCTG 23 61 0 CAGCAACGTA 0.65817 -34 TAATAGGTGCCAGCAATGGCTGCAA 27 6 0 CAGCAATGGC 0.970979 -66 TAGGATTTATCCGCAATGGAAGCAAGGCAT 28 153 0 CCGCAATGGA 0.93928 -58 GCTTTACAGCCCGAAAAGGCCGGAAGATAC 32 138 1 CCGAAAAGGC 0.708635 -58 AGATACTTGCCCGCAACGAAGATTCCTTCA 32 162 1 CCGCAACGAA 0.786253 -34 ********** Masking position 1 Map Score: 4.7089 Number of sites scoring better than the average of aligned sites = 915 Number in coding regions = 880 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 11 GATTATTATTTTGAACGCATTTATAAAATTA 8 5 0 TAACATAAAA 0.837383 -296 CATATTGTATTGTTTTTCAATGAAAAAATATTATTCG 8 151 1 TTTCATAAAA 0.837382 -150 TTAAAATGATTGGATCGCATTAAAAAAGTAGGATTTA 8 264 0 TATCATAAAA 0.941313 -37 TCCAGGCTTATCTAACACGCTGATAAACAAGAGGACG 9 15 0 TAACGTAAAA 0.722168 -187 TTACGCATTATTGTTTTCGTTGACAAATTGCGCAACA 13 120 0 TTTCGTAAAA 0.722188 -139 TTTGTTGCTTTTGATCACAATAAGAAAACAAT 16 209 1 TATCATAAAA 0.941307 -22 TCACCTATCTTAATTCACAATAAAAAATAACCATATT 21 264 1 TTTCATAAAA 0.837382 -37 TTAACACACCTTTATGACAGTCAGGAATTGACTGTTT 25 11 1 TATCATAGAA 0.706655 -290 TTAAGTGTAGTGAATTTCAATGAGAAACGTTACGCTT 26 82 1 TATCATAAAA 0.941313 -121 TTGGGCGATTTTTATTACGATAATAAAGTCTGTTTTT 28 38 1 TATCGTAAAA 0.882911 -173 CATTACAGGCTTAATTTAAATAACAAAATCCTAAGCA 28 119 0 TATAATAAAA 0.53507 -92 TTAAATTTATTTGAAGGCAATAAAAAAGTAGGATTTA 28 174 0 TAACATAAAA 0.837384 -37 GACAACGATATAAATCGGAATCAAAAACT 29 143 1 TATGATAAAA 0.630413 -19 * ** ** * * *** Masking position 13 Map Score: 4.50419 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 79 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 12 ATTGCATGAAATAAAAACGAGCAGAAAAAAG 1 35 0 AAAAAACGAG 0.867154 -266 GTTAAATGCCGAAAAAACAGGACTTTGGTCC 4 25 1 GAAAAACAGG 0.935152 -160 GGAAGGTATAAAAAAAACAGGACCAAAGTCC 4 44 0 AAAAAACAGG 0.823049 -141 CTCACGTCTTGCAAAAACAGCCTGCGTTTTC 4 83 1 GAAAAACAGC 0.756054 -102 ATGTCGCCAGAAATAAACGGGCATACGGCCC 6 189 1 AATAAACGGG 0.763651 -86 AGCATTTTTTGCAAAAAGGGGTAGATGCAAT 15 79 1 GAAAAAGGGG 0.905739 -83 TATCTGCCCCGATAAAACGGGGCAGATAATA 16 21 1 GTAAAACGGG 0.909235 -210 TTCAGGAAATGGATAAAGGAGTTATTTAGAA 19 179 0 GATAAAGGAG 0.493544 -102 GGGCGCTCTTGTAAAAACAAGAGTTTTCTCG 20 64 1 GAAAAACAAG 0.867154 -57 CTTACTCCGTGTTAAAACGAGCCAGCAACGT 23 72 0 GTAAAACGAG 0.81931 -23 AATCCTAAGCAGAAAAACGACTTTTTATAAT 28 99 0 AAAAAACGAC 0.58383 -112 CGGGGCGCCCGAAAAAACGGGCATACAGGTT 29 108 1 GAAAAACGGG 0.978123 -54 * ********* Masking position 6 Map Score: 4.19699 Number of sites scoring better than the average of aligned sites = 585 Number in coding regions = 496 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 13 GCGTTTTCCAGAACAGGTTAGATGATCTTT 1 81 1 GAACAGGTTA 0.913166 -220 TCTTGTTTATCAGCGTGTTAGATAAGCCTG 9 20 1 CAGCGTGTTA 0.833877 -182 GTTTCAGTAGCAACGGGTTAGCTTTAAGGA 9 152 1 CAACGGGTTA 0.956034 -50 AATTCTAAATCAGCAGGTTATTCAGTCGAT 15 24 1 CAGCAGGTTA 0.956069 -138 TATCCCCGAAGGGCGGGTTACTATCGACTG 15 46 0 GGGCGGGTTA 0.922723 -116 ATAACTAAAGCAACAGGTTAGGGGGAGTTA 16 130 0 CAACAGGTTA 0.913166 -101 CAGGATTCAAGAGCTGGTTACAGTTACTGA 20 23 1 GAGCTGGTTA 0.89599 -98 CATCCCATGTGACCGGGTTAGCCGGCCAGA 29 12 0 GACCGGGTTA 0.927365 -150 ********** Masking position 10 Map Score: 2.31621 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 229 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 14 CTTTTTGTCGCTTAATGCCTGTAAAACATGC 1 107 1 CTTAAGCCTG 0.788756 -194 TAAAAGTCAACTTAATGGCGGGATTTTTTAT 1 155 0 CTTAAGGCGG 0.868109 -146 CAAAACACTGCTTCACGCCGGGCCGCCAATG 2 136 1 CTTCAGCCGG 0.98301 -131 TCTGCTTTATGCCTGATGCGACGCT 3 5 1 CTTTAGCCTG 0.829408 -198 TCTTTTTGTTCTGTAAGCCGGGTAAGCGCAA 6 11 1 CTGTAGCCGG 0.953078 -264 ATTCAAGTTGCATCAAGGCGGCAAGTGAGCG 6 69 1 CATCAGGCGG 0.718447 -206 ACACTTCATCCTTCAAGCCGCCTCTGCCTTG 6 149 0 CTTCAGCCGC 0.84958 -126 GATCCCCGGGCCGTATGCCCGTTTATTTCTG 6 196 0 CCGTAGCCCG 0.804012 -79 TTGGGCGCTTTTTCAAGCCCGTGAACGAAAC 9 57 1 TTTCAGCCCG 0.689513 -145 CTTCGCCCGACTTCATGTCGGGCGATTTATA 14 15 1 CTTCAGTCGG 0.834841 -54 CTTGCTATCCCCGAAGGGCGGGTTACTATCG 15 50 0 CCGAAGGCGG 0.652053 -112 GTCGGTCAACCTGTATGCCCGTTTTTTCGGG 29 115 0 CTGTAGCCCG 0.9221 -47 TTAGATACCCCTCCAAGCCCGAAGACCTGCC 31 198 1 CTCCAGCCCG 0.887357 -103 ***** ***** Masking position 5 Map Score: 4.83655 Number of sites scoring better than the average of aligned sites = 806 Number in coding regions = 693 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 15 TTTAAACTCCTTAAAATGATTGGATCGCATT 8 280 0 CTCCTAATTT 0.973102 -21 AGGGAACTCCTTAACGTTATTGTCTCTGCTA 10 7 1 CTCCTAATTT 0.973102 -229 TCCCGCCTGATTCCTCAATGTAGTTCGGGTTTCTA 13 159 0 TTCCTAATTT 0.958346 -100 CTTTATCCATTTCCTGAATTTTCTTCTCCTTCGCC 19 192 1 TTCCTAATTT 0.958346 -89 TGTTGAGCGCTTCCTTAACCTCTTTAACCAGGACT 26 17 0 TTCCTAATTT 0.958346 -186 TTCGAACTCCTTAAATTTATTTGAAGGCAAT 28 190 0 CTCCTAATTT 0.973102 -21 ***** ** * ** Masking position 8 Map Score: 1.95684 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 5 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