AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00630_ecoli_reg_100.orf -o00630_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 acnB 300 aconitate hydrase B #2 prpC 41 putative citrate synthase; propionate metabolism? #3 ybbT 229 orf, hypothetical protein #4 ybbU 77 putative regulator #5 gcl 89 glyoxylate carboligase #6 folD 300 5,10-methylene-tetrahydrofolate dehydrogenase; 5,10-methylene-tetrahydrofolate cyclohydrolase #7 gltA 300 citrate synthase #8 hyaA 300 hydrogenase-1 small subunit #9 purU 49 formyltetrahydrofolate deformylase; for purT-dependent FGAR synthesis #10 ychJ 73 orf, hypothetical protein #11 acnA 300 aconitate hydrase 1 #12 fdnG 231 formate dehydrogenase-N, nitrate-inducible, alpha subunit #13 yeaU 81 putative tartrate dehydrogenase #14 eda 36 2-keto-3-deoxygluconate 6-phosphate aldolase and 2-keto-4-hydroxyglutarate aldolase #15 edd 234 6-phosphogluconate dehydratase #16 hycB 124 probable small subunit of hydrogenase-3, iron-sulfur protein (part of formate hydrogenlyase (FHL) complex) #17 fucO 24 L-1,2-propanediol oxidoreductase #18 fucA 300 L-fuculose-1-phosphate aldolase #19 glcB 21 malate synthase G #20 glcD 250 glycolate oxidase subunit D #21 b2997 188 putative hydrogenase subunit #22 ttdA 206 L-tartrate dehydratase, subunit A #23 mdh 300 malate dehydrogenase #24 def 129 peptide deformylase #25 dam 106 DNA adenine methylase #26 fdoG 193 formate dehydrogenase-O, major subunit #27 aceB 268 malate synthase A #28 aceA 29 isocitrate lyase #29 fdhF 197 selenopolypeptide subunit of formate dehydrogenase H Motif number 1 GGCAGGCGATTCTCTTCACGCTCCTGTGAG 1 249 0 TCTCTTCACG 0.910054 -52 TTGATGTTGTTCTCTTAAGGTTTTAGATTG 3 143 1 TCTCTTAAGG 0.862865 -87 TGGTAATTTACCGCTTCAGGTCTATATTTG 6 25 0 CCGCTTCAGG 0.878861 -276 CAGCGACGGTGCGCCTCACCTTCGCAAGAG 6 175 1 GCGCCTCACC 0.718567 -126 TCGCAAGAGGTCGCTTCACGCGATAAATCT 6 196 1 TCGCTTCACG 0.972058 -105 AGGCAAACCATCGCTTCACGTGAGATGCTG 8 206 0 TCGCTTCACG 0.972058 -95 AGGACACCGGGCGCTTATGGTCGGCAAGCG 8 250 0 GCGCTTATGG 0.916794 -51 CTCTGTCGATGCTCTTCTGGGCCGAACTCC 11 98 1 GCTCTTCTGG 0.83748 -203 AACACAAACATCGCGTAACGATTTGATAAC 11 220 0 TCGCGTAACG 0.85311 -81 AAGCCCTGATTCTCTTCAGGGTGAATATTA 11 255 0 TCTCTTCAGG 0.910054 -46 TATCTGCGCTTATCCTTTATGGTTA 15 6 1 GCGCTTATCC 0.836345 -229 TAATTAACAGTCGCTTATGCATTAGCGCAA 23 120 0 TCGCTTATGC 0.824898 -181 ACAGCATCCAGCGCTTCAGGCAACTCCCGC 25 42 0 GCGCTTCAGG 0.974186 -65 TTTCTCTTAACCAGATAAGAAC 26 3 1 TCTCTTAACC 0.744788 -191 AGGTGCTGAATCGCTTAACGATCGACTATC 27 19 0 TCGCTTAACG 0.955819 -250 GTAGTCGAGAGCGCGTATGCGTGATTTGAT 29 161 1 GCGCGTATGC 0.578402 -37 ********** Masking position 6 Map Score: 16.7689 Number of sites scoring better than the average of aligned sites = 1234 Number in coding regions = 990 Number in noncoding regions = 244 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 2 ACCAAGCTGACCGGTCGGCGGTGGTTGAACGGA 3 185 1 CCGTCGCGGG 0.974085 -45 CTGTCGCATCCCGCTCTGCGGAGCGGGTTTTTT 5 14 1 CCGTCGCGGG 0.948087 -76 AGCTTTCAGTCTCAGCGACGGTGCGCCTCACCT 6 163 1 CTCGCACGGG 0.838097 -138 TTTCTTTTGGCCGGGCGGTGGGGATGTTTAGCC 8 42 0 CCGGCGTGGG 0.991304 -259 AAGCTCATCCTTCTGCACTGGCGCACGTCGCCA 8 166 0 TTCGCCTGGG 0.824181 -135 ACTATGTTAACCGAGCAGTAGCGAT 10 3 0 CCGGCGTAGG 0.901356 -71 TGATCCTTGACCCCGCTGCGGCGGGGTTGTCAT 11 145 1 CCCGCGCGGG 0.503851 -156 AACTGGCCTGTCAGGCAGTGGTGCGTTTTTCTA 12 70 1 TCAGCGTGGG 0.88451 -162 GATATCATGATACTGCGGCGGGGCGCTAAAACG 21 64 0 TACGCGCGGG 0.753854 -125 CATTGCCATTCCCTGCTCTGGCGCAATATTCAT 22 56 1 CCCGCCTGGG 0.988558 -151 GGATTAAGGTCGCGGCAGCGGAGCAACATATCT 23 249 1 CGCGCGCGGG 0.655394 -52 AACTCCTGAACACATCTCTGGAGATTT 24 113 1 CACTCCTGGG 0.764534 -17 TTACACCTTCTCCGGCTGTGGAGAAAGCTCCGA 25 71 0 TCCGCGTGGG 0.987094 -36 *** ** **** * Masking position 6 Map Score: 15.8416 Number of sites scoring better than the average of aligned sites = 872 Number in coding regions = 813 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 3 AGTCAAAATTTAAACTACCGCCTCTTTATACTCG 1 18 0 TAAACACCCC 0.659859 -283 CAGAGGATAAGAAAATCACGCAACTTGCGGATTT 3 29 0 GAAAACCCAC 0.964884 -201 TTTTGTCAAAAAAACCCGCTCCGCAGAGCGGGAT 5 21 0 AAAACCCCCC 0.963033 -69 AGCAACCGGCTAAACATCCCCACCGCCCGGCCAA 8 35 1 TAAACTCCAC 0.692397 -266 TACGGTTTAGCAAACACTCTCAACAAGGTTTTTC 9 21 1 CAAACCCCAC 0.879491 -29 ATCGACAGAGAAAACGCGCCCATCCAGGACCAAT 11 74 0 AAAACCCCAC 0.941863 -227 CAAAGCAAATGACAACCCCGCCGCAGCGGGGTCA 11 152 0 GACAACCCCC 0.945289 -149 AATAGCGGTAGAAAAACGCACCACTGCCTGACAG 12 77 0 GAAAACCCCC 0.977868 -155 GACACTCATCGACACGCCCATCCCCAAACAGGCG 16 41 0 GACACCCTCC 0.651964 -84 CTTAACTCGCAAAACACGCACATCACGTAAGTGA 20 50 1 AAAACCCCAC 0.941863 -201 TATTTGTCTGGAAAAATTCACCGCCACAAACTAC 22 166 0 GAAAATCCCC 0.919705 -41 TTCTATTCTAGACAAATCCCCCTCTGATTGACAG 24 65 0 GACAATCCCC 0.817485 -65 AGCGCTTCAGGCAACTCCCGCAACGATAAACCAT 25 29 0 GCAACCCCAC 0.884354 -78 TAACCAGATAAGAACACACACACCAACATTATGG 26 18 1 AGAACCCCAC 0.687316 -176 TGTGCTGAACGAAAAGAGCACAACGATCCTTCGT 27 202 1 GAAAAACCAC 0.792434 -67 TCATGGATCCGAAAACTTCCCCACTGTGAACGAA 27 231 0 GAAAATCCCC 0.919705 -38 ***** * * ** * Masking position 4 Map Score: 12.2569 Number of sites scoring better than the average of aligned sites = 499 Number in coding regions = 440 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 4 CCAGTACCGCAACGGGCAGAATAGCAGGAT 1 196 0 AACGGGCAGA 0.803533 -105 TGACAATGAGAGCGAGGAGAACCGTC 1 285 1 AGCGAGGAGA 0.941669 -16 TTTTGTCAGAAGCGGGGCGCGCTGTCAGGT 6 234 0 AGCGGGGCGC 0.967289 -67 TCTTTCACAGAGCGGCGAGCCAAATAAAAA 7 201 1 AGCGGCGAGC 0.927943 -100 CCGGTGTCGCAAGGAGGAGAGACGTGCGAT 8 281 1 AAGGAGGAGA 0.811771 -20 CAAATTGATAAAAGAGGAGAAACCTTGTGG 11 186 0 AAAGAGGAGA 0.520493 -115 CCCTGTCATTAAGGAGGAGCT 11 290 1 AAGGAGGAGC 0.898437 -11 AGAGAGACAAAACAGCGAGC 12 1 0 AACAGCGAGC 0.792681 -231 TTCGTAAAGCAACAAGGAGAAGG 17 12 1 AACAAGGAGA 0.827381 -13 GCGAAAACGAGGAGATAAACA 19 6 1 AACGAGGAGA 0.942792 -16 TGTTCACAGAAGCAGCGCGCAAAAATCAGC 20 199 1 AGCAGCGCGC 0.675325 -52 ATGATACTGCGGCGGGGCGCTAAAACGAAG 21 61 0 GGCGGGGCGC 0.920403 -128 GGCTGCTTATGGCAGGGAGATAAGG 24 6 0 GGCAGGGAGA 0.746986 -124 TTCTTTGCGGAAGGGGCCGCAAAGGTCCAG 26 98 0 AAGGGGCCGC 0.549384 -96 ACAATGTCGAAACAAGGAGCAATCC 26 179 1 AACAAGGAGC 0.907677 -15 TCGGATCCATGACGAGGAGCTGCACG 27 253 1 GACGAGGAGC 0.92967 -16 ********** Masking position 9 Map Score: 11.9435 Number of sites scoring better than the average of aligned sites = 1221 Number in coding regions = 1088 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 5 AGGTGATTATCACCATGCGAATTAACGAAG 1 73 1 CACCATGCGA 0.741415 -228 TGTCATAGTGCGGCAGGCGATTCTCTTCAC 1 260 0 CGGCAGGCGA 0.983045 -41 CTCCGCAGAGCGGGATGCGACAGACA 5 7 0 CGGGATGCGA 0.96904 -83 AGATTTATCGCGTGAAGCGACCTCTTGCGA 6 196 0 CGTGAAGCGA 0.91162 -105 CAGCATCTCACGTGAAGCGATGGTTTGCCT 8 206 1 CGTGAAGCGA 0.91162 -95 CGCTTATGGTCGGCAAGCGACGTCCCTGTA 8 239 0 CGGCAAGCGA 0.990328 -62 TAATTTTTAACGGCAAGAGAGACAAAACAG 12 16 0 CGGCAAGAGA 0.909402 -216 TTTTGATGGTCAGGAAGTGAGAACCCA 13 65 1 CAGGAAGTGA 0.791218 -17 GCCTGCGTCACGGCATGCAAATTCTGCTTA 23 14 1 CGGCATGCAA 0.808858 -287 CCTGCACACGCAGCAAGCGAATGTAAATGG 26 143 1 CAGCAAGCGA 0.974105 -51 AAACGTACCTCAGCAGGTGAATAAATTTTA 27 85 1 CAGCAGGTGA 0.786438 -184 ********** Masking position 5 Map Score: 11.7452 Number of sites scoring better than the average of aligned sites = 470 Number in coding regions = 419 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 6 GAGAACAACATCAATACAAAAGTTGGAATA 3 127 0 TCAATACAAA 0.849544 -103 AAATATATTCAACACAAATATAGACCTG 6 9 1 TCAACACAAA 0.966301 -292 TTTGCACAAAACAATACAAACTGTGTGGAT 8 105 0 ACAATACAAA 0.874317 -196 GTTATCTCAACACAAAATAATAACCG 11 7 1 TCAACACAAA 0.966301 -294 TAGCCTATGATCAACACAAATATGAAATAT 11 46 1 TCAACACAAA 0.966301 -255 CGATTTGATAACAACCCAAATTGATAAAAG 11 202 0 ACAACCCAAA 0.89194 -99 AATATTAAAGATAACACAAACATCGCGTAA 11 232 0 ATAACACAAA 0.797778 -69 AAAAAACACAAATCAGATGACC 18 3 1 AAAACACAAA 0.797778 -298 CAGCTGCCACACAACACAACAAAGCGAAGC 20 225 1 ACAACACAAC 0.89194 -26 ********** Masking position 4 Map Score: 7.4324 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 31 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 ATCTAGTTTTGGAAAAATATTCCAACTTTTGTAT 3 110 1 GGAAATTTCA 0.955569 -120 GTGGTTGAACGGAATTATGTTACAAGGACAAAAA 3 205 1 GGATATTTCA 0.900167 -25 TTTGAAAGTTGGAAAAATTTTCCAATAAATAGAG 5 55 1 GGAAATTTCA 0.955398 -35 CGATAAAAATGGACCTATTTTTCTTTTGGCCGGG 8 60 0 GGATATTTCT 0.922322 -241 CAAACTGTGTGGATTTATCTTTTAGCGATAAAAA 8 85 0 GGATATTTTA 0.700372 -216 TGCTGGAAAAACCTTGTTGAGAGTGTTT 9 32 0 GGAAACTTTT 0.830011 -18 CGCCCATCCAGGACCAATATTTCATATTTGTGTT 11 58 0 GGAAATTTCA 0.955689 -243 AGCTCATAGGGCAAAAACGTTTCAGTCAGTGTAA 15 124 0 GCAAACTTCA 0.603323 -111 TAGTGTGAAAGGAACAACATTATTGCCCTGTTTT 18 257 1 GGAAACTTTT 0.830011 -44 TGCACAGGTAGGACCAATTTTTCTGTTCTTAACT 20 23 1 GGAAATTTCT 0.965986 -228 TCGCGGCAGCGGAGCAACATATCTTAGTTTATCA 23 258 1 GGAAACTACT 0.649589 -43 TAGAATAGAAGAAATAATCTTTCTAACTCCTGAA 24 89 1 GAAAATTTCT 0.782323 -41 GCAGGGAGTGGGAGTTATTTTTCTTTGCGGAAGG 26 114 0 GGATATTTCT 0.922322 -80 CTCAGCAGGTGAATAAATTTTATTCATATTGTTA 27 93 1 GAAAATTTTT 0.482319 -176 *** *** ** ** Masking position 7 Map Score: 8.50937 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 107 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 8 GCTTTACCCGTTTTTTATTTGGCTCGCCGCTC 7 210 0 TTTTATTTGG 0.84206 -91 AATGGACCTATTTTTCTTTTGGCCGGGCGGTG 8 55 0 TTTTTTTTGG 0.887214 -246 TTCTCCTCTTTTATCAATTTGGGTTGTTATCA 11 195 1 TTTCATTTGG 0.852587 -106 ACAGATGTTCTTTTTGATTTCGCGCAAAAAGA 12 151 1 TTTTATTTCG 0.901467 -81 GATGGTGATGTTGTCAATTTTGATGGTCAGGA 13 48 1 TTTCATTTTG 0.784777 -34 TGCCGATGAAATGTCATTTTCGACACTCATCG 16 64 0 ATTCTTTTCG 0.717625 -61 CCTCAGGTGATTGTCATTTTTGACGAAAACAT 16 95 0 TTTCTTTTTG 0.843259 -30 TGTTTATCTCCTCGTTTTCGC 19 2 0 TCTCTTTTCG 0.665192 -20 TTAAGCGGGCTTTTCGTTTTCGTCTATCTCTT 20 163 0 TTTCTTTTCG 0.936075 -88 ATCGATCGCATTATTGATTTTGCGATTGAGGC 21 129 1 TTTTATTTTG 0.770711 -60 GCAATATTCATTCTTATTTTCGCGTTGATTCA 22 78 1 TTTTTTTTCG 0.931028 -129 TATCAAATTGATGTTGTTTTGGCTGAACGGTA 23 60 1 ATTTTTTTGG 0.577209 -241 GTGGGAGTTATTTTTCTTTGCGGAAGGGGCCG 26 109 0 TTTTTTTGCG 0.663196 -85 TCGGGTGCCTTTTTTATTTCCGAAACGTACCT 27 63 1 TTTTTTTCCG 0.663196 -206 ATGGAAATTGTTTTTGATTTTGCATTTTAAAT 27 157 1 TTTTATTTTG 0.770711 -112 ** ** ****** Masking position 8 Map Score: 6.92811 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 171 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 9 AAGCGACCTCTTGCGAAGGTGAGGCGCACC 6 182 0 TTGCGAAGGT 0.915694 -119 CCAGGTTGATGTGCGAAGGCAAATTTAAGT 7 241 1 GTGCGAAGGC 0.962734 -60 TCTCTCCTCCTTGCGACACCGGCAGGACAC 8 273 0 TTGCGACACC 0.818138 -28 TTGAGAGTGTTTGCTAAACCGTACCGTCAA 9 14 0 TTGCTAAACC 0.79483 -36 AATGACAGGGTTGCGAAGCCCTGATTCTCT 11 270 0 TTGCGAAGCC 0.986676 -31 GTAGGTCAATTTGCGAAGGCGGATTATTTT 12 114 1 TTGCGAAGGC 0.989823 -118 AGTTATTCCGTTGCGAAGACCTGGCATATA 21 165 0 TTGCGAAGAC 0.949079 -24 ATCGCAAAGATTGCTAAGGCTGCTTATGGC 24 23 0 TTGCTAAGGC 0.956984 -107 ********** Masking position 6 Map Score: 6.61949 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 123 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 10 CCATCCTTAACGATTCAGCCACTTTTTTATG 1 130 1 CGTTCAGCCA 0.988503 -171 TAACATAATTCCGTTCAACCACCGCCGACCG 3 196 0 CCTTCAACCA 0.831904 -34 GGATTAATTCCTTTTCAGTCAATTATAGGAT 13 20 1 CTTTCAGTCA 0.896526 -62 AGGGCAAAAACGTTTCAGTCAGTGTAATAAA 15 120 0 CGTTCAGTCA 0.98525 -115 CGGTTACAGGCGTTTCAGTCATAAATCCTCT 15 159 1 CGTTCAGTCA 0.98525 -76 ATTCACAACGCGTTTCATTCAGAGGATTTAT 15 179 0 CGTTCATTCA 0.929345 -56 ATATACCCTACCGTTCAGCCAAAACAACATC 23 69 0 CCTTCAGCCA 0.977934 -232 CAGCATCCAGCGCTTCAGGCAACTCCCGCAA 25 40 0 CGTTCAGGCA 0.960667 -67 GGCTCAATTTCCCTCCATCCAGGAAGGGTTT 26 63 0 CCTCCATCCA 0.789582 -131 CGGTCTCGCTCCAGTTAATCAAATCAC 29 181 0 CGTCCAGTTA 0.715046 -17 ** ******** Masking position 7 Map Score: 8.52045 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 203 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 11 GGTTTTAGATTGCCTGTTATTGAAACCAAG 3 161 1 TGCCTGTTAT 0.871598 -69 AACCTGGCTTTACCCGTTTTTTATTTGGCT 7 218 0 TACCCGTTTT 0.833312 -83 GCTGAGGCTTTGCCCGTTTTGCAGGCGTTA 16 11 1 TGCCCGTTTT 0.982824 -114 ACAAATCAGATGACCGTATTAATTGTTTGT 18 18 1 TGACCGTATT 0.817786 -283 AAGCCCGGAATGACCGTTTTCGGCACAAAC 18 42 0 TGACCGTTTT 0.941675 -259 AATAGAAAAATGACCGTTTTGATAAATATT 18 77 1 TGACCGTTTT 0.941675 -224 TTACGTGATGTGCGTGTTTTGCGAGTTAAG 20 50 0 TGCGTGTTTT 0.759732 -201 CACCTTCGGGTGCCTTTTTTATTTCCGAAA 27 58 1 TGCCTTTTTT 0.680862 -211 AACTGACGACAGCCTGTTTTTCGTCAGAGT 29 62 1 AGCCTGTTTT 0.774572 -136 GAATAAATAGTGCCCGTAATATCAGGGAAT 29 95 1 TGCCCGTAAT 0.815552 -103 ********** Masking position 7 Map Score: 6.00495 Number of sites scoring better than the average of aligned sites = 546 Number in coding regions = 471 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 12 TTATGCAAGTCGGTTGCAGGCG 4 3 0 CGGTTGCAGG 0.955402 -75 TGTTTATGCTCACTTGTAGGTCGGAGTTAA 4 51 1 CACTTGTAGG 0.697123 -27 TGGTAATTTACCGCTTCAGGTCTATATTTG 6 25 0 CCGCTTCAGG 0.747467 -276 AAGCGGGGCGCGCTGTCAGGTTTCGTTTCA 6 225 0 CGCTGTCAGG 0.904165 -76 GAGCTCTGGGCGCTTGCAGGTAAAGGATCC 7 153 0 CGCTTGCAGG 0.96937 -148 CTCCTTGCGACACCGGCAGGACACCGGGCG 8 267 0 CACCGGCAGG 0.875341 -34 CAGTTACGGGGATTAATTCC 13 1 1 CAGTTACGGG 0.71944 -81 ACAATTTTTACACTTTCAGGCCTCGTGCGG 15 71 1 CACTTTCAGG 0.957787 -164 CTATGAGCTCCGGTTACAGGCGTTTCAGTC 15 149 1 CGGTTACAGG 0.878621 -86 TCTGACAACTCAATTTCAGGAGCCTTT 15 218 1 CAATTTCAGG 0.74639 -17 TTACCTCAGGCACCTTCGGGTGCCTTTTTT 27 48 1 CACCTTCGGG 0.84506 -221 ********** Masking position 1 Map Score: 3.99014 Number of sites scoring better than the average of aligned sites = 778 Number in coding regions = 717 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 13 CAGAGAGAGGATTCCATCTG 6 291 0 CAGAGAGAGG 0.942909 -10 TGGGCGCTTGCAGGTAAAGGATCCATTGAT 7 147 0 CAGGTAAAGG 0.780968 -154 ACTGGCCTGTCAGGCAGTGGTGCGTTTTTC 12 71 1 CAGGCAGTGG 0.952074 -161 TTTTGATGGTCAGGAAGTGAGAACCCA 13 65 1 CAGGAAGTGA 0.814568 -17 TGTTTTGAATCAGAGAGAGGTAGCTA 18 285 1 CAGAGAGAGG 0.942909 -16 TGCGCCAGAGCAGGGAATGGCAATGTTTTG 22 51 0 CAGGGAATGG 0.971319 -156 CTGCTTATGGCAGGGAGATAAGG 24 4 0 CAGGGAGATA 0.729352 -126 GCTGCGTGTGCAGGGAGTGGGAGTTATTTT 26 127 0 CAGGGAGTGG 0.990415 -67 CCCGTAATATCAGGGAATGACCCCACATAA 29 107 1 CAGGGAATGA 0.917351 -91 ********** Masking position 6 Map Score: 6.41477 Number of sites scoring better than the average of aligned sites = 363 Number in coding regions = 306 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 14 CTCCGCAGAGCGGGATGCGACAGACA 5 6 0 CGGGATGGAC 0.811357 -84 GTAGATCGAAGGGGATGCGCCTATTTTGTCA 6 256 0 GGGGATGGCC 0.984269 -45 GTAAAGCCAGGTTGATGTGCGAAGGCAAATT 7 235 1 GTTGATGGCG 0.95437 -66 AATACTTTCTGGCGACGTGCGCCAGTGCAGA 8 157 1 GGCGACGGCG 0.9558 -144 AATATTGGTCCTGGATGGGCGCGTTTTCTCT 11 71 1 CTGGATGGCG 0.974388 -230 ACGCCTGTTTGGGGATGGGCGTGTCGATGAG 16 40 1 GGGGATGGCG 0.991844 -85 GGATGGGCGTGTCGATGAGTGTCGAAAATGA 16 52 1 GTCGATGGTG 0.840317 -73 TAATCACTTACGTGATGTGCGTGTTTTGCGA 20 56 0 CGTGATGGCG 0.961915 -195 CAATAATGCGATCGATGCGCCATTTACCACA 21 114 0 ATCGATGGCC 0.789779 -75 ******* *** Masking position 5 Map Score: 2.72211 Number of sites scoring better than the average of aligned sites = 619 Number in coding regions = 592 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 15 GTTGGAATATTTTTCCAAAACTAGATTTAG 3 106 0 TTTTCCAAAA 0.593842 -124 AGCGGGTTTTTTTGACAAAATTTGAAAGTT 5 35 1 TTTGACAAAA 0.733456 -55 GCGCCCCGCTTCTGACAAAATAGGCGCATC 6 244 1 TCTGACAAAA 0.714987 -57 GTTCCGGCAGTCTTACGCAATAAGGCGCTA 7 269 1 TCTTACGCAA 0.736251 -32 GTAGTGAAACTTTTGCACAAAACAATACAA 8 116 0 TTTTGCACAA 0.63828 -185 TGTCATTTGCTTTGCCACAAGGTTTCTCCT 11 172 1 TTTGCCACAA 0.905557 -129 AGAACATCTGTTTGCCACAAAATAATCCGC 12 132 0 TTTGCCACAA 0.905557 -100 TTCTTTTTGATTTCGCGCAAAAAGATTCAG 12 158 1 TTTCGCGCAA 0.740473 -74 GATTGTCATTTTTGACGAAAACATGCCGAT 16 89 0 TTTGACGAAA 0.85338 -36 ATTAATTGTTTGTGCCGAAAACGGTCATTC 18 35 1 TGTGCCGAAA 0.698502 -266 TGGCATATATTTTGCCTCAATCGCAAAATC 21 144 0 TTTGCCTCAA 0.665651 -45 AATGGCAATGTTTTGCGAAATACACTGCGC 22 36 0 TTTTGCGAAA 0.496096 -171 CATTCCCTGCTCTGGCGCAATATTCATTCT 22 62 1 TCTGGCGCAA 0.925927 -145 TCAAGGTTATCTCCCGCAATGGTTTATCG 25 10 1 TCTCCCGCAA 0.814866 -97 TATTCAAAACTCTGACGAAAAACAGGCTGT 29 70 0 TCTGACGAAA 0.84158 -128 ********** Masking position 9 Map Score: 5.72563 Number of sites scoring better than the average of aligned sites = 861 Number in coding regions = 789 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493