AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00020_bsub_reg_300.orf -o00020_bsub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: mmgC 27 acyl-CoA dehydrogenase Input sequences: #1 citA 108 citrate synthase I #2 yjlC 300 yjlC #3 yjlD 39 similar to NADH dehydrogenase #4 yjmA 197 similar to glucuronate isomerase #5 yjmB 67 similar to Na+:galactoside symporter #6 yjmC 104 similar to malate dehydrogenase #7 pdhA 300 pyruvate dehydrogenase (E1 alpha subunit) #8 pdhC 114 pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit) #9 ylaM 102 similar to glutaminase #10 ylaN 97 ylaN #11 ylaO 205 similar to cell-division protein #12 pycA 74 pyruvate carboxylase #13 ylxM 176 similar to hypothetical proteins #14 rpsP 105 ribosomal protein S16 (BS17) #15 ylqD 121 ylqD #16 rplS 130 ribosomal protein L19 #17 ylqF 142 similar to hypothetical proteins #18 rnh 70 ribonuclease H #19 ylqG 31 ylqG #20 sucC 172 succinyl-CoA synthetase (beta subunit) #21 sucD 28 succinyl-CoA synthetase (alpha subunit) #22 citB 227 aconitate hydratase #23 odhB 29 2-oxoglutarate dehydrogenase complex (dihydrolipoamide transsuccinylase, E2 subunit) #24 odhA 227 2-oxoglutarate dehydrogenase (E1 subunit) #25 yojN 63 similar to nitric-oxide reductase #26 yojM 92 similar to superoxide dismutase #27 yojL 300 similar to cell wall-binding protein #28 yqiS 124 similar to phosphate butyryltransferase #29 yqiR 152 similar to transcriptional regulator (sigma-L-dependent) #30 mmgD 33 citrate synthase III #31 mmgB 149 3-hydroxybutyryl-CoA dehydrogenase #32 mmgA 137 acetyl-CoA acetyltransferase #33 yqiK 78 similar to glycerophosphodiester phosphodiesterase #34 yqiH 300 alternate gene name: yzpA; similar to lipoprotein #35 sdhA 33 succinate dehydrogenase (flavoprotein subunit) #36 sdhC 292 succinate dehydrogenase (cytochrome b558 subunit) #37 citH 43 malate dehydrogenase #38 citC 163 isocitrate dehydrogenase #39 citZ 300 citrate synthase II #40 pckA 300 phosphoenolpyruvate carboxykinase #41 citG 300 fumarate hydratase Motif number 1 TTCTATTCTCCCTCTGATTAATATTT 1 7 1 TCTCCCTCTG 0.618333 -102 AAGGGTAGTGCCTCTCCCTGTCTCACGCTT 2 237 0 CCTCTCCCTG 0.907071 -64 CGTATATCCTCCGTCCTTTATATCAAT 3 23 0 CCTCCGTCCT 0.731302 -17 GCAAGTGCCTCCTTCCTTTTCAGTTTT 6 88 0 CCTCCTTCCT 0.744261 -17 ACTAAGTCACCTCTTCCTTTCTTTTAAAC 7 282 0 CCTCTTCCTT 0.913349 -19 AAACGTTCATCTTCCCTCTCGATTATGCAG 8 16 0 CTTCCCTCTC 0.428648 -99 AACATCCTCTTCCCTGCTTCTAACT 11 191 0 CCTCTTCCCT 0.879433 -15 ACTTTTCTCCCCCTTACCCGAATGG 12 60 0 TCTCCCCCTT 0.977326 -15 TTGAGCTCTCCCCTTTGTTAAGTCAA 13 161 0 TCTCCCCTTT 0.905349 -16 AGGTGCCGGCCCTCTCCCTT 15 1 0 CCTCTCCCTT 0.974417 -121 AGGGCCGGCACCTCCCCTTTTTTTACACGC 15 18 1 CCTCCCCTTT 0.958322 -104 TTTCTCTTCTCCCTTACTGTATGTA 18 56 0 CTTCTCCCTT 0.848171 -15 TTTTTCATTTCCCCCTTAGTTTTTGCG 23 13 0 TTTCCCCCTT 0.863424 -17 ACTGTCTCCCCCTTGTTTTTTCTA 26 79 0 TCTCCCCCTT 0.977326 -14 CGAAGCAGTTTCTCCTCCTTTCTTGTCTAT 27 28 0 TCTCCTCCTT 0.922651 -273 TCTTGTTTCGACTCCGCCTTTTATTATGCA 28 92 0 ACTCCGCCTT 0.714239 -33 ATCCTCAACCTCCGTTTTTGCGTTTTTT 30 16 0 CCTCCGTTTT 0.466029 -18 ATGACCACCTCTTCCTGATGTTTGGCT 34 284 0 CCTCTTCCTG 0.729815 -17 GATAGCCCCTCTCCCTCTAGTAATCTA 35 17 0 CCTCTCCCTC 0.927645 -17 ATCTGTCTCCCCTCTCTCCTGCGTA 36 6 1 TCTCCCCTCT 0.868752 -287 ATTCTGTAATCCTCCCCCCTGTTTGAGCTA 36 41 0 CCTCCCCCCT 0.986245 -252 ATTTCATTTTACTCCTCCCTCAAAAGGGCG 36 182 0 ACTCCTCCCT 0.649056 -111 ATGTGCTAAATCTCTTCCCCCACTTCTTTC 36 244 0 TCTCTTCCCC 0.505283 -49 GTCTCTCTTCTCCTTTATGGCTAGTT 37 28 0 CTTCTCCTTT 0.553504 -16 TGCAAGTATTTCTCTCCCCCAAAAAGAAAA 39 206 0 TCTCTCCCCC 0.786815 -95 TTTCAATAAATTTCCCCTTTAAGAGTGTTG 39 267 0 TTTCCCCTTT 0.583833 -34 CACTTCGTATCCTCCGCTTTCATAAAAAAA 41 32 0 CCTCCGCTTT 0.856129 -269 ********** Masking position 3 Map Score: 31.7892 Number of sites scoring better than the average of aligned sites = 1001 Number in coding regions = 688 Number in noncoding regions = 313 Number of orfs with sites within 600 bp upstream = 351 Fraction of orfs with sites within 600 bp upstream = 0.0563765 Motif number 2 TCAGAGAGAGTAAAGGATTTTGACTTATTCAA 2 88 1 TAAAGGTTTG 0.96717 -213 AAAGAATATTTAAAATAATTTGTAAATAAAAT 6 22 1 TAAAATTTTG 0.857621 -83 CTATCCTACATAAAAGGTTTTGGCAAACTGGG 7 163 1 TAAAAGTTTG 0.964302 -138 CTCAAAATTATAAAAGTTTTCGCATGAATTGT 9 27 1 TAAAAGTTCG 0.768007 -76 TAAGTTATCGTAAAGGGATTTGACTTAACAAA 13 142 1 TAAAGGTTTG 0.969335 -35 AAAGTGTTTGTAAAGTGTTTTTTCTTAACAAC 14 32 0 TAAAGTTTTT 0.745293 -74 TTAACAATGATAAAAGTGTTTGTAAAGTGTTT 14 44 0 TAAAAGTTTG 0.965285 -62 TTAGAAGGATTAAAAGATTTTGCATCGAACTG 20 72 1 TAAAAGTTTG 0.963103 -101 TTGTTTTTTATAAAGGTTTTTTACTATTTTGT 24 61 1 TAAAGGTTTT 0.931808 -167 AAAAAGCCTATAAAAGGCTTTTTGTCATACTC 26 15 0 TAAAAGTTTT 0.916508 -78 AATGAAAAGATAAAGGGGTTTTCTGAAG 29 7 0 TAAAGGTTTT 0.932728 -146 GTCCAGCGGAAAAAATATTTTGTCAAGAGAAG 29 48 1 AAAAATTTTG 0.454334 -105 ATATAGAAAATAAAATGATTTTTCCTAACATT 38 89 0 TAAAATTTTT 0.725837 -75 AACCCGCAAATAAAGGCGTTTTTTCGGGGAAA 39 15 1 TAAAGGTTTT 0.930758 -286 CTGCTGGAACTAAAACCCTTTGCTTTTGAAAG 39 157 0 TAAAACTTTG 0.722316 -144 TATCTTATCGTAAAAGGGTTTGCAATGTCAAT 40 131 1 TAAAAGTTTG 0.96526 -170 TCGAAAAATAAAAAGGATTTTTTGTGTCATTG 41 234 1 AAAAGGTTTT 0.541258 -67 ****** **** Masking position 4 Map Score: 21.1008 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 185 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 3 CGAATTGGAGTTTTTTGTGTTTGCTATTTT 2 59 1 TTTTTTGTGT 0.965316 -242 GGCAATGTCTTTTTTTATGTTTATGACAGC 4 63 1 TTTTTTATGT 0.81063 -135 TGTATTTATCTTTTTTATTTTACTACAATT 11 141 0 TTTTTTATTT 0.669026 -65 AGTTTACCCTTTTTTTGCGTGTAAAAAAAG 15 34 0 TTTTTTGCGT 0.874205 -88 TATGGCTTCTTTTATTGTGTTATATGAGAG 22 31 1 TTTATTGTGT 0.850399 -197 AATGATTAAATTTTTTGTTTTTTATAAAGG 24 47 1 TTTTTTGTTT 0.929291 -181 TTTTATAGGCTTTTTTGTTTATACCAGACA 26 32 1 TTTTTTGTTT 0.929291 -61 TTTCTCCTCCTTTCTTGTCTATTTTTCTAA 27 20 0 TTTCTTGTCT 0.774001 -281 AAACAGCTAGTATTTTGTTTCCAAAAATGG 27 250 0 TATTTTGTTT 0.529308 -51 TGTTACCACCTTTCTTGTTTCGACTCCGCC 28 104 0 TTTCTTGTTT 0.858116 -21 CGTTTTTGCGTTTTTTGTCTA 30 2 0 TTTTTTGTCT 0.881547 -32 TCAATATATATTTCTTGCTTAATTTTTCAT 36 86 0 TTTCTTGCTT 0.601619 -207 TTCTCTGTTATTTATTATGTTCAACTGAGT 40 33 0 TTTATTATGT 0.466468 -268 CTATTTATTGTTTTTTGTGTGTGCATTTCC 40 205 0 TTTTTTGTGT 0.965316 -96 TCCTTTATCGTTTTTTGTGTTTTGCTAATT 40 272 0 TTTTTTGTGT 0.965316 -29 ATAAAAAGGATTTTTTGTGTCATTGGCGAA 41 241 1 TTTTTTGTGT 0.965316 -60 ********** Masking position 5 Map Score: 17.2723 Number of sites scoring better than the average of aligned sites = 395 Number in coding regions = 269 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 4 TTTGCTGATTTTTTTGGAAAGGGTAGTGCCTCTC 2 251 0 TTTGAAGGGT 0.879701 -50 AGCAAACTGCTTATAGTAAAGGAGAATTGGAT 2 279 1 TTTGAAGGAG 0.668225 -22 ATAAAAGGTTTTGGCAAACTGGGGATCGGCTAAA 7 172 1 TTGAATGGGG 0.619786 -129 TTTATAATTTTGAGAGAAGGGGGTCATATC 9 7 0 TGGGAGGGGT 0.60135 -96 ATTCTTCTATTTATCATAAAGGGTATCAACAGAA 10 42 0 TTTAAAGGGT 0.791263 -56 AAAACAAGTGTGTACAGGGGAAGGATATTC 12 7 1 AGGGAAGGGG 0.765507 -68 TTATATTCCATTCGGGTAAGGGGGAGAAAAGT 12 53 1 TTGGAGGGGG 0.829472 -22 GTAAACTAAGTTATCGTAAAGGGATTTGACTTAA 13 136 1 TTTGAAGGGA 0.602884 -41 TTTTTTTGCGTGTAAAAAAAGGGGAGGTGCCGGC 15 21 0 TGAAAAGGGG 0.863937 -101 CGAGTAAAAGTTTTAAAAGCGGGGAGCTTGGTGC 15 97 1 TTTAACGGGG 0.625468 -25 CCTTTTGTATTGAGCATACAGGGGCTTTTTTAGT 25 23 1 TGGAAAGGGG 0.937022 -41 CTGCGCCAAATGTTTGAAAAGGGTTTAACTTGCT 27 188 1 TGTGAAGGGT 0.899063 -113 GAAGAAAACGTGGTAACATAGGGTTGTGCAAATT 29 76 1 TGTAAAGGGT 0.821978 -77 TGCAAATTTTTTCATACAAAGGGGTATCGGG 29 132 1 TTAAAAGGGG 0.839044 -21 AACATGATGAAAAAGGGGATTTGAATGG 31 5 1 TGTAAAGGGG 0.94774 -145 TTTTAAAAAATTTGAGAATAGGGTGAGCAAATCG 34 54 0 TTGGAAGGGT 0.857133 -247 ACTAGATTACTAGAGGGAGAGGGGCTATC 35 15 1 TAAGAAGGGG 0.516943 -19 CGTATATTATAGCTCAAACAGGGGGGAGGATTAC 36 32 1 AGTAAAGGGG 0.673485 -261 TGCTTACAATTGAAAGAAGTGGGGGAAGAGATTT 36 233 1 TGAGATGGGG 0.620435 -60 CATTTCGCACTTATCAAACAGGGGGTAAAGTA 36 271 1 TTTAAAGGGG 0.937062 -22 AAGGGGAAATTTATTGAAAAGGAGATGTTATAT 39 278 1 TTTGAAGGAG 0.668225 -23 ATGAAATATCTTATCGTAAAAGGGTTTGCAATGT 40 125 1 TTTGAAAGGG 0.521139 -176 ** * * * ***** Masking position 8 Map Score: 16.2818 Number of sites scoring better than the average of aligned sites = 361 Number in coding regions = 242 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 5 TATTCCCCCTATCCTTTTCTGTTATTATAGTAAATATAATATTTA 1 71 0 ATTTTTAGAT 0.832733 -38 GACTTATTCAATTGTTTATTTTTAGATAAAAATAATACTGAATAT 2 109 1 ATTTTAAAAA 0.749643 -192 TGACAGCGTTAACATTTCATTTTCAAAAAAGAGATTGATCCCAAA 4 86 1 ATTTTAAAAT 0.882412 -112 GTCCTCACCGTCTTTCATTCTATTTCAAAATGTTAACGTTAAC 4 165 0 CTTTTTAAAT 0.621584 -33 TATCATTGTTAATATACTATCTTGTTGAAATATTTTCGGAGGTGC 14 64 1 ATCTTTAAAT 0.621584 -42 CCTTCTTTGAAATTTATGTTTTTAATAAAGTAAAAGTTTGAATGT 20 27 1 ATTTTTAGAA 0.665121 -146 AGTTCGATGCAAAATCTTTTAATCCTTCTAAACATTCAAACTTTT 20 58 0 ATTTTTTAAT 0.525678 -115 CTGCGCTTTCATTCTATAATAATACTGGAAGAATTGTCTACAGTT 20 99 0 ATTTTTAAAT 0.93608 -74 TCATAAGTCGAACTTATTGTATTTAATAAAAACATTGATATTTAC 22 95 1 ATTTTAAAAT 0.880186 -133 CAATTTTCTCACAATTTCATATTAAAACAAAATCATACATAAGTA 22 137 0 ATTTTAAAAA 0.749643 -91 ACTTTCGAAAAACATATCGTGCTTATGTAAAATGTTAGATGTTTA 27 108 1 ATTTTTAAAT 0.936079 -193 TCAACCTCCTAAACTGTTTTTTTGCAAAAACAGCTAGTATTTTGT 27 262 0 ATTTTAAAAT 0.882444 -39 GAAAGAAGCAACTTTTTATTCATTTTAAAAAATTTGAGAATAGGG 34 65 0 ATTTTTAAAT 0.934074 -236 TTACAGAATGATCCTGTAATTCTTATGAAAAATTAAGCAAGAAAT 36 62 1 ATTTTTAAAA 0.853852 -231 TTAAGCAAGAAATATATATTGATAAAATAAAATTTTTCAATCAAC 36 94 1 ATTTTAAAAT 0.882406 -199 TTTAGAAAACATTTTATTTTTCTTATATAGAAAATAAAATGATTT 38 100 0 ATTTTTAGAT 0.832697 -64 AGCTTATAAAAATTTGTTATGTTCTTTCAAAAGCAAAGGGTTTTA 39 134 1 ATTTTTAAAA 0.853851 -167 CGATCTTGGCAGATTTTAATTTTAATTCAAGATATACGCGGGAAT 41 192 0 ATTTTTAAAT 0.936045 -109 * * * * * * ** * * Masking position 13 Map Score: 11.9018 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 106 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 6 GAATATAAAGGTAAAATAAAAACAAATCAAA 4 132 1 GTAAAATAAA 0.77244 -66 ATAAATTGTAGTAAAATAAAAAAGATAAATA 11 138 1 GTAAAATAAA 0.77244 -68 GTTCAGCCAAGAAAAAATAAAGACCCGCATT 18 22 0 GAAAAAAAAA 0.953912 -49 TTAATCATTCGAAAAAACAAACGCCAAAAAG 24 25 0 GAAAAAAAAA 0.953912 -203 ACTATTTTGTGAACAATCAAGGTAGAATCAA 24 83 1 GAACAATAAG 0.609372 -145 CACACTGTTAGAAAAAACAAGGGGGAGACAG 26 71 1 GAAAAAAAAG 0.948672 -22 AGGCGGAGTCGAAACAAGAAAGGTGGTAACA 28 103 1 GAAACAAAAA 0.711308 -22 TAAAGGAAATGAAAAGATAAAGGGGTTTTCT 29 15 0 GAAAAGAAAA 0.711308 -138 ATGAATGAATGAAAAAAGAAGGCTGCGTCAA 32 40 0 GAAAAAAAAG 0.948672 -98 GAGTGGAGCCGACAAAATAAGTATAATGGAG 33 32 1 GACAAAAAAG 0.700948 -47 GCGCCAATTAGAAAAAATTAGCGGAAAGAAG 34 102 0 GAAAAAATAG 0.597502 -199 TAATTCTTATGAAAAATTAAGCAAGAAATAT 36 78 1 GAAAAATAAG 0.9291 -215 AATATATATTGATAAAATAAAATTTTTCAAT 36 104 1 GATAAAAAAA 0.63912 -189 TGAGGGAGGAGTAAAATGAAATTGTCAATAA 36 190 1 GTAAAATAAA 0.77244 -103 TTCTATATAAGAAAAATAAAATGTTTTCTAA 38 113 1 GAAAAATAAA 0.936205 -51 TCACAGAATGGAAAAAAAAAATTATAGGTAA 39 47 1 GAAAAAAAAA 0.953912 -254 TGCCAAGATCGAAAAATAAAAAGGATTTTTT 41 226 1 GAAAAATAAA 0.936205 -75 ******* *** Masking position 10 Map Score: 12.6491 Number of sites scoring better than the average of aligned sites = 499 Number in coding regions = 403 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 7 ATTCACGTTCAAATTTTGTTCAAAAAG 2 6 1 CGTCAAATTT 0.874933 -295 ACACATTTTATTTACAAATTATTTTAAATATT 6 26 0 TTTCAAATTT 0.937571 -79 TGTCACTTTGTGTACAAATTATGTGTATTGAA 9 56 1 TGTCAAATTT 0.960161 -47 CTGTCCGGCATTTTCAAATTCTGTATAAAAAA 17 52 0 TTTCAAATTT 0.937571 -91 TCGAACGCTGTGTCAAAATTATGTAATAAAAA 24 147 0 TGTAAAATTT 0.594665 -81 AACATAGGGTTGTGCAAATTATTGCAACGGAA 29 90 1 TGTCAAATTT 0.960161 -63 AATAAATAGGTGTGCAAATTTTTTCATACAAA 29 120 1 TGTCAAATTT 0.960161 -33 ATAGACAGCGCTTACAATTTCTAGTTGTCTTC 32 96 0 CTTCAATTTT 0.449953 -42 GCTCACCCTATTCTCAAATTTTTTAAAATGAA 34 60 1 TTCCAAATTT 0.686596 -241 TCGCGTTGTCTTTACAAATTCTCCATTCTGGT 34 242 1 TTTCAAATTT 0.937571 -59 ATAACATATATTTTCAAATAGTCTATACTATT 40 230 0 TTTCAAATAT 0.615119 -71 TTTTTTGTGTTTTGCTAATTGTGAATTAGTAT 40 260 0 TTTCTAATTT 0.59647 -41 TCTAATGAGCTGTTCAATTTCTTCTTGTTTTC 41 81 0 TGTCAATTTT 0.818928 -220 ATCATAATGCTGTTCAAATGATCTAATGAGCT 41 102 0 TGTCAAATGT 0.791725 -199 *** ****** * Masking position 7 Map Score: 9.49593 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 51 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 TTTGTTCAAAAAGTGTTATCATATAGAAGG 2 25 1 AAGTGTTATC 0.671856 -276 TTACAAAAATAAATGTTTACTACCCAGTTT 2 165 0 AAATGTTTAC 0.957165 -136 TTTGAAAATGAAATGTTAACGCTGTCATAA 4 83 0 AAATGTTAAC 0.929453 -115 AAACAAATCAAAATGTTAACGTTAACATTT 4 151 1 AAATGTTAAC 0.929453 -47 TTCTATTTCAAAATGTTAACGTTAACATTT 4 161 0 AAATGTTAAC 0.929453 -37 TATCTGTTTTCAATGCTTACGATGTAAACT 8 59 1 CAATGCTTAC 0.724945 -56 AAAACAAGTGTGTACAGGGGAAGGA 12 6 1 AAGTGTGTAC 0.724945 -69 AATCTTAATAAAGTGCTTACAATTGAAAGA 36 220 1 AAGTGCTTAC 0.897601 -73 AAGAAAAATAAAATGTTTTCTAAATATGAA 38 121 1 AAATGTTTTC 0.847197 -43 GACATTTGTTAAATGTTTACCTATAATTTT 39 64 0 AAATGTTTAC 0.957165 -237 CCCAAAAAGAAAATGCTTACATTTTACTGG 39 189 0 AAATGCTTAC 0.933313 -112 ********** Masking position 2 Map Score: 8.01253 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 30 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 CTGAGGGAACGAGGGTGTTTGC 9 91 1 GAGGTGTTTG 0.972123 -12 GTTCCGCTGTGCCGGTTTTTGTGGCCAAGAG 16 94 1 GCCGTTTTTG 0.796864 -37 AACAGTTTAGGAGGTTGAATGA 27 289 1 GAGGTGAATG 0.695844 -12 AAACATTCGTGCAGATGTTTGCGTTTATTCT 28 16 0 GCAGTGTTTG 0.920457 -109 AGCCGCGTCGGCGGCTGTTTGAGCAATTCCG 31 82 0 GCGGTGTTTG 0.988915 -68 GCTTTTATGTGCGGATGTATGATGTGAATCC 31 110 1 GCGGTGTATG 0.970291 -40 TTGTTAGAAGGAGGCTGTTTGACGCAGCCTT 32 22 1 GAGGTGTTTG 0.972123 -116 GCCTTTATTTGCGGGTTTTTG 39 1 0 GCGGTTTTTG 0.953282 -300 **** ****** Masking position 6 Map Score: 5.90589 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 73 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 10 GTATATCCTCCGTCCTTTATATCAATTTGA 3 19 0 CGTCCTTTAT 0.92374 -21 GTCCTCACCGTCTTTCATTCTATTTCAA 4 180 0 CGTCTTTCAT 0.839011 -18 TAGACGTGCATTCCTTTTATACATACAAAC 7 246 0 TTCCTTTTAT 0.667469 -55 AAAAAAAGACCGTCTTTTATGAGATGAGAG 11 65 0 CGTCTTTTAT 0.942845 -141 GATTCATTGTTGTCCTTTATGTATTTTACG 17 88 0 TGTCCTTTAT 0.845749 -55 TTTGGTCCCCTGCCTTTCATTCTTTC 21 7 0 TGCCTTTCAT 0.688099 -22 CATAATATGGCTTCTTTTATTGTGTTATAT 22 26 1 CTTCTTTTAT 0.825836 -202 TATGACAAAAAGCCTTTTATAGGCTTTTTT 26 18 1 AGCCTTTTAT 0.632724 -75 GTTTCGACTCCGCCTTTTATTATGCAAGTT 28 88 0 CGCCTTTTAT 0.939125 -37 TATCTTTTCATTTCCTTTATTGTCCAGCGG 29 27 1 TTTCCTTTAT 0.611807 -126 GCCGCCGACGCGGCTTTTATGTGCGGATGT 31 98 1 CGGCTTTTAT 0.889666 -52 TCCTGATGTTTGGCTTTTATCTTTGACCAG 34 269 0 TGGCTTTTAT 0.784939 -32 ATGAAACCTTCCTTTATCGTTTTTTGT 40 284 0 CTTCCTTTAT 0.776877 -17 ********** Masking position 9 Map Score: 7.43484 Number of sites scoring better than the average of aligned sites = 267 Number in coding regions = 234 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 11 TTGTATTCCCCCTATCCTTTTCTGT 1 94 0 GTTCCCCCTT 0.934995 -15 CAAAGTGTCCGCTCAGTATCGCTGAGC 5 5 1 GTTCGCTCAT 0.93389 -63 GTTCCACCTCTGTGTCTTAAGAA 5 55 0 GTCACCTCTT 0.71909 -13 GAAGATGAACGTTTTCCCTCTATTATATATCTG 8 32 1 GTTCCCTCTT 0.980219 -83 GCTTCTATCAGTTTACCCTTTTTTTGCGTGTAA 15 40 0 GTTCCCTTTT 0.851968 -82 CATTATCACCTCAATCATAATATGG 22 3 1 TTTACCTCAT 0.516491 -225 AATTTTTACTGTTTACGCTCTCTCATATAACAC 22 47 0 GTTCGCTCTT 0.93389 -181 ACTGTCTCCCCCTTGTTTTTTCTAAC 26 77 0 GTTCCCCTTT 0.625547 -16 GGTTTCACCTCATTCAGAAGATAG 32 124 0 GTTACCTCAT 0.946087 -14 CGTTTCACCTCAAACCCTAAAGTT 33 65 0 GTTACCTCAA 0.633318 -14 ATCTGTCTCCCCTCTCTCCTGCGTATA 36 5 1 GTTCCCTCTT 0.980219 -288 CTGAACAAGAGGCTAACCTCATTGACGCAAGCC 38 27 0 GGTACCTCAT 0.71909 -137 CGGGATAAGAGTATCCGCTCAATGAAATATCTT 40 104 1 GTTCGCTCAT 0.93389 -197 CATTTCCATTGTTTTCCCTCAATATAGGTGCCT 40 179 0 GTTCCCTCAT 0.980219 -122 ** * ****** * Masking position 8 Map Score: 12.3433 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 144 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 12 ATTTTAAAGGGAATTAATTAAAAATATTAATCAG 1 24 0 GAATTAAAAA 0.717284 -85 TTCGCTTGGAGAGTGCCCAAAAAACTGAAAAGGA 6 68 1 GAGTGAAAAA 0.96096 -37 GATTCGGAAGGAATGTGTAAAAAAAGACCGTCTT 11 79 0 GAATGAAAAA 0.957841 -127 TTCCATTAACGAGTATACTAAAAAAGCCCCTGTA 25 39 0 GAGTAAAAAA 0.828973 -25 AAATGAGTATGACAAAAAGCCTTTTATA 26 5 1 GAGTAAAAAA 0.828973 -88 AAACGGGCATGAATGAATGAAAAAAGAAGGCTGC 32 45 0 GAATGAAAAA 0.957841 -93 ACTTTAAATTGAATGTTAGGAAAAATCATTTTAT 38 78 1 GAATGGAAAA 0.825729 -86 GGAAATCACAGAATGGAAAAAAAAAATTATAGGT 39 42 1 GAATGAAAAA 0.957841 -259 TCCCCTTTAAGAGTGTTGTAAAAACATGAGGCTT 39 251 0 GAGTGAAAAA 0.96096 -50 CATAATTCGCCAATGACACAAAAAATCCTTTTTA 41 242 0 CAATGAAAAA 0.74632 -59 ***** ***** Masking position 4 Map Score: 5.38215 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 76 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 13 TGCTTTCTGGCAATGTCTTTTTTTATGTTTA 4 55 1 CATGTCTTTT 0.733425 -143 CCTTTGGGATCAATCTCTTTTTTGAAAATGA 4 102 0 CATCTCTTTT 0.861135 -96 TCTCATAAAAGACGGTCTTTTTTTACACATT 11 71 1 GAGGTCTTTT 0.788859 -135 TTACAGGTAACAAGCTCTTTTCGTTCGTTAT 17 13 0 CAGCTCTTTT 0.969223 -130 TTACCTGTAACAAGCTCTTTTTTTATACAGA 17 34 1 CAGCTCTTTT 0.969223 -109 TATCATCCAGGCCCTTTTGTATTGAGCA 25 8 1 CAGCCCTTTT 0.975929 -56 ATTGAGCATACAGGGGCTTTTTTAGTATACT 25 31 1 CAGGGCTTTT 0.836303 -33 TTCATTCATTCATGCCCGTTTCAAAGCATAC 32 58 1 CAGCCCGTTT 0.894241 -80 GCGTTTTCTTGACGCCCTTTTGAGGGAGGAG 36 170 1 GAGCCCTTTT 0.915552 -123 ATTGACATTGCAAACCCTTTTACGATAAGAT 40 132 0 CAACCCTTTT 0.819083 -169 ** ******** Masking position 9 Map Score: 5.61169 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 180 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 14 TATTTCGAAGTTGTAAAAAACTAATACAACA 7 109 0 TTTAAAAAAC 0.82591 -192 AAATAGCGGTTATAAAAAAACCCAAACTGTT 11 32 0 TAAAAAAAAC 0.442356 -174 AAACCGTTGTTAAGAAAAAACACTTTACAAA 14 27 1 TAGAAAAAAC 0.90079 -79 AATTTAATCATTCGAAAAAACAAACGCCAAA 24 28 0 TTGAAAAAAC 0.930538 -200 TAAAAAACCTTTATAAAAAACAAAAAATTTA 24 53 0 TTTAAAAAAC 0.82591 -175 GTTCACAAAATAGTAAAAAACCTTTATAAAA 24 66 0 TATAAAAAAC 0.762776 -162 GACCACACTGTTAGAAAAAACAAGGGGGAGA 26 68 1 TTGAAAAAAC 0.930538 -25 AAACTGTTTTTTTGCAAAAACAGCTAGTATT 27 266 0 TTGCAAAAAC 0.64509 -35 TACCCCTTTGTATGAAAAAATTTGCACACCT 29 127 0 TAGAAAAAAT 0.743581 -26 TTTTTATTCATTTTAAAAAATTTGAGAATAG 34 67 0 TTTAAAAAAT 0.602418 -234 GAGGCGCCAATTAGAAAAAATTAGCGGAAAG 34 105 0 TTGAAAAAAT 0.810555 -196 CTGTAATTCTTATGAAAAATTAAGCAAGAAA 36 75 1 TAGAAAAATT 0.43812 -218 AATTGAATGTTAGGAAAAATCATTTTATTTT 38 84 1 TAGAAAAATC 0.70942 -80 TTAAATAAGCTTATAAAAATTTGTTATGTTC 39 127 1 TTTAAAAATT 0.289479 -174 ACCCTTTGCTTTTGAAAGAACATAACAAATT 39 144 0 TTGAAAGAAC 0.64509 -157 ** ******** Masking position 6 Map Score: 6.69442 Number of sites scoring better than the average of aligned sites = 641 Number in coding regions = 514 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 15 AATAAAATGTGTTTGTAGGGGTTTCGCTTGG 6 46 1 GTTGTAGGGG 0.774793 -59 AAATAATACAGTTCAAAGCAGAGTGTAACTA 7 135 1 GTTAAAGCAG 0.641897 -166 GATAATGGAAGTTAGAAGCAGGGAAGAGGAT 11 182 1 GTTGAAGCAG 0.957894 -24 AAGAGCATCTGTTGGAAGGAG 16 120 1 GTTGAAGGAG 0.975024 -11 AGTTTGAATGTTTAGAAGGATTAAAAGATTT 20 61 1 TTTGAAGGAT 0.617915 -112 TGTTACATAAGTTAGGAGGATGGGAA 20 157 1 GTTGGAGGAT 0.810621 -16 GTAAAATATCGTTGGAAGCGTTTTTATTACA 24 127 1 GTTGAAGCGT 0.882234 -101 ATGAATAGTTGTTAGAAGGAGGCTGTTTGAC 32 14 1 GTTGAAGGAG 0.975024 -124 GAAGGAGGCTGTTTGACGCAGCCTTCTTTTT 32 28 1 GTTGACGCAG 0.897237 -110 TGAGCAAATCGTTTGACGGGTGGGTCAGCCA 34 34 0 GTTGACGGGT 0.831473 -267 ATTTCCTGTTGTTAGAAAGATAACGAGCAGA 34 161 0 GTTGAAAGAT 0.617915 -140 *** ******* Masking position 3 Map Score: 3.1977 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 194 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727