AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -inarL_ecoli_bsub_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 dmsA 300 anaerobic dimethyl sulfoxide reductase subunit A #2 narK 300 nitrite extrusion protein #3 narG 300 nitrate reductase 1, alpha subunit #4 fdnG 231 formate dehydrogenase-N, nitrate-inducible, alpha subunit #5 ccmC 41 heme exporter protein C #6 napF 300 ferredoxin-type protein: electron transfer #7 yhfC 270 putative transport #8 nirB 261 nitrite reductase (NAD(P)H) subunit #9 nirC 300 nitrite reductase activity #10 nrfA 300 periplasmic cytochrome c(552): plays a role in nitrite reduction #11 nrfB 38 formate-dependent nitrite reductase; a penta-haeme cytochrome c #12 nrfE 79 formate-dependent nitrite reductase; possible assembly function #13 frdA 294 fumarate reductase, anaerobic, flavoprotein subunit #14 nasF 60 uroporphyrin-III C-methyltransferase #15 nasE 31 assimilatory nitrite reductase (subunit) #16 nasD 121 assimilatory nitrite reductase (subunit) #17 nasB 179 assimilatory nitrate reductase (electron transfer subunit) #18 cysH 300 phosphoadenosine phosphosulfate #19 ylnB 48 similar to sulfate adenylyltransferase #20 ylnD 98 similar to uroporphyrin-III C-methyltransferase #21 citB 227 aconitate hydratase #22 yneN 71 similar to thiol:disulfide interchange protein #23 yoaE 300 similar to formate dehydrogenase #24 resC 135 essential protein similar to cytochrome c biogenesis protein #25 resA 131 essential protein similar to cytochrome c biogenesis protein #26 ypuL 91 similar to hypothetical proteins #27 dacB 122 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5*) #28 ypuI 54 similar to hypothetical proteins from B. subtilis #29 ypuG 280 similar to hypothetical proteins #30 spoIIIAC 22 spoIIIAC #31 spoIIIAA 75 spoIIIAA #32 yqhV 144 alternate gene name: yqgE #33 efp 24 elongation factor P #34 yqhS 86 similar to 3-dehydroquinate dehydratase #35 yqhR 226 yqhR #36 nadB 102 L-aspartate oxidase #37 sdhA 33 succinate dehydrogenase (flavoprotein subunit) #38 sdhC 292 succinate dehydrogenase (cytochrome b558 subunit) #39 gerBA 264 gerBA #40 narJ 25 nitrate reductase (protein J) #41 narG 195 nitrate reductase (alpha subunit) #42 ywiD 143 ywiD #43 narK 135 nitrite extrusion protein #44 ywiB 300 ywiB #45 ywcJ 300 alternate gene name: ipa-48r; similar to nitrite transporter #46 yyaE 300 similar to formate dehydrogenase Motif number 1 ACCACACGGCAAATAAGGAGTAACTCTTTC 2 81 0 AAATAAGGAG 0.789134 -220 TACCCCTGAAAAAAGAGGAAAGCA 4 218 1 AAAAGAGGAA 0.908199 -14 ATTTAACACTAAAAGAGCAGGTAAAATTGT 6 14 0 AAAAGAGCAG 0.958996 -287 ACAGAGCAGAAAAAAAGCAAGTGAAGAGAT 7 27 1 AAAAAAGCAA 0.639069 -244 ATGCTGTTGAAAAAGAGGAAGATACTGACT 10 107 1 AAAAGAGGAA 0.908199 -194 GCCAGAAAAGAGGTGGTTTCTGGAC 12 6 1 AAAAGAGGTG 0.879272 -74 TTGTACCTATAAAGGAGCAGTGGAATAGCG 13 201 1 AAAGGAGCAG 0.93541 -94 TTTGTCTCCGAAAGGAGGAAAGAAGAA 18 284 1 AAAGGAGGAA 0.859669 -17 TTGTGTCATAAAAAGAAGAGAAAGCGAAAT 22 33 0 AAAAGAAGAG 0.817783 -39 GTCAATTCTGAAAAAAAGAGATTGACATCA 23 221 0 AAAAAAAGAG 0.627686 -80 AATAAAGATAAAAAGGGCAGGCCAAACCG 24 117 1 AAAAGGGCAG 0.947519 -19 ACTCTCCCTGAAAAAGGGAGAGTAAACG 27 9 0 AAAAAGGGAG 0.934363 -114 AAAGCACATTAAAGGAGGAAGCACC 29 6 0 AAAGGAGGAA 0.859669 -275 CAATCGGTAGAAAGGAGGAGGCTCTG 31 60 1 AAAGGAGGAG 0.96815 -16 ATCATATAAAAAAATGGGAGGTTGGGAGAG 32 121 1 AAAATGGGAG 0.667002 -24 AACCCTCGCGAAAAGGAGAGATTGT 34 72 1 AAAAGGAGAG 0.776012 -15 AATCCTAAAGAAATAGGCAGGTTGATAAT 35 10 0 AAATAGGCAG 0.579197 -217 TTGTCATAGGAAAAAGGCAGCTTATACGGG 39 75 0 AAAAAGGCAG 0.871502 -190 AATTTGTATCAAAAAAGGAGAATTATTCTT 39 207 0 AAAAAAGGAG 0.948561 -58 CTTTTGATAAATGAGGTGTAACAAG 40 9 1 AAATGAGGTG 0.596457 -17 ACATTTTGTGAAAAAAGCAGAGTGTGTGAC 41 101 1 AAAAAAGCAG 0.89781 -95 ATAATGAAAGAAAAAAGGAGGATTTCG 42 8 0 AAAAAAGGAG 0.948561 -136 TGAATCATTGAAAGGGGCAAGCCAA 43 121 1 AAAGGGGCAA 0.692601 -15 TGTTTAAATAAAAGGGGGAGAAATA 45 6 0 AAAGGGGGAG 0.959126 -295 GCAGTTTAGGAAAAGAGGTGAAGGGTCTTG 46 27 1 AAAAGAGGTG 0.879272 -274 ********** Masking position 3 Map Score: 26.9073 Number of sites scoring better than the average of aligned sites = 314 Number in coding regions = 212 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 2 CGGTTTTCTCCTGTGGGAGCCT 3 289 0 GTTTTCTCCT 0.896905 -12 TCGTCGTCCGGCCTTTTCCTCTCTTCCCCC 8 33 1 GCCTTTTCCT 0.945915 -229 CTTATCAAATGTTTTTTCCAGCGTAGCACA 16 88 0 GTTTTTTCCA 0.759862 -34 ACTTACACATGTCTTTTCCAGAAAATAATG 17 69 0 GTCTTTTCCA 0.74418 -111 AAGCTCGTAAGTTTTCTCCTATTAAAAATT 17 140 0 GTTTTCTCCT 0.896905 -40 TCTGCCGGTTGTCTTTTCCCATGTAATGTG 18 241 0 GTCTTTTCCC 0.567184 -60 TTCTTCTTTCCTCCTTTCGGAGACA 18 286 0 CTTTCCTCCT 0.524527 -15 TAACAAACAAGCTTTTTCAAATTCCTATGC 26 34 0 GCTTTTTCAA 0.498589 -58 TATTATCTTACTTTTTTCAACCTTAACAAA 26 57 0 CTTTTTTCAA 0.235514 -35 AATGAATCGCGCTTTTTCATCATCATAAGA 28 17 1 GCTTTTTCAT 0.824122 -38 GATAGCTTCTTCCTTATATCTTAT 28 41 0 GCTTCTTCCT 0.859214 -14 GGTGCTTCCTCCTTTAATGTGCT 29 4 1 GCTTCCTCCT 0.780739 -277 GCCGGGCGTTCTTTTTTCCTTTTATCCCTT 29 49 0 CTTTTTTCCT 0.854944 -232 CAGAGCCTCCTCCTTTCTACCGAT 31 62 0 GCCTCCTCCT 0.766001 -14 GAACAGACTTCTTTTTTCCTTT 32 3 0 CTTTTTTCCT 0.854944 -142 TGCTGAAGTAGTCTTGTCATTTCCGTATAA 32 80 0 GTCTTGTCAT 0.410711 -65 GTATAAGCTGCCTTTTTCCTATGACAACAT 39 78 1 CCTTTTTCCT 0.882625 -187 CTTTGTTTCAGCCTTTTCCTCGATAAGAAT 39 183 1 GCCTTTTCCT 0.945915 -82 AAGTCTTCGGGCTTTGTCCTTTTTTTATGA 43 28 1 GCTTTGTCCT 0.797036 -108 ACACAGCGATCCTTTTTCATTTACGCAAAT 45 68 1 CCTTTTTCAT 0.649388 -233 TGTCTTTTCCTGCTTTCTTTC 45 290 0 GTCTTTTCCT 0.93201 -11 GACCCTTCACCTCTTTTCCTAAACTGCTGT 46 24 0 CTCTTTTCCT 0.844198 -277 CATGGATGCGGTTTTTTCATTTCTACGATA 46 83 0 GTTTTTTCAT 0.78599 -218 CGACACTCATGCTTTTTCATATAGAAGGTA 46 267 1 GCTTTTTCAT 0.824122 -34 CGCCGTCTTCTCCTTACCTTCTAT 46 287 0 GTCTTCTCCT 0.888863 -14 ********** Masking position 4 Map Score: 24.3622 Number of sites scoring better than the average of aligned sites = 639 Number in coding regions = 546 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 3 TTCGGTATCAAAGGGAGACAAAAAAAGCGCCCGCA 1 16 0 AAGGGCAAAA 0.975941 -285 TTTTAACGGCAAGAGAGACAAAACAGCGAGC 4 7 0 AAGGGCAAAA 0.975941 -225 TTAAATTCTAATGAGAGAGCAAACCAGCAGAAATA 6 38 1 ATGGGGAAAC 0.594208 -263 GAGTGGCGGGAAGCGTGGCAAAAACGGGCTTTTGC 6 126 0 AAGGGCAAAC 0.915896 -175 TCTGAAAATTGAGAGCGACCAAATAAACCGCATAA 6 252 0 GAGGGCAAAA 0.957497 -49 AAAGCAAGTGAAGAGATTCTAAATAGCCTTCAAGA 7 40 1 AAGGTCAAAA 0.681952 -231 TAGATGCACGTAGCGGGGGAAGAGAGGAAAAGGCC 8 42 0 TAGGGGAGAA 0.742293 -220 TCCGCCTCGCAAGGGGCGGAAAACACAATGGA 11 17 1 AAGGCGAAAA 0.739048 -22 ATGTAAAATAATGAGGGTCTAGAAAGGGGAATCTT 17 11 0 ATGGGCAGAA 0.82087 -169 TGTGTTATATGAGAGAGCGTAAACAGTAAAAATTA 21 46 1 GAGGGGAAAA 0.952554 -182 GCCTGTAACAGAGCGCGCCTATATATGAATCTCTT 23 14 0 GAGGGCATAA 0.72294 -287 CTCCCTGAAAAAGGGAGAGTAAACG 27 1 0 AAGGGGAAAG 0.906586 -122 CGGAGCGCAGAAGCGGGAGAAAAAGCCTTTGCTTC 29 107 0 AAGGGGAAAG 0.906586 -174 CCTCCAGTTAAAGTGTGCCCAAAAAATGAAATGTC 35 198 0 AAGGGCAAAA 0.975941 -29 ATATACGCAGGAGAGAGGGGAGACAGAT 38 4 0 GAGGGGAGAA 0.937623 -289 CCTCCCTCAAAAGGGCGTCAAGAAAACGCGTACAT 38 164 0 AAGGGCAGAA 0.968124 -129 CAATTGAAAGAAGTGGGGGAAGAGATTTAGCACAT 38 239 1 AAGGGGAGAA 0.964371 -54 *** * * * *** * Masking position 11 Map Score: 14.3102 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 86 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 4 TCATAAAAATTATGAGATTTTTCACGGTGCTGTAA 2 142 0 TTGATTTCAC 0.761506 -159 CACTATGGGTAATGATAAATATCAATGATAGATAA 2 189 1 ATGAAATCAA 0.505504 -112 TATCTTATCGTTTGATTTACATCAAATTGCCTTTA 2 227 1 TTGATATCAA 0.902273 -74 TTCTACCGCTATTGAGGTAGGTCAATTTGCGAAGG 4 98 1 ATGATATCAA 0.71961 -134 CTTTTTATTCCGTGATCAAAATCACCTCTTAAAAT 7 133 1 CTGAAATCAC 0.700477 -138 TAAAGGTGAATTTGATTTACATCAATAAGCGGGGT 8 189 1 TTGATATCAA 0.902273 -73 AAGCAGAGTGTGTGACATAGTTCACAAGGAAACAC 41 115 1 TTGATATCAC 0.961729 -81 TCACAGCCTGTATGATGAATGTCACTTATCAGGAG 42 51 0 TTGAAATCAC 0.909169 -93 TCATACAGGCTGTGAAATACATCACTGCTGTACAG 42 71 1 TTGATATCAC 0.961729 -73 GAGAAAAACGTGTGATGTAATTCACAATCCTGTTT 43 56 1 TTGATATCAC 0.961729 -80 AAAAATTAATTGTGAAATACTTCACAATATCGTGC 45 237 1 TTGATATCAC 0.961729 -64 * *** ** **** Masking position 5 Map Score: 6.04643 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 31 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 5 TGACAGGCCAGTTAAAAAAATGCTATAAAATTCAGCTTAA 4 43 0 GTAAAAAAAA 0.842735 -189 CATTTAAACAGATCACAAAATCACCTAAAATCGCCCGCTC 7 195 1 GTAAAAAAAA 0.842769 -76 ATTTCATGTTTGTGCAAAAAATAGACAAAATGAGCGGGTT 8 85 0 TTCAAAAAAA 0.873733 -177 GATTATCCTTTAAAAAATAAAAACAAAAAATAAAACAAAA 9 17 0 TAAAAAAAAA 0.770704 -284 ACCCCGAGACTTAACAACAACGCCAGAAAACCGACTTCAG 12 46 0 TACAAAAAAA 0.734087 -34 TGTAACAAAATATACGAAAAGTTCTAAAAATTTTATGAAA 16 14 0 TTCAAAAAAA 0.873734 -108 TTAAGATACATGTTATAAAATGTAACAAAATATACGAAAA 16 34 0 TTAAAAAAAA 0.893882 -88 GTTTACGCTCTCTCATATAACACAATAAAAGAAGCCATAT 21 30 0 TTAAAAAAAA 0.8939 -198 GCTTTCTAAATTTCACATAACCTTCAAAAAGTAAGAAATG 25 46 1 TTAAAAAAAA 0.893899 -86 GTGTACCATAGAAGGGATAAAAGGAAAAAAGAACGCCCGG 29 38 1 GAGAAAAAAA 0.519118 -243 CTGGCTACCCTATAGTATAAGCCACCAAAAAGCTCTCGTC 29 210 0 TTGAAAAAAA 0.809639 -71 CGAGGAAAAGGCTGAAACAAAGCTTGAAAAGCTGCACATA 39 165 0 GTAAAAAAAA 0.842769 -100 ATTCTCCTTTTTTGATACAAATTAATAAAAACCGTCAATA 39 214 1 TTAAAAAAAA 0.893864 -51 ACAACATAGATCTGCTAGAAAAACAAAAAAAGG 44 4 0 TTCAAAAAAA 0.873734 -297 AATACATATATTTTGAAAAAAATGTGAAAAGGAAATGATA 44 77 1 TTGAAAAAAA 0.809612 -224 CCCTTTTATTTAAACAAAAAAGACCTAAAATTCGCCAACG 45 20 1 TACAAAAAAA 0.734087 -281 GATATAACATGTAGACAAAAATTCGTAAAAATTAATTGTG 45 211 1 GAAAAAAAAA 0.681366 -90 GAGAAGAGAATTTGAAAGAAAACTAAAAAAAGTACTAGTC 46 197 1 TTAAAAAAAA 0.893899 -104 * * * * ** **** Masking position 10 Map Score: 14.7274 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 55 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 6 CAAACCACGGCGACTCACCTCAGCAGCCAAT 1 250 0 CGACTCCCTC 0.642151 -51 CCCCGTTCCGCCTCGCAAGGGGCG 11 4 1 CGTTCCCCTC 0.928588 -35 GTCCATTCCTCCTCAATGATAGTT 15 18 0 CATTCCCCTC 0.765962 -14 TAGGGCCAGTCCCTCCACCTCTCTGGATAGA 23 130 1 CCCTCCCCTC 0.974042 -171 TGCCCCCTTCCCCCTATTGCAGATCC 25 116 0 CCTTCCCCTA 0.81724 -16 GTCTTTCACCTCAAGTATTATC 26 80 0 TCTTTCCCTC 0.609942 -12 ATGCCATCCTCCTGTTGTTTACAC 36 89 0 CCATCCCCTG 0.932119 -14 GATAGCCCCTCTCCCTCTAGTAATCTA 37 17 0 CCCTCTCCTC 0.801106 -17 ATCTGTCTCCCCTCTCTCCTGCGTATATTAT 38 11 1 CCTCTCCCTG 0.922745 -282 ATTCTGTAATCCTCCCCCCTGTTTGAGCTAT 38 40 0 CCTCCCCCTG 0.973957 -253 GATCCGTACCCCTCCCCTGTAAATAACTG 39 9 1 CCCCTCCCTG 0.90763 -256 ATGACCCAAGCGTCCTGCCTGAACGCAGCCT 41 52 1 CGTCCTCCTG 0.533661 -144 CTGAACGCAGCCTTCCTTCTCCTTTGTGTGA 41 70 1 CCTTCCTCTC 0.72074 -126 ATAAATGCATTCACCCTCCTGATAAGTGACA 42 36 1 TCACCCCCTG 0.615227 -108 TCCGCCAAGACCCTTCACCTCTTTTCCTAAA 46 31 0 CCCTTCCCTC 0.922985 -270 ****** **** Masking position 10 Map Score: 8.34514 Number of sites scoring better than the average of aligned sites = 408 Number in coding regions = 347 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 7 ACAAAAAAAGCGCCCGCAGGCGC 1 2 0 CGCCCCAGGG 0.931873 -299 GGCCGACAGGCTCCCACAGGAGAAAACCG 3 282 1 CTCCCCAGGG 0.928681 -19 CACCTAAAATCGCCCGCTCGCGGCATATCCCG 7 216 1 CGCCCCTCGG 0.961941 -55 TCCATCCGTACGCCCTTTGGTGATGGGCGCGA 9 217 1 CGCCCTTGGG 0.973246 -84 TGACATTGCTCGCCCCTATGTGTAACAAATAA 10 198 0 CGCCCTATGG 0.967917 -103 GTGATAATTTAGCCCTCTTGCGCACTAAAAAA 13 126 1 AGCCCCTTGG 0.937474 -169 TCTCCAAAATCCCCCTTCAGATCAGATCAT 21 208 0 ATCCCCTTCG 0.595633 -20 AAGGCTTTTTCTCCCGCTTCTGCGCTCCGAGC 29 113 1 CTCCCCTTCG 0.905314 -168 AAAAAGCCTGCTCCCATTTGGGAACAGACTTC 32 22 0 CTCCCTTTGG 0.949483 -123 GTTTTCTTGACGCCCTTTTGAGGGAGGAGTAA 38 172 1 CGCCCTTTGG 0.980822 -121 CTCTTACAAACGCCCGTATAAGCTGCCTTTTT 39 63 1 CGCCCTATAG 0.747322 -202 ***** **** * Masking position 5 Map Score: 7.99657 Number of sites scoring better than the average of aligned sites = 282 Number in coding regions = 248 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 8 TTTTCACTCGAAAGTAGTATTACGTGTAAG 1 67 0 AAAGTAGTAT 0.799034 -234 GCAGACATCGAAACGAGTATCAGAGGTGTC 2 280 1 AAACGAGTAT 0.589721 -21 AGATGGGTATTAAGGAGTATTCCCCATGGG 3 45 0 TAAGGAGTAT 0.747589 -256 TAATTATCCTAAAGGGGTATCTTAGGAATT 3 150 1 AAAGGGGTAT 0.917289 -151 ATATACCCATTAAGGAGTATATAAAGGTGA 8 168 1 TAAGGAGTAT 0.747589 -94 AGGAGTATATAAAGGTGAATTTGATTTACA 8 180 1 AAAGGTGAAT 0.651497 -82 TTTATTTTTTAAAGGATAATCAAATGTTTA 9 36 1 AAAGGATAAT 0.634026 -265 TCACGCAAAAGTAGAATTGTGCAAATA 10 8 1 AAAGTAGAAT 0.777657 -293 GACTAACTCTAAAGTGGTATTTTACATGCA 10 133 1 AAAGTGGTAT 0.706167 -168 AGCACAGCAAAAAGGAATATTTAAGATACA 16 64 0 AAAGGAATAT 0.527603 -58 GAGGGTCTAGAAAGGGGAATCTT 17 4 0 AAAGGGGAAT 0.907026 -176 TCATACTGGAAAAGGATTATACA 34 4 0 AAAGGATTAT 0.663235 -83 TTGTATCAAAAAAGGAGAATTATTCTTATC 39 204 0 AAAGGAGAAT 0.941656 -61 ATGTTCACACAAAGGAGAAGGAAGGCTGCG 41 75 0 AAAGGAGAAG 0.671788 -121 ATGAAAGAAAAAAGGAGGATTTCG 42 5 0 AAAGGAGGAT 0.810851 -139 TATTCAAGTCAAAGTGGAATGATGAAAAGG 44 271 1 AAAGTGGAAT 0.678879 -30 ********** Masking position 3 Map Score: 8.0307 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 68 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 9 AGGGAGACAAAAAAAGCGCCCGCAGGCGC 1 9 0 AAAAAGCGCC 0.682735 -292 CTCTTAAAATAAAAAACTTTCAATCCGGCGG 18 175 0 AAAAAACTTC 0.69188 -126 TTAAGAGGTAAAAAGGCTATCTGTATATCAG 18 199 1 AAAAGGCTTC 0.845219 -102 GATCACGGTAAAAACGCTTTCTAAATTTCAC 25 31 1 AAAACGCTTC 0.965993 -101 AGCAAACATAAAAAAACTCTCCCTGAAAAAG 27 23 0 AAAAAACTTC 0.691881 -100 AGATATAAGGAAGAAGCTATC 28 44 1 AAGAAGCTTC 0.769703 -11 ATAAGCCACCAAAAAGCTCTCGTCCAATACT 29 203 0 AAAAAGCTTC 0.94666 -78 AATGTCAATAAAAAAGCTCACACTTTTTGGC 35 173 0 AAAAAGCTAC 0.814936 -54 GGGCGTCAAGAAAACGCGTACATAAATTATA 38 156 0 AAAACGCGAC 0.690085 -137 CCCTTCAAAGAAAACGCTTCCTATCTATTAT 39 135 1 AAAACGCTCC 0.915981 -130 TTCACAAGGAAACACGCTGTCTCTGTTTATA 41 135 1 AACACGCTTC 0.842504 -61 TCAGATTAAGAATACGCTTTCATCATAAATC 45 138 1 AATACGCTTC 0.783046 -163 ATAGTTGACGAAAACGCTATCATGATTTATG 45 161 0 AAAACGCTTC 0.965993 -140 ******** ** Masking position 4 Map Score: 7.09287 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 204 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 10 TCCCTGATGCGGTATTGGCTGCTGAGGTGAG 1 237 1 GGTTTGGCTG 0.916295 -64 AGTATTCTCGGCTATTGGCTGAAGTATACCC 2 43 1 GCTTTGGCTG 0.864485 -258 ATAAGGAGTAACTCTTTCCGGGTATGGGTAT 2 68 0 ACTTTTCCGG 0.666695 -233 TTGCTCATGCCGGACGGCACTAT 8 3 1 GCTATGCCGG 0.736335 -259 GGTGTGTCCGGTGAACAGTTC 9 290 0 GGTTGTCCGG 0.896682 -11 CGGTTTGGCCTGCCCTTTTTAT 24 124 0 GGTTGGCCTG 0.946244 -12 TAGGGTAGCCAGTTTTTCCGGCAATGAGAGT 29 238 1 AGTTTTCCGG 0.77439 -43 GAGGTTTAGCGGTGTTTCCTGTACAATAGAG 35 58 0 GGTTTTCCTG 0.911705 -169 GCAAATTTTAGGTCTTGCCTGCTTTACCAGT 45 92 1 GGTTTGCCTG 0.965641 -209 AGAGGTGAAGGGTCTTGGCGGATAAAGACTT 46 40 1 GGTTTGGCGG 0.936266 -261 GCGGATAAAGACTTTGGCCTGAATGATATCG 46 57 1 ACTTGGCCTG 0.717591 -244 *** ******* Masking position 3 Map Score: 4.21363 Number of sites scoring better than the average of aligned sites = 752 Number in coding regions = 702 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 11 CTTTACATCGGTAAGGGTAGGGATTTTACAGCAC 2 117 1 GAGGGAGGAT 0.98323 -184 ACTGTACTCACTATGGGTAATGATAAATATCAAT 2 181 1 CAGGGATGAT 0.946518 -120 CTCTGAAACAGCGTGGGAATTGATAACGATCAAG 3 205 0 GGGGGATGAT 0.966147 -96 CAGAAAAAAAGCAAGTGAAGAGATTCTAAATAGC 7 33 1 GAGTGAAGAT 0.85173 -238 GCGAAAAGGGAGTGATGTCATGGCAG 24 3 1 GAAGGATGAT 0.919623 -133 AATGTGAAATGAACGTGCAATGATATAATTGAAT 25 82 1 GAGTGATGAT 0.947858 -50 ATTGAAAGAAGTGGGGGAAGAGATTTAGCACATT 38 241 1 GGGGGAAGAT 0.900185 -52 TATTTACAGGGGAGGGGTACGGATC 39 2 0 GAGGGAGGAT 0.98323 -263 CGTTTTCTTTGAAGGGGTAATGAAAAGATGATGC 39 117 0 GAGGGATGAA 0.905106 -148 AAAAAAATGTGAAAAGGAAATGATAGATTTCGGA 44 92 1 GAAGGATGAT 0.919623 -209 CTATTCAAGTCAAAGTGGAATGATGAAAAGGACG 44 270 1 CAGTGATGAT 0.796202 -31 AAAATTATACGCATGGGAATGGATATTCGAATTA 46 129 1 GAGGGAGGAT 0.98323 -172 * * *** * **** Masking position 9 Map Score: 10.0587 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 83 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 GGCTCTTAATGAAATCCGGCGA 3 3 0 GAAATCCGGC 0.874586 -298 TTATCAGAGGGCCGACAGGCTCCCACAGGA 3 273 1 GCCGACAGGC 0.907324 -28 CGACGATAGTGCCGTCCGGCATGAGCAA 8 9 0 GCCGTCCGGC 0.912427 -253 CGGCACTATCGTCGTCCGGCCTTTTCCTCT 8 25 1 GTCGTCCGGC 0.923336 -237 CGGGTTATTTGCCGACAGGCGTGCAATGCG 9 101 0 GCCGACAGGC 0.907324 -200 CTGGACCTATGAAGCCCGGCAACCTGCATA 18 68 1 GAAGCCCGGC 0.946324 -233 CATGGGAAAAGACAACCGGCAGAAAGCTAC 18 248 1 GACAACCGGC 0.942298 -53 GTTCTCGCTTGCATTCCGGCATCTGAGAAG 20 28 0 GCATTCCGGC 0.780162 -71 AGGAAAAAAGAACGCCCGGCCTCTAGTGCT 29 59 1 AACGCCCGGC 0.87721 -222 AAAGATCAAAAAAAACCGGCTCTAT 41 6 0 AAAAACCGGC 0.546595 -190 ********** Masking position 6 Map Score: 4.01262 Number of sites scoring better than the average of aligned sites = 716 Number in coding regions = 673 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 13 CCTGCGGGCGCTTTTTTTGTCTCCCTTTGA 1 14 1 CTTTTTTTGT 0.880947 -287 GCAATGGCGGTTTTTATTGTTTTTCACGAC 10 252 0 TTTTTATTGT 0.761786 -49 CAGATCGTGCTTTTTTTAGTCACTGCCCAC 13 66 0 TTTTTTTAGT 0.867265 -229 ACGAGATCGATTTTTTTAGTGCGCAAGAGG 13 139 0 TTTTTTTAGT 0.867265 -156 AATATGGCTTCTTTTATTGTGTTATATGAG 21 29 1 CTTTTATTGT 0.724579 -199 AAACGGCGTTTTTTTTAGATTTGGCATAG 26 10 1 TTTTTTTAGA 0.699065 -82 TGGGAGCAGGCTTTTTTTGTGCCCAAAAAC 32 38 1 CTTTTTTTGT 0.880947 -107 AGTGTGAGCTTTTTTATTGACATTTCATTT 35 180 1 TTTTTATTGA 0.532045 -47 ATAGAGCCGGTTTTTTTTGATCTTTGAATG 41 11 1 TTTTTTTTGA 0.761786 -185 CCTTTTTTTGTTTTTCTAGCA 44 2 1 CTTTTTTTGT 0.880947 -299 TCGTCAACTATTTTTTTAGTTAAATAGTTT 45 181 1 TTTTTTTAGT 0.867265 -120 TGACTAGTACTTTTTTTAGTTTTCTTTCAA 46 208 0 TTTTTTTAGT 0.867265 -93 ********** Masking position 5 Map Score: 7.83768 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 27 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 14 TGCACGTAGCGGGGGAAGAGAGGAAAAGGC 8 43 0 GGGGGAAGAG 0.86464 -219 CCCTTGCGAGGCGGAACGGGG 11 2 0 GCGGAACGGG 0.81254 -37 AAGAGCGGCTGAGGGACTGGACCTATGAAG 18 52 1 GAGGGACTGG 0.922205 -249 CAGAGAGGTGGAGGGACTGGCCCTATGAAA 23 125 0 GAGGGACTGG 0.922205 -176 TAACTAGAGAGAGGAACTGGGCC 23 288 1 GAGGAACTGG 0.745959 -13 TCTGCAATAGGGGGAAGGGGGCA 25 119 1 GGGGAAGGGG 0.959043 -13 GATTACTAGAGGGAGAGGGGCTATC 37 19 1 GGGAGAGGGG 0.935747 -15 ATATACGCAGGAGAGAGGGGAGACAGAT 38 9 0 GAGAGAGGGG 0.901306 -284 ACGCCCTTTTGAGGGAGGAGTAAAATGAAA 38 181 1 GAGGGAGGAG 0.936239 -112 TGAAAGAAGTGGGGGAAGAGATTTAGCACA 38 243 1 GGGGGAAGAG 0.86464 -50 AGTTATTTACAGGGGAGGGGTACGGATC 39 9 0 AGGGGAGGGG 0.881634 -256 ********** Masking position 6 Map Score: 6.77255 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 155 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 15 AATAGTGTCTGTAAACATTTGATTATCCTT 9 47 0 GTAAACATTT 0.843656 -254 GGTGTGTCCGGTGAACAGTTCAGAACCGGC 9 281 0 GTGAACAGTT 0.926931 -20 TTCACTTCTCGTGAACATTTTATCATACTG 34 26 0 GTGAACATTT 0.965707 -61 TTCACGAGAAGTGAACATTTTTTACATGAG 34 41 1 GTGAACATTT 0.965707 -46 TCTCCTTTGTGTGAACATTTTGTGAAAAAA 41 87 1 GTGAACATTT 0.965707 -109 ********** Masking position 5 Map Score: 2.15071 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 9 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0