AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00190_bsub_reg_300.orf -o00190_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/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 Input sequences: #1 ndhF 300 NADH dehydrogenase (subunit 5) #2 ctaB 300 cytochrome caa3 oxydase assembly factor #3 ctaC 239 cytochrome caa3 oxidase (subunit II) #4 ctaD 32 cytochrome caa3 oxidase (subunit I) #5 flgB 300 flagellar basal-body rod protein #6 fliF 45 flagellar basal-body M-ring protein #7 fliH 117 flagellar assembly protein #8 qcrA 142 menaquinol:cytochrome c oxidoreductase (iron-sulfur subunit) #9 ypiF 54 ypiF #10 ypiB 71 ypiB #11 ypiA 300 similar to hypothetical proteins #12 yrhE 300 similar to formate dehydrogenase #13 sdhA 33 succinate dehydrogenase (flavoprotein subunit) #14 sdhC 292 succinate dehydrogenase (cytochrome b558 subunit) #15 yteU 21 similar to hypothetical proteins from B. subtilis #16 yteQ 94 similar to sugar transport protein #17 yteP 215 similar to hypothetical proteins from B. subtilis #18 yufT 300 similar to NADH dehydrogenase #19 atpC 23 ATP synthase (subunit epsilon) #20 atpD 25 ATP synthase (subunit beta) #21 atpG 76 ATP synthase (subunit gamma) #22 atpF 162 ATP synthase (subunit b) #23 atpE 45 ATP synthase (subunit c) #24 atpI 300 ATP synthase (subunit i) Motif number 1 ATGAGTTTTAAAAAAGGGAGAATTTAGA 1 283 1 AAAAAGGGAG 0.843427 -18 CCGCCTGATTAAACAAGAGGTCAAGGCGGC 3 68 0 AAACAAGAGG 0.842418 -172 TCATAATTTAAGAGAAGAGGAAATGTAAGT 3 138 1 AGAGAAGAGG 0.748036 -102 TGTATTGACCAGAAAAGGGGTTGGGTGAA 3 221 1 AGAAAAGGGG 0.872273 -19 GGAAGAAAGGGAGATATTGGGGG 4 4 1 AGAAAGGGAG 0.74947 -29 GAAAAAAACTGAAATGGAGGTAAGTGGAT 5 282 1 GAAATGGAGG 0.626522 -19 AAAACTTTCTATACAAGAGGTGCGTATTGA 7 56 1 ATACAAGAGG 0.697519 -62 CAGGGGTGACTTAGAGGGGGGAGAAGAG 8 125 1 TTAGAGGGGG 0.726863 -18 GCTTGTTGCCGTAAAGGGGGAGAACG 9 39 1 GTAAAGGGGG 0.929849 -16 TATACGAACGATAGAGGAGGGAATTAC 10 55 1 ATAGAGGAGG 0.900569 -17 ATAGAAAAACGAAAAGGGGGGATGTGCTTT 11 47 1 GAAAAGGGGG 0.968482 -254 TAGAAAATGAAAAAAGGAAGATCGCCCTCT 11 116 0 AAAAAGGAAG 0.820122 -185 ATTATAGCTCAAACAGGGGGGAGGATTACA 14 37 1 AAACAGGGGG 0.961252 -256 CTTACAATTGAAAGAAGTGGGGGAAGAGAT 14 235 1 AAAGAAGTGG 0.521958 -58 CGCACTTATCAAACAGGGGGTAAAGTA 14 276 1 AAACAGGGGG 0.961252 -17 TGCAAAAAAGGAGGGGGCGCC 15 5 1 AAAAAGGAGG 0.976122 -17 CAAGAATCCGTGAAAGGAGGCTAGGAAAAA 17 196 1 TGAAAGGAGG 0.849529 -20 TAAGTCTAACAAAAAAGAGGTTATTTGTAT 18 45 0 AAAAAAGAGG 0.912344 -256 TTGAGAACGAGAAAAGGAGGTCTTATCTTT 18 202 1 GAAAAGGAGG 0.962974 -99 CAGATGAAGAGAAAAGGTGGTGAAATCT 21 59 1 GAAAAGGTGG 0.841572 -18 GGATAACATTTTAAAGGAGGAACTTTTTC 23 27 1 TTAAAGGAGG 0.814309 -19 ********** Masking position 3 Map Score: 24.9015 Number of sites scoring better than the average of aligned sites = 988 Number in coding regions = 530 Number in noncoding regions = 458 Number of orfs with sites within 600 bp upstream = 503 Fraction of orfs with sites within 600 bp upstream = 0.0807902 Motif number 2 ATGAGTTTTAAAAAAGGGAGAATTTAGA 1 283 1 AAAAAGGGAG 0.752097 -18 AAATGCCGAAAAGAAAGGAGAAAAAACAGA 5 67 1 AAGAAAGGAG 0.752097 -234 GGGTGACTTAGAGGGGGGAGAAGAG 8 128 1 GAGGGGGGAG 0.992054 -15 TTGTTGCCGTAAAGGGGGAGAACG 9 41 1 AAAGGGGGAG 0.920441 -14 ACGAACGATAGAGGAGGGAATTAC 10 58 1 GAGGAGGGAA 0.922994 -14 GAAAAACGAAAAGGGGGGATGTGCTTTACT 11 50 1 AAGGGGGGAT 0.968732 -251 TTACTAGAGGGAGAGGGGCTATC 13 21 1 GAGAGGGGCT 0.687806 -13 ATACGCAGGAGAGAGGGGAGACAGAT 14 7 0 GAGAGGGGAG 0.981323 -286 ATAGCTCAAACAGGGGGGAGGATTACAGAA 14 40 1 CAGGGGGGAG 0.987137 -253 ACGCCCTTTTGAGGGAGGAGTAAAATGAAA 14 181 1 GAGGGAGGAG 0.930564 -112 TGCAAAAAAGGAGGGGGCGCC 15 8 1 AAGGAGGGGG 0.907384 -14 GTATTTTGCCAAGAAGGGAATGATAAAAGC 18 272 0 AAGAAGGGAA 0.813235 -29 AAGATTTTGTCAGGAGGGATAGCG 20 12 1 CAGGAGGGAT 0.932183 -14 TTCAGCCGGCAAGGCGGGATGCTTATCAGA 22 80 0 AAGGCGGGAT 0.836805 -83 GAAAAACCTGCAGAAGGGAGTTGCCGTAGT 22 141 1 CAGAAGGGAG 0.95266 -22 ********** Masking position 2 Map Score: 18.6446 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 192 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 3 CGTTTATTTTGAAGCGATAAAACAAGCATCAT 3 20 0 GAAGGAAAAA 0.966995 -220 GCCGAAAAGAAAGGAGAAAAAACAGAAATTCT 5 71 1 AAGGGAAAAA 0.947113 -230 AAGGATATTGAGGGTGAAAAAAACTGAAATGG 5 267 1 AGGGGAAAAA 0.883338 -34 ATTTCTCCACAAAAGGAAAAAAGAAAACTTTC 7 33 1 AAAAGAAAAA 0.896113 -85 TCGAGGCGAAAAAACATAGCTTGT 11 3 1 GAGGGAAAAA 0.951045 -298 CTTGAGATAGAAAATGAAAAAAGGAAGATCGC 11 121 0 AAAAGAAAAA 0.896113 -180 TTTCTTTCAAGAAGTCAAAAAAAGCCATGTAT 12 260 0 GAAGCAAAAA 0.710732 -41 AGCACAAACGAAAGCGATACAACAATGACCCA 16 54 0 AAAGGAACAA 0.878795 -41 CCTTGATTATAAAGGGATAAAACAGGATGTGA 17 118 1 AAAGGAAAAA 0.964296 -98 TTTTCAATTGAGAACGAGAAAAGGAGGTCTTA 18 195 1 AGAAGAAAAA 0.784811 -106 GCAAATAAAAAAGGCGATAAAATAGCAAGATG 18 242 0 AAGGGAAAAA 0.947113 -59 TGCCAAGAAGGGAATGATAAAAGCAAATAAAA 18 264 0 GGAAGAAAAA 0.798238 -37 CTCGAATGCTGATGAGAGAAAAAGGTTCTCTT 21 11 1 GATGGAAAAA 0.788255 -66 ATCTGCGTAAAAAGAGAGAAAAAGAGAACCTT 21 32 0 AAAGGAAAAA 0.964296 -45 CTTGCCGGCTGAAAAGAGACAAGTGCGGCTGC 22 97 1 GAAAGAACAA 0.715265 -66 **** ** **** Masking position 7 Map Score: 17.6547 Number of sites scoring better than the average of aligned sites = 536 Number in coding regions = 448 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 4 ATTGAAATAAATAATAGACAAATATGATCTGATTG 1 229 1 ATAAAGAATT 0.584128 -72 TGAAGCGATAAAACAAGCATCATATCTATTTT 3 8 0 AAACAGCATT 0.916142 -232 CTTTTTGAAGAAAAATGCAAAATTTATTAAAATTA 5 26 0 AAAATGCATT 0.956706 -275 TATAAGCCTGAAAATAGCAGAATTTCTGTTTTTTC 5 86 0 AAAAAGCATT 0.971898 -215 TATCATTAAACAAGAATCATCTATTTCTCCAC 7 8 1 AAACAGAATT 0.580267 -110 CAACCATACAAAAAAAGCTTTATTTGTTCGGGTTA 11 243 0 AAAAAGCATT 0.971893 -58 CAAGAAGTCAAAAAAAGCCATGTATAGATACACCT 12 250 0 AAAAAGCGTT 0.844271 -51 CCCCTGTTTGATAAGTGCGAAATGTGCTAAATCTC 14 260 0 ATAATGCATT 0.876468 -33 ACCCAAGACATAAAATGCGGGATATAAATCAGCGT 16 24 0 TAAATGCATT 0.701652 -71 CAGCTTGCAGAAAAGTGCGATATAATTTGGACTAG 18 127 1 AAAATGCATA 0.701652 -174 TTCTCAATTGAAAAATGCGCTATGTATAAAATATA 18 174 0 AAAATGCATT 0.956709 -127 AAAAGGCGATAAAATAGCAAGATGTAAGAGCTGCA 18 231 0 AAAAAGCATT 0.971898 -70 GCATAAAAGCCTTATATGAACTAAAAA 22 3 1 ATAAAGCATT 0.91726 -160 **** *** ** * Masking position 3 Map Score: 11.0834 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 174 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 5 ATGTGACCTCCCCCAATATCTCCC 4 19 0 GACCTCCCCC 0.975191 -14 GTTAACCCCCGGTCATTCCA 6 36 0 GTTAACCCCC 0.845147 -10 CTCTTCTCCCCCCTCTAAGTCA 8 131 0 CTTCTCCCCC 0.990385 -12 CGTTCTCCCCCTTTACGGCAA 9 44 0 GTTCTCCCCC 0.984451 -11 GTAAGTAAAGCACATCCCCCCTTTTCGTTT 11 53 0 CACATCCCCC 0.945787 -248 TCATTCTGTAATCCTCCCCCCTGTTTGAGC 14 43 0 ATCCTCCCCC 0.969048 -250 TTTCATTTTACTCCTCCCTCAAAAGGGCGT 14 181 0 CTCCTCCCTC 0.952015 -112 TGTGCTAAATCTCTTCCCCCACTTCTTTCA 14 243 0 CTCTTCCCCC 0.982209 -50 TACTTTACCCCCTGTTTGATAA 14 281 0 CTTTACCCCC 0.89878 -12 ********** Masking position 6 Map Score: 11.134 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 48 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 CATTTTGAGTAAAAAAACTCATAATTTAAGAGAAG 3 120 1 AACTCATAAT 0.965983 -120 TCGTGTAAAAAAATGTCCTCACAATTATCTATTTT 5 171 0 AACTCACAAT 0.934793 -130 AAACACTTACATTTCCTTATAAACAATATTTTG 8 9 1 AACTTATAAA 0.880915 -134 CAATAACTCTAGACACCCTCATAATATATGAATCT 8 64 0 AACTCATAAT 0.965983 -79 TTGTTCGGGTTAATCTTATCATAATTCAGACGAAT 11 220 0 TAATCATAAT 0.580083 -81 CGATATTGCCTTATAAAGGCTTTTCCC 12 3 1 AACTTATAAA 0.880915 -298 TTTTCCTGCCATATTGTATTATAATAAATATCACA 12 70 1 AAATTATAAT 0.821021 -231 ATTATAATAAATATCACATTATAATAAAAGCAGTG 12 87 1 AAATTATAAT 0.821021 -214 ACTCATAACAAGATCCTATTACAAATCCATCAACA 12 120 0 AAATTACAAA 0.491891 -181 ATGTGTGTTTACACCTTCTTAGAATTAAGGGCAGG 12 218 1 AACTTAGAAT 0.76918 -83 TAAATCTTAATAAAGTGCTTACAATTGAAAGAAGT 14 218 1 TACTTACAAT 0.62635 -75 TTTTGAGGTCAAAAGAACTCATAAAAATCCATTAC 18 75 1 AACTCATAAA 0.922307 -226 AAAGCTATGAAAACCTTCTCATAATACCCTCGTTT 24 56 0 AACTCATAAT 0.965983 -245 ATTCGCTTAAATAAATCCTCATAATACGGGTTTGC 24 126 0 AACTCATAAT 0.965983 -175 * * ******** Masking position 11 Map Score: 8.04907 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 86 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 7 TATCATACAAGATAACATCTTGTAAAAAAAC 2 226 0 GAAACATCTT 0.813965 -75 TTTATACATAGATGGCATTTTGAGTAAAAAA 3 105 1 GAGGCATTTT 0.903131 -135 AGATAATTGTGAGGACATTTTTTTACACGAA 5 176 1 GAGACATTTT 0.955913 -125 GCGTTTTCTTGACGCCCTTTTGAGGGAGGAG 14 170 1 GAGCCCTTTT 0.905975 -123 TATGATTGTAGACGGACTTTTGCCTGCTGCG 17 153 1 GAGGACTTTT 0.814555 -63 TATCCCTCCTGACAAAATCTTT 20 2 0 GAAAAATCTT 0.520106 -24 GAGAGAAAAAGAGAACCTTTTTCTCTCATCA 21 20 0 GAAACCTTTT 0.955912 -57 TATCCAAACGGATAACATTTTAAAGGAGGAA 23 18 1 GAAACATTTT 0.919355 -28 CATTTTAAAGGAGGAACTTTTTC 23 33 1 GAGAACTTTT 0.910836 -13 TGAAAGCTATGAAAACCTTCTCATAATACCC 24 62 0 GAAACCTTCT 0.803277 -239 ACCCTTAGTAGAAGACCTTTTTTGACCGGCA 24 217 0 GAGACCTTTT 0.976326 -84 ** ******** Masking position 2 Map Score: 6.27427 Number of sites scoring better than the average of aligned sites = 338 Number in coding regions = 287 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 8 AGTTAGTTGAAGTGAAGCCGACAATTTTCA 1 120 1 AGTGAAGCCG 0.767508 -181 TTTTTCCAACAAAAAAGCCGACAACTTCAA 1 182 0 AAAAAAGCCG 0.922941 -119 ATAAGGTAAACGCAATGCCGATTTGGAGAT 2 122 1 CGCAATGCCG 0.479989 -179 TATGTATAAAAGTAAAGCCGCCTGATTAAA 3 85 0 AGTAAAGCCG 0.929681 -155 TGTATTGACCAGAAAAGGGGTTGGGTGAA 3 221 1 AGAAAAGGGG 0.814104 -19 AAAAAGTTTCAAAAATGCCGAAAAGAAAGG 5 55 1 AAAAATGCCG 0.807449 -246 TGCAGGCTGAAGAGAACCCGGAGCGCTT 7 100 1 AGAGAACCCG 0.713209 -18 CCCTCTGTACAGTAAAGCAGCTCTTTGACC 11 92 0 AGTAAAGCAG 0.705615 -209 AAGGGCGTCAAGAAAACGCGTACATAAATT 14 159 0 AGAAAACGCG 0.908755 -134 TGCAAAAAAGGAGGGGGCGCC 15 4 1 AAAAAAGGAG 0.684682 -18 ATTGAGAACGAGAAAAGGAGGTCTTATCTT 18 201 1 AGAAAAGGAG 0.881879 -100 AAAAGCAAATAAAAAAGGCGATAAAATAGC 18 248 0 AAAAAAGGCG 0.922941 -53 GCAGATGAAGAGAAAAGGTGGTGAAATCT 21 58 1 AGAAAAGGTG 0.747142 -19 TATATGAACTAAAAATGGCGAAGATCATTC 22 23 1 AAAAATGGCG 0.807449 -140 TCAGACATAAAGCAATGGCGAAGGTTCTCT 22 55 0 AGCAATGGCG 0.879205 -108 AAATCCTCTCAGCAAACCCGTATTATGAGG 24 115 1 AGCAAACCCG 0.834102 -186 ********** Masking position 5 Map Score: 12.6298 Number of sites scoring better than the average of aligned sites = 1420 Number in coding regions = 1223 Number in noncoding regions = 197 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 9 ATAAAATAACCTGCAACTCTATCATACAAG 2 246 0 CTGCAACTCT 0.94325 -55 TTTAGTCAGTTTGCAGGGGTGACTTAGAGG 8 112 1 TTGCAGGGGT 0.814365 -31 TTGCAATTCACTGCAAGGCTGGTCATA 9 8 0 CTGCAAGGCT 0.98433 -47 TTGCAGTGAATTGCAAGGCTTGTTGCCGTA 9 22 1 TTGCAAGGCT 0.953678 -33 GGACTTTTGCCTGCTGCGCTACAGTGAATG 17 166 1 CTGCTGCGCT 0.921264 -50 TTTCTGCAAGCTGCCACGCTTCGAACTGCT 18 110 0 CTGCCACGCT 0.930892 -191 GGTCTTATCTTTGCAGCTCTTACATCTTGC 18 220 1 TTGCAGCTCT 0.875206 -81 CAACTCCCTTCTGCAGGTTTTTCTTTGCTG 22 134 0 CTGCAGGTTT 0.747467 -29 AACAGCATCCCTGCAAGGCTTGCGGATGAA 24 163 1 CTGCAAGGCT 0.98433 -138 ********** Masking position 2 Map Score: 6.24165 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 271 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 10 TCAAAAGACCTTTCAATCAGATCATATTTGTC 1 245 0 TTTCATCAGT 0.908522 -56 AAGTGTACATTTTCCAGAAGCCGTCATTCTAT 2 64 0 TTTCAGAAGC 0.915538 -237 GTTTACCTTATTTCTATCAGACCCGGCATGAA 2 101 0 TTTCATCAGC 0.968545 -200 TGGCGATAGATTTCGATCCGCTTTCCGCCTTT 3 190 1 TTTCATCCGT 0.92003 -50 CCTTTTCGTTTTTCTATCCGTTCTATAAGACA 11 32 0 TTTCATCCGT 0.92003 -269 TGTGCTTTACTTACAAGCCGGCAGGTCAAAGA 11 69 1 TTACAGCCGC 0.927244 -232 CTAGCAAGTCTTACTAACAGACCAATCCTTGA 12 172 0 TTACAACAGC 0.750078 -129 TCCATCTTTCTTTCAAGAAGTCAAAAAAAGCC 12 266 0 TTTCAGAAGC 0.915538 -35 ATGTACGCGTTTTCTTGACGCCCTTTTGAGGG 14 164 1 TTTCTGACGC 0.737765 -129 CTTTCCTTCAGCTTGATCAGGAT 18 2 1 TTTCTTCAGT 0.689942 -299 CACTTGTCTCTTTTCAGCCGGCAAGGCGGGAT 22 90 0 TTTTAGCCGC 0.803202 -73 TGAATGATTTTTTCGAACAGGCCCGTTTTGCC 24 189 1 TTTCAACAGC 0.930532 -112 **** ***** * Masking position 2 Map Score: 5.93253 Number of sites scoring better than the average of aligned sites = 538 Number in coding regions = 502 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 11 ACTCATTATTGGTCAAAAGACCTTTCAATCAG 1 257 0 GGTCAAAAAC 0.985143 -44 CCCCTTTTCTGGTCAATACAAAGGCGGAAAGC 3 209 0 GGTCAATAAA 0.834948 -31 GGATATTGAGGGTGAAAAAAACTGAAATGGAG 5 269 1 GGTGAAAAAC 0.91528 -32 CTCTCAGCAAGGTCAATATAGCCAAAATATTG 8 34 0 GGTCAATAAC 0.97498 -109 TCTTTCAAGAAGTCAAAAAAAGCCATGTATAG 12 258 0 AGTCAAAAAG 0.74604 -43 AAAATGAAATTGTCAATAAATCTTAATAAAGT 14 202 1 TGTCAATAAC 0.813275 -91 CTTATTTTGAGGTCAAAAGAACTCATAAAAAT 18 71 1 GGTCAAAAAC 0.986697 -230 TAAAATATACGGTCAAACGACCTAGTCCAAAT 18 151 0 GGTCAAACAC 0.944051 -150 CCGTTTTGCCGGTCAAAAAAGGTCTTCTACTA 24 211 1 GGTCAAAAAG 0.963379 -90 ******** * * Masking position 6 Map Score: 6.79123 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 53 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 12 TATGCTATGTTTTCATTTCCTTTAATATAGT 1 44 0 TTTCTTTCCT 0.976301 -257 AATAAAGCACTTACATTTCCTCTTCTCTTAA 3 145 0 TTACTTTCCT 0.910887 -95 AGAATTTCTGTTTTTTCTCCTTTCTTTTCGG 5 72 0 TTTTTCTCCT 0.740283 -229 TAGAAAGTTTTCTTTTTTCCTTTTGTGGAGA 7 36 0 TCTTTTTCCT 0.759413 -82 AAACACTTACATTTCCTTATAAACAAT 8 7 1 TTACTTTCCT 0.910887 -136 ATCTTCCTTTTTTCATTTTCTATCTCAAGAT 11 124 1 TTTCTTTTCT 0.821441 -177 GGACCGGTCCTTTCTTTTCCTATACAACATC 11 277 0 TTTCTTTCCT 0.976301 -24 TTATCGCCTTTTTTATTTGCTTTTATCATTC 18 254 1 TTTTTTTGCT 0.870387 -47 TATTTGCTTTTATCATTCCCTTCTTGGCAAA 18 267 1 TATCTTCCCT 0.6899 -34 TTCTGCAGGTTTTTCTTTGCTGATCCAGCAG 22 125 0 TTTTTTTGCT 0.870387 -38 AGGGATGCTGTTTCATTCGCTTAAATAAATC 24 144 0 TTTCTTCGCT 0.875233 -157 **** ****** Masking position 6 Map Score: 6.01943 Number of sites scoring better than the average of aligned sites = 471 Number in coding regions = 394 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 13 AAACAAGAGGTCAAGGCGGCATTTACTAGT 3 58 0 TCAAGGCGGC 0.938132 -182 CTCTTGTTTAATCAGGCGGCTTTACTTTTA 3 79 1 ATCAGGCGGC 0.966679 -161 CCGGGTTCTCTTCAGCCTGCAAAAGGTGAG 7 91 0 TTCAGCCTGC 0.941249 -27 TGCTTTACTTACAAGCCGGCAGGTCAAAGA 11 71 1 ACAAGCCGGC 0.939366 -230 TAATCAAGGGTTCAGCCGGTCCACCTGAAA 17 97 0 TTCAGCCGGT 0.941178 -119 CTTGTCTCTTTTCAGCCGGCAAGGCGGGAT 22 90 0 TTCAGCCGGC 0.990426 -73 ********** Masking position 4 Map Score: 2.54379 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 212 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 14 GCAATTCACTGCAAGGCTGGTCATA 9 6 0 GCAAGGCTGG 0.964009 -49 GCAGTGAATTGCAAGGCTTGTTGCCGTAAA 9 24 1 GCAAGGCTTG 0.9842 -31 AGGCGAAAAAACATAGCTTGTCTTATAGAA 11 14 1 ACATAGCTTG 0.772538 -287 ACCCGAACAAATAAAGCTTTTTTTGTATGG 11 245 1 ATAAAGCTTT 0.474561 -56 TGGTCTGTTAGTAAGACTTGCTAGTGAACT 12 180 1 GTAAGACTTG 0.699023 -121 GTGTATCTATACATGGCTTTTTTTGACTTC 12 252 1 ACATGGCTTT 0.772538 -49 TTTAGTTCATATAAGGCTTTTATGC 22 6 0 ATAAGGCTTT 0.761959 -157 TTTTCAGCCGGCAAGGCGGGATGCTTATCA 22 82 0 GCAAGGCGGG 0.848159 -81 CAGCATCCCTGCAAGGCTTGCGGATGAATG 24 165 1 GCAAGGCTTG 0.9842 -136 AAAAAATAATGTATAGCTTGGATACGGCAA 24 261 0 GTATAGCTTG 0.772538 -40 ********** Masking position 3 Map Score: 3.12717 Number of sites scoring better than the average of aligned sites = 609 Number in coding regions = 579 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 15 TTGTTGGAAAAAAATAGAGATAAATAAAAAT 1 200 1 AAAATAGAAT 0.933722 -101 GAGATAAATAAAAATTGAAATAAATAATAGA 1 216 1 AAAATTGAAT 0.777556 -85 ATTGAAATAAATAATAGACAAATATGATCTG 1 229 1 ATAATAGAAA 0.680219 -72 AAAATAGATATGATGCTTGTT 3 1 1 AAAATAGAAT 0.933722 -239 GAAAGGAGAAAAAACAGAAATTCTGCTATTT 5 79 1 AAAACAGAAT 0.888611 -222 ACCTAGTTGCAAAATAGATAATTGTGAGGAC 5 161 1 AAAATAGAAA 0.943634 -140 GAGGGTGAAAAAAACTGAAATGGAGGTAAGT 5 276 1 AAAACTGAAT 0.664361 -25 CCACAAAAGGAAAAAAGAAAACTTTCTATAC 7 39 1 AAAAAAGAAA 0.776564 -79 CAAACTGACTAAAATAGAAAATATTGCAATA 8 94 0 AAAATAGAAA 0.943634 -49 CATCTGCGTAAAAAGAGAGAAAAAGAGAACC 21 34 0 AAAAGAGAAA 0.90458 -43 TTGCCGGCTGAAAAGAGACAAGTGCGGCTGC 22 98 1 AAAAGAGAAA 0.90458 -65 ******** ** Masking position 4 Map Score: 8.63213 Number of sites scoring better than the average of aligned sites = 354 Number in coding regions = 262 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829