AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i259_ecoli_bsub_300.orf -o259_ecoli_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 flgB 154 flagellar biosynthesis, cell-proximal portion of basal-body rod #2 flgE 24 flagellar biosynthesis, hook protein #3 BIME65 28 BIME #4 flgG 44 flagellar biosynthesis, cell-distal portion of basal-body rod #5 flhB 130 putative part of export apparatus for flagellar proteins #6 BIME88 37 BIME #7 tap 45 methyl-accepting chemotaxis protein IV, peptide sensor receptor #8 tar 144 methyl-accepting chemotaxis protein II, aspartate sensor receptor #9 motA 126 proton conductor component of motor; no effect on switching #10 flhD 300 regulator of flagellar biosynthesis, acting on class 2 operons; transcriptional initiation factor #11 fliA 178 flagellar biosynthesis; alternative sigma factor 28; regulation of flagellar operons #12 BIME89 108 BIME #13 fliC 265 flagellar biosynthesis; flagellin, filament structural protein #14 fliF 214 flagellar biosynthesis; basal-body MS(membrane and supramembrane)-ring and collar protein #15 fliL 104 flagellar biosynthesis #16 fliO 62 flagellar biosynthesis #17 flgB 300 flagellar basal-body rod protein #18 fliF 45 flagellar basal-body M-ring protein #19 fliH 117 flagellar assembly protein #20 fliK 160 fliK #21 flgE 21 flagellar hook protein #22 fliL 251 flagellar protein #23 fliM 33 flagellar motor switch protein #24 cheY 25 two-component response regulator #25 flhA 32 flagella-associated protein #26 cheW 21 cheW #27 sigD 22 RNA polymerase sigma-28 factor (sigma-D) #28 flhO 224 flagellar basal-body rod protein #29 mbl 165 MreB-like protein #30 usd 224 usd Motif number 1 TGGTTTGAGTAAGGGGCAAAACAGGCGGGAT 5 52 0 AAGGGCAAAA 0.722274 -79 TATCGGCAAGGAGGGGGGAAACTTTATTGCT 8 92 0 GAGGGGGAAA 0.969244 -53 GGTAAATTCCAGGCAGAAAAAAACCCCGCCG 11 52 0 AGGCGAAAAA 0.670479 -127 CGGGAATAAGGGGCAGAGAAAAGAGTATTTC 13 104 1 GGGCGAGAAA 0.901938 -162 GAGCGCAACAAAGCGGGGAAAAGACGCGGAT 15 30 0 AAGCGGGAAA 0.886112 -75 GCCGAAAAGAAAGGAGAAAAAACAGAAATTC 17 71 1 AAGGGAAAAA 0.938078 -230 GGCTTATATCAGGGCGAGAAATGTAGTTCTA 17 113 1 AGGGGAGAAA 0.974889 -188 AAGGATATTGAGGGTGAAAAAAACTGAAATG 17 267 1 AGGGGAAAAA 0.893765 -34 CAGCCTGCAAAAGGTGAGAATGATCAATACG 19 78 0 AAGGGAGAAT 0.856768 -40 GGAGGGAGGGGAGGCGAGTAATCGCTTCTCC 22 11 1 GAGGGAGTAA 0.870801 -241 ACAGAATACGGAGGTGAGGAAA 23 22 1 GAGGGAGGAA 0.948411 -12 CGAAACACAAGGAGAGAGATAGATT 24 9 1 AAGGGAGAGA 0.945817 -17 TTCGATTTAAAAGGAGAGAAAAAACAGC 25 15 1 AAGGGAGAAA 0.985897 -18 GCCATTTTTAGAGGTGGGAAAT 28 213 1 GAGGGGGAAA 0.969244 -12 CAATAAGGACAAGGGGTGAAACGAACTTTTT 30 127 0 AAGGGTGAAA 0.890076 -98 GAGAGTGTTTGAGGTGAGGGATC 30 212 1 GAGGGAGGGA 0.821123 -13 **** ****** Masking position 6 Map Score: 18.946 Number of sites scoring better than the average of aligned sites = 341 Number in coding regions = 287 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 2 TAGGGCTTTTGCTGCCACACATCAAGCATAGTG 5 18 0 GCTGCCACCC 0.989011 -113 CTTTATTGCTGATGCCACCCGCCGCGAAATTGA 8 69 0 GATGCCACCC 0.912746 -76 CAGCAATAAAGTTTCCCCCCTCCTTGCCGATAA 8 91 1 GTTTCCCCCC 0.992626 -54 CTGCTGGAATGTTGCGCCTCACCGTATCAG 9 8 0 GTTGCGCCCC 0.975638 -119 ATTGAAAATCGCAGCCCCCCTCCGTTGTATGTG 10 63 1 GCAGCCCCCC 0.981782 -238 TTTTACCGGGGCTTCCCGGCGACATCACGGGGT 10 240 1 GCTTCCCGCC 0.973999 -61 TTTTTATGCGGTTTCACCGCACCCCGTGATGTC 10 260 0 GTTTCACCCC 0.929548 -41 TCAGCAACGTGCTTCCCCGCCACCGGCGGGGTT 11 29 1 GCTTCCCCCC 0.997235 -150 TACGTATTGGGTTTCCACCCGTCGGCTCAATCG 13 212 0 GTTTCCACCC 0.967444 -54 GCCGGTTTCTGCTGCGCCACTGCTGCAG 16 45 1 GCTGCGCCCC 0.986702 -18 GCGATTACTCGCCTCCCCTCCCTCC 22 3 0 GCCTCCCCCT 0.905546 -249 GCGAGTAATCGCTTCTCCGCTGTTTTATGATTA 22 24 1 GCTTCTCCCT 0.833077 -228 ******** * * Masking position 5 Map Score: 17.149 Number of sites scoring better than the average of aligned sites = 305 Number in coding regions = 277 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 3 CGTTTATTCCGCCGATAACGCGCGCGTAAAG 1 91 1 GCCGTAACGC 0.994749 -64 CCCCCTCCTTGCCGATAACGAGATCAACTTG 8 106 1 GCCGTAACGA 0.97665 -39 ACATTCCAGCAGCGGTAACGACGTACCGCTG 9 29 1 AGCGTAACGA 0.687528 -98 TCAGTCGTCAGGCGTTAACGCGCGATTGGGG 9 70 0 GGCGTAACGC 0.978298 -57 CCGTGATGTCGCCGGGAAGCCCCGGTAAAAA 10 239 0 GCCGGAAGCC 0.876688 -62 CCTGGAATTTACCTGTAACCCCCAAATAACC 11 70 1 ACCTTAACCC 0.734268 -109 GGATAATCATGCCGATAACTCATATAACGCA 11 146 1 GCCGTAACTC 0.960901 -33 AACTGAGACTGACGGCAACGCCAAATTGCCT 12 27 1 GACGCAACGC 0.864004 -82 CGCAATTCAGACCGATAACCCCGGTATTCGT 13 41 0 ACCGTAACCC 0.972275 -225 CGGCTCAATCGCCGTCAACCCTGTTATCGTC 13 192 0 GCCGCAACCC 0.983802 -74 GTTCCACTTTGCCAATAACGCCGTCCATAAT 14 177 1 GCCATAACGC 0.93722 -38 AGGATAATTAGCCGATAAGCAGTAGCGACAC 15 68 1 GCCGTAAGCA 0.882861 -37 **** ****** Masking position 7 Map Score: 12.5465 Number of sites scoring better than the average of aligned sites = 1205 Number in coding regions = 1140 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 4 TTGCCGCCTGATGGGGAGCGTTG 7 33 1 ATGGGGAGCG 0.86433 -13 GAAATAAAAAACCCGATGCGCAGATCATCG 8 41 0 ACCCGATGCG 0.782282 -104 TGCTGATGCCACCCGCCGCGAAATTGAAAT 8 66 0 ACCCGCCGCG 0.95063 -79 GGCGCAACATTCCAGCAGCGGTAACGACGT 9 23 1 TCCAGCAGCG 0.840498 -104 TGGGGCAAAAAAAAGCAGCGGTACGTCGTT 9 45 0 AAAAGCAGCG 0.662072 -82 CGGCGACATCACGGGGTGCGGTGAAACCGC 10 256 1 ACGGGGTGCG 0.967309 -45 TAGGCCTGATAAGCGCAGCGCATCAGGCAA 12 52 0 AAGCGCAGCG 0.960139 -57 AAGCACAAATAATGGGAGCGTCAATTTTTC 14 120 1 AATGGGAGCG 0.799213 -95 ATAATCAGCCACGAGGTGCGCG 14 203 1 ACGAGGTGCG 0.958304 -12 GCGCAGCAGAAACCGGCGCGGAAGATTGCA 16 32 0 AACCGGCGCG 0.942343 -31 CTTTCTATACAAGAGGTGCGTATTGATCAT 19 60 1 AAGAGGTGCG 0.925163 -58 GCTGAAGAGAACCCGGAGCGCTT 19 105 1 ACCCGGAGCG 0.986047 -13 ACCCGTTTGAACGGGCAGCCCTTTACACTG 22 62 1 ACGGGCAGCC 0.765353 -190 TATTTCATTTTACAGGAGCGATCAATAGTT 30 53 1 TACAGGAGCG 0.817278 -172 ********** Masking position 9 Map Score: 10.0187 Number of sites scoring better than the average of aligned sites = 1431 Number in coding regions = 1335 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 5 CCTCAATATCCTTGTCGAGAATTGTAAAAC 17 250 0 CTTGTCGAGA 0.942055 -51 GTTCCCTTTCCTTGTTCTGAAAGTTCCTTC 20 112 0 CTTGTTCTGA 0.93443 -49 AAGCTGCGATCTTTTCCAGAACAGCTTCTT 22 180 0 CTTTTCCAGA 0.976448 -72 GTTTAGGAAGCTTGTCCATATTATCAGCAT 28 29 0 CTTGTCCATA 0.945926 -196 AAACCTCATTCTTTTTCAGAATGAGGTTTG 28 78 0 CTTTTTCAGA 0.954755 -147 TTCGTGAAGGCTTTTTCATAAAAAAACCTC 28 101 0 CTTTTTCATA 0.873672 -124 CATTTAACATCTTTTCGTGAAGGCTTTTTC 28 114 0 CTTTTCGTGA 0.868838 -111 GTGAAACGAACTTTTTCAGATTCAGCAAAC 30 113 0 CTTTTTCAGA 0.954755 -112 CGTTTCACCCCTTGTCCTTATTGAGTTTTT 30 135 1 CTTGTCCTTA 0.901733 -90 ********** Masking position 5 Map Score: 8.02402 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 109 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 TGGATTAGTGACAAAGTGCATATGTCTTCT 4 5 0 ACAAGCTGTC 0.868898 -40 CAAAAGCCCTAAATCCCGCCTGTTTTGCCCCTTACT 5 40 1 AAACGCTTTT 0.550941 -91 AACATAAAGCGCAATTTGTCAGCAACG 11 2 1 ACAAGCATTT 0.645537 -177 AATTAAACGTAAACTTTGCGCAATTCAGACCGATAA 13 54 0 AAATGCATTC 0.825961 -212 GCGACTAACAAAAAATGGCTGTTTTTGAAAAAAATT 13 136 1 AAAAGCTTTT 0.496553 -130 TAATTTTAATAAATTTTGCATTTTTCTTCAAAAAGT 17 26 1 AAATGCTTTC 0.90649 -275 GAAAAAACAGAAATTCTGCTATTTTCAGGCTTATAT 17 86 1 AAATGCTTTC 0.90649 -215 TCTTGTATAGAAAGTTTTCTTTTTTCCTTTTGTGGA 19 38 0 AAATTCTTTC 0.508219 -80 AGTTTTGAAAACTCCTGGCTACTTTTCATGTTTTTA 20 54 0 ACTCGCTTTT 0.673327 -107 AGGAGTTTTCAAAACTGGCTTATGTCTGAGGCTGGA 20 74 1 AAACGCTGTC 0.859243 -87 AGCCCTTTACACTGAATGCGCTATTTATTGAACAGA 22 78 1 ACTAGCATTT 0.418532 -174 CTGTTCTGGAAAAGATCGCAGCTTTCTACCGAAAAA 22 186 1 AAAAGCTTTC 0.957522 -66 TCCTAAACGCAAACTAAGCTGATTTCACAAACCTCA 28 51 1 AAATGCTTTC 0.947366 -174 TGACAACTGGAAAAAATGCCATTTTTAGAGGTGGGA 28 196 1 AAAAGCTTTT 0.496553 -29 GTTCTTTACAAATTTTTGCGGATGTTTTATGAACGA 29 35 0 AATTGCTGTT 0.565403 -131 TACCTAAGTAACTAATTGCTTATTTCATTTTACAGG 30 33 1 ACTAGCTTTC 0.855799 -192 *** * ** **** Masking position 15 Map Score: 8.76953 Number of sites scoring better than the average of aligned sites = 502 Number in coding regions = 387 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 7 AATTTTGATACCTGCGGAGGAGAT 1 141 1 CCTGGAGGAG 0.986492 -14 AAAATGTCCTGTAGTGGATTAGTGACAAA 4 26 0 CCTGGTGGAT 0.927051 -19 AATACTCTTTCCAGGATTGGCGAC 5 117 1 CCAGTTGGCG 0.86177 -14 TTTGTATTGCCTGATGTGGCGTGACCACGTC 6 10 1 CCTGGTGGCG 0.993414 -28 GTCATTGCCGCCTGATGGGGAGCGTTG 7 29 1 CCTGGGGGAG 0.977189 -17 GAAAAAAACCCCGCCGGTGGCGGGGAAGCACG 11 36 0 CCGCGTGGCG 0.933934 -143 CAGAAATTATCCGGGAGACGAGA 14 2 0 CCGGGACGAG 0.907877 -213 CTGCAGCAGTGGCGCAGCAGAAAC 16 49 0 GCAGGTGGCG 0.902344 -14 TTTCTTTTTTCCTTTTGTGGAGAAATAGATGA 19 27 0 CCTTGTGGAG 0.978498 -91 ATTAGCCGGACCTTTCGTCGAGACCGACGACG 20 11 1 CCTTGTCGAG 0.915573 -150 CCATTCGAGGAGGTGTCTCAC 26 1 1 CCATGAGGAG 0.915321 -21 **** ****** Masking position 2 Map Score: 7.96567 Number of sites scoring better than the average of aligned sites = 801 Number in coding regions = 582 Number in noncoding regions = 219 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 8 ATAGCGACCCATTTTGCGTTTATTCCGCCGA 1 75 1 ATTTTCGTTT 0.956555 -80 CATCAAGCATAGTGTGCGTTT 5 1 0 AGTGTCGTTT 0.930121 -130 TATCGGCATGATTATCCGTTTCTGCAGGGTT 11 132 0 ATTATCGTTT 0.889629 -47 CGATAACCCCGGTATTCGTTTTACGTGTCGA 13 29 0 GGTATCGTTT 0.787235 -237 AATTGCGCAAAGTTTACGTTTAATTGTTTTT 13 65 1 AGTTTCGTTT 0.977405 -201 ATTTTAATAAATTTTGCATTTTTCTTCAAAA 17 28 1 ATTTTCATTT 0.710873 -273 TTGTATAGAAAGTTTTCTTTTTTCCTTTTGT 19 41 0 AGTTTCTTTT 0.828491 -77 ATTTTTCGATTTAAAAGGAGA 25 1 1 ATTTTCGATT 0.77633 -32 AAATCAGCTTAGTTTGCGTTTAGGAAGCTTG 28 45 0 AGTTTCGTTT 0.977405 -180 ***** ***** Masking position 5 Map Score: 4.49353 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 79 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 9 GCCAATCCTGGAAAGAGTATTAAGCGTGAATG 5 106 0 GAAGAGTTTA 0.754852 -25 TATGTTAAGTAATTGAGTGTTTTGTGTGATCT 10 19 1 AATGAGTTTT 0.947385 -282 TTACAAATAGAAATGGGTCTTTACACTTATCT 10 139 0 AATGGGTTTT 0.755565 -162 AGGGGCAGAGAAAAGAGTATTTCGGCGACTAA 13 112 1 AAAGAGTTTT 0.903274 -154 GCTGACCCGGGAGTGAGTCTTGTTCCACTTTG 14 156 1 GATGAGTTTG 0.941838 -59 TTATTGAACAGATTGAATGTTTTCCGGATACT 22 102 1 GATGAATTTT 0.751701 -150 CTTACCATTTGACAGAGTAATTGTAGTATCCG 22 126 0 GAAGAGTATT 0.717088 -126 TTCTTTTTCAGAATGAGGTTTGTGAAATCAGC 28 68 0 GATGAGGTTG 0.848764 -157 TTCTGAAAAAGAATGAGGTTTTTTTATGAAAA 28 87 1 GATGAGGTTT 0.935991 -138 TAGGATAAAATACTGAGTTTTTATTATAGAAC 28 151 1 TATGAGTTTT 0.906108 -74 CCCTTGTCCTTATTGAGTTTTTAGCATATTCC 30 143 1 TATGAGTTTT 0.906108 -82 AAACCTAACAAAGAGAGTGTTTGAGGTGAGGG 30 200 1 AAAGAGTTTT 0.903277 -25 ** ***** *** Masking position 2 Map Score: 4.71161 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 121 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 10 AATGACCATCAACGGCATAAATAGCGACCCAT 1 55 1 AACGGCATAT 0.790024 -100 AAATTCTGCCATCAGCTTAAATGCCTTTACGC 1 114 0 ATCAGCTTAT 0.729178 -41 TGCGCAGATCATCGGGTTCATTTCAATTGAGG 8 23 0 ATCGGGTTTT 0.97217 -122 TGATCTGCGCATCGGGTTTTTTATTTCAATTT 8 44 1 ATCGGGTTTT 0.97217 -101 TATATGAGTTATCGGCATGATTATCCGTTTCT 11 140 0 ATCGGCATTT 0.957801 -39 GCAACAAAAAAACGGGTTTATTGGCGGATAGA 14 79 1 AACGGGTTTT 0.948251 -136 CTCCTTTCTTTTCGGCATTTTTGAAACTTTTT 17 55 0 TTCGGCATTT 0.781567 -246 TGCCCGTTCAAACGGGTTACTTTAATCATAAA 22 47 0 AACGGGTTTT 0.948251 -205 GGTTTGTGAAATCAGCTTAGTTTGCGTTTAGG 28 52 0 ATCAGCTTTT 0.894961 -173 ******** ** Masking position 8 Map Score: 3.59505 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 240 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 11 TCGCTATTTATGCCGTTGATGGTCATTGCGGACA 1 48 0 TCCTATGGTC 0.946833 -107 ATTGAAATGAACCCGATGATCTGCGCATCGGGTT 8 28 1 ACCTATCTGC 0.946839 -117 AAACAAGTTGATCTCGTTATCGGCAAGGAGGGGG 8 106 0 ACTTATCGGC 0.916053 -39 ACGACTGAACATCCTGTCATGGTCAACAGTGGAA 9 93 1 ACCTATGGTC 0.975207 -34 TACCCATTTATGTTAAGTAATTGAG 10 2 1 ACCTATGTTA 0.52072 -299 CCCTCATTTCACCCACTAATCGTCCGATTAAAAA 11 100 1 ACCTATCGTC 0.988766 -79 GCGATTTCCTTTTATCTTTCGACACGTAA 13 6 1 TCCTATCTTT 0.526165 -260 ATCGCCGTCAACCCTGTTATCGTCTGTCGTAAAA 13 182 0 ACCTATCGTC 0.988846 -84 CCTGTGTCGCTACTGCTTATCGGCTAATTATCCT 15 68 0 TCTTATCGGC 0.831682 -37 TCAGTATTTTATCCTATTATCGTCATTTAACATC 28 133 0 ACCTATCGTC 0.988846 -92 * ** * ****** Masking position 7 Map Score: 5.30868 Number of sites scoring better than the average of aligned sites = 331 Number in coding regions = 312 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 12 ACTACACGCACATACAACGGAGGGGGGCTGCG 10 72 0 CATACCGGAG 0.883732 -229 AGTGGCGCAGCAGAAACCGGCGCGGAAGATTG 16 34 0 CAGAACGGCG 0.991912 -29 GCAGGCTGAAGAGAACCCGGAGCGCTT 19 101 1 GAGAACGGAG 0.953933 -17 TTTTTAGCGGCAGAACCCGTCGTCGGTCTCGA 20 28 0 CAGAACGTCG 0.931948 -133 AAGGAACTTTCAGAACAAGGAAAGGGAACTCC 20 113 1 CAGAAAGGAA 0.761657 -48 AGCTGATCTTCAGAATTAGGAGTTCCCTTTCC 20 131 0 CAGAAAGGAG 0.966236 -30 TTACTTTAATCATAAAACAGCGGAGAAGCGAT 22 31 0 CATAACAGCG 0.758003 -221 CATAATTTGACAGAATACGGAGGTGAGGAAA 23 13 1 CAGAACGGAG 0.992071 -21 ***** ***** Masking position 4 Map Score: 2.50176 Number of sites scoring better than the average of aligned sites = 436 Number in coding regions = 407 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 13 GCGCGTTATCGGCGGAATAAACGCAAAATGGGT 1 81 0 GGGGAATACG 0.979275 -74 GGCAAAACAGGCGGGATTTAGGGCTTTTGCTGC 5 36 0 GCGGATTAGG 0.943427 -95 TCCCCATCAGGCGGCAATGACCGCGTTAGTAAA 7 17 0 GCGCAATACG 0.952241 -29 TTTCGCGGCGGGTGGCATCAGCAATAAAGTTTC 8 73 1 GGGGCATACA 0.73642 -72 GTTGCGATAAGCTGCAATAAGCAGAACCACCTT 10 188 0 GCGCAATACA 0.754406 -113 GGGGCTTCCCGGCGACATCACGGGGTGCGGTGA 10 247 1 GGGACATAGG 0.876373 -54 ACGATTAGTGGGTGAAATGAGGGGTTATTTGGG 11 90 0 GGGAAATAGG 0.948639 -89 TTTTTTAATAGCGGGAATAAGGGGCAGAGAAAA 13 93 1 GCGGAATAGG 0.98534 -173 AAAAACGAAAGCACAAATAATGGGAGCGTCAAT 14 112 1 GCCAAATAGG 0.720091 -103 TTAGAGAAAGAGTGGAATGACCGGGGGTTAAC 18 24 1 AGGGAATACG 0.788276 -22 TATGTCTGAGGCTGGATTGAAGGAACTTTCAGA 20 94 1 GCGGATTAGG 0.943426 -67 ** ***** * ** Masking position 10 Map Score: 3.73711 Number of sites scoring better than the average of aligned sites = 888 Number in coding regions = 831 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 14 ATTGTACCTGTCCGCAATGACCATCAACGGCA 1 40 1 TCGCAAGACC 0.962312 -115 GTATCAAAATTCTGCCATCAGCTTAAATGCCT 1 120 0 TCGCCACAGC 0.870594 -35 TCCCCATCAGGCGGCAATGACCGCGTTAGTAA 7 18 0 GCGCAAGACC 0.827838 -28 GATCTCGTTATCGGCAAGGAGGGGGGAAACTT 8 99 0 TCGCAAGAGG 0.987371 -46 CAACTTGTTTTCAGGAAGGTGCCTT 8 130 1 TCGGAAGTGC 0.818634 -15 GCGCAATTTGTCAGCAACGTGCTTCCCCGCCA 11 19 1 TCGCAAGTGC 0.97478 -160 CACTCCCGGGTCAGCAAACTCGAAAAATTGAC 14 139 0 TCGCAACTCG 0.827624 -76 GACGGCGTTATTGGCAAAGTGGAACAAGACTC 14 170 0 TTGCAAGTGG 0.919478 -45 CCGTCCATAATCAGCCACGAGGTGCGCG 14 197 1 TCGCCAGAGG 0.96775 -18 AATTATCTATTTTGCAACTAGGTATAAAGTCC 17 152 0 TTGCAATAGG 0.655011 -149 GTGAAACAGATTTTCAAGGAGGATATAAATAG 29 144 1 TTTCAAGAGG 0.604117 -22 ** **** **** Masking position 7 Map Score: 2.47314 Number of sites scoring better than the average of aligned sites = 997 Number in coding regions = 935 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 15 GATTTCCTCAATTGAAATGAACCCGATGATC 8 18 1 ATTGAAAGAA 0.812362 -127 CCGCCGCGAAATTGAAATAAAAAACCCGATG 8 53 0 ATTGAAAAAA 0.948793 -92 GTGAAACCGCATAAAAATAAAGTTGGTTATT 10 276 1 ATAAAAAAAA 0.747579 -25 TATTCCCGCTATTAAAAAAAACAATTAAACG 13 81 0 ATTAAAAAAA 0.78489 -185 AATGGCTGTTTTTGAAAAAAATTCTAAAGGT 13 149 1 TTTGAAAAAA 0.744957 -117 AAGGCGCTAAATAGCAACAAAAAAACGGGTT 14 66 1 ATAGCAAAAA 0.799791 -149 TTATTGGCGGATAGAAAAAAACGAAAGCACA 14 96 1 ATAGAAAAAA 0.937657 -119 CTATATGCTTATTGTAAGAAATAACAGGCAT 17 220 0 ATTGTAAAAA 0.768544 -81 ATCATAAAATATAGAAAAAAAGTTGGAAGCA 29 77 0 ATAGAAAAAA 0.937657 -89 ******* *** Masking position 6 Map Score: 2.13459 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 40 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911