AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -icpxR_bsub_opreg_100.orf -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 yacB 194 similar to hypothetical proteins #2 yacC 85 similar to hypothetical proteins #3 yacD 46 similar to protein secretion PrsA homolog #4 ybdE 105 similar to hypothetical proteins #5 yczA 300 yczA #6 ycbL 96 similar to two-component response regulator [YcbM] #7 yclJ 212 similar to two-component response regulator [YclK] #8 yerI 161 yerI #9 htrA 168 serine protease Do (heat-shock protein) #10 ykoG 300 similar to two-component response regulator [YkoH] #11 motA 300 motility protein A #12 fliL 251 flagellar protein #13 fliM 33 flagellar motor switch protein #14 cheY 25 two-component response regulator #15 flhA 32 flagella-associated protein #16 cheW 21 cheW #17 resD 80 two-component response regulator #18 resC 135 essential protein similar to cytochrome c biogenesis protein #19 ppiB 253 peptidyl-prolyl isomerase #20 yrkP 267 similar to two-component response regulator [YrkQ] #21 phoP 211 two-component response regulator #22 yvqA 277 similar to two-component response regulator [YvqB] #23 yvrI 300 yvrI #24 cydA 300 cytochrome bd ubiquinol oxidase (subunit I) #25 yyxA 68 alternate gene name: yycK; similar to serine protease Do #26 yycJ 21 yycJ #27 yycF 300 similar to two-component response regulator [YycG] Motif number 1 TGTAAAAAGTAAAGTAGAGAAACTATTCAAAA 1 160 1 AAAGAGAAAA 0.957379 -35 TAACCTTTACAAAATCAAAAAACACACACGTA 6 54 0 AAAACAAAAA 0.70379 -43 AAAGGTATGAAAAAAATATGAACAATCTATTT 7 92 1 AAAAATAGAA 0.545193 -121 TAGACATGTGAAAATAGAGAAACGGAGTGAAC 9 144 1 AAAAAGAAAA 0.976033 -25 TTTTTTTGGTAAAATAAAAAACTGCATATCCT 10 16 1 AAAAAAAAAC 0.70379 -285 GTTTGTAGTAAAAGAAGATGAAGAAGCTGTTC 12 160 1 AAAGAGAGAA 0.883191 -92 TCTCTCCTTTTAAATCGAAAAAT 15 2 0 TAAACGAAAA 0.507357 -31 TTTCGATTTAAAAGGAGAGAAAAAACAGC 15 14 1 AAAGAGAAAA 0.957379 -19 CATACGCGGGAATAAAGATAAAAAGGGCAGGC 18 107 1 AATAAGAAAA 0.705124 -29 GAGCTTTACTAAAAAATAAAAATGAAACCTGA 19 118 0 AAAAATAAAA 0.780765 -136 TTTGAAAATTAAAATAAAGAAAGTAGGCATAC 19 230 1 AAAAAAAAAA 0.906787 -24 TAAAAAGAGAGAAAGGCTTGCTTA 21 3 1 AAAAAGAAAA 0.976033 -209 TCATTTATAGTAAAAAGAGAAAGGCTGTATTA 21 33 0 TAAAAGAAAA 0.808306 -179 CATCATTTTTAAAAGAAATAAAGACGTTTATG 21 74 0 AAAAAAAAAA 0.906787 -138 AAGATGACATAAAATAGAGAAATAGGATGTCG 21 164 1 AAAAAGAAAA 0.976033 -48 TAAGGGAAGAAAGGAAGAGAAAAAGAGCGAGG 22 140 0 AAGGAGAAAA 0.661577 -138 GTAAGTGAGGAAAACCGATAAAACGTAAACTG 23 193 1 AAAACGAAAA 0.908646 -108 TAAATGAAGGAAAGCAAAAAAAAGTAAACTAC 23 261 0 AAAGAAAAAA 0.842912 -40 AATAAGCAACAAAATAGACAAAAATCCGTCAC 24 20 1 AAAAAGAAAA 0.976033 -281 AGTAATTCACAAAATAGACGAAAAAAATATTG 24 207 0 AAAAAGAGAA 0.932009 -94 CGGCCGGTTCAAAGAAGAAGACGTCATTGATA 27 28 1 AAAGAGAGAC 0.648714 -273 AACTTTTTTTAAAAAAGATAACTTTATTGAAA 27 84 0 AAAAAGAAAC 0.908646 -217 GACCAGCATGACAATAGATAAACAACTGGCGA 27 116 1 ACAAAGAAAA 0.772318 -185 GTCAAAAGATAAAAAAAATAAAGGTTTAGAAA 27 170 0 AAAAAAAAAA 0.906787 -131 **** *** *** Masking position 8 Map Score: 27.7412 Number of sites scoring better than the average of aligned sites = 741 Number in coding regions = 558 Number in noncoding regions = 183 Number of orfs with sites within 600 bp upstream = 191 Fraction of orfs with sites within 600 bp upstream = 0.0306778 Motif number 2 AAAAGGGGCTGAAAGCAGGT 3 37 1 GAAAGCAGGT 0.892379 -10 CAACTATTCCTGAAGGATGTTCATGCTCGT 4 14 0 TGAAGGATGT 0.608232 -92 CCGTTACCAAGAGAGGAGTATCGAAACATA 5 111 1 GAGAGGAGTA 0.627251 -190 TTGTGTTTCTTAAAGGAGGTGACGGCCAAT 5 230 1 TAAAGGAGGT 0.905423 -71 AGATGAGTTAGAAAGGAGGATATCAA 5 285 1 GAAAGGAGGA 0.97811 -16 ATAGGGACGGGAGAGGATGGTCAAAT 10 285 1 GAGAGGATGG 0.852423 -16 TAAAAAAGTGTAAAGGATGAAGGGAAGTAG 11 15 0 TAAAGGATGA 0.737325 -286 ACTTTTTTAAGGAGGGATGGAACATGTTTA 11 36 1 GGAGGGATGG 0.807554 -265 GGAGGGAGGGGAGGCGAGTA 12 1 1 GGAGGGAGGG 0.93469 -251 GTAACAGAAGGAAAGCAGGGGGAAAAC 17 64 1 GAAAGCAGGG 0.919717 -17 CTTGTGAAATTGAAGGAGGTCAAACTGCT 19 10 0 TGAAGGAGGT 0.841143 -244 TGATAAATGGGAAAGGAGTATTGAT 20 6 0 GAAAGGAGTA 0.840593 -262 TTATTTTAGCGAAAGCAGGACATTCCGACA 21 118 0 GAAAGCAGGA 0.892379 -94 GAATAACCGTTAAAGGAGTGTAAGAAC 22 8 0 TAAAGGAGTG 0.60952 -270 GTTAAGGGAAGAAAGGAAGAGAAAAAGAGC 22 144 0 GAAAGGAAGA 0.731176 -134 TAATGACGTTGAAAGGATGTGAAGAGCC 22 260 1 GAAAGGATGT 0.929084 -18 TGCAGAAAAAGAAGGGAGGTATTTTCCTAT 23 154 0 GAAGGGAGGT 0.949312 -147 AACGTTCTTGGAAAGGATGGAAT 25 56 1 GAAAGGATGG 0.947646 -13 GCACTCCGGTGAGGGGAGGTTTCAATAAAG 27 65 1 GAGGGGAGGT 0.856662 -236 GAAGTCATTCGGCAGGAGGAAAATCAAAAT 27 280 1 GGCAGGAGGA 0.746319 -21 ********** Masking position 7 Map Score: 21.0261 Number of sites scoring better than the average of aligned sites = 729 Number in coding regions = 392 Number in noncoding regions = 337 Number of orfs with sites within 600 bp upstream = 382 Fraction of orfs with sites within 600 bp upstream = 0.0613556 Motif number 3 TTCGCTTTCTTTCTAAAAAAACTGCCGG 1 6 1 TTTTTTAAAA 0.848274 -189 ACGCTGGCAGTTTTTTTATGTAAATGATTGGCT 1 42 1 TTTTTTGTAA 0.810745 -153 TCCTACGCGGTTTCTTTCATAAATCAATTCCAG 2 43 0 TTTTTTTAAA 0.941171 -43 TAGCGGGTTTTTAATTTGAGAAAAGGGGCTGAA 3 17 1 TTATTTGAAA 0.573013 -30 GGGGGTTTTTTGTGTTTCTTAAAGGAGGTGACG 5 221 1 TGTTTTTAAA 0.772729 -80 GAAAAACGTGTGTGTTTTATAAAAA 6 3 0 TGTTTTTAAA 0.772727 -94 ATTGTTAGTTTTTATTTCATCAACTAGAAATAG 7 118 0 TTTTTTTCAA 0.802561 -95 TCCCACAGTTTTTGTTTATGATAAACTCAAGTC 9 92 1 TTTTTTGATA 0.897345 -77 TCCTGTTTTTTTGGTAAAATAAAAAACT 10 6 1 TTTTTTTAAA 0.9457 -295 AACGAAATCATTTTTTTCATATAGGGACGGGAG 10 265 1 TTTTTTTATA 0.884807 -36 ACATTGTGAATTTGTTCATGAAATATTCAAGGA 11 207 0 TTTTTCGAAA 0.665834 -94 GTATGCCTACTTTCTTTATTTTAATTTTCAAAG 19 229 0 TTTTTTTTTA 0.624194 -25 AGAGTCATCATTTTTTTTAGAAAATGTGACAAA 20 115 1 TTTTTTGAAA 0.950678 -153 AACGTCTTTATTTCTTTTAAAAATGATGTAAAA 21 78 1 TTTTTTAAAA 0.844259 -134 TCCCACAATGTTTGTTTATGATATGGTTAAGGG 22 166 0 TTTTTTGATA 0.897345 -112 TATTTTAGGCTTTATTTTTGAAATGAATCGTTG 24 72 1 TTTTTTGAAA 0.951917 -229 TTGAGCAATATTTTTTTCGTCTATTTTGTGAAT 24 202 1 TTTTTTTCTA 0.641965 -99 GCTGGTCAACTTTTTTTAAAAAAGATAACTTTA 27 90 0 TTTTTTAAAA 0.784623 -211 GAAACATGTGTTTTTTTTCTAAACCTTTATTTT 27 155 1 TTTTTTTAAA 0.9457 -146 TTTCTAAACCTTTATTTTTTTTATCTTTTGACC 27 170 1 TTTTTTTTTA 0.624197 -131 *** *** **** Masking position 6 Map Score: 16.4929 Number of sites scoring better than the average of aligned sites = 586 Number in coding regions = 366 Number in noncoding regions = 220 Number of orfs with sites within 600 bp upstream = 230 Fraction of orfs with sites within 600 bp upstream = 0.0369419 Motif number 4 GGAAATTGTGAAAAAGTGCGGAAAACGGTACACTT 9 38 0 AAAAGGAAAA 0.867164 -131 ATAAAAATGAAAAGATTATGGGAAATTGTGAAAAA 9 58 0 AAAAAGGAAA 0.931249 -111 TATCATAAACAAAAACTGTGGGATAAAAATGAAAA 9 80 0 AAAAGGGATA 0.945056 -89 CGAAACACAAGGAGAGAGATAGATT 14 3 1 AAAAAGGAGA 0.936204 -23 TAACAACAAGAATCATGAGGTGAGAGAGAC 20 248 1 AATAAGGAGA 0.85984 -20 TATTTCTTTTAAAAATGATGTAAAAGGCGAATTGT 21 86 1 AAAAAGAAAA 0.778339 -126 CAATTGTCCCAATAATGAGGAGAAAAGCAAAGCAC 22 72 1 AATAAGGAAA 0.849904 -206 AGGAAGAGAAAAAGAGCGAGGAAGATGTAGGATGA 22 126 0 AAAAGGAAGA 0.876124 -152 TATCATAAACAAACATTGTGGGATAAAAATGAAAA 22 176 1 AAAAGGGATA 0.945056 -102 ATAAAAATGAAAAGAATATGTGAAATTATGAAAAT 22 198 1 AAAAAGGAAA 0.931249 -80 GATACATTGCAATCAGCGCGGGAAACCCCAAATTG 23 80 1 AATAGGGAAA 0.913248 -221 CACATTTGTGAAATATTGAGCAATATTTTTTTCGT 24 187 1 AAAAGGAATA 0.816815 -114 AAATAATGGAGTGAGACAAAC 26 2 1 AATAGGGAGA 0.919389 -20 GACAATAGATAAACAACTGGCGATAAAGGTGAAAC 27 125 1 AAAATGGATA 0.657623 -176 *** * * * **** Masking position 5 Map Score: 10.1952 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 263 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 5 ACCTGCTTTCAGCCCCTTTTCTCA 3 33 0 GCTTTCAGCC 0.906864 -14 AAAGCAATCAGCTTTCCTAATGCCTCTTCA 4 57 0 GCTTTCCTAA 0.806743 -49 GATAATGATTGTTTTCACACGATTTCCAGC 8 122 0 GTTTTCACAC 0.519036 -40 GAAGTGTACCGTTTTCCGCACTTTTTCACA 9 37 1 GTTTTCCGCA 0.931613 -132 CACCCCTAGTGCTTTCCGTATACAATTTTT 10 193 1 GCTTTCCGTA 0.82864 -108 AGTTTTCACCAAATCCTTTTT 11 290 0 GTTTTCACCA 0.704428 -11 CAGATTGAATGTTTTCCGGATACTACAATT 12 110 1 GTTTTCCGGA 0.638203 -142 TTTTCCCCCTGCTTTCCTTCTGTTACTTTC 17 60 0 GCTTTCCTTC 0.895426 -21 GTTTTCCCCCTGCTTTCCTT 17 71 0 GTTTTCCCCC 0.957553 -10 CGGGAGATTCGTTTTCCCCCGAAAGGTGTG 19 149 1 GTTTTCCCCC 0.957553 -105 GCGAGCATCAGCTTTCATAAATTGGTAAGA 20 154 1 GCTTTCATAA 0.47496 -114 TTGGTGCTTTGCTTTTCTCCTCATTATTGG 22 80 0 GCTTTTCTCC 0.672158 -198 CGTTTTATCGGTTTTCCTCACTTACATACA 23 188 0 GTTTTCCTCA 0.92163 -113 GTAAACTACTACTTTCCGCCTAGTGTCTTC 23 240 0 ACTTTCCGCC 0.817622 -61 ACTTTTTTTTGCTTTCCTTCATTTAATTTA 23 268 1 GCTTTCCTTC 0.895426 -33 CATTTTGATTTTCCTCCTGCCGAATGA 27 284 0 ATTTTCCTCC 0.706465 -17 ********** Masking position 5 Map Score: 11.6739 Number of sites scoring better than the average of aligned sites = 1211 Number in coding regions = 1078 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 6 AAAAACTAACAATTGTGAAACGCAAAACCTT 7 138 1 AATGTGAAAC 0.891044 -75 AATTAACAGGAAAAGGGAAAATATTTTCACT 8 55 1 AAAGGGAAAA 0.666058 -107 GTGTTTCGGCAGAAGTGAAAATATTTTCCCT 8 68 0 AGAGTGAAAA 0.804715 -94 GATTATGGGAAATTGTGAAAAAGTGCGGAAA 9 49 0 AATGTGAAAA 0.932524 -120 ACTGTGGGATAAAAATGAAAAGATTATGGGA 9 70 0 AAAATGAAAA 0.903859 -99 ATATAAATAGACATGTGAAAATAGAGAAACG 9 137 1 ACAGTGAAAA 0.691273 -32 CCCTCCTTAAAAAAGTGTAAAGGATGAAGGG 11 21 0 AAAGTGTAAA 0.792412 -280 CGGGCTCTCCAAAATTGAAAAGCCCGGGGGT 11 146 0 AAATTGAAAA 0.597107 -155 CATTTTATCAAATCGTGAGAAAGTTTGAGAA 17 30 0 AATGTGAGAA 0.621954 -51 TGAGGACCTGAATCATGAAAAATACAGTTCC 19 61 1 AATATGAAAA 0.87354 -193 ACTAAAAAATAAAAATGAAACCTGAATCTCT 19 112 0 AAAATGAAAC 0.847637 -142 TTTTTTTAGAAAATGTGACAAATTTGTGGCG 20 126 1 AAAGTGACAA 0.804715 -142 TTCTTTTAAAAATGATGTAAAAGGCGAATTG 21 89 1 AATATGTAAA 0.583656 -123 GCTAAAATAAAATCATGAAACATGTTAAGAT 21 138 1 AATATGAAAC 0.803443 -74 ATTGTGGGATAAAAATGAAAAGAATATGTGA 22 190 1 AAAATGAAAA 0.903859 -88 GAATATGTGAAATTATGAAAATTGCCTGCCG 22 211 1 AATATGAAAA 0.87354 -67 AATATTTCACAAATGTGTCAAAAAGTCATCC 24 173 0 AAAGTGTCAA 0.455418 -128 AACTGGCGATAAAGGTGAAACATGTGTTTTT 27 139 1 AAAGTGAAAC 0.917562 -162 ATGGGCCATAAGTGATGAAACGAATGTTATA 27 239 1 AGTATGAAAC 0.472435 -62 *** ******* Masking position 10 Map Score: 13.3382 Number of sites scoring better than the average of aligned sites = 738 Number in coding regions = 548 Number in noncoding regions = 190 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 7 TCCTATGCAAAGGACGAGGGTCTCGCGGTA 5 190 0 AGGACGAGGG 0.9731 -111 TCCTTTGCATAGGACGGGGGTTTTTTGTGT 5 206 1 AGGACGGGGG 0.985674 -95 GTGCCAATATGGCACAAGGGTTTTCTA 8 8 0 GGCACAAGGG 0.945564 -154 GTGCCATATTGGCACAAGGGTTTTTATGTT 8 23 1 GGCACAAGGG 0.945564 -139 TACAATTAACAGGAAAAGGGAAAATATTTT 8 52 1 AGGAAAAGGG 0.727427 -110 GTATACGGAAAGCACTAGGGGTGCTGTTTT 10 186 0 AGCACTAGGG 0.797333 -115 TTTTCATATAGGGACGGGAGAGGATGGTCA 10 278 1 GGGACGGGAG 0.971366 -23 AAAATTGAAAAGCCCGGGGGTCTACTGAAA 11 137 0 AGCCCGGGGG 0.923254 -164 GGAGGGAGGGGAGGCGAGTAATC 12 4 1 GGGAGGGGAG 0.831338 -248 TTTTTAGTAAAGCTCGGGAGATTCGTTTTC 19 135 1 AGCTCGGGAG 0.748887 -119 CGTGATAAATGGGAAAGGAGTATTGAT 20 8 0 GGGAAAGGAG 0.7145 -260 ********** Masking position 8 Map Score: 5.90874 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 163 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 TTATGTAAATGATTGGCTCAGCTGCGGCTT 1 57 1 GATTGGCTCA 0.959751 -138 ATCAGGGGAGGATCGGTTCACACCTGCCAC 5 20 0 GATCGGTTCA 0.92709 -281 CCTTGTGCCATATTGGCACAAGGGTTTTTA 8 19 1 TATTGGCACA 0.740998 -143 GTATTATCCAGATCGGGTCATAAGGGATCA 10 125 1 GATCGGGTCA 0.978997 -176 CCCCGCCGAAGATTGGGACAGCGATTAAAT 18 76 0 GATTGGGACA 0.967366 -60 TTCTCCTCATTATTGGGACAATTGAACTTG 22 66 0 TATTGGGACA 0.871467 -212 CTTCTTTTCGAATCGGGTCAGCAGATACAT 23 57 1 AATCGGGTCA 0.858075 -244 CACAATCTCTGACTGGTTCATATTAAGTAC 24 109 0 GACTGGTTCA 0.782692 -192 ACCAGTCAGAGATTGTGTCATTTGGTCAGT 24 122 1 GATTGTGTCA 0.847093 -179 ********** Masking position 2 Map Score: 3.33851 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 165 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 9 CGATGCCGGGTTTCTCTCCCCGTTACCAAGA 5 92 1 TTCTCTCCCC 0.900288 -209 TATGCGCTGCATCTCCTCACCTAACCTT 6 79 0 TCATCTCCTC 0.728735 -18 AGCATCAACATACCTCCCCTTGATTTGTGTT 8 94 0 TCCTCCCCTT 0.964046 -68 TTTTTGTTTATTTCTCCCTTCTATGCCTCTT 11 177 1 TTCTCCCTTC 0.914198 -124 AGCGATTACTCGCCTCCCCTCCCTCC 12 6 0 CCCTCCCCTC 0.902859 -246 TTTCCTCACCTCCGTATTCTGT 13 22 0 TCCTCACCTC 0.970086 -12 AATCTATCTCTCTCCTTGTGTTTCG 14 9 0 TTCTCTCCTT 0.934009 -17 GCTGTTTTTTCTCTCCTTTTAAATCGAA 15 15 0 TTCTCTCCTT 0.934009 -18 GCGGCTATTATACCACACCTTTCGGGGGAAA 19 161 0 TCCACACCTT 0.555424 -93 GGTTATAGCCTGTCTCTCCTTGTCGCGGCTA 19 185 0 TTCTCTCCTT 0.934009 -69 GTCTCTCTCACCTCATGATTCTTG 20 254 0 TTCTCACCTC 0.958285 -14 TAAGCAAGCCTTTCTCTCTTTTTA 21 4 0 TTCTCTCTTT 0.769649 -208 CATAGGAAAATACCTCCCTTCTTTTTCTGCA 23 153 1 TCCTCCCTTC 0.93766 -148 GTTTGTCTCACTCCATTATTT 26 8 0 TTCTCACTCC 0.59281 -14 ACTTTATTGAAACCTCCCCTCACCGGAGTGC 27 65 0 ACCTCCCCTC 0.862466 -236 * ********* Masking position 6 Map Score: 15.6755 Number of sites scoring better than the average of aligned sites = 293 Number in coding regions = 183 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 10 GCCAGCGTCAGCCGGCAGTTTTTTTAGAAAG 1 19 0 GCCGCAGTTT 0.977402 -176 GCCGGCTGACGCTGGCAGTTTTTTTATGTAA 1 34 1 GCTGCAGTTT 0.756303 -161 ATAAATCAATTCCAGCCCTTTTAGGGTTAAG 2 27 0 TCCGCCCTTT 0.957621 -59 GTGTACCGTTTTCCGCACTTTTTCACAATTT 9 40 1 TTCGCACTTT 0.630209 -129 TTCATTTTTATCCCACAGTTTTTGTTTATGA 9 82 1 TCCACAGTTT 0.680437 -87 CGTTTGAACGGGCAGCCCTTTACACTGAATG 12 65 1 GGCGCCCTTT 0.896035 -187 CGGTTTGGCCTGCCCTTTTTATCTTTAT 18 118 0 GCCGCCCTTT 0.973094 -18 GCTGTGCCTCCAGTATTATAATTCCC 21 196 0 GCCCCAGTAT 0.723739 -16 TATGAAAATTGCCTGCCGTATGTTAAAACTA 22 224 1 GCCGCCGTAT 0.962944 -54 CAAAATACTTTGCAGCAGTTTACGTTTTATC 23 209 0 TGCGCAGTTT 0.865588 -92 ACCTAAAAAGTCCCGCACTATGTGACGGATT 24 42 0 TCCGCACTAT 0.910049 -259 TTGATTTTCCTCCTGCCGAATGACTTCATTT 27 276 0 TCCGCCGAAT 0.652845 -25 *** ******* Masking position 11 Map Score: 5.80974 Number of sites scoring better than the average of aligned sites = 896 Number in coding regions = 811 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 11 TAGCAGATGAGTTAGAAAGGAGGATATCAA 5 281 1 GTAGAAAGGA 0.650744 -20 ATGGTGCTATTATATAAAAAAGCATCAAAACAAC 7 178 1 TTATAAAAGA 0.500172 -35 CAAAAACTGTGGGATAAAAATGAAAAGATTATGG 9 72 0 GGATAAAAGA 0.973101 -97 AGGCATAGAAGGGAGAAATAAACAAAAACGGGCT 11 171 0 GGAGAAAAAA 0.786819 -130 ACACATTGCCGTGATAAATGGGAAAGGAGTATTG 20 13 0 GGATAAAGGA 0.948086 -255 AGCCTTACAATGGATAAATATAAAGACCGAATCT 20 68 1 TGATAAAAAA 0.50014 -200 ACTTGTACATGCGATGAATATGTAACGATAAATG 22 37 0 GGATGAAAGA 0.948085 -241 GAGAAAAAGAGCGAGGAAGATGTAGGATGATCAA 22 122 0 GGAGGAAAGA 0.930605 -156 CAAACATTGTGGGATAAAAATGAAAAGAATATGT 22 185 1 GGATAAAAGA 0.973101 -93 ATGTATGTAAGTGAGGAAAACCGATAAAACGTAA 23 187 1 GGAGGAAACA 0.610298 -114 GCCGACATAAATAAGCAACAAAATAGA 24 4 1 GCATAAAAGA 0.808601 -297 GAAGACGTCATTGATAAAGACGCACTCCGGTGAG 27 44 1 TGATAAAAGA 0.878082 -257 TAAACAACTGGCGATAAAGGTGAAACATGTGTTT 27 134 1 GGATAAAGGA 0.948086 -167 * ****** * * * Masking position 7 Map Score: 4.27193 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 297 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 12 AGCTTTCCTAATGCCTCTTCAGCCGCAAACGGAGCAA 4 41 0 ACTTCAGCGA 0.986243 -65 AGGAAAGCTGATTGCTTTTCAGCTGAAAGATAAGGAG 4 69 1 ACTTCAGCGA 0.986243 -37 ACCTTTATTAACAGCTATACAGCCGTTCACTCTAAGT 5 151 0 ACTTCAGCGT 0.992579 -150 GAGGCGAGTAATCGCTTCTCCGCTGTTTTATGATTAA 12 21 1 ACTCCCGCGT 0.947043 -231 CTCACAAAGCAGCACTATCCAGCTGCTTGTGAAATTG 19 28 0 ACTTCAGCGT 0.992579 -226 TGTCTTCCAAAATACTTTGCAGCAGTTTACGTTTTAT 23 210 0 ACTTCAGCGT 0.992579 -91 * ** * **** * * Masking position 6 Map Score: 2.60557 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 17 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 13 ATTCTACAATACCATACACGATCAGCGGCTCATT 1 123 0 ACATAGATCA 0.941444 -72 GGCTGGTGGTGGCATAGCAGATGAGTTAGAAAGG 5 267 1 GCATAGATGA 0.979744 -34 TCCAGATCGGGTCATAAGGGATCAAAGCGCGTTT 10 131 1 GCATAGATCA 0.96195 -170 TTATTTTAACATCATAATAGATGATAAGAATCAT 10 222 1 ACATAGATGA 0.968514 -79 GCAATCTTGCATCATATTGGATGACTTTTTGACA 24 155 1 ACATAGATGA 0.968514 -146 CTTTACATGGGCCATAAGTGATGAAACGAATGTT 27 233 1 GCATAGATGA 0.979744 -68 * **** ***** Masking position 6 Map Score: 2.21786 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 33 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 14 TATCGATTTGTTTACAAATGAGCCGCTGATC 1 107 1 TTTCAAATGA 0.752294 -88 ACCCCCGTCCTATGCAAAGGACGAGGGTCTC 5 196 0 TATCAAAGGA 0.829753 -105 AATACAAATATTTGCAATGGATCAAGGAATA 12 220 1 TTTCAATGGA 0.944299 -32 AACTGTGTCGCTTTCAAAGGA 17 1 0 CTTCAAAGGA 0.963844 -80 TTTATTTTAATTTTCAAAGGAGATTATGTAT 19 217 0 TTTCAAAGGA 0.964535 -37 AAACTTGAGCCTTACAATGGATAAATATAAA 20 61 1 CTTCAATGGA 0.943237 -207 AGGGAGGTATTTTCCTATGGATCAGGTTTTT 23 141 0 TTTCTATGGA 0.752359 -160 TATTAACGTTCTTGGAAAGGATGGAAT 25 52 1 CTTGAAAGGA 0.815226 -17 *** ******* Masking position 7 Map Score: 2.40934 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 80 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 15 CAGGAATAGTTGCTCCGTTTGCGGCTGAAG 4 32 1 TGCTCCGTTT 0.865236 -74 CCTTTCAGTCCTCCTTATCTTTCAGCTG 4 88 0 TCCTCCTTAT 0.94555 -18 TTGATATCCTCCTTTCTAACTCATCT 5 285 0 TCCTCCTTTC 0.833297 -16 TTATGTTCCTCCGTATAGGTATTTTT 7 7 1 TCCTCCGTAT 0.972875 -206 TATATCCTCCGGTTGTTTTGATGC 7 199 0 TCCTCCGGTT 0.911693 -14 TTTCCTCACCTCCGTATTCTGTCAAAT 13 17 0 ACCTCCGTAT 0.849713 -17 TTTGCTTTTCTCCTCATTATTGGGACAATT 22 73 0 TCCTCATTAT 0.629961 -205 TTTTTTGCTTTCCTTCATTTAATTTAGTAG 23 272 1 TCCTTCATTT 0.594115 -29 GCTTTCTCCTCCATTTCCGGTTAAAA 24 285 0 TCCTCCATTT 0.937229 -16 ********** Masking position 4 Map Score: 1.90541 Number of sites scoring better than the average of aligned sites = 392 Number in coding regions = 240 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655