AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -icpxR9_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 yyxA 68 alternate gene name: yycK; similar to serine protease Do #25 yycJ 21 yycJ #26 yycF 300 similar to two-component response regulator [YycG] Motif number 1 TGTAAAAAGTAAAGTAGAGAAACTATTCAAAA 1 160 1 AAGAGAGAAA 0.922614 -35 ATAAAAACTAACAATTGTGAAACGCAAAACCT 7 136 1 AAATGTGAAA 0.663764 -77 TATCAAATCTATAGCAATGAAAGG 8 148 1 AAGAATGAAA 0.787848 -14 AAACTGTGGGATAAAAATGAAAAGATTATGGG 9 71 0 AAAAATGAAA 0.912964 -98 TAGACATGTGAAAATAGAGAAACGGAGTGAAC 9 144 1 AAAAGAGAAA 0.971161 -25 ATCCCTCCTTAAAAAAGTGTAAAGGATGAAGG 11 22 0 AAAAGTGTAA 0.883244 -279 GAAGAGGCATAGAAGGGAGAAATAAACAAAAA 11 177 0 AAAGGAGAAA 0.942771 -124 TTTCGATTTAAAAGGAGAGAAAAAACAGC 15 14 1 AAGAGAGAAA 0.922614 -19 TTACTAAAAAATAAAAATGAAACCTGAATCTC 19 113 0 AAAAATGAAA 0.912964 -141 TTTGAAAATTAAAATAAAGAAAGTAGGCATAC 19 230 1 AAAAAAGAAA 0.931232 -24 CTTGAGCCTTACAATGGATAAATATAAAGACC 20 64 1 AAAGGATAAA 0.746672 -204 TAAAAAGAGAGAAAGGCTTGCTTA 21 3 1 AAAAGAGAAA 0.971161 -209 TCATTTATAGTAAAAAGAGAAAGGCTGTATTA 21 33 0 TAAAGAGAAA 0.664132 -179 CATCATTTTTAAAAGAAATAAAGACGTTTATG 21 74 0 AAAAAATAAA 0.707846 -138 ATTTCTTTTAAAAATGATGTAAAAGGCGAATT 21 87 1 AAAGATGTAA 0.598091 -125 AAGATGACATAAAATAGAGAAATAGGATGTCG 21 164 1 AAAAGAGAAA 0.971161 -48 AATAACCGTTAAAGGAGTGTAAGAAC 22 5 0 AAGAGTGTAA 0.728127 -273 ACATTGTGGGATAAAAATGAAAAGAATATGTG 22 188 1 AAAAATGAAA 0.912964 -90 GAAGGAAAGCAAAAAAAAGTAAACTACTACTT 23 256 0 AAAAAAGTAA 0.797044 -45 GACCAGCATGACAATAGATAAACAACTGGCGA 26 116 1 AAAAGATAAA 0.857654 -185 ACAACTGGCGATAAAGGTGAAACATGTGTTTT 26 137 1 AAAGGTGAAA 0.927329 -164 GTCAAAAGATAAAAAAAATAAAGGTTTAGAAA 26 170 0 AAAAAATAAA 0.707846 -131 CTTGTCTATTATAACGGTTTAAGGTCAAAAGA 26 193 0 AAAGGTTTAA 0.398357 -108 * ** ******* Masking position 3 Map Score: 24.3087 Number of sites scoring better than the average of aligned sites = 970 Number in coding regions = 731 Number in noncoding regions = 239 Number of orfs with sites within 600 bp upstream = 258 Fraction of orfs with sites within 600 bp upstream = 0.0414391 Motif number 2 ACCTGCTTTCAGCCCCTTTT 3 37 0 ACCTGCTTTC 0.920373 -10 ACGAGCATGAACATCCTTCAGGAATAGTTG 4 14 1 ACATCCTTCA 0.675466 -92 TATGTTTCGATACTCCTCTCTTGGTAACGG 5 111 0 TACTCCTCTC 0.667356 -190 ATTGGCCGTCACCTCCTTTAAGAAACACAA 5 230 0 ACCTCCTTTA 0.929022 -71 TTGATATCCTCCTTTCTAACTCATCT 5 285 0 TCCTCCTTTC 0.976085 -16 ATTTGACCATCCTCTCCCGTCCCTAT 10 285 0 CCATCCTCTC 0.89701 -16 AGCGCTACTTCCCTTCATCCTTTACA 11 7 1 ACTTCCCTTC 0.828678 -294 TAAACATGTTCCATCCCTCCTTAAAAAAGT 11 36 0 CCATCCCTCC 0.827708 -265 TACTCGCCTCCCCTCCCTCC 12 1 0 CCCTCCCTCC 0.946314 -251 GTTTTCCCCCTGCTTTCCTTCTGTTAC 17 64 0 CCCTGCTTTC 0.911672 -17 AGCAGTTTGACCTCCTTCAATTTCACAAG 19 10 1 ACCTCCTTCA 0.884215 -244 ATCAATACTCCTTTCCCATTTATCA 20 6 1 TACTCCTTTC 0.803963 -262 CTTGCTTAATACAGCCTTTCTCTTTTTACT 21 27 1 ACAGCCTTTC 0.769752 -185 TGTCGGAATGTCCTGCTTTCGCTAAAATAA 21 118 1 TCCTGCTTTC 0.865748 -94 GTTCTTACACTCCTTTAACGGTTATTC 22 8 1 CACTCCTTTA 0.540106 -270 GCTCTTTTTCTCTTCCTTTCTTCCCTTAAC 22 144 1 TCTTCCTTTC 0.853698 -134 GGCTCTTCACATCCTTTCAACGTCATTA 22 260 0 ACATCCTTTC 0.952241 -18 CTGTTTTACGACTTCCTCTATAAAAACCTG 23 120 1 ACTTCCTCTA 0.47792 -181 ATAGGAAAATACCTCCCTTCTTTTTCTGCA 23 154 1 ACCTCCCTTC 0.971291 -147 ACCGCCTCCCTACTAAATTA 23 291 0 ACCGCCTCCC 0.777829 -10 ATTCCATCCTTTCCAAGAACGTT 24 56 0 CCATCCTTTC 0.946821 -13 CTTTATTGAAACCTCCCCTCACCGGAGTGC 26 65 0 ACCTCCCCTC 0.943022 -236 ATTTTGATTTTCCTCCTGCCGAATGACTTC 26 280 0 TCCTCCTGCC 0.727595 -21 ********** Masking position 6 Map Score: 23.358 Number of sites scoring better than the average of aligned sites = 937 Number in coding regions = 527 Number in noncoding regions = 410 Number of orfs with sites within 600 bp upstream = 429 Fraction of orfs with sites within 600 bp upstream = 0.0689046 Motif number 3 CGTCAGCCGGCAGTTTTTTTAGAAAGAAAGCGAA 1 10 0 CATTTTTAAA 0.925519 -185 CTGACGCTGGCAGTTTTTTTATGTAAATGATTGGC 1 39 1 CATTTTTATA 0.960202 -156 ATAAAACACACACGTTTTTCAATTACAATAAGTGT 6 16 1 CATTTTTATA 0.960202 -81 ATAGATTGTTCATATTTTTTTCATACCTTTGGACT 7 87 0 CATTTTTTTA 0.964823 -126 TTAGGATATGCAGTTTTTTATTTTACCAAAAAAAC 10 15 0 CATTTTTTTA 0.964822 -286 TTTCCGTATACAATTTTTTATTTTAACATCATAAT 10 205 1 CATTTTTTTA 0.964822 -96 ACAACGAAATCATTTTTTTCATATAGGGACGGGAG 10 263 1 CATTTTTATA 0.960202 -38 TCATCCTTTACACTTTTTTAAGGAGGGATGGAACA 11 25 1 CATTTTTAAG 0.782929 -276 ACAGCTTCTTCATCTTCTTTTACTACAAACTTCTT 12 155 0 CATTCTTTTA 0.788196 -97 ATTCAGGTTTCATTTTTATTTTTTAGTAAAGCTCG 19 116 1 CATTTATTTA 0.715167 -138 TTGTAAGGCTCAAGTTTTTCAGATCCGCACTACAC 20 43 0 CATTTTTATC 0.7919 -225 GAAGAGTCATCATTTTTTTTAGAAAATGTGACAAA 20 113 1 CATTTTTAAA 0.925519 -155 TAACATGTTTCATGATTTTATTTTAGCGAAAGCAG 21 130 0 CAATTTTTTA 0.715166 -82 TCCTATGGATCAGGTTTTTATAGAGGAAGTCGTAA 23 125 0 CATTTTTTAG 0.803932 -176 TCATGCTGGTCAACTTTTTTTAAAAAAGATAACTT 26 92 0 CATTTTTTAA 0.933889 -209 ** ***** * ** Masking position 2 Map Score: 13.6701 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 179 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 4 TTCGCTTTCTTTCTAAAAAAACTG 1 5 1 CTTTCTTTCT 0.914074 -190 CTTTTGAATAGTTTCTCTACTTTACTTTTT 1 163 0 GTTTCTCTAC 0.781474 -32 TTCCTACGCGGTTTCTTTCATAAATCAATT 2 47 0 GTTTCTTTCA 0.545845 -39 GCGATGCCGGGTTTCTCTCCCCGTTACCAA 5 91 1 GTTTCTCTCC 0.946967 -210 TGTTCACTCCGTTTCTCTATTTTCACATGT 9 147 0 GTTTCTCTAT 0.826881 -22 TTCTTCCGCGCTTTATCTCAGCCAAAACAG 10 163 1 CTTTATCTCA 0.719184 -138 GCCCGTTTTTGTTTATTTCTCCCTTCTATG 11 172 1 GTTTATTTCT 0.631198 -129 AATCTATCTCTCTCCTTGTGTTT 14 13 0 CTATCTCTCT 0.866756 -13 GCTGTTTTTTCTCTCCTTTTAAATCG 15 17 0 TTTTCTCTCC 0.698442 -16 ACCTGAATCTCTTTATCTCCGTCTAACCTA 19 94 0 CTTTATCTCC 0.903737 -160 AGGTTATAGCCTGTCTCTCCTTGTCGCGGC 19 187 0 CTGTCTCTCC 0.803675 -67 TGTATGCCTACTTTCTTTATTTTAATTTTC 19 233 0 CTTTCTTTAT 0.680561 -21 TTAAGCAAGCCTTTCTCTCTTTTTA 21 6 0 CTTTCTCTCT 0.977331 -206 TTAATACAGCCTTTCTCTTTTTACTATAAA 21 32 1 CTTTCTCTTT 0.724093 -180 TCATAAACGTCTTTATTTCTTTTAAAAATG 21 73 1 CTTTATTTCT 0.755736 -139 CCCCGACATCCTATTTCTCTATTTTATGTC 21 169 0 CTATTTCTCT 0.451467 -43 CTTCCTCGCTCTTTTTCTCTTCCTTTCTTC 22 137 1 CTTTTTCTCT 0.845079 -141 ATCGCCAGTTGTTTATCTATTGTCATGCTG 26 119 0 GTTTATCTAT 0.581444 -182 ********** Masking position 6 Map Score: 11.5903 Number of sites scoring better than the average of aligned sites = 942 Number in coding regions = 738 Number in noncoding regions = 204 Number of orfs with sites within 600 bp upstream = 201 Fraction of orfs with sites within 600 bp upstream = 0.032284 Motif number 5 CATAAATCAATTCCAGCCCTTTTAGGGTTAA 2 28 0 TTCCGCCCTT 0.710967 -58 ACCTGCTTTCAGCCCCTTTTCTCAAAT 3 30 0 TTTCGCCCCT 0.937068 -17 AAACATAGGTTTTCTGTACTTAGAGTGAACG 5 134 1 TTTCGTACTT 0.678923 -167 ATGCGCTGCATCTCCTCACCTAACCTTTACA 6 75 0 TCTCTCACCT 0.75497 -22 TTCATATTTTTTTCATACCTTTGGACTACTA 7 83 0 TTTCTACCTT 0.791445 -130 TTAGTTTTTATTTCATCAACTAGAAATAGAT 7 116 0 TTTCTCAACT 0.842788 -97 AGTGTACCGTTTTCCGCACTTTTTCACAATT 9 39 1 TTTCGCACTT 0.943542 -130 AGAAACGCGCTTTGATCCCTTATGACCCGAT 10 136 0 TTTGTCCCTT 0.832775 -165 TTTCCTCACCTCCGTATTCTG 13 23 0 TTTCTCACCT 0.957822 -11 GAGCATCAGCTTTCATAAATTGGTAAGATTT 20 156 1 TTTCTAAATT 0.452304 -112 TTTCTCTTCCTTTCTTCCCTTAACCATATCA 22 150 1 TTTCTCCCTT 0.967735 -128 CGAAAAGAAGTTTGATCAACTAATAGAACTA 23 36 0 TTTGTCAACT 0.470924 -265 TTTTATCGGTTTTCCTCACTTACATACATGA 23 185 0 TTTCTCACTT 0.965095 -116 TTTTTTTTGCTTTCCTTCATTTAATTTAGTA 23 270 1 TTTCTTCATT 0.472534 -31 ATAACATTCGTTTCATCACTTATGGCCCATG 26 238 0 TTTCTCACTT 0.965095 -63 **** ****** Masking position 1 Map Score: 9.37175 Number of sites scoring better than the average of aligned sites = 878 Number in coding regions = 705 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 6 GCCAATCATTTACATAAAAAAACTGCCAGC 1 44 0 TACATAAAAA 0.452193 -151 CCCTTTTCTCAAATTAAAAACCCGCTAAAG 3 14 0 AAATTAAAAA 0.834614 -33 TCCTTTAAGAAACACAAAAAACCCCCGTCC 5 217 0 AACACAAAAA 0.68795 -84 ACACTTATTGTAATTGAAAAACGTGTGTGT 6 21 0 TAATTGAAAA 0.424488 -76 AACCTTTACAAAATCAAAAAACACACACGT 6 55 0 AAATCAAAAA 0.78078 -42 TGTTAATTGTAACATAAAAACCCTTGTGCC 8 33 0 AACATAAAAA 0.757501 -129 CTGTGGGATAAAAATGAAAAGATTATGGGA 9 70 0 AAAATGAAAA 0.835585 -99 GAGTTTATCATAAACAAAAACTGTGGGATA 9 90 0 TAAACAAAAA 0.631498 -79 TTTTTTTGGTAAAATAAAAAACTGCATATC 10 16 1 AAAATAAAAA 0.901851 -285 TTATGATGTTAAAATAAAAAATTGTATACG 10 209 0 AAAATAAAAA 0.901851 -92 GGGCTCTCCAAAATTGAAAAGCCCGGGGGT 11 146 0 AAATTGAAAA 0.73623 -155 AAGGGAGAAATAAACAAAAACGGGCTCTCC 11 167 0 TAAACAAAAA 0.631498 -134 CTCTCCTTTTAAATCGAAAAAT 15 3 0 AAATCGAAAA 0.66329 -30 CGCGGGAATAAAGATAAAAAGGGCAGGCCA 18 111 1 AAGATAAAAA 0.681984 -25 GCTTTACTAAAAAATAAAAATGAAACCTGA 19 118 0 AAAATAAAAA 0.901851 -136 TCTCCTTTGAAAATTAAAATAAAGAAAGTA 19 225 1 AAATTAAAAT 0.491089 -29 TGCTTTCGCTAAAATAAAATCATGAAACAT 21 131 1 AAAATAAAAT 0.637291 -81 TTGTGGGATAAAAATGAAAAGAATATGTGA 22 191 1 AAAATGAAAA 0.835585 -87 TTAAGGTCAAAAGATAAAAAAAATAAAGGT 26 177 0 AAGATAAAAA 0.681984 -124 GGCAGGAGGAAAATCAAAATG 26 290 1 AAATCAAAAT 0.405133 -11 ********** Masking position 7 Map Score: 15.8914 Number of sites scoring better than the average of aligned sites = 1211 Number in coding regions = 853 Number in noncoding regions = 358 Number of orfs with sites within 600 bp upstream = 372 Fraction of orfs with sites within 600 bp upstream = 0.0597494 Motif number 7 CTTAACCCTAAAAGGGCTGGAATTGATTTAT 2 27 1 AAAGGCTGGA 0.875667 -59 CGTCCTATGCAAAGGACGAGGGTCTCGCGGT 5 191 0 AAAGGCGAGG 0.953632 -110 CGTCCTTTGCATAGGACGGGGGTTTTTTGTG 5 204 1 ATAGGCGGGG 0.883913 -97 ATTGTATATGAAAGGACTGAGTCG 9 4 0 AAAGGCTGAG 0.835918 -165 AAATTGTGAAAAAGTGCGGAAAACGGTACAC 9 40 0 AAAGTCGGAA 0.734155 -129 TGGCTGAGATAAAGCGCGGAAGAAACGCGCT 10 156 0 AAAGCCGGAA 0.923512 -145 TTGTATACGGAAAGCACTAGGGGTGCTGTTT 10 187 0 AAAGCCTAGG 0.882715 -114 CCAAAATTGAAAAGCCCGGGGGTCTACTGAA 11 138 0 AAAGCCGGGG 0.990628 -163 CAATGTCCCTAAAGTTCCGGGCACCAAAACC 11 234 1 AAAGTCCGGG 0.86604 -67 TAACAGAAGGAAAGCAGGGGGAAAAC 17 65 1 AAAGCGGGGG 0.911652 -16 ATTTTTTAGTAAAGCTCGGGAGATTCGTTTT 19 133 1 AAAGCCGGGA 0.976746 -121 GGAGAAAAGCAAAGCACCAAAATAGAATATG 22 90 1 AAAGCCCAAA 0.481335 -188 AGGAAGAGAAAAAGAGCGAGGAAGATGTAGG 22 130 0 AAAGACGAGG 0.797616 -148 ***** ***** Masking position 3 Map Score: 8.69992 Number of sites scoring better than the average of aligned sites = 431 Number in coding regions = 353 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 8 ATTGTAAAAGCCGCAGCTGAGCCAATCATTT 1 63 0 CCGCACTGAG 0.863871 -132 AATTAAAAACCCGCTAAAGAGC 3 2 0 CCGCTAAGAG 0.871559 -45 GCTCCGTTTGCGGCTGAAGAGGCATTAGGAA 4 43 1 CGGCTAAGAG 0.929414 -63 GAAGCCCATTCGGCATCAGGGGAGGATCGGT 5 33 0 CGGCACAGGG 0.990069 -268 ATTGATAAGACCGCCTCTGGGGCGCGTCCCC 7 37 1 CCGCCCTGGG 0.916139 -176 TGTGCCAATATGGCACAAGGGTTTTCTA 8 8 0 TGGCAAAGGG 0.938452 -154 TGTGCCATATTGGCACAAGGGTTTTTATGTT 8 22 1 TGGCAAAGGG 0.938452 -140 ATTTGTGTTTCGGCAGAAGTGAAAATATTTT 8 72 0 CGGCAAAGTG 0.922952 -90 TTCTTTGAACCGGCCGCAGGGCCGGTTCTCC 26 13 0 CGGCCCAGGG 0.985312 -288 ***** ***** Masking position 4 Map Score: 5.15551 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 204 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 GTGTGAACCGATCCTCCCCTGATGCCGAAT 5 27 1 ATCCTCCCCT 0.953054 -274 TGTTTCGATACTCCTCTCTTGGTAACGGGG 5 109 0 CTCCTCTCTT 0.728292 -192 TGCGCTGCATCTCCTCACCTAACCTTTACA 6 75 0 CTCCTCACCT 0.964716 -22 GCCTCTGGGGCGCGTCCCCTTGCTGATAAA 7 49 1 CGCGTCCCCT 0.885808 -164 AGCATCAACATACCTCCCCTTGATTTGTGT 8 95 0 TACCTCCCCT 0.974278 -67 AGCGATTACTCGCCTCCCCTCCCTCC 12 7 0 CGCCTCCCCT 0.986476 -245 TTTCCTCACCTCCGTATTCTG 13 23 0 TTCCTCACCT 0.944889 -11 GCGGCTATTATACCACACCTTTCGGGGGAA 19 162 0 TACCACACCT 0.617135 -92 CATAGGAAAATACCTCCCTTCTTTTTCTGC 23 153 1 TACCTCCCTT 0.924341 -148 TTTATCGGTTTTCCTCACTTACATACATGA 23 185 0 TTCCTCACTT 0.846861 -116 ACCGCCTCCCTACTAAATTAAA 23 289 0 CGCCTCCCTA 0.73155 -12 ACTTTATTGAAACCTCCCCTCACCGGAGTG 26 66 0 AACCTCCCCT 0.942785 -235 ********** Masking position 6 Map Score: 11.4578 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 133 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 10 TTCGCTTTCTTTCTAAAAAAACTGCCGGCTG 1 11 1 TTTAAAAAAA 0.929227 -184 AGCGGCTCATTTGTAAACAAATCGATACCAG 1 103 0 TTTAAACAAA 0.938562 -92 AACGTGTGTGTTTTATAAAAA 6 1 0 TTTATAAAAA 0.741037 -96 AATAGCACCATTTTAAACAGAAGGTTTTGCG 7 158 0 TTTAAACAGA 0.723897 -55 AATGGTGCTATTATATAAAAAAGCATCAAAA 7 177 1 TTTATAAAAA 0.746995 -36 CTTGAGTTTATCATAAACAAAAACTGTGGGA 9 92 0 TCTAAACAAA 0.841147 -77 AAGAATCATTTTGTAAACAACGAAATCATTT 10 247 1 TTTAAACAAC 0.723977 -54 TTGTCACATTTTCTAAAAAAAATGATGACTC 20 116 0 TTTAAAAAAA 0.929227 -152 TTTACATCATTTTTAAAAGAAATAAAGACGT 21 79 0 TTTAAAAGAA 0.692356 -133 CTTAACCATATCATAAACAAACATTGTGGGA 22 168 1 TCTAAACAAA 0.841147 -110 AAGTTATCTTTTTTAAAAAAAGTTGACCAGC 26 92 1 TTTAAAAAAA 0.92779 -209 AAATAAAGGTTTAGAAAAAAAACACATGTTT 26 156 0 TTGAAAAAAA 0.693608 -145 ** ******** Masking position 5 Map Score: 5.44383 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 84 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 11 ACATCGTTGATCCATTCTTAACCCTA 2 7 1 TTGATCCATT 0.815088 -79 ACCTGCTTTCAGCCCCTTTTCTCAAAT 3 30 0 TTCAGCCCCT 0.597174 -17 TCATATTTTTTTCATACCTTTGGACTACTA 7 83 0 TTCATACCTT 0.828572 -130 TAGTTTTTATTTCATCAACTAGAAATAGAT 7 116 0 TTCATCAACT 0.830193 -97 GAAACGCGCTTTGATCCCTTATGACCCGAT 10 136 0 TTGATCCCTT 0.861547 -165 GCTACTTCCCTTCATCCTTTACACTTTTTT 11 14 1 TTCATCCTTT 0.780934 -287 CCTCTATTCCTTGATCCATTGCAAATATTT 12 225 0 TTGATCCATT 0.815088 -27 TTTCCTCACCTCCGTATTCTG 13 23 0 TTCCTCACCT 0.64947 -11 GGTCTTTATATTTATCCATTGTAAGGCTCA 20 66 0 TTTATCCATT 0.457899 -202 ATGATGACTCTTCATAAATTGTTAAGATTC 20 96 0 TTCATAAATT 0.654879 -172 AGCATCAGCTTTCATAAATTGGTAAGATTT 20 157 1 TTCATAAATT 0.654879 -111 GTTCTTACACTCCTTTAACGG 22 2 1 TTCTTACACT 0.290154 -276 TTCTCTTCCTTTCTTCCCTTAACCATATCA 22 151 1 TTCTTCCCTT 0.758568 -127 GCAGGCAATTTTCATAATTTCACATATTCT 22 210 0 TTCATAATTT 0.345324 -68 GAAAAGAAGTTTGATCAACTAATAGAACTA 23 36 0 TTGATCAACT 0.626933 -265 TTTATCGGTTTTCCTCACTTACATACATGA 23 185 0 TTCCTCACTT 0.729254 -116 TAACATTCGTTTCATCACTTATGGCCCATG 26 238 0 TTCATCACTT 0.909365 -63 ********** Masking position 2 Map Score: 5.51746 Number of sites scoring better than the average of aligned sites = 1514 Number in coding regions = 1292 Number in noncoding regions = 222 Number of orfs with sites within 600 bp upstream = 244 Fraction of orfs with sites within 600 bp upstream = 0.0391905 Motif number 12 TATGTAAATGATTGGCTCAGCTGCGGCTTTT 1 58 1 ATTGGTCAGC 0.973005 -137 TAGGGTTAAGAATGGATCAACGATGT 2 6 0 AATGGTCAAC 0.716302 -80 ATCGCCTACTATCCGTTCAGCAAAGCAATTC 5 65 0 ATCCGTCAGC 0.982809 -236 AAAATACACCATTCGGTCAACCTGCACTTCC 10 86 1 ATTCGTCAAC 0.933727 -215 TAAAGAAAATTTCCGCTCAGCTCTGCCATGA 18 28 0 TTCCGTCAGC 0.911076 -108 CCCGCCGAAGATTGGGACAGCGATTAAATAC 18 74 0 ATTGGACAGC 0.865938 -62 GGCTCTTCACATCCTTTCAACGTCATTATAA 22 257 0 ATCCTTCAAC 0.713922 -21 TTCTTTTCGAATCGGGTCAGCAGATACATTG 23 58 1 ATCGGTCAGC 0.982809 -243 ***** ***** Masking position 9 Map Score: 2.11404 Number of sites scoring better than the average of aligned sites = 374 Number in coding regions = 357 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 13 TGGTACCGCGAGACCCTCGTCCTTTGCATA 5 187 1 AGACCCTCGT 0.979778 -114 GAAACACAAAAAACCCCCGTCCTATGCAAA 5 209 0 AAACCCCCGT 0.979778 -92 TAGAAAACCCTTGTGCCATATTGG 8 5 1 AAACCCTTGT 0.952199 -157 TGTAACATAAAAACCCTTGTGCCAATATGG 8 26 0 AAACCCTTGT 0.952199 -136 TAATTTCAGTAGACCCCCGGGCTTTTCAAT 11 134 1 AGACCCCCGG 0.959287 -167 ********** Masking position 3 Map Score: 1.0759 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 9 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 14 GCTGGAAATCGTGTGAAAACAATCATTATC 8 122 1 GTGTGAAAAC 0.725042 -40 TGTGAAAAAGTGCGGAAAACGGTACACTTC 9 37 0 TGCGGAAAAC 0.951982 -132 AAAAAGGATTTGGTGAAAACT 11 290 1 TGGTGAAAAC 0.914867 -11 AATTGTAGTATCCGGAAAACATTCAATCTG 12 110 0 TCCGGAAAAC 0.893227 -142 AAGGAAAGCAGGGGGAAAAC 17 71 1 GGGGGAAAAC 0.986759 -10 CACACCTTTCGGGGGAAAACGAATCTCCCG 19 149 0 GGGGGAAAAC 0.986759 -105 TGCAATCAGCGCGGGAAACCCCAAATTGCC 23 87 1 GCGGGAAACC 0.893074 -214 TGTATGTAAGTGAGGAAAACCGATAAAACG 23 188 1 TGAGGAAAAC 0.879059 -113 ********** Masking position 6 Map Score: 4.75056 Number of sites scoring better than the average of aligned sites = 241 Number in coding regions = 175 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 15 AAAACTGTGGGATAAAAATGAAAAGATTATGG 9 72 0 GATAAAATAA 0.644927 -97 TCTATTCCTTGATCCATTGCAAATATTTGTAT 12 221 0 GATCCATGAA 0.933303 -31 CTCACGATTTGATAAAATGAAAGTAACAGAAG 17 42 1 GATAAAAGAA 0.921812 -39 ACATTGCCGTGATAAATGGGAAAGGAGTATTG 20 13 0 GATAAATGAA 0.933378 -255 TCTTTATATTTATCCATTGTAAGGCTCAAGTT 20 62 0 TATCCATGAA 0.524384 -206 TACGTTATAAGATACTACGTAAATCTTACCAA 20 175 0 GATACTAGAA 0.704919 -93 TACTATGAACGATATATAGTAAGGACACACGA 20 212 1 GATATATGAA 0.7756 -56 AACATTGTGGGATAAAAATGAAAAGAATATGT 22 187 1 GATAAAATAA 0.644927 -91 CGGGTCAGCAGATACATTGCAATCAGCGCGGG 23 70 1 GATACATGAA 0.957158 -231 ATAAAAACCTGATCCATAGGAAAATACCTCCC 23 139 1 GATCCATGAA 0.933303 -162 GAGGAAAACCGATAAAACGTAAACTGCTGCAA 23 199 1 GATAAAAGAA 0.921812 -102 ******* * ** Masking position 2 Map Score: 3.23294 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 193 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405