AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00300_hinf_reg_100.orf -o00300_hinf_100.ace -a/home/amcguire/genomes/ORF_hinf.txt -z/home/amcguire/genomes/hinf.fna -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: HI0102 27 succinyl-diaminopimelate desuccinylase (dapE) Input sequences: #1 HI0089 300 aspartokinase I / homoserine dehydrogenase I (thrA) #2 HI0103 78 conserved hypothetical protein #3 HI0104 216 heat shock protein (htpG) #4 HI0195.1 26 conserved hypothetical transmembrane protein (aefA) #5 HI0197 84 penicillin-insensitive murein endopeptidase (mepA) #6 HI0199 46 lipid A biosynthesis (kdo)2-(lauroyl)-lipid IVA acyltransferase (msbB) #7 HI0255 100 dihydrodipicolinate synthetase (dapA) #8 HI0301 300 hemolysin, putative #9 HI0646 158 aspartate-semialdehyde dehydrogenase (asd) #10 HI0727 260 diaminopimelate decarboxylase (lysA) #11 HI0750 143 diaminopimelate epimerase (dapF) #12 HI0836 181 lysyl-tRNA synthetase analog (genX) #13 HI0916 107 outer membrane protein, putative #14 HI0949 300 aminotransferase #15 HI1129 201 conserved hypothetical protein #16 HI1130 30 conserved hypothetical protein #17 HI1166 87 histidinol-phosphate aminotransferase (hisH) #18 HI1167 190 phosphoserine aminotransferase (serC) #19 HI1211 300 lysyl-tRNA synthetase (lysU) #20 HI1303 147 riboflavin synthase, beta chain (ribH) #21 HI1527 84 lipid A biosynthesis lauroyl acyltransferase (htrB) #22 HI1634 274 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase (dapD) Motif number 1 GATTACGGATAAAGTGCGGTTATTTTTCAT 1 132 0 AAAGTGCGGT 0.998525 -169 TATTTCATTTAAAGTGCGGTTTAAATTCCT 3 109 1 AAAGTGCGGT 0.998525 -108 TTTAAGAGGAAAAGTGCGGTAAAAAAACAC 3 140 0 AAAGTGCGGT 0.998525 -77 AAAGCGCGCAAAAGTGCGGTTAAAATTAAT 6 16 1 AAAGTGCGGT 0.998525 -31 GTTTAAACCTAAAGTGCGGTTAAAAATACA 8 175 0 AAAGTGCGGT 0.998525 -126 GTTTAAACCCAATGTGCGGTTATTTTTTAT 8 197 1 AATGTGCGGT 0.989615 -104 ATTAAATAAAAAAGTGTGGTTAATTTAAAA 9 37 0 AAAGTGTGGT 0.98338 -122 AGGAATGAATAAAGTGCGGTAAAAATTTAC 11 21 1 AAAGTGCGGT 0.998525 -123 TAGTATAAGCAAAGTGCGGTAAAAATACCG 11 50 0 AAAGTGCGGT 0.998525 -94 TGTAGAAACAAAACTGCGGTGATAATAAAA 22 248 0 AAACTGCGGT 0.988725 -27 ********** Masking position 5 Map Score: 40.3852 Number of sites scoring better than the average of aligned sites = 1115 Number in coding regions = 700 Number in noncoding regions = 415 Number of orfs with sites within 600 bp upstream = 285 Fraction of orfs with sites within 600 bp upstream = 0.0457758 Motif number 2 AAAGTGACAAATTTTTCAGAAATTTTCTTAGTCAAT 1 32 0 ATTTTTGTTT 0.917169 -269 AAGTGCGGTTATTTTTCATTGTGTTTTATCTTGAAA 1 115 0 ATTTTTTTTT 0.943918 -186 GAGGATTTTTCTTTTTTAGGTGAAAT 2 63 1 CTTTTTGAAT 0.784372 -16 GGGATAAGAAATTTTTTATTTCATTTAAAGTGCGGT 3 93 1 ATTTTTTTTT 0.943918 -124 TGAAATCTTTCTTTTTATTCTTATATCTGTGACGTT 3 177 1 CTTTTTTTAT 0.881832 -40 TAATTTGCAAATTTTTTTTCATTAAAGGAGTTTTTT 7 11 0 ATTTTTTAAA 0.673405 -90 TGAATAATGGATTTTTGATTGTGAATTGATCTCGTA 8 50 0 ATTTTTTAAT 0.895798 -251 ATGTGCGGTTATTTTTTATTGATTTTCCTCTTTTCG 8 208 1 ATTTTTTTTT 0.943918 -93 GCGTTTTGCGATTTTTTCTAAAATATGATAATTTTT 8 243 1 ATTTTTTTAT 0.876974 -58 AAATATGATAATTTTTCGCCGTCAATAAGACATCAA 8 263 1 ATTTTTCAAT 0.687811 -38 ATTAACCACACTTTTTTATTTAATTTCTTTCGCGAA 9 43 1 CTTTTTTTTT 0.915444 -116 AAAATCAAGTATTTTTAATGAAAATTGATCTTTCGC 9 74 0 ATTTTTTATT 0.862274 -85 TGAGCTTGATCTTTTTCAGGAAAATATAAAGAACCT 10 175 0 CTTTTTGATA 0.558512 -86 AATACCGTAAATTTTTACCGCACTTTATTCATTCCT 11 21 0 ATTTTTCTTT 0.81179 -123 AATTTACGGTATTTTTACCGCACTTTGCTTATACTA 11 44 1 ATTTTTCTTT 0.81179 -100 ATTTGCCATGATTTTTGCTGCTCTTTATAATGCAAA 11 89 1 ATTTTTTTTT 0.943918 -55 TAGGGGATTTATTTTTACTTTCTATTGATTGGAGGA 12 15 0 ATTTTTTATT 0.925777 -167 GCATTGTGCCATTTTTCGTTACAAATTAATAACGTN 12 70 1 ATTTTTTAAT 0.878201 -112 ACAATTGTATATTTTTTTTGCAATATGAAAAGTAAA 14 69 0 ATTTTTTTAT 0.920565 -232 CACCCGACTTATTTTTTTTCACCTCTTTTAGAAGGT 14 264 1 ATTTTTTTCT 0.628574 -37 TTCAAACGGCTTTTTTCATAAAATTTTATTGA 15 7 0 TTTTTTTTTT 0.486009 -195 ATTCAAACGGCTTTTTTATTTTGATAAAAATCAGTT 15 49 1 CTTTTTTATA 0.65803 -153 AATAAGTTCAATTTTTAAGGCGTAAT 15 186 1 ATTTTTGAAT 0.849765 -16 GTTAGTATGTATTTTTAAATAAATTTGGGCGTAGTA 17 36 0 ATTTTTATTT 0.656378 -52 CGTAATTTAGCTTTTTTTTAATCAATCGTCAAAATT 18 46 1 CTTTTTTAAT 0.846861 -145 TATTTCCTTGCTTTTTATGAAAATAATGATGTCTTT 18 163 0 CTTTTTGTAA 0.540748 -28 TTAATAAGAAATTTTTATTTTCTTTGTTTACTTTAG 19 254 0 ATTTTTTTTG 0.553983 -47 ATTGTTTACCTTTTTTATAAATTAATAAGAAATTT 19 276 0 CTTTTTTTAA 0.641545 -25 CCAACACTATATTTTTATGGAAAATTTCCTTCATTA 20 34 0 ATTTTTGATT 0.883421 -114 TTTAGGACTCATTTTTAAGGCGATTTTATTGTTCAT 20 78 0 ATTTTTGTTT 0.917175 -70 ATCCCTAAAAATTTTTCCTATTATAAAGGTTTGTTG 22 19 1 ATTTTTTTAA 0.735616 -256 AAAATCACTTCTTTTTATAAAAAATTTGCAATAAAG 22 68 0 CTTTTTAATT 0.476815 -207 AAAAGAAGTGATTTTTTCGTATTATTCTTGCTAGAA 22 89 1 ATTTTTGATT 0.891375 -186 ****** * *** Masking position 6 Map Score: 33.7275 Number of sites scoring better than the average of aligned sites = 916 Number in coding regions = 617 Number in noncoding regions = 299 Number of orfs with sites within 600 bp upstream = 245 Fraction of orfs with sites within 600 bp upstream = 0.0393511 Motif number 3 TGTCAAACAGAAAGTGACAAATTTTTCAGAAATTT 1 43 0 AAATGATTTT 0.943888 -258 AATAAAATGTAATTAATTTTAACCGCACTT 6 27 0 AATTAATTTT 0.93197 -20 AAAATTTGCAAATTAACGTTATTTTAGCGACTATA 7 32 1 AATAAATTTT 0.835451 -69 CATATAAACAAAATAAGAATATTTTGTTGTCTAGA 8 116 1 AAAAAATTTT 0.874437 -185 AGTGCGGTTAAAAATACACAATTTTTACGGAGAGG 8 158 0 AAATAATTTT 0.74015 -143 TGACGGCGAAAAATTATCATATTTTAGAAAAAATC 8 252 0 AAATAATTTT 0.783569 -49 ATTTTCATTAAAAATACTTGATTTTSCTAACGCTA 9 85 1 AAATAATTTT 0.74015 -74 TATCAGATTTAAACAGGAAAATTTT 10 1 0 AAAAGATTTT 0.872661 -260 AAGGCTTTATAATTTGCCGCATTTTATCAGATTTA 10 25 0 AATTGATTTT 0.911158 -236 GTGCGGTAAAAATTTACGGTATTTTTACCGCACTT 11 34 1 AATTAATTTT 0.928696 -110 AAATCCCCTAAAAGGGTAATATTGTGTGGGCATTG 12 41 1 AAAGGATTGT 0.647856 -141 TAAAGATGGAAANGTATCGGATTTTGTGATCTACC 12 115 1 AANTAATTTT 0.959974 -67 TAAATTGAACTTTTTTCTTCATCAGA 13 2 1 AAATGTTTTT 0.592271 -106 TATTGCAAAAAAAATATACAATTGTCCCCGTTTTG 14 80 1 AAATAATTGT 0.796941 -221 ATTCCACATTAAAGCAACTGATTTTTATCAAAATA 15 65 0 AAACAATTTT 0.76517 -137 ACGCCTTAAAAATTGAACTTATTTTTAGAAAATCT 15 174 0 AATGAATTTT 0.890239 -28 ATTTAAGATAAAAGTACTACATTATTTT 16 4 0 AAATAATTAT 0.720536 -27 ACTGTGCCGTAATTTAGCTTTTTTTTAATCAATCG 18 39 1 AATTATTTTT 0.575304 -152 GTAGTGATAAAAAAGACATCATTATTTTCATAAAA 18 152 1 AAAGAATTAT 0.604626 -39 AGTTTACCTTAATGAAGGAAATTTTCCATAAAAAT 20 25 1 AATAAATTTT 0.835744 -123 ATTAATATTGAATATACGCGATTTT 20 133 1 AATTAATTTT 0.927172 -15 TTGGTTATTCAAATAGAGAGATTTTAAA 21 4 0 AAAAGATTTT 0.872661 -81 AAACCTTTATAATAGGAAAAATTTTTAGGGATTTA 22 16 0 AATGGATTTT 0.862272 -259 ATTTTTTATAAAAAGAAGTGATTTTTTCGTATTAT 22 79 1 AAAGAATTTT 0.928994 -196 TGAGGAGAACAAAATGAGCGATTTTGGTTATGCAA 22 143 1 AAATGATTTT 0.732124 -132 *** ** ***** Masking position 12 Map Score: 30.9687 Number of sites scoring better than the average of aligned sites = 472 Number in coding regions = 311 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 4 TATTTTTCCCTAATCTAAATGGTAAA 4 11 0 TTCCCTATCT 0.820362 -16 ATAAGGATCTTTGCCCTCTTTTTACGAGATCA 8 28 1 TTCCCTCTTT 0.987586 -273 TTTTTATTGATTTTCCTCTTTTCGCGTTTTGC 8 220 1 TTTCCTCTTT 0.929775 -81 CGGCGAAAAATTATCATATTTTAGAAAAAATC 8 252 0 TTTCATATTT 0.63271 -49 TGTTGTTTCCTTAGTTTGTTGTGCTTG 9 142 0 TTCCTTATTT 0.88826 -17 AAAATTTTCCTGTTTAAATCTGATAA 10 5 1 TTTCCTGTTA 0.729832 -256 AGTTCTTTATTTGCCATGATTTTTGCTGCTCT 11 81 1 TTCCATGTTT 0.930198 -63 TTTTCCATCCTTTGTATAAATTC 11 131 0 TTCCATCTTT 0.958102 -13 ATCCGATACTTTCCATCTTTAGACATAAAA 12 105 0 TTCCATCTTA 0.888969 -77 TTTTTTGTTTTTACCCTAGTTTGCCCATTGGA 14 154 0 TTCCCTATTT 0.97298 -147 CTTATTTTTTTTCACCTCTTTTAGAAGGTTTT 14 271 1 TTACCTCTTT 0.839743 -30 TCGTCAAAATTTACCCTCTATTTTATGAATGA 18 71 1 TTCCCTCATT 0.871912 -120 TGTATTTCCTTGCTTTTTATGAAAAT 18 175 0 TTCCTTGTTT 0.910987 -16 ATTTCTTGCCTTCCCCTGTTTACGGGGAAAGT 19 163 1 TTCCCTGTTA 0.941969 -138 TTATGGAAAATTTCCTTCATTAAGGTAAACTA 20 24 0 TTCCTTCTTA 0.860117 -124 TAATAAGGCTTTACCCTATTTTATTTAGGACT 20 105 0 TTCCCTATTT 0.97298 -43 ** ***** *** Masking position 7 Map Score: 16.2922 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 160 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 5 CCCGCGATTCAACTGAATAGCGGGTTTTTTTATAAAT 1 244 1 AATAAAGTTT 0.926286 -57 ACTTTAAATGAAATAAAAAATTTCTTATCCCCCTTGA 3 87 0 AATAAAATTA 0.818838 -130 AACACAAGGAATTTAAACCGCACTTTAAATGAAATAA 3 108 0 ATTAACGTTA 0.749357 -109 AAAAAGAAAGATTTCAAGAGGAATTTAAGAGGAAAAG 3 156 0 ATTAAAGTTA 0.859385 -61 AATGTAATTAATTTTAACCGCACTTTTGCGCGCTTTC 6 15 0 ATTAACGTTT 0.837356 -32 TGTGGATAACTTGTGAATAATGGATTTTTGATTGTGA 8 62 0 TTTAAAATTT 0.716093 -239 AAATTGTGTATTTTTAACCGCACTTTAGGTTTAAACC 8 169 1 TTTAACGTTA 0.536322 -132 AAGAAAATTTAATTTAATCACTCTTTTT 9 2 0 AATAACATTT 0.792013 -157 AAGTGTGGTTAATTTAAAAGAAAATTTAATTTAATCA 9 19 0 AATAAAGTTT 0.926286 -140 CTAAGTACTAAAATTAATAGTAATTTTTTCATTTTTT 10 102 0 AATAAAGTTT 0.926261 -159 TTTCAGGAAAATATAAAGAACCTTTTACGCCACATCC 10 161 0 ATTAAAATTA 0.791057 -100 AAGCTCAACAAACTCAATAATCTATTATCTAATATCA 10 204 1 AATAAAATTA 0.818846 -57 TTTTCGTTACAAATTAATAACGTNTTTTATGTCTAAA 12 82 1 AATAAAATTT 0.88616 -100 TTTTTTTGCAATATGAAAAGTAAATTTAGCTTCTTAC 14 56 0 ATTAAAGTTT 0.913226 -245 ACTCGCTACTTATTAAAAAAAGCGTTTCAGCTTTTTT 14 180 0 TATAAAATTT 0.750721 -121 TGTGTCTGTTTTATAAACAGTAAATTTATCGCAAGGC 14 228 1 TTTAAAGTTT 0.802805 -73 TTGAATAAACAATTCAAACGGCTTTTTTCATAAAATT 15 18 0 AATAACGTTT 0.860083 -184 ATTTTTATCAAAATAAAAAAGCCGTTTGAATAAACAA 15 43 0 AATAAAATTT 0.88616 -159 CCTTTTTTATAAATTAATAAGAAATTTTTATTTTCTT 19 266 0 AATAAAATTT 0.886136 -35 CGTATATTCAATATTAATAAGGCTTTACCCTATTTTA 20 114 0 ATTAAAATTA 0.791057 -34 GATGACTAAATTCTCAACAAACCTTTATAATAGGAAA 22 32 0 TTTAAAATTA 0.594275 -243 ACTGCGGTGATAATAAAAAGTTGGTTTGATTAAAAGA 22 229 0 TATAAAGTTT 0.829369 -46 ** * ** ** *** Masking position 4 Map Score: 24.2927 Number of sites scoring better than the average of aligned sites = 384 Number in coding regions = 254 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 6 TTTTCTTAGTCAATAAATTTCGTGTAAACT 1 16 0 CAATAAATTT 0.860803 -285 ATTTATTGACTAAGAAAATTTCTGAAAAAT 1 28 1 TAAGAAAATT 0.867954 -273 TCAAGGGGGATAAGAAATTTTTTATTTCAT 3 87 1 TAAGAAATTT 0.893293 -130 TAAAAAAACACAAGGAATTTAAACCGCACT 3 121 0 CAAGGAATTT 0.663723 -96 CCTTTAATGAAAAAAAATTTGCAAATTAAC 7 19 1 AAAAAAATTT 0.520991 -82 TGAAACCAAATAATAAAATTAAAAACCGAC 7 72 1 TAATAAAATT 0.723145 -29 ATAAACAAAATAAGAATATTTTGTTGTCTA 8 119 1 TAAGAATATT 0.359971 -182 GGTTAATTTAAAAGAAAATTTAATTTAATC 9 20 0 AAAGAAAATT 0.775181 -139 CAGATTTAAACAGGAAAATTTT 10 3 0 CAGGAAAATT 0.753168 -258 GTTTTATAAACAGTAAATTTATCGCAAGGC 14 235 1 CAGTAAATTT 0.606961 -66 TCAATAAAATTTTATGAAAAA 15 2 1 CAATAAAATT 0.829235 -200 ATGTATTTTTAAATAAATTTGGGCGTAGTA 17 36 0 AAATAAATTT 0.63528 -52 TTACTGAAATCAAAAAAATTCTTTCTATCA 18 100 0 CAAAAAAATT 0.751677 -91 CAGGGGAAGGCAAGAAATTTCTACAAGCCC 19 151 0 CAAGAAATTT 0.939627 -150 TATAAATTAATAAGAAATTTTTATTTTCTT 19 266 0 TAAGAAATTT 0.893293 -35 CTTCTTTTTATAAAAAATTTGCAATAAAGA 22 67 0 TAAAAAATTT 0.674655 -208 ********** Masking position 6 Map Score: 9.71174 Number of sites scoring better than the average of aligned sites = 367 Number in coding regions = 294 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 7 ATTTGTCACTTTCTGTTTGACAAGCTCGGG 1 56 1 TTCTGTTTGA 0.941072 -245 TTATTTTTCATTGTGTTTTATCTTGAAAAA 1 113 0 TTGTGTTTTA 0.932536 -188 CTCCTAGATATTGTGTTTTTAAATTTATAA 1 273 0 TTGTGTTTTT 0.877589 -28 TTGAGGATTTTTCTTTTTTAGGTGAAAT 2 61 1 TTCTTTTTTA 0.580945 -18 ATATAATGAATTCTGTTTTAGATACTAGAT 3 40 0 TTCTGTTTTA 0.908907 -177 TTTAAATTCCTTGTGTTTTTTTACCGCACT 3 128 1 TTGTGTTTTT 0.877589 -89 ATTGATTTGTGTTTGATGTCTTATTG 8 285 0 TTGTGTTTGA 0.956755 -16 CCTTAGTTTGTTGTGCTTGAATAGCATTAT 9 131 0 TTGTGCTTGA 0.947918 -28 TAGTACTTAGTTCAGCTTGTATATTCGCTA 10 129 1 TTCAGCTTGT 0.707823 -132 ATTGAGTTTGTTGAGCTTGATCTTTTTCAG 10 192 0 TTGAGCTTGA 0.866144 -69 GCAGAGAACGTTGTTTTTGAGTTCTGATGA 13 29 0 TTGTTTTTGA 0.754537 -79 AAAAAAGCGTTTCAGCTTTTTTGTTTTTAC 14 172 0 TTCAGCTTTT 0.602163 -129 ********** Masking position 7 Map Score: 7.74435 Number of sites scoring better than the average of aligned sites = 332 Number in coding regions = 288 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 8 ACACAATATCTAGGAGAACCAATT 1 287 1 TAGAGAACAA 0.95445 -14 TTCAGTCCTATTGAAGAACTAACCTAGAGTAT 5 29 0 TTGAGAATAA 0.789809 -56 AAGATAGCGTTAGAAAATCAAGTATTTTTAA 9 92 0 TAGAAAACAA 0.840724 -67 TAAAGAACTCTAGTATAAGCAAAGTGCGGTAA 11 58 0 TAGATAACAA 0.944206 -86 AAAAAGCCGTTTGAATAAACAATTCAAACGGC 15 33 0 TTGATAACAA 0.930661 -169 ATCTCTCTATTTGAATAACCAAAATTGTGGCG 21 17 1 TTGATAACAA 0.930661 -68 ACCATAATCATTGCATAACCAAAATCGCTCAT 22 156 0 TTGATAACAA 0.930661 -119 CGCACTTTGTAGAAACAAAACTGCGGTG 22 257 0 TTGAGAACAA 0.969743 -18 *** **** *** Masking position 7 Map Score: 6.86836 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 51 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 9 CTATTCAGTTGAATCGCGGGTTTTCTGTATCTT 1 231 0 GAATGGGTTT 0.969667 -70 CGATTCAACTGAATAGCGGGTTTTTTTATAAAT 1 248 1 GAATGGGTTT 0.969811 -53 CAATCTAATCAGACTGAGGATTTTAACCCTTAT 2 31 0 AGACGGGTTT 0.804186 -48 CAGTCTGATTAGATTGAGGATTTTTCTTTTTTA 2 48 1 AGATGGGTTT 0.93925 -31 GATAACTTGTGAATAATGGATTTTTGATTGTGA 8 62 0 GAATAGGTTT 0.864589 -239 CTCTCCGTAAAAATTGTGTATTTTTAACCGCAC 8 159 1 AAATGGTTTT 0.479981 -142 TCAAGCTTGTGAAAGGCGGATTTACCGATAAGT 10 62 1 GAAAGGGTTT 0.965196 -199 AATTAGGCAGAGAACGTTGTTTTTGAGTTCTGA 13 32 0 AGAAGTGTTT 0.60735 -76 ATCCTTAATTAAATGATGGGTTTAATATTTTCT 13 76 0 AAATAGGTTT 0.750721 -32 GGGCTAGGTTGGAAACAGGTTTTGATGTAGGGT 14 120 0 GGAACGGTTT 0.767461 -181 CAGAAGTGGAGAAAAGTGGTGTTTTGTGGAGAT 15 135 1 GAAAGGGGTT 0.801839 -67 TACGGCTTGCGTATTACGGTTTTCTACGCCAGT 19 74 0 GTATAGGTTT 0.502128 -227 GCGAACGTACGGAAGGGGGCTTTCGATAATATA 19 198 1 GGAAGGGTTT 0.965831 -103 CGGTGATAATAAAAAGTTGGTTTGATTAAAAGA 22 229 0 AAAAGTGTTT 0.60293 -46 **** * ** *** Masking position 3 Map Score: 6.70557 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 145 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 10 TTTATCTTGAAAAATGAATGCGTAAAGAAA 1 97 0 AAAATGAATG 0.688208 -204 AACACAATGAAAAATAACCGCACTTTATCC 1 126 1 AAAATAACCG 0.867238 -175 TTAAATTTATAAAAAAACCCGCTATTCAGT 1 255 0 AAAAAAACCC 0.542995 -46 AAATCAATAAAAAATAACCGCACATTGGGT 8 203 0 AAAATAACCG 0.867238 -98 AAAAAGAGTGATTAAATTAA 9 1 1 AAAAAGAGTG 0.799409 -158 ATAGAAAGTAAAAATAAATCCCCTAAAAGG 12 26 1 AAAATAAATC 0.525658 -156 GCTACTTATTAAAAAAAGCGTTTCAGCTTT 14 183 0 AAAAAAAGCG 0.799409 -118 GAGGTGAAAAAAAATAAGTCGGGTGCCTTG 14 259 0 AAAATAAGTC 0.84912 -42 AGATTTTCTAAAAATAAGTTCAATTTTTAA 15 174 1 AAAATAAGTT 0.518864 -28 TAAAATAAATAAAATGACTGTGCCGTAATT 18 23 1 AAAATGACTG 0.867238 -168 AATCGCCTTAAAAATGAGTCCTAAATAAAA 20 89 1 AAAATGAGTC 0.851515 -59 ATTTTTTATAAAAAGAAGTGATTTTTTCGT 22 79 1 AAAAGAAGTG 0.696427 -196 TGAGGAGAACAAAATGAGCGATTTTGGTTA 22 143 1 AAAATGAGCG 0.9195 -132 ********** Masking position 4 Map Score: 5.01028 Number of sites scoring better than the average of aligned sites = 355 Number in coding regions = 241 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 11 CACTTATCGGTAAATCCGCCTTTCACAAGC 10 66 0 TAAATCCGCC 0.865838 -195 GTTCAGCTTGTATATTCGCTACAGGATGTG 10 138 1 TATATTCGCT 0.618676 -123 TTTATCAAAATAAAAAAGCCGTTTGAATAA 15 47 0 TAAAAAAGCC 0.49549 -155 GAACAAATTATAAACTTGCCAGAAGTGGAG 15 116 1 TAAACTTGCC 0.79808 -86 TTGGGCGTAGTAAATACGCCCATTGGAAAT 17 18 0 TAAATACGCC 0.88477 -70 TTGGGGAAGCCAAATTCGCTCTTATGTATT 19 16 1 CAAATTCGCT 0.829194 -285 AGCCCGCTTTTAAACTCGCTTCAATAAATC 19 126 0 TAAACTCGCT 0.920715 -175 ATAAAATTGCCGATAGTTTAC 20 2 1 TAAAATTGCC 0.874684 -146 TTATGAACAATAAAATCGCCTTAAAAATGA 20 76 1 TAAAATCGCC 0.978404 -72 TTTAAAATCTCTCTATTTGAAT 21 3 1 TAAAATCTCT 0.595379 -82 TGAGTTGTGGTAAAATCGCCACAATTTTGG 21 35 0 TAAAATCGCC 0.978404 -50 ATTGCATAACCAAAATCGCTCATTTTGTTC 22 149 0 CAAAATCGCT 0.876655 -126 ********** Masking position 4 Map Score: 6.11606 Number of sites scoring better than the average of aligned sites = 416 Number in coding regions = 366 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 12 TGATCGCTATAAATTTATGTATATAATGAAT 3 59 0 AAATTTAGTA 0.494351 -158 AAAGATAAAAATTGAACGTCACAGATATA 3 198 0 AAATTGACGT 0.86352 -19 AAAAATTTGCAAATTAACGTTATTTTAGCGA 7 31 1 AAATTAAGTT 0.582204 -70 ATTTAAAAGAAAATTTAATTTAATCACTCTT 9 14 0 AAATTTATTT 0.584113 -145 TTTTTAATGAAAATTGATCTTTCGCGAAAGA 9 68 0 AAATTGACTT 0.909913 -91 AGTGCGGTAAAAATTTACGGTATTTTTACCG 11 33 1 AAATTTAGGT 0.861524 -111 TAAATTGAACTTTTTTCTTCAT 13 2 1 AAATTGACTT 0.90818 -106 TATGAAAAGTAAATTTAGCTTCTTACGAGTC 14 51 0 AAATTTACTT 0.93209 -250 GCCTTGCGATAAATTTACTGTTTATAAAACA 14 234 0 AAATTTATGT 0.629138 -67 TACGCCTTAAAAATTGAACTTATTTTTAGAA 15 179 0 AAATTGACTT 0.90818 -23 AAATTTAAGATAAAAGTACTA 16 20 0 AAATTTAGAT 0.734006 -11 GACTGTGCCGTAATTTAGCTTTTTTTTAATC 18 38 1 TAATTTACTT 0.575262 -153 TCAATCGTCAAAATTTACCCTCTATTTTATG 18 67 1 AAATTTACCT 0.762767 -124 ACCACAACTCAAATTTACGATAAACTACGCC 21 54 1 AAATTTAGAT 0.734134 -31 ******* *** Masking position 7 Map Score: 6.31114 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 166 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 13 TGAGGATTTTAACCCTTATGCTACTTCATC 2 20 0 AACCCTTATG 0.76535 -59 GCAAATTATAAAGCCTTTCTCAAGCTTGTG 10 43 1 AAGCCTTTCT 0.766969 -218 GCTTTTTATTTAGCCGTTTGACTCGTAAGA 14 32 1 TAGCCGTTTG 0.904513 -269 TTTATGAAAAAAGCCGTTTGAATTGTTTAT 15 21 1 AAGCCGTTTG 0.978551 -181 CAAAATAAAAAAGCCGTTTGAATAAACAAT 15 42 0 AAGCCGTTTG 0.978551 -160 CGTAATACGCAAGCCGTATTAGACGGGGAT 19 89 1 AAGCCGTATT 0.944288 -212 AAATAGGGTAAAGCCTTATTAATATTGAAT 20 116 1 AAGCCTTATT 0.891476 -32 ********** Masking position 2 Map Score: 1.89809 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 56 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 14 AAATTTTTTATTTCATTTAAAGTGCGGTTT 3 101 1 TTTCATTTAA 0.678068 -116 GCAAATTTTTTTTCATTAAAGGAGTTTTTT 7 11 0 TTTCATTAAA 0.934086 -90 AAAGATCAATTTTCATTAAAAATACTTGAT 9 77 1 TTTCATTAAA 0.934086 -82 TTTTGATTAAAACCTTCTAAA 14 290 0 TTTGATTAAA 0.917118 -11 AAACGGCTTTTTTCATAAAATTTTATTGA 15 10 0 TTTCATAAAA 0.861507 -192 AAAAAAGCCGTTTGAATAAACAATTCAAAC 15 36 0 TTTGAATAAA 0.62337 -166 GCTTTTTTATTTTGATAAAAATCAGTTGCT 15 58 1 TTTGATAAAA 0.838014 -144 AATTTTGACGATTGATTAAAAAAAAGCTAA 18 52 0 ATTGATTAAA 0.744697 -139 TCTTTCTATCATTCATAAAATAGAGGGTAA 18 81 0 ATTCATAAAA 0.719814 -110 ATTTTTTTGATTTCAGTAAAAAGCATTGAT 18 111 1 TTTCAGTAAA 0.772506 -80 ACATCATTATTTTCATAAAAAGCAAGGAAA 18 167 1 TTTCATAAAA 0.861507 -24 ATTGCAAATTTTTTATAAAAAGAAGTGATT 22 72 1 TTTTATAAAA 0.414219 -203 AAAAAGTTGGTTTGATTAAAAGATTGAAAG 22 222 0 TTTGATTAAA 0.917118 -53 ********** Masking position 5 Map Score: 13.3571 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 132 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 15 TTATTATGATTAATGGTGCGGGTTAGTGCAGC 1 193 1 TATGTGCGGG 0.942998 -108 TCTAAAGTTTTGCTGTAGGTAAGTATATC 5 66 0 TTTGTGTAGG 0.964703 -19 TGGAAACAGGTTTTGATGTAGGGTTACGTCAA 14 112 0 TTTGTGTAGG 0.964703 -189 TATTTATAAATATTGATATGGGTTAGTATGTA 17 61 0 TTTGTATGGG 0.925998 -27 AAAAATATAGTGTTGGTGCGGGTTATGAACAA 20 54 1 TTTGTGCGGG 0.985306 -94 TTAGTATGTCTGTTGTCGTGGGGCTTGCACTT 22 193 1 TTTGCGTGGG 0.967294 -82 * *** ****** Masking position 4 Map Score: 0.887129 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 30 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701