AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00760_hinf_reg_300.orf -o00760_hinf_300.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 Input sequences: #1 HI0205 292 H. influenzae predicted coding region HI0205 #2 HI0206 22 5'-nucleotidase, putative #3 HI0518 83 purine-nucleoside phosphorylase (deoD) #4 HI0519 98 transport protein, putative #5 HI0521 212 conserved hypothetical protein #6 HI1126.1 181 H. influenzae predicted coding region HI1126.1 #7 HI1129 201 conserved hypothetical protein #8 HI1130 30 conserved hypothetical protein #9 HI1136 122 UDP-N-acetylmuramoylalanine--D-glutamate ligase (murD) #10 HI1137 21 cell division protein (ftsW) #11 HI1139 137 UDP-N-acetylmuramate--alanine ligase (murC) #12 HI1140 71 D-alanine--D-alanine ligase (ddlB) #13 HI1143 83 cell division protein (ftsZ) #14 HI1144 38 UDP-3-0-(3-hydroxymyristoyl) N-acetylglucosamine deacetylase (lpxC) #15 HI1334 126 cell division protein (ftsJ) #16 HI1335 90 cell division protein (ftsH) #17 HI1336 111 dihydropteroate synthase (folP-1) #18 HI1337 37 mrsA protein (mrsA) #19 HI1338 58 conserved hypothetical protein #20 HI1354 300 glutaminyl-tRNA synthetase (glnS) #21 HI1355 65 conserved hypothetical protein #22 HI1356 61 4-alpha-glucanotransferase (malQ) #23 HI1358 95 glycogen operon protein (glgX) #24 HI1360 107 glycogen synthase (glgA) #25 HI1361 245 glycogen phosphorylase (glgP) #26 HI1362 261 NAD(P) transhydrogenase, subunit alpha (pntA) Motif number 1 AATCAATTAAAAAGTGCGGTAAAAAATGAC 3 19 1 AAAGTGCGGT 0.998724 -65 AAAAATGAATAAAGTGCGGTCATTTTTTAC 3 37 0 AAAGTGCGGT 0.998724 -47 ACGTTTACAAAAAGTGCGGTGAAAATTCGC 4 11 1 AAAGTGCGGT 0.998724 -88 AATTTTATGAAAAAAGCCGTTTGAATTGTT 7 18 1 AAAAAGCCGT 0.88714 -184 TATCAAAATAAAAAAGCCGTTTGAATAAAC 7 45 0 AAAAAGCCGT 0.88714 -157 AACTCAACTAAAAGTGCGGTTAAAATTCGC 11 91 0 AAAGTGCGGT 0.998724 -47 TCCTAATAAAAAAGAGCGGTTGATTTTCTC 15 17 1 AAAGAGCGGT 0.996807 -110 AAAATGCGGTTAATTTTTAG 17 102 0 AAAATGCGGT 0.993181 -10 CGCACTTTACTAAGTGCGGTCAAAAA 19 7 0 TAAGTGCGGT 0.984337 -52 CGCACTTAGTAAAGTGCGGTTTATTTTTAT 19 19 1 AAAGTGCGGT 0.998724 -40 ACATCACATTAAAAAGCGGTATCGCCGTGA 20 28 1 AAAAAGCGGT 0.983083 -273 ATAAATGCACAAAGTGCGGTAAGTTTTTTG 20 124 0 AAAGTGCGGT 0.998724 -177 TTTAATCAACCAAGTGCGGTCAAAACAAAC 21 12 1 CAAGTGCGGT 0.989378 -54 ATACAAATAAAAAGTGCGGTCAAAATCACG 21 41 0 AAAGTGCGGT 0.998724 -25 TTAGGAAAAGTGCGGTCAAAATTAAC 24 7 1 AAAGTGCGGT 0.998724 -101 GGAGGTTCAGAAAGTGCGGTTAATTTTGAC 24 25 0 AAAGTGCGGT 0.998724 -83 TCACGTACTCAAAGAGCGGTCAAATTTTGA 25 141 1 AAAGAGCGGT 0.996807 -105 TTTTTTATGGAAAGTGCGGTAAATTTTTGA 26 52 1 AAAGTGCGGT 0.998724 -210 ********** Masking position 10 Map Score: 79.2603 Number of sites scoring better than the average of aligned sites = 1183 Number in coding regions = 748 Number in noncoding regions = 435 Number of orfs with sites within 600 bp upstream = 298 Fraction of orfs with sites within 600 bp upstream = 0.0478638 Motif number 2 TCATTTTTTACCGCACTTTTTAATTGATTAAGAT 3 14 0 CCGCACTTTT 0.994571 -70 TAAAAAATGACCGCACTTTATTCATTTTTATTCA 3 38 1 CCGCACTTTA 0.997827 -46 CGAATTTTCACCGCACTTTTTGTAAACGT 4 6 0 CCGCACTTTA 0.997827 -93 CTGTGATCTTCCTCACGTTTTCAAAATTGTCTAT 5 142 1 CCTCACGTTA 0.897929 -71 GTAAAAAAGGTCGCTCTTTCAAAAGTGAAAGAGC 9 28 0 TCGCTCTTTA 0.900841 -95 CGAATTTTAACCGCACTTTTAGTTGAGTTTTGTC 11 92 1 CCGCACTTTT 0.994571 -46 AGAAAATCAACCGCTCTTTTTTATTAGGAATCCT 15 12 0 CCGCTCTTTT 0.986502 -115 TAAAAATAAACCGCACTTTACTAAGTGCGGTCAA 19 14 0 CCGCACTTTA 0.997827 -45 CACGGCGATACCGCTTTTTAATGTGATGTAGTGG 20 23 0 CCGCTTTTTT 0.773424 -278 AAAAAACTTACCGCACTTTGTGCATTTATACATC 20 125 1 CCGCACTTTA 0.997827 -176 TTTGTTTTGACCGCACTTGGTTGATTAAAA 21 7 0 CCGCACTTGA 0.980954 -59 GTGATTTTGACCGCACTTTTTATTTGTATCAACT 21 42 1 CCGCACTTTT 0.994571 -24 TTAATTTTGACCGCACTTTTCCTAA 24 2 0 CCGCACTTTA 0.997827 -106 TCAAAATTAACCGCACTTTCTGAACCTCCTCTTT 24 26 1 CCGCACTTTA 0.997827 -82 TCGATCAACTCCTCTCTTTGCTAAAGAGGAGGTT 24 48 0 CCTCTCTTTA 0.941245 -60 CAAAATTTGACCGCTCTTTGAGTACGTGAATGTT 25 136 0 CCGCTCTTTA 0.994571 -110 TTCAAAATTTACGCACGTTTGCAAAAATCAATCA 25 168 0 ACGCACGTTA 0.833023 -78 CAAAAATTTACCGCACTTTCCATAAAAAAACACC 26 47 0 CCGCACTTTA 0.997827 -215 ********* * Masking position 8 Map Score: 58.4759 Number of sites scoring better than the average of aligned sites = 1299 Number in coding regions = 857 Number in noncoding regions = 442 Number of orfs with sites within 600 bp upstream = 292 Fraction of orfs with sites within 600 bp upstream = 0.0469001 Motif number 3 ATTTGAGAATATAGCTTACTTTTTTCTCTGTATATATAGACAA 1 64 1 ATTTTTTTAT 0.855899 -229 AAGCCTGCGAATTTTATACTTTTCAAGCAAAATTGCAAGTTTT 1 108 1 ATTTTTTCAT 0.732143 -185 ATAAAGTAGGTTGTATTCCTTTTAATTATCATTCACAATTTAT 1 157 1 TTTTTTTATT 0.890241 -136 TCATTCACAATTTATTTTGTTTTACGATATAATACGAGGCATC 1 185 1 TTTTTTTAAT 0.925446 -108 AATTTTTCCTTATTTTTAATAATGAATAAAAATGAAT 3 57 0 TTTTTTTAAT 0.925446 -27 ATTCGGCTTATTCTACTTGTTTTCTTATGAAAAGTCGGCGAAT 4 35 0 TTTTTTTCAA 0.624788 -64 ATTTATTACCTTTTATATTCCGTTTTATCATAAA 5 2 1 TTATTTTATT 0.820372 -211 GTTACTCAAAATAAATATGTTTTTGATATAAATGAACTGACAA 5 72 0 ATATTTTTAT 0.769822 -141 TCAAAATTGAATTTAAAGATTTTTATAAGATTTGTGACTTGTA 6 83 0 ATATTTTTTT 0.686048 -99 AAGTGGTGTTTTGTGGAGATTTTTAGAGATTTTCTAAAAATAA 7 148 1 TTATTTTTTT 0.795116 -54 AAAATAATGTAGTACTTTTATCTTAAATTT 8 7 1 ATTTTTTATT 0.820372 -24 ATTTCCATCAATGATATAATTTTAAAATTTATAGCAATTAAGA 9 81 1 ATTTTTTATA 0.610386 -42 AGCCTCAGTCATAAGTATTTTTTATATCCAAAAGTGCTAATAT 11 32 1 ATATTTTAAA 0.574486 -106 GCGGTTAAAATTCGCAACGTTTTTATTTCTAATATTAGCACTT 11 63 0 TTATTTTTAT 0.855899 -75 TTATTTTAATTTTTCATCTACAATAAAGGGAAT 13 1 1 TTTTTTTTAA 0.783476 -83 GCGGTTGATTTTCTCAATGTTTTTTACTGATTTCAATTAGCTT 15 32 1 TTATTTTTTT 0.795116 -95 AATCTTCTATTTTTTGTAGTCGTTTCGCCTATAT 15 103 0 ATTTTTTTTT 0.795116 -24 TTGCTTTGATAGCTTTTCATTGCTAATGATGTGTAGT 16 5 1 TTATTTTCAT 0.732143 -86 CGGTTAATTTTTAGAGTGATTTTGGTGGGCGATTATAGCGAAA 17 73 0 TTTTTTTGAT 0.644233 -39 AATAAAATTCCTTTAATTTTTTATCGTTATAAAACCA 18 8 0 TTTTTTTTAT 0.913408 -30 CGGTTTATTTTTATAAAGTTTTTAGGAAAGCAAA 19 35 1 TTATTTTAAA 0.705684 -24 GCGGTTTTTTATGGCAAGTTTTTACAATCTTTTATTTAAATCT 20 176 1 ATATTTTATT 0.720015 -125 ATAGCCGAATATTTTTTTATTTTAACGAGAGAAA 20 277 1 ATTTTTTAAA 0.705688 -24 AGCGGTGTGATTGGGCTTGTTTTTTGCAAAGATAAGCATAAAA 25 64 1 TTTTTTTTAT 0.913408 -182 AGTAAAAAACTTGTGGTGCTTTTAATTTTATTA 26 1 0 TTTTTTTATA 0.735609 -261 CGGTAAATTTTTGAGATGTTTTTTATGTGGGATTTTTCGTGAT 26 68 1 TTTTTTTTAT 0.913408 -194 AGGTAACGTTTTTAAGTGGTTTTACAAGATATTGTGATAGGGA 26 110 0 TTTTTTTATT 0.890241 -152 TCCGTTTGACTTTTTGTCATTTTAACGATGAATAGACGAAGGT 26 182 1 TTTTTTTAAT 0.925449 -80 ** * ***** ** Masking position 12 Map Score: 24.9119 Number of sites scoring better than the average of aligned sites = 795 Number in coding regions = 579 Number in noncoding regions = 216 Number of orfs with sites within 600 bp upstream = 183 Fraction of orfs with sites within 600 bp upstream = 0.0293929 Motif number 4 ATCACTTTCGAATTTGAGAATATTCTTTTAGTA 1 33 0 ATTAGAATAT 0.766891 -260 GCGGTATTTTAGCTTGATAAAATATCAGTTAAA 1 258 1 ATTATAAAAT 0.948375 -35 TAGATTAGTTAAGTTAATAAAATTCGGCTTATT 4 66 0 ATTATAAAAT 0.947158 -33 GGAAGATCACAGTTTTAGAAAATAAACATTATG 5 121 0 ATTAGAAAAT 0.968252 -92 GACTTGTATCACATTTGTAAAATCTAAAACATC 6 58 0 ATTGTAAAAT 0.744951 -124 GAATTTAAAGATTTTTATAAGATTTGTGACTTG 6 85 0 ATTATAAGAT 0.650235 -97 TCAATAAAATTTTATGAAAAAAGCCGTTTGA 7 9 1 ATTTGAAAAA 0.510766 -193 CGGCTTTTTTATTTTGATAAAAATCAGTTGCTT 7 56 1 ATTATAAAAA 0.830432 -146 AATTGAACTTATTTTTAGAAAATCTCTAAAAAT 7 166 0 ATTAGAAAAT 0.861059 -36 TAAGCTGACTAAATATATAAAATATAAATTCCC 13 38 0 ATAATAAAAT 0.629217 -46 TAAGTTTCAGAAAATACCTAGTAAA 14 3 1 ATTAGAAAAT 0.866765 -36 TCAGTAAAAAACATTGAGAAAATCAACCGCTCT 15 29 0 ATTAGAAAAT 0.96943 -98 CTTTCCTAAAAACTTTATAAAAATAAACCGCAC 19 32 0 ATTATAAAAA 0.832895 -27 GCTAAAGAGGAGGTTCAGAAAGTGCGGTTAATT 24 30 0 ATTAGAAAGT 0.818741 -78 AAACGTGCGTAAATTTTGAAAATTCACACACCC 25 182 1 ATTTGAAAAT 0.862668 -64 * ** ******* Masking position 9 Map Score: 15.0313 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 113 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 5 AATTTTTCCTTATTTTTAATAATGA 3 69 0 ATTTCCTTAT 0.922388 -15 ATTACCTTTTATATTCCGTTTTATCATAAAAGGA 5 15 1 ATTCCGTTTT 0.748291 -198 CTGTTTTTGCATCTTTCCTTTTATGATAAAACGG 5 30 0 ATTTCCTTTT 0.973697 -183 GCATATAAATACTTTTACTTTATTTT 6 166 1 ATTTACTTTT 0.709153 -16 ATGGAAATATAAATTTCCTTTACTAACGTAAAAA 9 55 0 ATTTCCTTTT 0.973697 -68 TTATTTTTCCTTTTCTCCCAATGACA 11 122 0 ATTTCCTTTT 0.973697 -16 TATAAAATATAAATTCCCTTTATTGTAGATGAAA 13 22 0 ATTCCCTTTT 0.968207 -62 AGTCTAACCTACCTTTCCTAAGTTAAAAAATTTC 16 58 0 ATTTCCTAAT 0.846173 -33 AATAAAATTCCTTTAATTTTTTATCGT 18 21 0 AATTCCTTTT 0.797546 -17 AAAAACAGCAAAATTTCCTATCAAATGGGAGCTG 20 66 1 ATTTCCTATA 0.777788 -235 ATGAACCTTTATTTTCCCTTAGATTTGTATAGAA 20 244 1 ATTCCCTTAT 0.907209 -57 TGAGTTTTTTATTTTCCCTATAAATATAAATAAT 24 84 0 ATTCCCTATA 0.742234 -24 CCACTTAAAAACGTTACCTATTTTCATTCAATTA 26 134 1 ATTACCTATT 0.729741 -128 * ******** * Masking position 1 Map Score: 10.4449 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 104 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 6 TGAAAAGTATAAAATTCGCAGGCTTTTTGTCT 1 101 0 AAATCGCAGG 0.369784 -192 AAGTGCGGTAAAAAATGACCGCACTTTATTCA 3 30 1 AAAAGACCGC 0.835524 -54 AAGTGCGGTGAAAATTCGCCGACTTTTCATAA 4 22 1 AAATCGCCGA 0.888677 -77 GAAAACAAGTAGAATAAGCCGAATTTTATTAA 4 54 1 AAATAGCCGA 0.680642 -45 AAAAATCTCCACAAAACACCACTTTTCTCCAC 7 140 0 AAAACACCAC 0.950312 -62 GAGGCTATTTATAAAACGCCACAACCC 11 6 0 AAAACGCCAC 0.95201 -132 AAGTGCGGTTAAAATTCGCAACGTTTTTATTT 11 78 0 AAATCGCAAC 0.733532 -60 TCTCCCAATGACAAAACTCAACTAAAAGTGCG 11 103 0 AAAACTCAAC 0.217275 -35 AAACATTGAGAAAATCAACCGCTCTTTTTTAT 15 22 0 AAATAACCGC 0.938969 -105 AATCACTCTAAAAATTAACCGCATTTT 17 95 1 AAATAACCGC 0.938969 -17 AAACTTTATAAAAATAAACCGCACTTTACTAA 19 24 0 AAATAACCGC 0.938969 -35 TTGTGCATTTATACATCGCCACGATAATTTCG 20 142 1 AACACGCCAC 0.677791 -159 ACTTGCCATAAAAAACCGCCACGAAATTATCG 20 163 0 AAAACGCCAC 0.95201 -138 CATTCGCCTGATAAACCACCGATGTTTTTGGG 23 41 1 AAAACACCGA 0.874211 -55 AAGTGCGGTCAAAATTAACCGCACTTTCTGAA 24 18 1 AAATAACCGC 0.938969 -90 AACTTTCTTAACAATCCACCGCTTGTGAAAGA 25 22 1 AAATCACCGC 0.982943 -224 TAATAAAATTAAAAGCACCACAAGTTTTTTA 26 10 1 TAAACACCAC 0.577767 -252 ACTTTCCATAAAAAAACACCGCAAGTAAAAAA 26 35 0 AAAACACCGC 0.981145 -227 AAACATCTCAAAAATTTACCGCACTTTCCATA 26 57 0 AAATTACCGC 0.791476 -205 * *** ****** Masking position 3 Map Score: 23.4273 Number of sites scoring better than the average of aligned sites = 1004 Number in coding regions = 707 Number in noncoding regions = 297 Number of orfs with sites within 600 bp upstream = 220 Fraction of orfs with sites within 600 bp upstream = 0.0353357 Motif number 7 TGAATGATAATTAAAAGGAATACAACCTAC 1 162 0 TTAAAAGGAA 0.643317 -131 AAAACGGAATATAAAAGGTAATAAAT 5 7 0 ATAAAAGGTA 0.774713 -206 CCGTTTTATCATAAAAGGAAAGATGCAAAA 5 30 1 ATAAAAGGAA 0.948254 -183 TTGAATAGGTATAAAAGCAAAT 6 3 0 ATAAAAGCAA 0.911887 -179 GTAATTCCACATTAAAGCAACTGATTTTTA 7 73 0 ATTAAAGCAA 0.859192 -129 TTTTTACGTTAGTAAAGGAAATTTATATTT 9 55 1 AGTAAAGGAA 0.929235 -68 TGTCATTGGGAGAAAAGGAAAAATAA 11 122 1 AGAAAAGGAA 0.957029 -16 TTCATCTACAATAAAGGGAATTTATATTTT 13 23 1 ATAAAGGGAA 0.727756 -61 GAAAATACCTAGTAAATGAAGGTAGTAGA 14 20 1 AGTAAATGAA 0.603981 -19 AAAAACATTGAGAAAATCAACCGCTCTTTT 15 26 0 AGAAAATCAA 0.593633 -101 ATGAAAAGCTATCAAAGCAA 16 1 0 ATCAAAGCAA 0.733246 -90 TTTTTAACTTAGGAAAGGTAGGTTAGACTT 16 63 1 AGGAAAGGTA 0.671361 -28 ACGATAAAAAATTAAAGGAATTTTATT 18 21 1 ATTAAAGGAA 0.915287 -17 TAAAGTTTTTAGGAAAGCAAA 19 48 1 AGGAAAGCAA 0.860101 -11 ********** Masking position 5 Map Score: 11.5475 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 132 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 8 CAAAACTTGCAATTTTGCTTGAAAAGTATAAAATTC 1 116 0 AATTGTAAAG 0.467418 -177 TATTCCTTTTAATTATCATTCACAATTTATTTTGTT 1 170 1 AAATCTAAAT 0.939101 -123 TAGCTTGATAAAATATCAGTTAAATGAGGTTTATAT 1 267 1 AAATCTAATG 0.83935 -26 CCTTATTTTTAATAATGAATAAAAATGAATAAAGTG 3 51 0 AAATGTAAAT 0.704137 -33 GTAAAATCTAAAACATCCATTAAAATGCTAATAAAT 6 39 0 AAATCTAAAT 0.939101 -143 CTTATTTTTAGAAAATCTCTAAAAATCTCCACAAAA 7 156 0 GAATCTAAAT 0.762806 -46 GTTTTATAAATAGCCTCAGTCATAAGTATTTTTTAT 11 21 1 TACTCTAAAG 0.777841 -117 ATTAGAAAAGTATCATCAGTAAGAAGAAAAACAGGA 12 40 1 TAATCTAAAG 0.917235 -32 TATATTTGGGTACAATCTGTCAAATTCAAGCCGAAG 15 72 0 TAATCTAATT 0.702817 -55 GATGAACCTTTATTTTCCCTTAGATTTGTATAGAAT 20 243 1 TATTCTAATT 0.409027 -58 TCAGCTTAGCTATAATCCCTAACAAGAGTTATACAG 22 29 1 TAATCTAAAG 0.917235 -33 AATTTGCCTACAAAATCGATAAAAAT 23 80 1 CAATCTAAAT 0.762806 -16 CCGCTTGCAAAATATTCTTTCACAAGCGGTGGATTG 25 33 0 AATTCTAAAG 0.850448 -213 GCACGTTTGCAAAAATCAATCAAAATTTGACCGCTC 25 154 0 AAATCTAAAT 0.939101 -92 AGGTAAAACCTCTATTAGAATGCTAAGAAAT 25 225 0 AACTCTAAAT 0.829696 -21 TCATCAACCCAATCATCAATCAGAGGGAAACAGT 26 238 1 AAATCTAAGG 0.75398 -24 ** *** * * *** Masking position 10 Map Score: 7.8182 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 155 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 9 CCTACTTTATGCATACAAAACTTGCAATTT 1 137 0 GCATACAAAA 0.901514 -156 ACGTTTACAAAAAGTGCGGTGA 4 3 1 GTTTACAAAA 0.728548 -96 ATATAAATGAACTGACAAAATTATTTCTGT 5 60 0 ACTGACAAAA 0.651052 -153 TGCCAGATAAGCTGACTAAATATATAAAAT 13 48 0 GCTGACTAAA 0.776492 -36 TAGGCGAAACGACTACAAAAAATAGAAGAT 15 106 1 GACTACAAAA 0.622501 -21 CGCTATAATCGCCCACCAAAATCACTCTAA 17 76 1 GCCCACCAAA 0.629514 -36 TTTACTAAGTGCGGTCAAAAA 19 2 0 GCGGTCAAAA 0.946535 -57 CGCCGTGAATGCAGGCAAAAACAGCAAAAT 20 50 1 GCAGGCAAAA 0.878405 -251 TGAATGTTTAGCTTACCAAACCCAGCCAGC 20 96 0 GCTTACCAAA 0.870341 -205 TCAACCAAGTGCGGTCAAAACAAACGTGAT 21 17 1 GCGGTCAAAA 0.946535 -49 AATAAAAAGTGCGGTCAAAATCACGTTTGT 21 36 0 GCGGTCAAAA 0.946535 -30 AATGTAATTTGCCTACAAAATCGATAAAAA 23 75 1 GCCTACAAAA 0.9644 -21 TAGGAAAAGTGCGGTCAAAATTAACCGCAC 24 12 1 GCGGTCAAAA 0.946535 -96 CAATCACACCGCTTGCAAAATATTCTTTCA 25 47 0 GCTTGCAAAA 0.933232 -199 TGTTTACACAGCCTACAAAAGTAGTTCGAA 25 107 0 GCCTACAAAA 0.9644 -139 ATTTACGCACGTTTGCAAAAATCAATCAAA 25 166 0 GTTTGCAAAA 0.599858 -80 ********** Masking position 8 Map Score: 14.3101 Number of sites scoring better than the average of aligned sites = 348 Number in coding regions = 277 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 10 TTCTCAAATTCGAAAGTGATTTGAGAATAT 1 46 1 CGAAAGTGAT 0.95373 -247 TTAGATTTTACAAATGTGATACAAGTCACA 6 64 1 CAAATGTGAT 0.938218 -118 AAATTTAAGATAAAAGTACTACATTATTTT 8 11 0 TAAAAGTACT 0.510751 -20 GTCGCTCTTTCAAAAGTGAAAGAGCGAACC 9 23 0 CAAAAGTGAA 0.802897 -100 TTTTTATATCCAAAAGTGCTAATATTAGAA 11 50 1 CAAAAGTGCT 0.933997 -88 GCGGTCAAAACAAACGTGATTTTGACCGCA 21 27 1 CAAACGTGAT 0.89907 -39 ATAGCTAAGCTGAAAGTGATGACAACTGGC 22 12 0 TGAAAGTGAT 0.780858 -50 GTTTATCAGGCGAATGTAATTCGCCCCTAC 23 27 0 CGAATGTAAT 0.821883 -69 TGTTTTTGGGCAAATGTAATTTGCCTACAA 23 63 1 CAAATGTAAT 0.866323 -33 ACACAGCCTACAAAAGTAGTTCGAATTTTA 25 102 0 CAAAAGTAGT 0.766433 -144 ********** Masking position 4 Map Score: 3.37725 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 121 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 11 AACCTTCCTCTAAATGTTTAATTA 1 5 1 TTCCTCTAAA 0.815542 -288 ACGCGTAAATTTGACCTAAAACAGCTGGAT 1 225 0 TTGACCTAAA 0.788274 -68 TTGATTCCCCTAGATTAGTTAAGT 4 85 0 TTCCCCTAGA 0.861275 -14 AAATATGTTTTTGATATAAATGAACTGACA 5 73 0 TTGATATAAA 0.631025 -140 AAGTATTTATATGCCCTAAACAAGCGGCTG 6 150 0 ATGCCCTAAA 0.66901 -32 CTTTTTTATTTTGATAAAAATCAGTTGCTT 7 59 1 TTGATAAAAA 0.418904 -143 TTCTTCTTAATTGCTATAAATTTTAAAATT 9 98 0 TTGCTATAAA 0.904824 -25 TTTGCTTTCCTAAAAACTTTATAAAA 19 43 0 TTCCTAAAAA 0.644611 -16 TTGTAAAAACTTGCCATAAAAAACCGCCAC 20 173 0 TTGCCATAAA 0.952723 -128 TCTCCTGTTCTTGCCATAGAAATACTAGAT 20 215 0 TTGCCATAGA 0.930378 -86 AACCTTTATTTTCCCTTAGATTTGTATAGA 20 247 1 TTCCCTTAGA 0.489917 -54 CAAATTACATTTGCCCAAAAACATCGGTGG 23 56 0 TTGCCCAAAA 0.895671 -40 ACTCCTCTCTTTGCTAAAGAGGAGGTTCAG 24 45 0 TTGCTAAAGA 0.725121 -63 TTTACCGCACTTTCCATAAAAAAACACCGC 26 45 0 TTTCCATAAA 0.637672 -217 ********** Masking position 8 Map Score: 6.6243 Number of sites scoring better than the average of aligned sites = 541 Number in coding regions = 459 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 12 ATGCATACAAAACTTGCAATTTTGCTTGAA 1 129 0 AACTTGCAAT 0.959908 -164 TTGTTCGCTCAACTTGCAAGTAATTCCACA 7 92 0 AACTTGCAAG 0.973708 -110 ACAAATTATAAACTTGCCAGAAGTGGAGAA 7 118 1 AACTTGCCAG 0.982843 -84 AGATTGTAAAAACTTGCCATAAAAAACCGC 20 176 0 AACTTGCCAT 0.973708 -125 ********** Masking position 5 Map Score: 1.72782 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 5 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 13 AAGTGGTGTTTTGTGGAGATTTTTAGAGATT 7 148 1 TTGTGGAGTT 0.951798 -54 GGGTTGTGGCGTTTTATAAATAGC 11 4 1 TTGTGGCGTT 0.987414 -134 CACGAAATTATCGTGGCGATGTATAAATGCA 20 145 0 TCGTGGCGTG 0.959647 -156 CACGATAATTTCGTGGCGGTTTTTTATGGCA 20 161 1 TCGTGGCGTT 0.984858 -140 AGTAAAAAACTTGTGGTGCTTTTAATTTTAT 26 13 0 TTGTGGTGTT 0.972082 -249 AGTTTTTTACTTGCGGTGTTTTTTTATGGAA 26 33 1 TTGCGGTGTT 0.927175 -229 ******** ** Masking position 10 Map Score: 3.91405 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 28 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 14 CGTTTACAAAAAGTGCGGTGAAAATTCGCC 4 12 1 AAGTGCGGTG 0.902493 -87 TATGCCCTAAACAAGCGGCTGTATTCTATT 6 141 0 ACAAGCGGCT 0.795544 -41 AGAAGTGGAGAAAAGTGGTGTTTTGTGGAG 7 136 1 AAAAGTGGTG 0.879482 -66 AAAATGCGGTTAATTTTTAGA 17 101 0 AAATGCGGTT 0.873089 -11 CATCACATTAAAAAGCGGTATCGCCGTGAA 20 29 1 AAAAGCGGTA 0.827793 -272 ATATTCTTTCACAAGCGGTGGATTGTTAAG 25 28 0 ACAAGCGGTG 0.986452 -218 AGAATATTTTGCAAGCGGTGTGATTGGGCT 25 51 1 GCAAGCGGTG 0.944481 -195 CAAGTAAAAAACTTGTGGTGCTTTTAATTT 26 16 0 ACTTGTGGTG 0.809896 -246 CAAGTTTTTTACTTGCGGTGTTTTTTTATG 26 31 1 ACTTGCGGTG 0.955821 -231 ********** Masking position 5 Map Score: 4.22711 Number of sites scoring better than the average of aligned sites = 447 Number in coding regions = 337 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 15 ATAGCGGTATTTTAGCTTGATAAAATATCAG 1 255 1 TTTAGCTTAT 0.64631 -38 TTTATCTTAATCAATTAAAAA 3 1 1 TTTATCTTAT 0.930881 -83 ACTTTATTCATTTTTATTCATTATTAAAAAT 3 52 1 TTTTTATTAT 0.756677 -32 AATTTTTCCTTATTTTTAATAAT 3 71 0 TTTTTCCTAT 0.919183 -13 ATATAAATACTTTTACTTTATTTT 6 168 1 TTTTACTTAT 0.610934 -14 AAACGGCTTTTTTATTTTGATAAAAATCAGT 7 53 1 TTTATTTTAT 0.630182 -149 ATGTAGTACTTTTATCTTAAATTT 8 17 1 TTTATCTTAA 0.535373 -14 TTTCTTTCTTCTTAATTGCTATAAAT 9 107 0 TTCTTCTTAT 0.685069 -16 TTATTTTTCCTTTTCTCCCAATGA 11 124 0 TTTTTCCTTT 0.647392 -14 TTCTATCCTGTTTTTCTTCTTACTGATGATA 12 50 0 TTTTTCTTTT 0.734672 -22 TTCTCAATGTTTTTTACTGATTTCAATTAGC 15 42 1 TTTTTACTAT 0.673418 -85 AAGGCTTTATTTTTTCCTAATGATTTTGTTC 17 33 1 TTTTTCCTAT 0.919183 -79 CCTTTAATTTTTTATCGTTATAAAACCA 18 8 0 TTTATCGTAT 0.823561 -30 TAAAGTGCGGTTTATTTTTATAAAGTTTTTA 19 28 1 TTTATTTTAT 0.630183 -31 TCGAGCATTATTTATATTTATAGGGAAAATA 24 78 1 TTTATATTAT 0.709448 -30 TTATGTGGGATTTTTCGTGATCCCTATCACA 26 90 1 TTTTTCGTAT 0.856006 -172 ******** ** Masking position 8 Map Score: 8.06129 Number of sites scoring better than the average of aligned sites = 428 Number in coding regions = 329 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767