AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00710_hinf_reg_300.orf -o00710_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 HI0462 192 ATP-dependent proteinase (lon) #2 HI0463 115 oxygen-independent coproporphyrinogen III oxidase, putative #3 HI0464 132 ribose 5-phosphate isomerase A (rpiA) #4 HI0524 110 fructose-bisphosphate aldolase (fba) #5 HI0525 101 phosphoglycerate kinase (pgk) #6 HI0526 77 H. influenzae predicted coding region HI0526 #7 HI0566 116 ribulose-phosphate 3-epimerase (dod) #8 HI0567 150 DNA gyrase, subunit B (gyrB) #9 HI0568 95 transcription accessory protein (tex) #10 HI0678 165 triosephosphate isomerase (tpiA) #11 HI0809 172 phosphoenolpyruvate carboxykinase (pckA) #12 HI0810 144 conserved hypothetical protein #13 HI0811 134 argininosuccinate lyase (argH) #14 HI0812 21 glucosephosphate uridylyltransferase (galU) #15 HI0813 77 carbon storage regulator (csrA) #16 HI0814 187 alanyl-tRNA synthetase (alaS) #17 HI0815 101 universal stress protein A (uspA) #18 HI0817 170 conserved hypothetical protein #19 HI0819 37 galactokinase (galK) #20 HI0820 207 galactose-1-phosphate uridylyltransferase (galT) #21 HI1023 128 transketolase 1 (tktA) #22 HI1024 49 hexulose-6-phosphate synthase, putative #23 HI1027 58 L-xylulose kinase (lyx) #24 HI1028 30 conserved hypothetical protein #25 HI1030 71 conserved hypothetical transmembrane protein #26 HI1031 175 conserved hypothetical protein #27 HI1210 206 malate dehydrogenase (mdh) #28 HI1573 300 pyruvate kinase, type II (pykA) #29 HI1615 160 phosphoribosylaminoimidazole carboxylase, catalytic subunit (purE) #30 HI1616 69 phosphoribosylaminoimidazole carboxylase, ATPase subunit (purK) #31 HI1617 138 aspartate aminotransferase (aspC) #32 HI1635 274 purine nucleotide synthesis repressor (purR) #33 HI1636 182 phosphoenolpyruvate carboxylase (ppc) #34 HI1645 233 fructose-1,6-bisphosphatase (fbp) Motif number 1 CCGCACTTTTCCTCTATAAC 4 1 1 CCGCACTTTT 0.998818 -110 GTGGTTTTTTCCGCACTTTTTGTCTTGATC 12 95 0 CCGCACTTTT 0.998818 -50 GAAAAAACCACCGCACTTTTTATCTCAATT 12 114 1 CCGCACTTTT 0.998818 -31 TAAATTTTAACCGCACTTCTCAAATAGCGT 16 49 1 CCGCACTTCT 0.996925 -139 CAAAATAAAACCGCACTTCACGACGCTATT 16 71 0 CCGCACTTCA 0.987722 -117 TTAGATCTGACCGCACTTTTAAAGTGCGGT 30 19 1 CCGCACTTTT 0.998818 -51 TAAAAAATGACCGCACTTTTTGATGAATAT 31 13 1 CCGCACTTTT 0.998818 -126 TTTATTATCACCGCAGTTTTGTTTCTACAA 32 17 0 CCGCAGTTTT 0.989966 -258 CAAAAATAGACCGCACTTTTTAAAAAATCC 33 17 1 CCGCACTTTT 0.998818 -166 TAAAAAAGACCCGCACTTTTTAGGGATTTT 33 40 0 CCGCACTTTT 0.998818 -143 GCTACCATAACCGCACTTTATTAAGCCAAA 34 20 0 CCGCACTTTA 0.995252 -214 ********** Masking position 5 Map Score: 42.1819 Number of sites scoring better than the average of aligned sites = 654 Number in coding regions = 386 Number in noncoding regions = 268 Number of orfs with sites within 600 bp upstream = 208 Fraction of orfs with sites within 600 bp upstream = 0.0334083 Motif number 2 ATATTTTGTGAAATTTAATAAAATTTTTCATTA 1 17 1 AAATTAAAAA 0.858416 -176 GATAATGGCTAAAATAATGAAAAATTTTATTAA 1 31 0 AAAATAAAAA 0.910271 -162 ATAAAGTGGGTTTTAAACAAAAAAGAATTTTGG 1 74 0 TTTTAAAAAA 0.542332 -119 TATCATCTCTAAAATCAATAAAAGGCTTGTTTT 2 32 0 AAAATAAAAA 0.910271 -84 CATCAATATGTTATAGAGGAAAAGTGCGG 4 7 0 TTATAAAAAA 0.638498 -104 ACGAAGTAGGTATAATACGAAAAGTTTTCAATT 5 44 1 TATAAAAAAA 0.700079 -58 TTAAGTTAAAATTAAAATTAAAATTGAAAACTT 5 65 0 ATTAAAAAAA 0.762082 -37 TCATGAATATAAATAGACGAAAAT 7 2 0 AAATAAAAAA 0.753626 -115 TGCACTAAAAAATTGGAAAAAATAACAAGTT 8 9 1 AAAATGAAAA 0.830963 -142 ATTGGGCGAGATTATAGCAAAAAATCGCCGTTT 8 100 0 ATTATGAAAA 0.75467 -51 AATAAAAATAAAAGAAAGTTTTT 9 1 1 AATAAAAAAA 0.782534 -95 TGGCTCAAATATAATTCAAAAAACTTTCTTTTA 9 19 0 ATAATCAAAA 0.755356 -77 GTCGTACTTCTTTATTATAAAAAAACGAAGATA 9 72 0 TTTATAAAAA 0.804518 -24 AGAAGATCATAAAATTAAAAAAATTCTCACAGA 10 76 0 AAAATAAAAA 0.910271 -90 TGATATTGTGATATAGAGCAAAAATCCCGACAT 11 27 0 ATATAAAAAA 0.731389 -146 TCTATATCACAATATCACTAAAAAGAGGTAAAG 11 43 1 AATATAAAAA 0.877035 -130 ACCTCTAATATATAAGATTAAAATTTAACTGTG 11 145 0 TATAAAAAAA 0.700078 -28 GTGCCACCTATTTATAAGCAAAAACACTTAAAT 12 57 1 TTTATAAAAA 0.804625 -88 TAATACAAATAAAATGGACAAAATGAAAGATTT 13 18 1 AAAATGAAAA 0.830963 -117 TAATAAAACAAAAATGGACAAAATCTTTCATTT 13 38 0 AAAATGAAAA 0.830963 -97 AATATTCTATATTAATAATAAAACAAAAATGGA 13 53 0 ATTAAAAAAA 0.762082 -82 AATAATAGAATAATTAATTAAAACAAAAAGGAA 13 107 1 TAATTAAAAA 0.797278 -28 GTTATTTCAGATTATTCAAAAAACAATTTCTTG 16 15 0 ATTATCAAAA 0.68459 -173 CATATTTTTGAAATTTATAAAAAGGCTTTTTGC 16 109 0 AAATTAAAAA 0.858416 -79 TAAATTTCAAAAATATGCAAAAATAGGGCGACT 16 125 1 AAATAGAAAA 0.59714 -63 GTTACCCATAATAAAAATAAAAACTAAGTCGCC 16 151 0 ATAAAAAAAA 0.820013 -37 ACACAGTTTTTTATTGCTCAAAATGTTAGCATT 17 37 1 TTATTCAAAA 0.544796 -65 GCCATTATTTATAATAAAAATGTCATTACA 18 8 1 TTTATAAAAA 0.804518 -163 TCGTAAATTATTTATGATCAAAATATAAGATTT 20 35 0 TTTATAAAAA 0.804625 -173 AAGTATGAACTAAATCATAAAAAATTTTGCTTA 20 92 1 TAAATAAAAA 0.868084 -116 ACAAAATAAGAAAATAAGCAAAATTTTTTATGA 20 106 0 AAAATAAAAA 0.910271 -102 TTCCTCATATTATTTAAGGAAAAACG 22 34 1 TATTTAAAAA 0.734401 -16 TCTAGATCACAAAATCAGTAAAATTATTTTAAC 26 46 1 AAAATAAAAA 0.910271 -130 TTACGTTTCATAATTTACAAAAATAAGAAAGCT 26 123 0 TAATTAAAAA 0.797278 -53 TCTCTTAATTTTATATAGTAAAATTACGTTTCA 26 146 0 TTATAAAAAA 0.638456 -30 GAACACAAGTATTTTTCTTAAAACCCGATATAA 28 122 1 ATTTTCAAAA 0.562686 -179 CCATTGCAACTTTAAGGATAAAATTTTATCCTA 29 41 0 TTTAAGAAAA 0.500429 -120 GCTAAATGGCTTTTATAGGAAAATACCATTGCA 29 66 0 TTTTAAAAAA 0.553817 -95 TTTTAATTAGAAAATTGAGAAAATAGC 29 144 1 AAAATGAAAA 0.830963 -17 ATTTCTCGTTAAATTTACGAAAAAAACAACCGC 30 44 0 AAATTAAAAA 0.858416 -26 ATATTTTTAAATATTCATCAAAAAGTGCGGTCA 31 20 0 ATATTAAAAA 0.843675 -119 TTCTAGCAAGAATAATACGAAAAAATCACTTCT 32 171 1 AATAAAAAAA 0.782534 -104 TTATTGCAAATTTTTTATAAAAAGAAGTGATTT 32 193 0 TTTTTAAAAA 0.696084 -82 ACAAACCTTTATAATAGGAAAAATTTTTAGGGA 32 243 1 ATAATGAAAA 0.813983 -32 ATATTTAAATCCCTAAAAATTTTTCCTA 32 257 0 TAAATCAAAA 0.692307 -18 CACTTTTTAAAAAATCCCTAAAAAGTGCGGGTC 33 30 1 AAAATCAAAA 0.776217 -153 GAAAAGCTAAAAAATAGCTAAAAAAGACCCGCA 33 55 0 AAAATGAAAA 0.830963 -128 AATTTTGAAAATAATCAAGAAAAGCTAAAAAAT 33 73 0 ATAATAAAAA 0.900302 -110 TTGGCGATAGATATAACTAAAAATAGGGTGGAG 33 125 0 ATATACAAAA 0.482107 -58 AACCGCACTTTATTAAGCCAAAAGGTAAAAA 34 9 0 TATTAGAAAA 0.403323 -225 GAATGAGATCTTTATCACAAAAAATTCACATTT 34 134 0 TTTATAAAAA 0.804518 -100 ***** * **** Masking position 10 Map Score: 47.5308 Number of sites scoring better than the average of aligned sites = 1688 Number in coding regions = 1098 Number in noncoding regions = 590 Number of orfs with sites within 600 bp upstream = 392 Fraction of orfs with sites within 600 bp upstream = 0.0629618 Motif number 3 AATTTTATTAAATTTCACAAAATATTGAGTT 1 9 0 AATTAAAAAT 0.809906 -184 CAAGGAAAAGATTATAACAAAATCTGAGTTATA 1 104 0 ATATAAAAAT 0.752327 -89 TTCAATTTGGAAAAGTATAAATTAACCTTGTGT 2 76 0 AAAGAAAATT 0.609904 -40 CATGAATATAAATAGACGAAAAT 7 1 0 AAAGCAAAAT 0.695857 -116 TGCACTAAAAAATTGGAAAAAATAACAAGTTAT 8 11 1 AATGAAAAAT 0.826021 -140 TGGGCGAGATTATAGCAAAAAATCGCCGTTTTG 8 98 0 TAAGAAAAAT 0.609904 -53 TTCTTTGCAGAAGATCATAAAATTAAAAAAATT 10 84 0 AAATAAAAAT 0.9461 -82 TGTTTCTCCATAGTTGATAAAATTAACTTGCTT 10 140 0 TATTAAAAAT 0.332039 -26 TTCTTAAAAAAATGTTTAAAAATGAGATCTACT 11 76 1 AAGTTAAAAT 0.328803 -97 AATGGATGTCAATATAAAAAAATGTTAAGTAGA 11 103 0 AAATAAAAAT 0.945824 -70 CCTCTAATATATAAGATTAAAATTTAACTGTGG 11 144 0 ATAGTAAAAT 0.536292 -29 AATACAAATAAAATGGACAAAATGAAAGATTTT 13 19 1 AATGAAAAAT 0.826299 -116 AATAAAACAAAAATGGACAAAATCTTTCATTTT 13 37 0 AATGAAAAAT 0.826299 -98 AATTAAAACAAAAAGGAAAAATT 13 122 1 AAAGAAAATT 0.609904 -13 AAATTTCAAAAATATGCAAAAATAGGGCGACTT 16 126 1 AAATCAAAAT 0.712486 -62 TAAAAATGTTTAAATTGTGATCTAG 17 3 1 AAATTTAAAT 0.540263 -99 ATGTCATTACAAGATCTATAAATCAGGTTCATT 18 30 1 AAATTTAAAT 0.540263 -141 TTTCCTTGTTATAATCTATAAATCTTATATTTT 20 16 1 ATATTTAAAT 0.170727 -192 TCTTTGTCACAAAATAAGAAAATAAGCAAAATT 20 114 0 AAATAAAAAT 0.9461 -94 AGGCAGAATAGTATAAAATAGCTGCCACC 21 7 1 AAAGAAAAAT 0.941879 -122 TTGCAAGGTTACTATGTGAAAATTAGGTGGCAG 21 32 0 ACATTAAAAT 0.314128 -97 CAAGATTAGGAAAATAACAAAATATTCACAGGA 21 99 1 AAATAAAAAT 0.9461 -30 AAATAGGATCTAGATCACAAAATCAGTAAAATT 26 38 1 TAATAAAAAT 0.628732 -138 TTTATAAATCAATATGTTAAAATAATTTTACTG 26 61 0 AAATTAAAAT 0.876675 -115 CAATAAATGTAAAATAAATAAATTATTTATAAA 26 86 0 AAATATAAAT 0.742592 -90 AATAAGAACAAAGAGAAGAAAATATTTATCTCA 27 80 1 AAAGAAAAAT 0.941881 -127 TTGTAAGATGAACATTTTAAAATCAGTCTGTTT 27 156 1 AAATTAAAAT 0.877303 -51 TACTCCGTCAATAATTACAAAATTTTAAAGGTG 28 274 0 ATATAAAAAT 0.754597 -27 TTTAATTAGAAAATTGAGAAAATAGC 29 145 1 AATTAAAAAT 0.837222 -16 CTTTTTGATGAATATTTAAAAATATCAAAGCGT 31 28 1 AAATTAAAAT 0.876675 -111 AGCGTGGTTAATTTTTATAAAATCTTTCTTGAT 31 56 1 ATTTAAAAAT 0.393015 -83 ATTTTTTATGAGGAGAACAAAATGAGCGATTTT 32 128 0 AGAGAAAAAT 0.509354 -147 TAGCAAGAATAATACGAAAAAATCACTTCTTTT 32 174 1 AAACAAAAAT 0.593845 -101 ATTTGCAATAAAGATGACTAAATTCTCAACAAA 32 215 1 AAATATAAAT 0.742592 -60 AAACCTTTATAATAGGAAAAATTTTTAGGGATT 32 245 1 AAAGAAAATT 0.609894 -30 CTATTCAGAGAAATTTTGAAAATAATCAAGAAA 33 84 0 AATTTAAAAT 0.676819 -99 AGGAACTCCTAAAAGTAAAAAATAAAATTTGTC 33 160 0 AAAGAAAAAT 0.941881 -23 ** ** * ***** Masking position 10 Map Score: 36.7876 Number of sites scoring better than the average of aligned sites = 681 Number in coding regions = 473 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 182 Fraction of orfs with sites within 600 bp upstream = 0.0292323 Motif number 4 TATTGATGATGGCATTTTTGATGCCACCATCA 4 35 0 GATTTTTGAT 0.828233 -76 GTTATTTTTTCCAATTTTTTAGTGCA 8 5 0 CATTTTTTAG 0.746062 -146 AAATTATTCGCCCTTTTTTTATCGTTTTCCTT 8 50 1 CTTTTTTTAT 0.478629 -101 TATAATCTCGCCCAATTTTTATTTACAAAAGA 8 117 1 CAATTTTTAT 0.854356 -34 AATTGGTTATTTTTTATTGGTTCCATA 10 6 1 GATTTTTTAT 0.916636 -160 AAAAAACCACCGCACTTTTTATCTCAATTAGG 12 115 1 CACTTTTTAT 0.768613 -30 CCTATTTTTGCATATTTTTGAAATTTATAAAA 16 120 0 CATTTTTGAA 0.544104 -68 AATAGGGCGACTTAGTTTTTATTTTTATTATG 16 146 1 CAGTTTTTAT 0.643491 -42 GAAAATAAGCAAAATTTTTTATGATTTAGTTC 20 98 0 AATTTTTTAT 0.464204 -110 TTTGACTCCTGTTTTTTATCAATGTAAAC 20 189 0 CGTTTTTTAT 0.784825 -19 TTTTTATGGGCTGGATTTTTATTATGTAAAAT 23 23 0 CGATTTTTAT 0.600521 -36 CAATTCTTATGCAAATTTTGACTATTGAAAAA 27 16 0 GAATTTTGAC 0.290893 -191 GTTGATGAAAGTGAATTTTTATGCAATTCTTA 27 39 0 GAATTTTTAT 0.819228 -168 AAATAACTGAGCCGTTTTTGATTTCCAAAAGT 28 183 1 GGTTTTTGAT 0.552707 -118 ATAATGTGCACCGATTTTTTATCTGGCTAATA 28 224 1 CATTTTTTAT 0.934352 -77 TTATCCTAAGCACAATTTTTATAAGAATAGGT 29 17 0 CAATTTTTAT 0.854356 -144 AAAAAGTGCGGTCATTTTTTACA 31 2 0 GATTTTTTAC 0.694165 -137 TCAAAGCGTGGTTAATTTTTATAAAATCTTTC 31 52 1 GAATTTTTAT 0.819228 -87 TTTAATCAAACCAACTTTTTATTATCACCGCA 32 32 0 CACTTTTTAT 0.768613 -243 GAATGTCTGCGTTATTTTTTATGAGGAGAACA 32 142 0 GATTTTTTAT 0.916636 -133 ATCTTTATTGCAAATTTTTTATAAAAAGAAGT 32 198 0 CATTTTTTAT 0.934352 -77 GCACTTTTTAGGGATTTTTTAAAAAGTGCGGT 33 26 0 GATTTTTTAA 0.677687 -157 GTCTTTTTTAGCTATTTTTTAGCTTTTCTTGA 33 60 1 GATTTTTTAG 0.694165 -123 GAAACTATCGCTTATTTTTGAATAAATTTTGG 34 86 0 CATTTTTGAA 0.544104 -148 * ********* Masking position 6 Map Score: 19.5889 Number of sites scoring better than the average of aligned sites = 404 Number in coding regions = 237 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 5 CGGGATTTTTGCTCTATATCACAATATCACTAA 11 31 1 GTCTATCACA 0.988981 -142 TTAAAAATGAGATCTACTTAACATTTTTTTATA 11 91 1 GTCTATAACA 0.886898 -82 AAAAAACTGTGTACTAGATCACAATTTAAACAT 17 16 0 GACTATCACA 0.975985 -86 TCATAAGTATGAACTAAATCATAAAAAATTTTG 20 88 1 GACTATCATA 0.8754 -120 AATAAACCGTGATCTTTGTCACAAAATAAGAAA 20 126 0 GTCTTTCACA 0.975985 -82 AAGAAAATAGGATCTAGATCACAAAATCAGTAA 26 34 1 GTCTATCACA 0.988981 -142 TCTTCTCTTTGTTCTTATTCATATTTCAGTTGA 27 66 0 GTCTTTCATA 0.8754 -141 ATCATTCTATGATCTAGTTCACATTTCTGAGAT 27 107 0 GTCTATCACA 0.988981 -100 TCTATAATCACGACTACTTCACACAGTGCGACT 28 77 0 CACTATCACA 0.840322 -224 ATCAGAATGAGATCTTTATCACAAAAAATTCAC 34 138 0 GTCTTTCACA 0.975985 -96 * **** ***** Masking position 5 Map Score: 13.5712 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 7 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 6 TGTTTTAGGGCTTGTGAAAACAAGCCTTTTAT 2 16 1 CTTGTGAAAA 0.96827 -100 ATAAATTAACCTTGTGTAAAGATGAAATTATC 2 61 0 CTTGTGAAAA 0.968271 -55 AATAACATTGCTTGAGAAAAACGCCTGTTAAA 3 38 1 CTTGAGAAAC 0.865949 -95 TTATCTCATTCTTTTGTAAATAAAAATTGGGC 8 126 0 CTTTTGAAAA 0.924346 -25 AGATGATTATCTTGAGCTAAAAAGCTACAATT 10 43 0 CTTGAGTAAA 0.895684 -123 ATTTTATGATCTTCTGCAAAGAATAGGGGCGA 10 94 1 CTTCTGAAAA 0.76443 -72 ATTATTCCTAATTGAGATAAAAAGTGCGGTGG 12 121 0 ATTGAGTAAA 0.534315 -24 TTAGTGTAAACCTTTGTAAATAAAAAAGCCAT 18 123 0 CCTTTGAAAA 0.564392 -48 CCCTCTTTAGCTTTAGCAAAGAGGG 19 23 1 CTTTAGAAAA 0.852079 -15 AACTTTTTCCTTGTTATAATCTATAAATCTT 20 10 1 CTTGTTTAAC 0.584581 -198 AAAAGTCTCCTTGTGTTAAGAAAGTCTGTT 24 10 0 CTTGTGTAAA 0.947703 -21 ACGAATCACATTTGTGATAATCAATTGGAGGT 25 47 1 TTTGTGTAAC 0.299578 -25 ATCCTATTTTCTTGTGATAATATTTCATATTG 26 15 0 CTTGTGTAAA 0.947703 -161 ACGCTTAAAACTTTTGGAAATCAAAAACGGCT 28 192 0 CTTTTGAAAC 0.845103 -109 TAATTAGAAAATTGAGAAAATAGC 29 147 1 ATTGAGAAAA 0.65896 -14 TAAAATCTTTCTTGATAAAATAAAATGACTGA 31 73 1 CTTGATAAAA 0.715583 -66 AAAATCACTTCTTTTTATAAAAAATTTGCAAT 32 192 1 CTTTTTTAAA 0.557275 -83 ATAGACCGCACTTTTTAAAAAATCCCTAAAAA 33 22 1 CTTTTTAAAA 0.678449 -161 ATTCAGAGAAATTTTGAAAATAATCAAGAAAA 33 83 0 ATTTTGAAAA 0.620017 -100 ****** *** * Masking position 3 Map Score: 12.7579 Number of sites scoring better than the average of aligned sites = 442 Number in coding regions = 380 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 7 CCATTATCACTTCATTTGCCAAAATTCTTTTTTGT 1 56 1 TTTTTCAAAT 0.732093 -137 TCTCTTATAATTTCGTTCCGATAATTTGGGTAAAT 1 160 0 TTGTTCATAT 0.746024 -33 AAGTAAACGATTGTGTTACTTTATTACGAGAGTAT 3 89 0 TTGTTCTTAT 0.76174 -44 TTCTTTTCCTTATCTTAATAAGTAA 3 118 0 TTTTTCTATT 0.763997 -15 ACTTGTGTTTCCTTTTTATGTTTAGCG 4 94 0 TTGTTCTTTT 0.776774 -17 AAATTTTGTTTAGTTTTTGTCAATCAAG 6 60 0 TTGTTATTTT 0.625058 -18 TCTGTGAGAATTTTTTTAATTTTATGATCTTCTGC 10 76 1 TTTTTATTTT 0.74075 -90 ATTTTTCCTTTTTGTTTTAATTAATTATTCTATTA 13 109 0 TTTTTATTAT 0.724151 -26 TTTTATCTCCTTAGTTTGCATTTATTAGATATCCT 15 52 0 TTTTTCTTTT 0.856407 -26 AAGATCACGGTTTATTTACAATAATTTAGTATAAA 20 143 1 TTTTTCATAT 0.834282 -65 GAATATTTTGTTATTTTCCTAATCTTGACCGAAAG 21 91 0 TTTTTCAATT 0.748381 -38 AAAAGTCTCCTTGTGTTAAGAAAGTCTGTT 24 6 0 TTGTTAAAAT 0.433049 -25 ACAAATGTGATTCGTTTTATATTATGGCGTTTTAC 25 27 0 TTTTTAATTT 0.724151 -45 ATCAGTAAAATTATTTTAACATATTGATTTATAAA 26 59 1 TTTTTAATAT 0.70691 -117 AATAATTTATTTATTTTACATTTATTGACTGAGCT 26 92 1 TTTTTCTTTT 0.856407 -84 TATAGTAAAATTACGTTTCATAATTTACAAAAATA 26 131 0 TTGTTCTAAT 0.634412 -45 TTTTCCTCTCTTAATTTTATATAGTAAAATTACGT 26 150 0 TTTTTAATAT 0.70691 -26 CTTTATTTTTCAATAGTCAAAATTTGC 27 3 1 TTTTTCATAT 0.834286 -204 TTAAGCTGGTTTTGTTTACTTTTTTGCCAGTTATA 28 150 0 TTTTTCTTTT 0.856407 -151 TGAGCCGTTTTTGATTTCCAAAAGTTTTAAGCGTA 28 190 1 TTTTTCAAAT 0.732093 -111 ATGATTATGGTTGTTTTTAGTATGTCTGTTGTCGT 32 84 0 TTTTTATATT 0.607979 -191 CTTTTCTTGATTATTTTCAAAATTTCTCTGAATAG 33 82 1 TTTTTAAATT 0.58761 -101 AATTTCCTTTTAGTTTTTCATAATACGT 34 216 0 TTTTTATTTT 0.740751 -18 ** *** * *** * Masking position 7 Map Score: 21.6449 Number of sites scoring better than the average of aligned sites = 374 Number in coding regions = 286 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 8 CTAGTCGTGAAATAACATTGCTTGAGAAAAA 3 28 1 AATACATTGC 0.700075 -105 TCCTTTCCCGAAAAGCATCGCCAAAACGGCG 8 77 1 AAAACATCGC 0.955632 -74 GAGATTATAGCAAAAAATCGCCGTTTTGGCG 8 95 0 CAAAAATCGC 0.628253 -56 AAGTGCGGAAAAAACCACCGCACTTTTTATC 12 107 1 AAAACACCGC 0.971883 -38 AAAACTCCAAAATAAAACCGCACTTCACGAC 16 77 0 AATAAACCGC 0.886004 -111 TGTAAATAAAAAAGCCATCGCTTGACCAATT 18 110 0 AAAGCATCGC 0.862105 -61 CATACTTATGAAAGTAACCGCTTTCAATTTA 20 68 0 AAAGAACCGC 0.843668 -140 CAAAATTTGCATAAGAATTGCATAAAAATTC 27 28 1 ATAAAATTGC 0.467791 -179 TTTATAGGAAAATACCATTGCAACTTTAAGG 29 57 0 AATACATTGC 0.700075 -104 ATTTACGAAAAAAACAACCGCACTTTAAAAG 30 34 0 AAAAAACCGC 0.948959 -36 TGTAAAAAATGACCGCACTTTTTGAT 31 6 1 AAAAGACCGC 0.851208 -133 CCAACTTTTTATTATCACCGCAGTTTTGTTT 32 23 0 ATTACACCGC 0.808753 -252 AAAAACAACCATAATCATTGCATAACCAAAA 32 101 1 ATAACATTGC 0.620363 -174 AAATAGCTAAAAAAGACCCGCACTTTTTAGG 33 46 0 AAAAACCCGC 0.730611 -137 **** ****** Masking position 11 Map Score: 7.3019 Number of sites scoring better than the average of aligned sites = 596 Number in coding regions = 446 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 9 TTCTTTTTTGTTTAAAACCCACTTTATAACTCA 1 80 1 TTAAAACCAT 0.886857 -113 TCACTTAACGTCAAAAAACCAACAGTAATCCTT 7 85 0 TAAAAACCAC 0.973107 -32 CTTAGAGGCTTGTAAAATCCAATGTGATCTCTA 12 25 0 TTAAAACCAT 0.886857 -120 CAAAAAGTGCGGAAAAAACCACCGCACTTTTTA 12 103 1 GAAAAACCAC 0.939609 -42 TTCAGATTATTCAAAAAACAATTTCTTGTTAA 16 10 0 TAAAAACAAT 0.696803 -178 TTGGAGCCAGTTAAAAACCGAACCAATCAGTTA 17 68 1 TAAAAACGAC 0.840194 -34 CCTTTGTAAATAAAAAAGCCATCGCTTGACCAA 18 112 0 TAAAAACCAC 0.973107 -59 ATTTTTATTATGTAAAATCCAGCCTATTGA 23 8 0 TTAAAACCAC 0.955226 -51 ATTTTACATAATAAAAATCCAGCCCATAAAAAA 23 23 1 AAAAAACCAC 0.85084 -36 GGTATTTTCCTATAAAAGCCATTTAGCAAACGT 29 72 1 TTAAAACCAT 0.886857 -89 TTAAATTTACGAAAAAAACAACCGCACTTTAAA 30 36 0 GAAAAACAAC 0.728971 -34 * ***** *** * Masking position 7 Map Score: 7.1737 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 133 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 10 AAAATTTTTCATTATTTTAGCCATTATCAC 1 36 1 ATTATTTTAG 0.658772 -157 TCACGACTAGGTTATTTCACGATTAGG 3 8 0 GTTATTTCAC 0.935105 -125 CTCAAGCAATGTTATTTCACGACTAGGTTA 3 24 0 GTTATTTCAC 0.935105 -109 TGTTTATCTTGTTATTTCATATAAGGATTA 7 63 1 GTTATTTCAT 0.767465 -54 TCTTGATCGTTTTATTTAAGTGTTTTTGCT 12 73 0 TTTATTTAAG 0.592024 -72 TAAAATTTAAGTTATTTCAGATTATTCAAA 16 28 0 GTTATTTCAG 0.923659 -160 TGAATATTTTGTTATTTTCCTAATCTTGAC 21 97 0 GTTATTTTCC 0.6775 -32 CCTTCCTCATATTATTTAAGGAAAAACG 22 32 1 ATTATTTAAG 0.503151 -18 AAATAATTTATTTATTTTACATTTATTGAC 26 91 1 TTTATTTTAC 0.767399 -85 ATTATGAAACGTAATTTTACTATATAAAAT 26 142 1 GTAATTTTAC 0.585892 -34 AAACGGCTCAGTTATTTAAGCTGGTTTTGT 28 170 0 GTTATTTAAG 0.854116 -131 TTTTAAAGGTGTTATTTTACTTCGCTACAT 28 255 0 GTTATTTTAC 0.929791 -46 CTTCAGTCATTTTATTTTATCAAGAAAGAT 31 77 0 TTTATTTTAT 0.430084 -62 ********** Masking position 4 Map Score: 4.32999 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 78 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 11 TTCAAGGAAAAGATTATAACAAAATCTGAG 1 109 0 AGATTATAAC 0.933846 -84 AAATTGGGCGAGATTATAGCAAAAAATCGC 8 105 0 AGATTATAGC 0.789445 -46 TTAATATTATAACTTAGAGATCA 12 4 1 ATATTATAAC 0.846575 -141 TAAGATTTATAGATTATAACAAGGAAAAAG 20 13 0 AGATTATAAC 0.933846 -195 CACCTCCAATTGATTATCACAAATGTGATT 25 50 0 TGATTATCAC 0.891267 -22 ACAATATGAAATATTATCACAAGAAAATAG 26 14 1 ATATTATCAC 0.897459 -162 AACCAACTTTTTATTATCACCGCAGTTTTG 32 26 0 TTATTATCAC 0.762134 -249 CTCTAATGGCAGATTATCAGAATGAGATCT 34 156 0 AGATTATCAG 0.787496 -78 ********** Masking position 6 Map Score: 2.29471 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 35 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 12 AAGTGTAATTTTTAACAGGCGTTTTTCTCA 3 50 0 TTTAACAGGC 0.956725 -83 TGGTTCGGTTTTTAACTGGCTCCAATGCTA 17 63 0 TTTAACTGGC 0.969399 -39 TAAAACCCGATATAACTGGCAAAAAAGTAA 28 140 1 TATAACTGGC 0.956725 -161 GCACCGATTTTTTATCTGGCTAATATGTAG 28 231 1 TTTATCTGGC 0.956725 -70 ACATCTTACATATATCAGGCAAACGTTTGC 29 97 0 TATATCAGGC 0.915021 -64 ********** Masking position 4 Map Score: 1.77287 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 37 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 13 ACTTTTCCAAATTGAAAACTTGTTAATAAC 2 93 1 ATTGAAAACT 0.858034 -23 ACACTTGTTTATTAAATACTCTCGTAATAA 3 74 1 ATTAAATACT 0.634419 -59 TAAAATTAAAATTGAAAACTTTTCGTATTA 5 56 0 ATTGAAAACT 0.858034 -46 AAAAACGAAGATAGAATACTGGTTTTAGCG 9 55 0 ATAGAATACT 0.548571 -41 GGATGTCAATATAAAAAAATGTTAAGTAGA 11 103 0 ATAAAAAAAT 0.594424 -70 CCATAATAAAAATAAAAACTAAGTCGCCCT 16 149 0 AATAAAAACT 0.477906 -39 ATTTTGAGCAATAAAAAACTGTGTACTAGA 17 31 0 ATAAAAAACT 0.920533 -71 GAACTAAATCATAAAAAATTTTGCTTATTT 20 98 1 ATAAAAAATT 0.594424 -110 GTTTACATTGATAAAAAACAGGAGTCAAA 20 189 1 ATAAAAAACA 0.552115 -19 AATCCAGCCCATAAAAAACTAAGGAGAATA 23 38 1 ATAAAAAACT 0.920533 -21 AATTTTGACTATTGAAAAATAAAG 27 5 0 ATTGAAAAAT 0.433334 -202 ACTTTTGGAAATCAAAAACGGCTCAGTTAT 28 185 0 ATCAAAAACG 0.471755 -116 CAATTTTCTAATTAAAAACGTGGCGTAGAA 29 131 0 ATTAAAAACG 0.743747 -30 ACTTCTTTTTATAAAAAATTTGCAATAAAG 32 198 1 ATAAAAAATT 0.594424 -77 TCAACGTATTATGAAAAACTAAAAGGAAAT 34 213 1 ATGAAAAACT 0.754705 -21 ********** Masking position 5 Map Score: 2.96473 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 129 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 14 TGTGTTATTAACAAGTTTTCAATT 2 102 0 TTATTAACAA 0.645779 -14 CGCCCAATTTTTATTTACAAAAGAATGAGA 8 125 1 TTATTTACAA 0.944571 -26 CTATCTTCGTTTTTTTATAATAAAGAAGTA 9 71 1 TTTTTTATAA 0.678084 -25 TAAGTGCCACCTATTTATAAGCAAAAACAC 12 54 1 CTATTTATAA 0.628482 -91 TTGTGCATATTTATTCATAAAGCAATATTC 13 79 0 TTATTCATAA 0.828328 -56 TTATTTCAGATTATTCAAAAAACAATTTCT 16 17 0 TTATTCAAAA 0.641653 -171 GCCATTATTTATAATAAAAATGTC 18 5 1 TTATTTATAA 0.9003 -166 GATGGCTTTTTTATTTACAAAGGTTTACAC 18 122 1 TTATTTACAA 0.944571 -49 TTATCGTAAATTATTTATGATCAAAATATA 20 41 0 TTATTTATGA 0.628456 -167 AGATCACGGTTTATTTACAATAATTTAGTA 20 144 1 TTATTTACAA 0.944571 -64 AATAAATAAATTATTTATAAATCAATATGT 26 77 0 TTATTTATAA 0.9003 -99 TTACGTTTCATAATTTACAAAAATAAGAAA 26 126 0 TAATTTACAA 0.61231 -50 TTATTGCAAATTTTTTATAAAAAGAAGTGA 32 196 0 TTTTTTATAA 0.678084 -79 CTTTTCTTGATTATTTTCAAAATTTCTCTG 33 82 1 TTATTTTCAA 0.612311 -101 ACTCCAAAATTTATTCAAAAATAAGCGATA 34 83 1 TTATTCAAAA 0.641653 -151 ********** Masking position 10 Map Score: 9.14264 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 100 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 15 GTAATTGTAGCTTTTTAGCTCAAGATAATC 10 41 1 CTTTTTAGCT 0.706725 -125 TTTTGTTTCTCCATAGTTGATAAAATTA 10 148 0 CTCCATAGTT 0.878531 -18 CTTTTATCTCCTTAGTTTGCATTTATT 15 61 0 CTCCTTAGTT 0.967015 -17 AATCGACTCCTTAACTGATTGGTTCG 17 86 0 CTCCTTAACT 0.877023 -16 GTCAGTCTCCCTCTTTAGCTTTAGCAAAGA 19 15 1 CTCTTTAGCT 0.939674 -23 ATATTCTCCTTAGTTTTTTATGGGC 23 44 0 CTCCTTAGTT 0.967015 -15 ********** Masking position 6 Map Score: 0.669825 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 7 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493