AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00252_hinf_reg_300.orf -o00252_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 Purged sequences: HI0535 74 urease accessory protein (ureH) Input sequences: #1 HI0317 218 aspartyl-tRNA synthetase (aspS) #2 HI0534 177 aspartate ammonia-lyase (aspA) #3 HI0536 102 urease accessory protein (ureG) #4 HI0537 107 urease accessory protein (ureF) #5 HI0538 127 urease accessory protein (ureE) #6 HI0540 75 urease, beta subunit (ureB) #7 HI0541 162 urease, gamma subunit (ureA) #8 HI0564 153 aspartate--ammonia ligase (asnA) #9 HI0638 128 conserved hypothetical protein #10 HI0639 22 adenylosuccinate lyase (purB) #11 HI0675 110 aminoacyl-histidine dipeptidase (pepD) #12 HI0745 225 L-asparaginase II (ansB) #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 HI1302 147 asparaginyl-tRNA synthetase (asnS) #22 HI1573 300 pyruvate kinase, type II (pykA) #23 HI1574 33 replicative DNA helicase (dnaB) #24 HI1615 160 phosphoribosylaminoimidazole carboxylase, catalytic subunit (purE) #25 HI1616 69 phosphoribosylaminoimidazole carboxylase, ATPase subunit (purK) #26 HI1617 138 aspartate aminotransferase (aspC) #27 HI1632 300 H. influenzae predicted coding region HI1632 #28 HI1633 128 adenylosuccinate synthetase (purA) #29 HI1723 135 conserved hypothetical protein #30 HI1726 124 phosphoribosylaminoimidazole-succinocarboxamide synthase (purC) #31 HI1727 155 argininosuccinate synthetase (argG) Motif number 1 ACCGCTCTTTAACGGATTTA 4 1 1 ACCGCTCTTT 0.986994 -107 TTATATAGAAACCGCACTTACAAATTATTA 7 26 0 ACCGCACTTA 0.989491 -137 CTCAAGTATAACCGCACTTGGGTTATCTTT 12 46 1 ACCGCACTTG 0.992885 -180 TTAAATTTTAACCGCACTTCTCAAATAGCG 16 48 1 ACCGCACTTC 0.996121 -140 CCAAAATAAAACCGCACTTCACGACGCTAT 16 72 0 ACCGCACTTC 0.996121 -116 TTTAGATCTGACCGCACTTTTAAAGTGCGG 25 18 1 ACCGCACTTT 0.998328 -52 GAAAAAAACAACCGCACTTTAAAAGTGCGG 25 29 0 ACCGCACTTT 0.998328 -41 GTAAAAAATGACCGCACTTTTTGATGAATA 26 12 1 ACCGCACTTT 0.998328 -127 ATAAAAATTAACCACGCTTTGATATTTTTA 26 44 0 ACCACGCTTT 0.939858 -95 GTGATTTTTCACCGCACTTTAGGTTTAAAT 28 12 0 ACCGCACTTT 0.998328 -117 GTGAAAAATCACCACACTTTTTCTTTTATA 28 30 1 ACCACACTTT 0.988093 -99 ATAGAGTATAACCGCACTTTTCCTCTTTGT 31 75 0 ACCGCACTTT 0.998328 -81 ********** Masking position 1 Map Score: 39.4425 Number of sites scoring better than the average of aligned sites = 1218 Number in coding regions = 781 Number in noncoding regions = 437 Number of orfs with sites within 600 bp upstream = 292 Fraction of orfs with sites within 600 bp upstream = 0.0469001 Motif number 2 ACAAGCGGCATAATATAACAAAAAATCTGATGATA 1 40 1 TAAAAAAAAA 0.804694 -179 AAAATCTGATGATATGGCACAAAAAAGCCTTTATT 1 61 1 GATTCAAAAA 0.77595 -158 AAAAGTAATAAATATTCAAAATAAAGGCTTTTTTG 1 80 0 AATTAATAAA 0.745224 -139 TTTATGCTGACAAATCAATCAAAAAAGCAAAGAAA 1 112 0 CAATAAAAAA 0.474587 -107 GTACTCTTTTAATTATGCTCAAAAATCTGTCGCAA 1 181 0 AATACAAAAA 0.79691 -38 AGATAGAACATTTTTCCCTAAAAAAACTAATCCGA 2 49 1 TTTTCAAAAA 0.764511 -129 ATTATAGAAATTTCAAGAAGAAAAAACTTGATGAA 2 127 0 TTTAAAAAAA 0.787847 -51 TTGAAATTTCTATAATGACGATAAATTAACTAACC 2 146 1 TATAAATAAA 0.769133 -32 GACGATAAATTAACTAACCCAAAAAG 2 162 1 TAATCAAAAA 0.819631 -16 CTACAAGTAAAATCTCAATAAAAAATAACCGCAC 3 10 0 AATTAAAAAA 0.887829 -93 AAAGTCAGCGAATTTTACGTAAAAAATCTAAAATA 7 112 0 AATTCAAAAA 0.854069 -51 TTATTTACTGAATAATACTCAAAAATATTACTCCT 8 109 1 AATACAAAAA 0.79691 -45 AATATTGACGAAATAATAGCATAAAACGCCATTTC 11 66 0 AAAAAATAAA 0.472657 -45 ATTTCGTCAATATTTTCAGTAAAAAGGAGCAATT 11 87 1 TATTAAAAAA 0.930428 -24 GCACTTGGGTTATCTTTCAAAAAAATTATGCTTAA 12 59 1 TATTCAAAAA 0.908611 -167 AAGGTTATACAATCAACAAAAAAAATTATGTGATC 12 110 1 AATAAAAAAA 0.841435 -116 AGATTTCTCCTAAGATGAATAAAAATTTCTCCAAA 12 201 0 TAAAAAAAAA 0.804694 -25 AGCAATATTCTATATTAATAATAAAACAAAAATGG 13 54 0 TATTAATAAA 0.832354 -81 ATAGAATAATTAATTAAAACAAAAAGGAAAAATT 13 111 1 TAATAAAAAA 0.860047 -24 CTTTTTGCCAAAACTCCAAAATAAAACCGCACTTC 16 82 0 AAATAATAAA 0.572076 -106 TTGTTACCCATAATAAAAATAAAAACTAAGTCGCC 16 151 0 TAAAAAAAAA 0.804694 -37 ATGCTAACATTTTGAGCAATAAAAAACTGTGTACT 17 34 0 TTTAAAAAAA 0.787847 -68 GCCATTATTTATAATAAAAATGTCATTACA 18 6 1 TATTAAAAAA 0.930428 -165 AGTGTAAACCTTTGTAAATAAAAAAGCCATCGCTT 18 118 0 TTTTAAAAAA 0.84664 -53 ATTTATAGATTATAACAAGGAAAAAGTT 20 4 0 TATAAAAAAA 0.900147 -204 ATAAATCTTATATTTTGATCATAAATAATTTACGA 20 33 1 TATTAATAAA 0.832158 -175 TCATAAGTATGAACTAAATCATAAAAAATTTTGCT 20 88 1 GAATAATAAA 0.441679 -120 TTTATTTACAATAATTTAGTATAAATTAATGTAAT 20 153 1 ATATAATAAA 0.355136 -55 GTTGGTGCGGGTTATGAACAATAAAATCGCCTTAA 21 69 0 GTTTAATAAA 0.416181 -79 TAATGAAGGAAATTTTCCATAAAAATATAGTGTTG 21 100 0 AATTCAAAAA 0.854069 -48 CTTCGCTACATATTAGCCAGATAAAAAATCGGTGC 22 231 0 TATACATAAA 0.711271 -70 TATTTCTCGTTAAATTTACGAAAAAAACAACCGCA 25 43 0 TAATAAAAAA 0.860049 -27 GATATTTTTAAATATTCATCAAAAAGTGCGGTCAT 26 19 0 AATTAAAAAA 0.887828 -120 CGTCAAATACTTTTTTACAAAAAAAGTAATTTTAT 27 61 1 TTTTCAAAAA 0.764511 -240 ATAAGTTGTTTAAATGAATAAAAAATAAGTGATAT 27 119 0 TAATAAAAAA 0.860049 -182 TAATTAAAATTTATTTGACAAAAAATGCCTAAATC 27 225 1 TTATAAAAAA 0.716571 -76 TAATCTCAATGATATAAAAGAAAAAGTGTGGTGAT 28 37 0 GATTAAAAAA 0.824055 -92 TATCATTGAGATTAAAGCCGAAAAAGAGTAAAGTA 28 58 1 ATTACAAAAA 0.617802 -71 CATTTAACTAATTTAACCGAATAAAAGGCGGAAAT 28 103 1 ATTACATAAA 0.373971 -26 ATTATAGCACGATTTCTAGGAAAAAACTGGATTGC 29 44 1 GATTAAAAAA 0.824054 -92 GCTATTTTTTAAAAAGAAATAAAAATCCTCTGAAA 30 74 0 AAAAAAAAAA 0.708057 -51 TTTTAAATCAAATAAAGCAAACGTTT 30 109 0 TTTACATAAA 0.503609 -16 TTTATTTAGCTTTGTGCATAAAAAATCCTAATTT 31 10 0 TTTTAAAAAA 0.84664 -146 GTGTTTTGTGCATTAAAAGCAAAAATCTTTATTTA 31 37 0 CATAAAAAAA 0.569898 -119 TCTATAGAATTTTTATTCACAAAAATCGATTATTT 31 100 1 TTTACAAAAA 0.732777 -56 *** * * ***** Masking position 11 Map Score: 40.6633 Number of sites scoring better than the average of aligned sites = 1285 Number in coding regions = 784 Number in noncoding regions = 501 Number of orfs with sites within 600 bp upstream = 387 Fraction of orfs with sites within 600 bp upstream = 0.0621587 Motif number 3 CTAAATCCGTTAAAGAGCGGT 4 2 0 TAAAGAGCGG 0.944707 -106 TTAATAATTTGTAAGTGCGGTTTCTATATA 7 25 1 GTAAGTGCGG 0.936656 -138 GAAAGATAACCCAAGTGCGGTTATACTTGA 12 47 0 CCAAGTGCGG 0.956362 -179 ACGCTATTTGAGAAGTGCGGTTAAAATTTA 16 49 0 AGAAGTGCGG 0.991016 -139 AATAGCGTCGTGAAGTGCGGTTTTATTTTG 16 71 1 TGAAGTGCGG 0.985665 -117 ACCGCACTTTAAAAGTGCGGTCAGATCTAA 25 19 0 AAAAGTGCGG 0.994893 -51 ATATTCATCAAAAAGTGCGGTCATTTTTTA 26 13 0 AAAAGTGCGG 0.994893 -126 AATTTAAACCTAAAGTGCGGTGAAAAATCA 28 11 1 TAAAGTGCGG 0.991832 -118 ATATAAAAGAAAAAGTGTGGTGATTTTTCA 28 31 0 AAAAGTGTGG 0.944501 -98 GACAAAGAGGAAAAGTGCGGTTATACTCTA 31 74 1 AAAAGTGCGG 0.994893 -82 ********** Masking position 4 Map Score: 19.5163 Number of sites scoring better than the average of aligned sites = 1355 Number in coding regions = 886 Number in noncoding regions = 469 Number of orfs with sites within 600 bp upstream = 303 Fraction of orfs with sites within 600 bp upstream = 0.0486669 Motif number 4 TGTTGAGATTAAATTACGTTAAGGATAACCAC 1 10 0 AAATTATAAG 0.631727 -209 TTTCTTCTTGAAATTTCTATAATGACGATAAAT 2 139 1 AAATTTTAAT 0.575012 -39 TAAAAAATCTAAAATAGGAAAAATATTTTGTCA 7 95 0 AAAATAAAAA 0.8318 -68 CATTGTGAAAAAATTAAATAAAATCTAAAGGAG 8 19 0 AAATTAAAAA 0.864577 -135 CCAAGAAAAGAAAGTAAATAAAATACTTGAAAT 8 69 1 AAAGTAAAAA 0.714001 -85 CGAGAAATAAAAAATTGCGTAAGGATAACCCGA 11 35 1 AAAATTTAAG 0.369446 -76 TAATACAAATAAAATGGACAAAATGAAAGATTT 13 18 1 AAAATGAAAA 0.777294 -117 TAATAAAACAAAAATGGACAAAATCTTTCATTT 13 38 0 AAAATGAAAA 0.777294 -97 CATATTTTTGAAATTTATAAAAAGGCTTTTTGC 16 109 0 AAATTTAAAA 0.737887 -79 ATAAATTTCAAAAATATGCAAAAATAGGGCGAC 16 124 1 AAAATAAAAA 0.8318 -64 TAAAAATGTTTAAATTGTGATCTAG 17 3 1 AAAATGAAAT 0.694256 -99 TTGACCAATTAAATTAGATTAAGAGGCTGGTGG 18 87 0 AAATTATAAG 0.631727 -84 AGTAAATTTGAAATTAGTGTAAACCTTTGTAAA 18 135 0 AAATTATAAA 0.825061 -36 ACAAAATAAGAAAATAAGCAAAATTTTTTATGA 20 106 0 AAAATAAAAA 0.8318 -102 AATTTATACTAAATTATTGTAAATAAACCGTGA 20 147 0 AAATTATAAA 0.825061 -61 AATTTAGTATAAATTAATGTAATCGTTTACATT 20 165 1 AAATTATAAT 0.754202 -43 AGTCCTAAATAAAATAGGGTAAAGCCTTATTAA 21 31 0 AAAATATAAA 0.785097 -117 AACTGGCAAAAAAGTAAACAAAACCAGCTTAAA 22 153 1 AAAGTAAAAA 0.714001 -148 TAACACCTTTAAAATTTTGTAATTATTGACGGA 22 271 1 AAAATTTAAT 0.51173 -30 TTTAATTAGAAAATTGAGAAAATAGC 24 145 1 AAATTGAAAT 0.745641 -16 ATTTCTCGTTAAATTTACGAAAAAAACAACCGC 25 44 0 AAATTTAAAA 0.737887 -26 AGGATCATCAAAATTAGCATAATACGCCCCGCA 27 28 0 AAATTATAAT 0.754202 -273 TATTTGACAAAAAATGCCTAAATCGTTATTTCT 27 236 1 AAAATGAAAT 0.694256 -65 TTATTCGGTTAAATTAGTTAAATGAACAGCCGT 28 94 0 AAATTAAAAT 0.80596 -35 TTTTTTCAAAAAAGTGAGATAAAA 29 2 0 AAAGTGTAAA 0.565521 -134 TTATTATTGGAAATTTAGTAAATCCTACGGCTT 30 13 0 AAATTTAAAT 0.646833 -112 ****** **** Masking position 5 Map Score: 19.6911 Number of sites scoring better than the average of aligned sites = 1101 Number in coding regions = 763 Number in noncoding regions = 338 Number of orfs with sites within 600 bp upstream = 294 Fraction of orfs with sites within 600 bp upstream = 0.0472213 Motif number 5 AGATAGAACATTTTTCCCTAAAAAAACTAATC 2 49 1 TTTTCCTAAA 0.768308 -129 TGAAGATCACATTTTCAAAAAATGCTCTCAAG 2 99 0 ATTTAAAAAA 0.862368 -79 CTTACAAAAAATTCTGACAAAATATTTTTCCT 7 81 1 ATTTACAAAA 0.73878 -82 CATCTAATTCATTGTGAAAAAATTAAATAAAA 8 29 0 ATTTAAAAAA 0.861892 -125 TTTCAAAAAAATTATGCTTAAATTCCGTACTT 12 73 1 ATTTCTTAAA 0.804939 -153 TTGTTTTTCCATTGTTTATAAATAACTTAATT 12 157 1 ATTTTATAAA 0.522883 -69 ATTGTGCATATTTATTCATAAAGCAATATTCT 13 78 0 TTTTCATAAA 0.501385 -57 GTTATTTCAGATTATTCAAAAAACAATTTCTT 16 16 0 ATTTCAAAAA 0.846095 -172 ATAAAAAGGCTTTTTGCCAAAACTCCAAAATA 16 94 0 TTTTCCAAAA 0.713103 -94 GCCATTATTTATAATAAAAATGTCATTAC 18 8 1 TTTTATAAAA 0.714515 -163 AGTGTAAACCTTTGTAAATAAAAAAGCCATCG 18 121 0 TTTTAATAAA 0.827182 -50 AACCGTGATCTTTGTCACAAAATAAGAAAATA 20 123 0 TTTTACAAAA 0.708697 -85 ATACTAAATTATTGTAAATAAACCGTGATCTT 20 143 0 ATTTAATAAA 0.863431 -65 AATGAAGGAAATTTTCCATAAAAATATAGTGT 21 102 0 ATTTCATAAA 0.895452 -46 GAACACAAGTATTTTTCTTAAAACCCGATATA 22 122 1 ATTTCTTAAA 0.805165 -179 AATTTGACCTATTCTTATAAAAATTGTGCTTA 24 11 1 ATTTATAAAA 0.751505 -150 AGGATAAAATTTTATCCTTAAAGTTGCAATGG 24 42 1 TTTTCTTAAA 0.77996 -119 TTTTCTCAATTTTCTAATTAAAAACGTGGCGT 24 135 0 TTTTATTAAA 0.722169 -26 AGCGTGGTTAATTTTTATAAAATCTTTCTTGA 26 56 1 ATTTATAAAA 0.75095 -83 GTCAAATACTTTTTTACAAAAAAAGTAATTTT 27 62 1 TTTTCAAAAA 0.605614 -239 ATAAATTTTAATTACAATAAATGAACGCATA 27 207 0 ATTAATAAA 0.0693501 -94 TATACCCACTATTCTAAAAAAACACAACATCT 27 268 1 ATTTAAAAAA 0.863431 -33 TCTCGTAAAGTTTTTTCAAAAAAGTGAGATAA 29 13 0 TTTTCAAAAA 0.501385 -123 AACGTTTGCTATTTTTTAAAAAGAAATAAAAA 30 84 0 ATTTTAAAAA 0.495333 -41 TTTATTTAGCTTTGTGCATAAAAAATCCTAAT 31 13 0 TTTTCATAAA 0.770042 -143 ATAATCGATTTTTGTGAATAAAAATTCTATAG 31 101 0 TTTTAATAAA 0.738359 -55 *** * ****** Masking position 5 Map Score: 32.3862 Number of sites scoring better than the average of aligned sites = 647 Number in coding regions = 429 Number in noncoding regions = 218 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987 Motif number 6 ATATGGCACAAAAAAGCCTTTATTTTGAATAT 1 72 1 AAAACCTTTA 0.764795 -147 TTGTCAGCATAAATAACCTTTTTATCTCTCTT 1 134 1 AATACCTTTT 0.615684 -85 TTAAAAGAGTACAAAGGATTTTGAA 1 204 1 ACAAGATTTT 0.801849 -15 GTTTCTATATAAGGAGGATTTTTTTTCTTTCA 7 44 1 AAGAGATTTT 0.81407 -119 TTATTCAGTAAATAATGATTTTATTTCAAGTA 8 92 0 AAAAGATTTT 0.965224 -62 AATGGACAAAATGAAAGATTTTGTCCATTTTT 13 30 1 ATAAGATTTT 0.732062 -105 TGAAATTTATAAAAAGGCTTTTTGCCAAAACT 16 102 0 AAAAGCTTTT 0.951998 -86 TATTATGGGTAACAAGGATTCTTTTTA 16 171 1 AAAAGATTCT 0.790199 -17 ATTCAATATTAATAAGGCTTTACCCTATTTTA 21 23 1 AAAAGCTTTA 0.896784 -125 TTATTTTATCAAGAAAGATTTTATAAAAATTA 26 64 0 AAAAGATTTT 0.965224 -75 TGGGTATAGAAATAACGATTTAGGCATTTTTT 27 244 0 AAAAGATTTA 0.913629 -57 GCCATTATCTAATAACCCTTTACTCCATTCAA 29 81 0 AAAACCTTTA 0.764888 -55 AATTTCCAATAATAAACATTTTCCCCCTATAC 30 31 1 AAAACATTTT 0.912233 -94 AAATTAGGATTTTTTATGCACAA 31 2 1 AATAGATTTT 0.838948 -154 CACAAAGCTAAATAAAGATTTTTGCTTTTAAT 31 29 1 AAAAGATTTT 0.965224 -127 ** ** ****** Masking position 5 Map Score: 10.422 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 114 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 7 ATTTTACTTGTAGGGGCAAATCACATTTGCC 3 32 1 TAGGGCAAAT 0.951656 -71 CGTTGATATATAGGGGCAAATGTAACTTGCC 3 73 1 TAGGGCAAAT 0.951656 -30 GGGTGTAGGGGCAAGTTACATTTGCC 3 87 0 TAGGGCAAGT 0.917675 -16 ACAAATTATTAAGAAGGAAATTAATC 7 6 0 AAGAGGAAAT 0.776733 -157 GTTTCTATATAAGGAGGATTTTTTTTCTTTC 7 44 1 AAGGGGATTT 0.726332 -119 ATAAAATCTAAAGGAGGAAGTTTT 8 4 0 AAGGGGAAGT 0.957535 -150 AATTTAAACTAAGGTGCAATT 11 1 0 AAGGGCAATT 0.945986 -110 TTTCAGTAAAAAGGAGCAATT 11 100 1 AAGGGCAATT 0.945986 -11 AACCGAATAAAAGGCGGAAATT 28 117 1 AAGGGGAAAT 0.975502 -12 AATTTTAGGAAAGTAGGAAATAGTT 29 121 1 AAGTGGAAAT 0.776733 -15 AGGGGAAGTATAGGGGGAAAATGTTTATTAT 30 39 0 TAGGGGAAAA 0.748942 -86 **** ****** Masking position 8 Map Score: 8.82642 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 64 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 TTTTTATTGAGATTTTACTTGTAGGGGCAA 3 21 1 GATTTTACTT 0.706084 -82 GCTACAATGATTTCTTATTTATCAAGTAAG 5 62 0 TTTCTTATTT 0.571294 -66 TGTAGCTGTAGTTTTTCTTTCGAAGAGAAG 5 86 1 GTTTTTCTTT 0.827871 -42 CACCATTGATATTTTTATTTTGTGGGCTAA 6 25 0 ATTTTTATTT 0.618791 -51 AAGGAGGATTTTTTTTCTTTCAAGGGGCTT 7 54 1 TTTTTTCTTT 0.8226 -109 TCCTCCTTTAGATTTTATTTAATTTTTTCA 8 17 1 GATTTTATTT 0.871559 -137 TTATTTCAAGTATTTTATTTACTTTCTTTT 8 74 0 TATTTTATTT 0.867411 -80 AGTAAATAATGATTTTATTTCAAGTATTTT 8 88 0 GATTTTATTT 0.871559 -66 CCTTACGCAATTTTTTATTTCTCGATAAAT 11 29 0 TTTTTTATTT 0.888237 -82 TCATTTTGTCCATTTTATTTGTATTAGTGC 13 14 0 CATTTTATTT 0.750662 -121 CGTGAAGTGCGGTTTTATTTTGGAGTTTTG 16 79 1 GGTTTTATTT 0.585945 -109 GGGCGACTTAGTTTTTATTTTTATTATGGG 16 150 1 GTTTTTATTT 0.891815 -38 AAGCGATGGCTTTTTTATTTACAAAGGTTT 18 118 1 TTTTTTATTT 0.888237 -53 TTTTGCTTATTTTCTTATTTTGTGACAAAG 20 116 1 TTTCTTATTT 0.571294 -92 GGCTTTACCCTATTTTATTTAGGACTCATT 21 38 1 TATTTTATTT 0.867411 -110 TTAAAGGTGTTATTTTACTTCGCTACATAT 22 253 0 TATTTTACTT 0.698442 -48 CGCTCTTTTATTTTAACATATTT 23 21 0 TCTTTTATTT 0.715169 -13 ATACTTCAGTCATTTTATTTTATCAAGAAA 26 80 0 CATTTTATTT 0.750662 -59 AGCTTTTCCTTATGTATGTGT 26 128 0 GCTTTTCCTT 0.349782 -11 CCTAATCCTATTTTTTCTTTTATGCGTTCA 27 187 1 TTTTTTCTTT 0.8226 -114 AATCACCACACTTTTTCTTTTATATCATTG 28 36 1 CTTTTTCTTT 0.680907 -93 ATTTCAGAGGATTTTTATTTCTTTTTAAAA 30 73 1 ATTTTTATTT 0.618791 -52 ATATTTTCCTTACTAATAATT 31 145 0 TATTTTCCTT 0.574708 -11 ********** Masking position 5 Map Score: 22.0511 Number of sites scoring better than the average of aligned sites = 595 Number in coding regions = 386 Number in noncoding regions = 209 Number of orfs with sites within 600 bp upstream = 176 Fraction of orfs with sites within 600 bp upstream = 0.0282686 Motif number 9 AATATCAGGAAAACGTTTCCGTTAAATATA 9 104 0 AAACGTTTCC 0.885802 -25 AAATGTTTGCTCCAGAATTG 10 13 0 AAATGTTTGC 0.92586 -10 TTATTGCTCAAAATGTTAGCATTGGAGCCA 17 47 1 AAATGTTAGC 0.880425 -55 TAAATCATAAAAAATTTTGCTTATTTTCTT 20 102 1 AAAATTTTGC 0.618293 -106 TATACGCTTAAAACTTTTGGAAATCAAAAA 22 197 0 AAACTTTTGG 0.859189 -104 GCCATTTAGCAAACGTTTGCCTGATATATG 24 89 1 AAACGTTTGC 0.952187 -72 CTCAACAGCCAAATTTTTCCTAATCCTATT 27 169 1 AAATTTTTCC 0.718893 -132 TTTTTTGAAAAAACTTTACGAGATTATAGC 29 22 1 AAACTTTACG 0.583552 -114 GGCGGGATTGAAATTTTAGGAAAGTAGGAA 29 110 1 AAATTTTAGG 0.692871 -26 AAATCCTCTGAAATGTTAGGGGAAGTATAG 30 57 0 AAATGTTAGG 0.810992 -68 AAAAAATAGCAAACGTTTGCTTTATTTGAT 30 99 1 AAACGTTTGC 0.952187 -26 ********** Masking position 3 Map Score: 6.04479 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 130 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 10 AAATGTTCTATCTATCAATCTTACACAGAT 2 32 0 TCTATCAATC 0.943748 -146 TACATTTGCCCCTATATATCAACGAATGTT 3 67 0 CCTATATATC 0.862071 -36 CTTTCCTCTATAAATCCACTTTCTTC 5 112 0 TCTATAAATC 0.961437 -16 TATTAGATATCCTATCAATCAAGGAACGGT 15 35 0 CCTATCAATC 0.952963 -43 CATTACAAGATCTATAAATCAGGTTCATTT 18 34 1 TCTATAAATC 0.961437 -137 CTTGTTATAATCTATAAATCTTATATTTTG 20 20 1 TCTATAAATC 0.961437 -188 CCAGTTTTTTCCTAGAAATCGTGCTATAAT 29 44 0 CCTAGAAATC 0.902573 -92 ********** Masking position 4 Map Score: 5.99666 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 5 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 11 GAAAATTGGTAGGCTATTGAAATCT 2 6 1 TTGGTAGGCT 0.910292 -172 CCGTAGGGTGGGCTTTAGCCCACA 6 5 1 AGGGTGGGCT 0.987937 -71 ATATTTTTATTTTGTGGGCTAAAGCCCACC 6 17 0 TTTGTGGGCT 0.910292 -59 AAAAATATCAATGGTGGGCTAAAGCCCACC 6 39 1 ATGGTGGGCT 0.986992 -37 TGTTCCTTGTAGGGTGGGCTTTAGCCCACC 6 51 0 AGGGTGGGCT 0.987937 -25 ********** Masking position 5 Map Score: 3.41605 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 18 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 12 CCATTGGAATGGTTAAATCCACCAATCGGT 4 63 0 GGTTAAATCC 0.928602 -45 TTATTTTGTGGGCTAAAGCCCACCCTACGG 6 11 0 GGCTAAAGCC 0.782083 -65 ATCAATGGTGGGCTAAAGCCCACCCTACAA 6 45 1 GGCTAAAGCC 0.782083 -31 AAATAAAATAGGGTAAAGCCTTATTAATAT 21 28 0 GGGTAAAGCC 0.96736 -120 ATATCATTGAGATTAAAGCCGAAAAAGAGT 28 57 1 GATTAAAGCC 0.929371 -72 ********** Masking position 5 Map Score: 3.22306 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 13 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 13 GATTTTTTGTTATATTATGCCGCTTGTTGAGA 1 35 0 TATATTATCG 0.737881 -184 TTGGTTTTCCGCTATAATTGCGACAGATTTTT 1 164 1 GCTATAATCG 0.971531 -55 TCTTGAAATTTCTATAATGACGATAAATTAAC 2 144 1 TCTATAATCG 0.965823 -34 GGCGTTTTATGCTATTATTTCGTCAATATTTT 11 71 1 GCTATTATCG 0.963246 -40 AATTAATTATTCTATTATTGTGCATATTTATT 13 94 0 TCTATTATTG 0.737881 -41 GTTAAAAATATCTATAATCACGACTACTTCAC 22 88 0 TCTATAATCG 0.965823 -213 TAGAAATCGTGCTATAATCTCGTAAAGTTTTT 29 30 0 GCTATAATCG 0.971531 -106 ******** ** Masking position 7 Map Score: 3.02378 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 10 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 14 TAAATTACGTTAAGGATAACCAC 1 4 0 TAAGGATAAC 0.750839 -215 ATTTCTATAATGACGATAAATTAACTAACC 2 151 1 TGACGATAAA 0.650336 -27 AGTTTAAATTTATCGAGAAATAAAAAATTG 11 22 1 TATCGAGAAA 0.623563 -89 AAAAATTGCGTAAGGATAACCCGAAATGGC 11 44 1 TAAGGATAAC 0.750839 -67 GTTAGACTACTTTGGAGAAATTTTTATTCA 12 191 1 TTTGGAGAAA 0.723314 -35 TTTATTCATCTTAGGAGAAATCT 12 213 1 TTAGGAGAAA 0.927538 -13 AAATGCAAACTAAGGAGATAAAAG 15 64 1 TAAGGAGATA 0.576663 -14 CATAAATAATTTACGATAAATTGAAAGCGG 20 52 1 TTACGATAAA 0.858045 -156 AAAATTGTGCTTAGGATAAAATTTTATCCT 24 30 1 TTAGGATAAA 0.905109 -131 ATTGCAACTTTAAGGATAAAATTTTATCCT 24 42 0 TAAGGATAAA 0.905109 -119 CTCGTTAAATTTACGAAAAAAACAACCGCA 25 43 0 TTACGAAAAA 0.688745 -27 TTCGTAAATTTAACGAGAAATATT 25 56 1 TAACGAGAAA 0.890249 -14 AAAAATAGGATTAGGAAAAATTTGGCTGTT 27 172 0 TTAGGAAAAA 0.777376 -129 ********** Masking position 6 Map Score: 7.12056 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 115 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 15 ********** No masking Map Score: 1.13569e-11 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0