AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -ifruR_hinf_opreg_300.orf -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HI0050 74 conserved hypothetical transmembrane protein #2 HI0051 38 conserved hypothetical transmembrane protein #3 HI0052 26 conserved hypothetical protein #4 HI0053 109 zinc-type alcohol dehydrogenase #5 HI0448 71 PTS system, fructose-specific IIA/FPr component (fruB) #6 HI0449 86 H. influenzae predicted coding region HI0449 #7 HI0451 71 conserved hypothetical protein #8 HI0452 50 conserved hypothetical protein #9 HI0453 26 conserved hypothetical protein #10 HI0454 54 conserved hypothetical protein #11 HI0457 69 conserved hypothetical protein #12 HI0458 70 stationary phase survival protein SurA, putative #13 HI0459 131 pyrimidine operon regulatory protein (pyrR) #14 HI0524 110 fructose-bisphosphate aldolase (fba) #15 HI0525 101 phosphoglycerate kinase (pgk) #16 HI0526 77 H. influenzae predicted coding region HI0526 #17 HI0809 172 phosphoenolpyruvate carboxykinase (pckA) #18 HI0810 144 conserved hypothetical protein #19 HI0811 134 argininosuccinate lyase (argH) #20 HI0812 21 glucosephosphate uridylyltransferase (galU) #21 HI0813 77 carbon storage regulator (csrA) #22 HI0814 187 alanyl-tRNA synthetase (alaS) #23 HI0815 101 universal stress protein A (uspA) #24 HI0817 170 conserved hypothetical protein #25 HI0819 37 galactokinase (galK) #26 HI0820 207 galactose-1-phosphate uridylyltransferase (galT) #27 HI0982 95 6-phosphofructokinase (pfkA) #28 HI0985 300 DNA processing chain A (dprA) #29 HI1711 59 PTS system, glucose-specific IIA component (crr) #30 HI1712 79 phosphoenolpyruvate-protein phosphotransferase (ptsI) #31 HI1713 158 phosphocarrier protein HPr (ptsH) #32 HI1714 70 conserved hypothetical protein Motif number 1 AGAAATAACAATAAGAATAAACTACACAAAATAATAGTAACA 1 21 0 ATAAAAAAAT 0.974556 -54 TAACATAATTTTGTAGAGAAATGGATAAAAATTTACCGCACT 7 12 0 TTAAAAAAAT 0.967154 -60 CTACAAAATTATGTTATAAAACCATAAAAAATTTGAGGTTAA 7 38 1 ATAAAAAAAT 0.974555 -34 TATCCAAAACATTCCATCAAAGGAAACCAAATT 13 2 0 ATAAACAAAT 0.859834 -130 AAATGCCATCATCAATACAAATTCTTCAAATTGTGGGCTTAT 14 50 1 ATAAAAAATT 0.943607 -61 CGAAGTAGGTATAATACGAAAAGTTTTCAATTTTAATTTTAA 15 45 1 ATAAACAATT 0.728262 -57 CAAAAACTTGATTGACAAAAACTAAACAAAATTT 16 54 1 ATAAAAAAAT 0.974544 -24 AGAGGTAAAGTTCTTAAAAAAATGTTTAAAAATGAGATCTAC 17 66 1 TTAAAAAAAA 0.706138 -107 GCTTATTATAATGGATGTCAATATAAAAAAATGTTAAGTAGA 17 103 0 ATCAAAAAAT 0.717284 -70 TGCCACCTATTTATAAGCAAAAACACTTAAATAAAACGATCA 18 58 1 TTAAATAAAT 0.892815 -87 ATAGCACTAATACAAATAAAATGGACAAAATGAAAGATTTT 19 10 1 ATAAAAAAAT 0.974555 -125 TATATTAATAATAAAACAAAAATGGACAAAATCTTTCATTTT 19 37 0 ATAAAAAAAT 0.974555 -98 AGAATAATTAATTAAAACAAAAAGGAAAAATT 19 113 1 ATAAAAAATT 0.943609 -22 TGTTTTTTGAATAATCTGAAATAACTTAAATTTTAACCGCAC 22 23 1 ATAAAAAATT 0.943609 -165 ATAAAAAGGCTTTTTGCCAAAACTCCAAAATAAAACCGCACT 22 84 0 TTAAAAAATA 0.512139 -104 CCTTTTTATAAATTTCAAAAATATGCAAAAATAGGGCGACTT 22 117 1 AAAAAAAAAT 0.777708 -71 TAAATTTGAAATTAGTGTAAACCTTTGTAAATAAAAAAGCCA 24 124 0 ATAAATAAAT 0.915484 -47 TCTTTGTCACAAAATAAGAAAATAAGCAAAATTTTTTATGAT 26 105 0 AAAAAAAAAT 0.889327 -103 ATTACATTAATTTATACTAAATTATTGTAAATAAACCGTGAT 26 146 0 TTAAATAAAT 0.892514 -62 CCATTTTCAATTATGGTTAAAAGTAGGTAAATT 27 73 1 TTAAATAAAT 0.892815 -23 AGGTTTATTTTTAATATAAAATGCCAAAAAATAGTTTGACAG 28 25 0 TTAAAAAAAT 0.96716 -276 AATATACATTTAACTAATAAACTTAATAAAATTAGCATATTT 28 82 1 TAAAAAAAAT 0.860699 -219 AAAATTTTTCTTATTTTGAAAATGTAAAAAATCCAATAAGAA 28 152 0 TTAAAAAAAT 0.967139 -149 ATTCTTTTTAATGAATAAAAAATTGCAAAATTTTTCTTATTT 28 178 0 ATAAAAAATT 0.943607 -123 CATACTAGATTTTCAAATAAAAAGGAAAAAAT 28 279 1 TTAAAAAAAT 0.96716 -22 TGGTTGCTATTTTAACGTAAAATCAAATAATTTTGT 29 5 0 TTAAATAATT 0.784441 -55 TTCTTACTTAGCCATAAAATTGTGAAATTTTATGGCTAT 30 8 1 TTAAAAAATT 0.927885 -72 AGCCTGAATTAAATCATAAAAATAAGCTAAATAGTTTATTTA 31 30 0 AAAAATAAAT 0.694446 -129 ATCAATAATTAAAAATATAAAACCAGAAAATTGCCCTAGTAT 31 111 0 AAAAAAAATT 0.778302 -48 TTTTCCCTTGTTTTTGGTAAAATGAAAAAAATTTTTGCATAG 32 24 0 TTAAAAAAAT 0.965121 -47 ** *** ***** Masking position 11 Map Score: 53.9592 Number of sites scoring better than the average of aligned sites = 367 Number in coding regions = 224 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 2 TTTGTTTCATCCGCAGCTTTCTTTTTAAAT 5 37 1 CCGCAGCTTT 0.947526 -35 AAGAAAACGACCGCACTTTGCGACCGTTTG 8 16 0 CCGCACTTTG 0.99215 -35 CCGCACTTTTCCTCTATAAC 14 1 1 CCGCACTTTT 0.997571 -110 GTGGTTTTTTCCGCACTTTTTGTCTTGATC 18 95 0 CCGCACTTTT 0.997571 -50 GAAAAAACCACCGCACTTTTTATCTCAATT 18 114 1 CCGCACTTTT 0.997571 -31 TAAATTTTAACCGCACTTCTCAAATAGCGT 22 49 1 CCGCACTTCT 0.995719 -139 CAAAATAAAACCGCACTTCACGACGCTATT 22 71 0 CCGCACTTCA 0.979712 -117 GAAAAAACGACCGCACTTTT 32 61 1 CCGCACTTTT 0.997571 -10 ********** Masking position 5 Map Score: 20.6388 Number of sites scoring better than the average of aligned sites = 684 Number in coding regions = 409 Number in noncoding regions = 275 Number of orfs with sites within 600 bp upstream = 213 Fraction of orfs with sites within 600 bp upstream = 0.0342114 Motif number 3 AACTTTCTCCTTATTGATTATGTTTT 3 1 0 TTATTTATTT 0.939807 -26 TTAAGCCCCTTTATTTTTGATACTTTG 11 2 0 TTATTTATTT 0.939806 -68 GCCCCTTTTGTTGTTTTTTATTTTCTCTTTCTTATA 11 40 1 TTGTTTATTT 0.819231 -30 ACCATTTTTCTTGTTCGTTATACTATCCAAAACATT 13 31 0 TTGTTTATTT 0.819231 -101 ACTTTACCTCTTTTTAGTGATATTGTGATATAGAGC 17 41 0 TTTTTTATTT 0.888928 -132 TATTTAAGTGTTTTTGCTTATAAATAGGTGGCACTT 18 55 0 TTTTTTATAA 0.907054 -90 TGATTATTCCTAATTGAGATAAAAAGTGC 18 126 0 TTATTTATAA 0.950096 -19 CATTTTTGTTTTATTATTAATATAGAATATTGCTTT 19 55 1 TTATTTATAA 0.948643 -80 TTGTGCATATTTATTCATAAAGCAATATTCTATATT 19 73 0 TTATTTAAAT 0.815586 -62 ACACAGTTTTTTATTGCTCAAAATGTTAGCATTGGA 23 37 1 TTATTTAATT 0.749092 -65 GCCATTATTTATAATAAAAATGTCATTACA 24 5 1 TTATTTATAA 0.932521 -166 TTATCGTAAATTATTTATGATCAAAATATAAGATTT 26 35 0 TTATTTATAA 0.950092 -173 ATAAGCAAAATTTTTTATGATTTAGTTCATACTTAT 26 90 0 TTTTTTATAT 0.922212 -118 TTGACTCCTGTTTTTTATCAATGTAAACGATTACAT 26 181 0 TTTTTTAATA 0.55747 -27 GTAAGTAGGTTTATTTTTAATATAAAATGCCAAAAA 28 37 0 TTATTTATAA 0.932521 -264 ATTTTGCAATTTTTTATTCATTAAAAAGAATTTTTG 28 189 1 TTTTTTATAA 0.905002 -112 AATTTTATGGCTATTGTTTATTTATTACTTTGTTAA 30 36 1 CTATTTATAT 0.699295 -44 GCTAAATAGTTTATTTATTATTCACAATCTCAATCG 31 11 0 TTATTTATAA 0.950096 -148 TTTTTAGTGTTTATTCTTGATTATTTTGCTTTGAAA 31 71 1 TTATTTATTT 0.939807 -88 TGGTTTTATATTTTTAATTATTGATTAGTCGAGGTA 31 128 1 TTTTTTATAT 0.922212 -31 ***** * ** * * Masking position 8 Map Score: 23.428 Number of sites scoring better than the average of aligned sites = 343 Number in coding regions = 206 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 4 AACTTTCTCCTTATTGATTATG 3 15 0 ATTTCTCCTT 0.744475 -12 ACTTTTCCCTTGTTAGAACTG 9 16 0 ATTTTCCCTT 0.874326 -11 AATTATTTTTCCTTATGCCTAAGG 10 41 0 TTTTTTCCTT 0.930756 -14 TGTTGTTTTTTATTTTCTCTTTCTTATAGCT 11 48 1 TTTTTCTCTT 0.432043 -22 TTTTCTTTATACTTTGTGCATTGAAATACTA 13 93 1 ATTTGTGCAT 0.818814 -39 TTTATTTAAGTGTTTTTGCTTATAAATAGGT 18 62 0 TTTTTTGCTT 0.90462 -83 AAAATCTTTCATTTTGTCCATTTTATTTGTA 19 21 0 ATTTGTCCAT 0.864953 -114 AAAATGAAAGATTTTGTCCATTTTTGTTTTA 19 37 1 ATTTGTCCAT 0.864953 -98 AATTATTCTATTATTGTGCATATTTATTCAT 19 91 0 TATTGTGCAT 0.44692 -44 AATTTTTCCTTTTTGTTTTAA 19 124 0 ATTTTTCCTT 0.960745 -11 TAAGTCGCCCTATTTTTGCATATTTTTGAAA 22 129 0 TTTTTTGCAT 0.855523 -59 AACTTTTTCCTTGTTATAATCT 26 2 1 ATTTTTCCTT 0.960745 -206 AAATCATAAAAAATTTTGCTTATTTTCTTAT 26 103 1 AATTTTGCTT 0.848994 -105 CCTAATCAACAAATTTTTCTTATTGGATTTT 28 136 1 AATTTTTCTT 0.613356 -165 TTCTTATTGGATTTTTTACATTTTCAAAATA 28 152 1 ATTTTTACAT 0.54628 -149 AAAAATTGCAAAATTTTTCTTATTTTGAAAA 28 172 0 AATTTTTCTT 0.613356 -129 TCTCTCCCTCGTTTTTTCCATACTAGATTTT 28 261 1 GTTTTTCCAT 0.690309 -40 ATTTTTTCCTTTTTATTTGAA 28 290 0 ATTTTTCCTT 0.960745 -11 TTATTCTTGATTATTTTGCTTTGAAAAAGGA 31 81 1 TATTTTGCTT 0.75537 -78 AAATGAAAAAAATTTTTGCATAGGATACCTG 32 16 0 ATTTTTGCAT 0.915124 -55 AGTGCGGTCGTTTTTTCCCTTGTTTTTGGTA 32 47 0 TTTTTCCCTT 0.79257 -24 * ********* Masking position 5 Map Score: 19.2625 Number of sites scoring better than the average of aligned sites = 577 Number in coding regions = 461 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 5 GTAGTTTATTCTTATTGTTATTTCTTGGTG 1 38 1 CTTATTGTTA 0.726109 -37 CAGAATAAAATTACTTGTTATGTTTAACTA 4 65 0 TTACTTGTTA 0.662349 -45 CATCCGCAGCTTTCTTTTTAAATTATTAAG 5 44 1 TTTCTTTTTA 0.928912 -28 ACTTTTCCCTTGTTAGAACTGTGCA 9 12 0 TCCCTTGTTA 0.864597 -15 TTGCACCATTTTTCTTGTTCGTTATACTAT 13 41 0 TTTCTTGTTC 0.771807 -91 ACTTGTGTTTCCTTTTTATGTTTAGCGG 14 93 0 TTCCTTTTTA 0.944246 -18 AATCTATCCTCTTGTTAAGTTAAAATT 15 85 0 CCTCTTGTTA 0.786718 -17 AAGAACTTTACCTCTTTTTAGTGATATTGT 17 51 0 CCTCTTTTTA 0.7574 -122 TTAAGTAGATCTCATTTTTAAACATTTTTT 17 82 0 CTCATTTTTA 0.744129 -91 AATTTTTCCTTTTTGTTTTAATTAA 19 120 0 TTCCTTTTTG 0.668446 -15 CAAAAAACAATTTCTTGTTAA 22 2 0 TTTCTTGTTA 0.939167 -186 CGACTTAGTTTTTATTTTTATTATGGGTAA 22 153 1 TTTATTTTTA 0.74981 -35 TAAAAAGAATCCTTGTTACCCATAATAA 22 170 0 ATCCTTGTTA 0.854144 -18 AACTTTTTCCTTGTTATAATCTATAA 26 7 1 TTCCTTGTTA 0.952403 -201 TGTAAGTAGGTTTATTTTTAATATAAAATG 28 44 0 TTTATTTTTA 0.74981 -257 GATCGCAAAAATTCTTTTTAATGAATAAAA 28 200 0 ATTCTTTTTA 0.792713 -101 ATTTTTTCCTTTTTATTTGAAAATC 28 286 0 TTCCTTTTTA 0.944246 -15 AACTATTTAGCTTATTTTTATGATTTAATT 31 36 1 CTTATTTTTA 0.691725 -123 TTGCCCTAGTATCCTTTTTCAAAGCAAAAT 31 93 0 ATCCTTTTTC 0.520582 -66 ********** Masking position 5 Map Score: 18.9991 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 107 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 6 AAGTGCGGTAAATTTTTATCCATTT 7 5 1 GCGGTAATTT 0.887959 -67 GTCGCAAAGTGCGGTCGTTTTCTTTTATATT 8 22 1 GCGGTGTTTT 0.991304 -29 TGGTGCAAATGCCGTCGCTTTTTAGGCGTAT 13 63 1 GCCGTGCTTT 0.963334 -69 GATAAAAAGTGCGGTGGTTTTTTCCGCACTT 18 107 0 GCGGTGTTTT 0.991304 -38 GTCGTGAAGTGCGGTTTTATTTTGGAGTTTT 22 77 1 GCGGTTTATT 0.82372 -111 AATTGGTCAAGCGATGGCTTTTTTATTTACA 24 110 1 GCGATGCTTT 0.946601 -61 TAAATTGAAAGCGGTTACTTTCATAAGTATG 26 68 1 GCGGTACTTT 0.976392 -140 TTGATTAGTCGAGGTAGCATT 31 148 1 GAGGTGCATT 0.848527 -11 AAAAGTGCGGTCGTTTTTTCCCTTGTT 32 54 0 GCGGTGTTTT 0.991304 -17 ***** ***** Masking position 5 Map Score: 9.8621 Number of sites scoring better than the average of aligned sites = 247 Number in coding regions = 193 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 7 GATCCCCTATGTTCAATTTTATAAATTGCTC 2 18 1 GTTAATTTTA 0.939977 -21 TACGAAAAGTTTTCAATTTTAATTTTAATTT 15 59 1 TTTAATTTTA 0.935217 -43 TCAATTTTAATTTTAATTTTAACTTAACAAG 15 71 1 TTTAATTTTA 0.935217 -31 ATAAGCCACAGTTAAATTTTAATCTTATATA 17 139 1 GTTAATTTTA 0.939977 -34 TTCTATTATTGTGCATATTTATTCATAAAGC 19 86 0 GTGATATTTA 0.567265 -49 GAGAAGTGCGGTTAAAATTTAAGTTATTTCA 22 39 0 GTTAAATTTA 0.889692 -149 TTTGCATATTTTTGAAATTTATAAAAAGGCT 22 115 0 TTTAAATTTA 0.881447 -73 GCGACTTAGTTTTTATTTTTATTATGGGTAA 22 152 1 TTTATTTTTA 0.795152 -36 TTTACACTAATTTCAAATTTACTCAGGAAAT 24 145 1 TTTAAATTTA 0.881447 -26 AAACTATTTTTTGGCATTTTATATTAAAAAT 28 30 1 TTGCATTTTA 0.716939 -271 GTGTAAGTAGGTTTATTTTTAATATAAAATG 28 44 0 GTTATTTTTA 0.808092 -257 CGCAAAATGCTTTTAAATTAATCGTTTCTCT 28 235 1 TTTAAATTAA 0.404988 -66 TTCAAGATGGTTGCTATTTTAACGTAAAATC 29 23 0 TTGTATTTTA 0.481485 -37 CCATAAAATTGTGAAATTTTATGGCTATTGT 30 22 1 GTGAATTTTA 0.904451 -58 GCAAAAATTTTTTTCATTTTACCAAAAACAA 32 28 1 TTTCATTTTA 0.807332 -43 *** ******* Masking position 11 Map Score: 11.294 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 177 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 8 ATCCATTTCTCTACAAAATTATGTTATAAAACCATAAAAA 7 28 1 CTACAAATAA 0.672529 -44 TTATAAAACCATAAAAAATTTGAGGTTAAAT 7 51 1 ATAAAAATAA 0.955021 -21 ATTATAGCCGACAAAAACTTGATTGACAAAAACTAAACAA 16 43 1 ACAAAAATAA 0.755934 -35 GGATGTCAATATAAAAAAATGTTAAGTAGATCTCATTTTT 17 93 0 ATAAAAATAA 0.955021 -80 GTTTTTGCTTATAAATAGGTGGCACTTAGAGGCTTGTAAA 18 42 0 ATAAATATAA 0.676348 -103 AAACACTTAAATAAAACGATCAAGACAAAAAGTGCGGAAA 18 78 1 ATAAAACTAA 0.907157 -67 ATAGCACTAATACAAATAAAATGGACAAAATGAAAGATT 19 10 1 ATACAAAAAA 0.725418 -125 TATATTAATAATAAAACAAAAATGGACAAAATCTTTCATT 19 39 0 ATAAAACAAA 0.647084 -96 ATTTTGAGCAATAAAAAACTGTGTACTAGATCACAATTTA 23 21 0 ATAAAAATAA 0.955021 -81 ATTATTTATAATAAAAATGTCATTACAAGATCTATAAATC 24 14 1 ATAAAAATAA 0.955021 -157 ATTATTTATGATCAAAATATAAGATTTATAGATTATAACA 26 22 0 ATCAAAATAA 0.755934 -186 ACATTAATTTATACTAAATTATTGTAAATAAACCGTGATC 26 145 0 ATACTAATAA 0.580828 -63 GAATAAAAAACTGGCTGTCAAACTATTTTTTG 28 3 1 ATAAAAATAA 0.955021 -298 TATTTAACCAATACAACCCTAATCAACAAATTTTTCTTAT 28 119 1 ATACAACTAA 0.86629 -182 ******* * * * Masking position 18 Map Score: 6.69714 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 64 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 9 TAAAGTTAATAAAACGCCGCCATTATACTGTC 6 58 0 AAAACCCGCA 0.973016 -29 TACTATCCAAAACATTCCATCAAAGGAAACCA 13 15 0 AACATCCACA 0.914259 -117 GGTGGCATCAAAAATGCCATCATCAATACAAA 14 39 1 AAAATCCACA 0.975696 -72 AAACAATCCCGACACAATGTCGGG 17 3 1 ACAATCCGCA 0.944175 -170 ATATAGAGCAAAAATCCCGACATTGTGTCGGG 17 18 0 AAAATCCGCA 0.984539 -155 GCTTTTTGCCAAAACTCCAAAATAAAACCGCA 22 86 0 AAAACCCAAA 0.838702 -102 TGTAGATCAAAATCCCGTCAAATTTTGCTA 27 9 1 AAAATCCGCA 0.984539 -87 TTTTTAATATAAAATGCCAAAAAATAGTTTGA 28 28 0 AAAATCCAAA 0.901791 -273 ***** *** ** Masking position 4 Map Score: 7.12912 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 38 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 10 GATCCCCTATGTTCAATTTTATAAATTGCT 2 18 1 GTTCAATTTT 0.645933 -21 GCAGCTTTCTTTTTAAATTATTAAGGAGCA 5 49 1 TTTTAAATTA 0.647482 -23 TACGAAAAGTTTTCAATTTTAATTTTAATT 15 59 1 TTTCAATTTT 0.920424 -43 TCAATTTTAATTTTAATTTTAACTTAACAA 15 71 1 TTTTAATTTT 0.82131 -31 TTCCTTTTTGTTTTAATTAATTATTCTATT 19 110 0 TTTTAATTAA 0.647482 -25 TTTACACTAATTTCAAATTTACTCAGGAAA 24 145 1 TTTCAAATTT 0.842635 -26 AAGTAACCGCTTTCAATTTATCGTAAATTA 26 58 0 TTTCAATTTA 0.908961 -150 TTATGCCCATTTTCAATTATGGTTAAAAGT 27 67 1 TTTCAATTAT 0.842635 -29 AAGAAAAATTTTGCAATTTTTTATTCATTA 28 182 1 TTGCAATTTT 0.645933 -119 CGCAAAATGCTTTTAAATTAATCGTTTCTC 28 235 1 TTTTAAATTA 0.647482 -66 CATACTAGATTTTCAAATAAAAAGGAAAAA 28 279 1 TTTCAAATAA 0.681508 -22 GGTTTTATATTTTTAATTATTGATTAGTCG 31 129 1 TTTTAATTAT 0.680289 -30 CAAAAATTTTTTTCATTTTACCAAAAACAA 32 29 1 TTTCATTTTA 0.515152 -42 ********** Masking position 5 Map Score: 6.13602 Number of sites scoring better than the average of aligned sites = 482 Number in coding regions = 370 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 11 ATAATGTTACTATTATTTTGTGTAGTTTAT 1 17 1 TATTATTTTG 0.940794 -58 TTCTTATTGTTATTTCTTGGTGTACCTGTA 1 46 1 TATTTCTTGG 0.738393 -29 CGTTATTGACTCTTTTTTGGATGAG 12 56 1 TCTTTTTTGG 0.830001 -15 TTAATTATTCTATTATTGTGCATATTTATT 19 94 0 TATTATTGTG 0.749528 -41 TGAAGTGCGGTTTTATTTTGGAGTTTTGGC 22 81 1 TTTTATTTTG 0.767384 -107 TTGCTTATTTTCTTATTTTGTGACAAAGAT 26 118 1 TCTTATTTTG 0.945102 -90 GCTGTCAAACTATTTTTTGGCATTTTATAT 28 24 1 TATTTTTTGG 0.818396 -277 GCAAAATTTTTCTTATTTTGAAAATGTAAA 28 166 0 TCTTATTTTG 0.945102 -135 TTCTTACTTAGCCATAAAATT 30 2 1 TCTTACTTAG 0.658971 -78 ATTGTTTATTTATTACTTTGTTAATTGTTT 30 48 1 TATTACTTTG 0.908696 -32 GTTTATTCTTGATTATTTTGCTTTGAAAAA 31 79 1 GATTATTTTG 0.749528 -80 ********** Masking position 4 Map Score: 4.67437 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 138 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 12 TGCGGTAAATTTTTATCCATTTCTCTACAAA 7 14 1 TTTATCCATT 0.803879 -58 GCGGTCGTTTTCTTTTATATTTTTGAGTA 8 32 1 TCTTTATATT 0.90546 -19 ATCTTATCTATTGTGAACCTTC 12 2 1 TCTATCTATT 0.924985 -69 TACTTAACATTTTTTTATATTGACATCCATT 17 105 1 TTTTTATATT 0.703477 -68 TAAATTTTAATCTTATATATTAGAGGTGACT 17 151 1 TCTATATATT 0.919233 -22 ATTATCATATCCATTGTTTAA 20 7 0 TCTATCCATT 0.943011 -15 AATCTATAAATCTTATATTTTGATCATAAAT 26 28 1 TCTATATTTT 0.591189 -180 ATTAATGTAATCGTTTACATTGATAAAAAAC 26 177 1 TCTTTACATT 0.927813 -31 TCTTATTGGATTTTTTACATTTTCAAAATAA 28 153 1 TTTTTACATT 0.76098 -148 ATTTTTTCCTTTTTATTTGAAAATCTA 28 284 0 TCTTTTTATT 0.66537 -17 TTTAATCTCCTATCCATTCAAGATGGTT 29 42 0 TCTATCCATT 0.943011 -18 ** ******** Masking position 6 Map Score: 5.57277 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 63 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 13 ATGGCATATAAGGAGTCTAAAA 4 98 1 AGGAGTCTAA 0.923988 -12 TACTGTCTAAAGGGGATTAAGCAAGGAAGC 6 35 0 AGGGGATTAA 0.945706 -52 TCAAAAATAAAGGGGCTTAATTGCCCCTTT 11 18 1 AGGGGCTTAA 0.910851 -52 ATGCAAACTAAGGAGATAAAAG 21 66 1 AGGAGATAAA 0.918438 -12 GATAAAAAACAGGAGTCAAA 26 198 1 AGGAGTCAAA 0.866935 -10 TTGAATGGATAGGAGATTAAA 29 49 1 AGGAGATTAA 0.954566 -11 ********** Masking position 9 Map Score: 1.08503 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 4 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 14 ********** No masking Map Score: -4.85057e-12 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 Motif number 15 GTTACTATTATTTTGTGTAGTTTATTCTTA 1 22 1 TTTTGTGTAG 0.787738 -53 AAATTACTTGTTATGTTTAACTATGATATG 4 58 0 TTATGTTTAA 0.843195 -52 TGATGGAATGTTTTGGATAGTATAACGAAC 13 25 1 TTTTGGATAG 0.727754 -107 TGTTTCCTTTTTATGTTTAGCGGGATAAGC 14 86 0 TTATGTTTAG 0.895107 -25 AAATTTTGTTTAGTTTTTGTCAA 16 65 0 TTTTGTTTAG 0.817401 -13 TTTATTTTTATTATGGGTAACAAGGATTCT 22 163 1 TTATGGGTAA 0.897503 -25 CCATTTTCAATTATGGTTAAAAGTAGGTAA 27 73 1 TTATGGTTAA 0.913498 -23 TTTCACAATTTTATGGCTAAGTAAGAA 30 8 0 TTATGGCTAA 0.897503 -72 TTGTGAAATTTTATGGCTATTGTTTATTTA 30 30 1 TTATGGCTAT 0.727038 -50 ********** Masking position 4 Map Score: 1.16196 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 54 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863