AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -icrp_hinf_opreg_100.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 HI0054 109 uxu operon regulator (uxuR) #2 HI0055 27 mannonate dehydratase (uxuA) #3 HI0079 102 peptidyl-prolyl cis-trans isomerase B (ppiB) #4 HI0098 216 iron(III) ABC transporter, permease protein (hitB) #5 HI0140 272 N-acetylglucosamine-6-phosphate deacetylase (nagA) #6 HI0141 285 glucosamine-6-phosphate isomerase (nagB) #7 HI0190 28 ferric uptake regulation protein (fur) #8 HI0191 96 flavodoxin (fldA) #9 HI0289 222 serine transporter (sdaC) #10 HI0351 172 UDP-glucose 4-epimerase (galE) #11 HI0518 83 purine-nucleoside phosphorylase (deoD) #12 HI0519 98 transport protein, putative #13 HI0521 212 conserved hypothetical protein #14 HI0604 300 adenylate cyclase (cyaA) #15 HI0615_HI0616 197 HI0615: L-fucose operon activator (fucR), HI0616: ATP-dependent helicase (hepA) #16 HI0618 26 glp protein, putative #17 HI0619 29 glycerol-3-phosphate regulon repressor (glpR) #18 HI0680 31 rarD protein, putative #19 HI0681 300 transcriptional activator (ilvY) #20 HI0685_HI0686 200 HI0685: anaerobic glycerol-3-phosphate dehydrogenase, subunit A (glpA), HI0686: glycerol-3-phosphatase transporter (glpT) #21 HI0687 99 conserved hypothetical protein #22 HI0688 94 H. influenzae predicted coding region HI0688 #23 HI0690 229 glycerol uptake facilitator protein (glpF) #24 HI0727.1 260 cyaY protein (cyaY) #25 HI0745 225 L-asparaginase II (ansB) #26 HI0819 37 galactokinase (galK) #27 HI0820 207 galactose-1-phosphate uridylyltransferase (galT) #28 HI0953 124 DNA/pantothenate metabolism flavoprotein (dfp) #29 HI0954 47 deoxyuridinetriphosphatase (dut) #30 HI0956 21 conserved hypothetical protein #31 HI0957 66 catabolite gene activator (crp) #32 HI1027 58 L-xylulose kinase (lyx) #33 HI1028 30 conserved hypothetical protein #34 HI1030 71 conserved hypothetical transmembrane protein #35 HI1031 175 conserved hypothetical protein #36 HI1116 110 deoxyribose-phosphate aldolase (deoC) #37 HI1164 300 outer membrane protein P5 (ompA) #38 HI1350 273 cytidine deaminase (cdd) #39 HI1678 300 kpsF protein (kpsF) #40 HI1713 158 phosphocarrier protein HPr (ptsH) Motif number 1 AGTGCTATAAAAGTGCGGTTTGTTTTTATTT 3 29 0 AAGTGCGGTT 0.968695 -74 GGATCATTATAAGTGCGGCAATTTTCTATCT 6 189 0 AAGTGCGGCA 0.992491 -97 TTTTTATAAAAAGTGCGGTAATTTTCAGCGA 9 62 0 AAGTGCGGTA 0.99705 -161 ATCAATTAAAAAGTGCGGTAAAAAATGACCG 11 20 1 AAGTGCGGTA 0.99705 -64 AAAATGAATAAAGTGCGGTCATTTTTTACCG 11 35 0 AAGTGCGGTA 0.99705 -49 CGTTTACAAAAAGTGCGGTGAAAATTCGCCG 12 12 1 AAGTGCGGTA 0.99705 -87 ATCTTCCTAAAAGTGCGGTCAATTTTTTGTG 15 85 0 AAGTGCGGTA 0.99705 -113 TAAAAAGTGCGGTTAGTTTTCTGGT 19 5 1 AAGTGCGGTA 0.99705 -296 CTTCAATTTAAAGTGCGGGTAAAATTTAGCG 19 49 0 AAGTGCGGGA 0.980122 -252 CATTGTAGGGAAGTGCGGCCAAAATTAACAA 20 128 0 AAGTGCGGCA 0.992491 -73 CACTCCTTAGAAGTGCGGTTGAAATGAAGAG 23 205 0 AAGTGCGGTG 0.988291 -25 AAATCTGATAAAATGCGGCAAATTATAAAGC 24 225 0 AAATGCGGCA 0.924924 -36 AAGATAACCCAAGTGCGGTTATACTTGAGCC 25 44 0 AAGTGCGGTA 0.99705 -182 TTTTAGGTAAAAGTACGGTTGGAA 29 4 0 AAGTACGGTG 0.887219 -44 GAACGTTCAAAAGTGCGCTTATTATCCTATA 37 112 0 AAGTGCGCTA 0.961307 -189 TAGGTCGTATAAATACGGTTAAGGGCTTCAA 39 170 1 AAATACGGTA 0.745966 -131 GGGCAATCACTAGTGCGGTCAATAAAATCCC 39 241 1 TAGTGCGGTA 0.964475 -60 ********* * Masking position 4 Map Score: 51.8121 Number of sites scoring better than the average of aligned sites = 1378 Number in coding regions = 936 Number in noncoding regions = 442 Number of orfs with sites within 600 bp upstream = 294 Fraction of orfs with sites within 600 bp upstream = 0.0472213 Motif number 2 CGGTTTTCACTTTTAGCTCTTGTTGAGATTATAGGGCGA 5 49 0 TTTTTTTTAT 0.915346 -224 AGTGCGGCAATTTTCTATCTTGTTTTTAAAAAGAAATTC 6 170 0 TTTTTTTTAA 0.953212 -116 TTATATTAAATTTAATCTATTGATTATAAGGCTTATCCA 8 54 0 TTTTTTATAA 0.890555 -43 TTTTATTTCCTTTTTTATATTAAATTTAATCTAT 8 73 0 TTTTTTTAAA 0.756111 -24 TTGTGATCAAGTTAAAATTTTTTTATAAAAAGTGCGGTA 9 73 0 GTTTTTTTAA 0.783445 -150 TAGCAACAGGTTTTTTATTTTATTGAAAATCACCATTCT 10 87 1 TTTTTTTTAA 0.95294 -86 AATTTTTCCTTATTTTTAATAATGAATAAAAA 11 62 0 TTTTTTTTAA 0.953212 -22 GTTTTCAAAATTGTCTATTTTGTTACCATTGCGTACAAT 13 158 1 TTGTTTTTAT 0.723075 -55 AGTGGATAGCTTGATATTTTTCTTATCAACGCAAAGTAT 14 48 0 TTGTTTTTAA 0.831072 -253 AAAAAAGTCATTTTGATTGTTGATAGGTAAAATTTATAG 14 171 1 TTTTTTATTA 0.797439 -130 ATAGGTAAAATTTATAGTATTTTTCGAAAAATTGTGATT 14 193 1 TTTTTTTTAA 0.953189 -108 TGCGGTTAGTTTTCTGGTATTTTTCAAAATACGCTAAAT 19 18 1 TTTTTTTTAA 0.953212 -283 AATTTCTTCTTTTATTTAATATCGGGTTTCG 19 280 0 TTTTTTTTTA 0.907891 -21 CACTTCACATTTTTGATTTTTTTTACTTTCTT 20 4 0 TTTTTTTTTT 0.839521 -197 AGAAAGCGATTTTGTGATATTGATCACAATAATTTTCGC 20 74 0 TTTTTTATAA 0.890551 -127 GATTACACTTTTTATATTATTTTTTCTTACATTTTGGGA 20 158 1 TTTTTTTTTA 0.907891 -43 GATACTTATCTTTTTATTATTCTTATGATAGTTACAAAA 21 52 0 TTTTTTTTAT 0.915346 -48 ATAGTAATTTTTTCATTTTTTCTTTCTCACTTATCGGTA 24 159 1 TTTTTTTTCA 0.649888 -102 GATCACATAATTTTTTTTGTTGATTGTATAACCTTTATG 25 106 0 TTTTTTATAT 0.811982 -120 TAAATTTGTTTTTCCATTGTTTATAAATAACTTAATTTA 25 152 1 TTTTTTATTA 0.797439 -74 AACTTTTTCCTTGTTATAATCTATAAATCTTAT 27 5 1 TTTTTTTATA 0.6001 -203 ATAAAAAATTTTGCTTATTTTCTTATTTTGTGACAAAGA 27 108 1 TTGTTTTTTT 0.558161 -100 CAAAAATTCCGTTTTATTTTTGATGTCAATGGATTCATG 31 15 0 GTTTTTATAA 0.590992 -52 GTAAAATTATTTTAACATATTGATTTATAAATAATTTAT 35 63 1 TTTTTTATTA 0.797439 -113 TTTTTCCTCTCTTAATTTTATATAGTAAAAT 35 155 0 TTTTTTATAT 0.811982 -21 TTTATTTATGTTTTACCTATTGTAGCAAAAATTCTTTAT 36 70 0 TTTTTTTAAA 0.756197 -41 TCAAATTCTTTTGAATTTTTTGTTTAGTTTTTATCCAAA 37 60 0 TTGTTTTTTT 0.558161 -241 GAATTTGATCTTTTCAATTTTTATAGGATAATAAGCGCA 37 91 1 TTTTTTATAT 0.811982 -210 ACAGTTATAATTTTTAATATTTTTCCTAAGGATATGTT 38 246 1 TTTTTTTTAA 0.953193 -28 AAGCTAAATAGTTTATTTATTATTCACAATCTCAATCG 40 10 0 GTTTTTTTAA 0.783413 -149 AAATAAACTATTTAGCTTATTTTTATGATTTAATTCAGG 40 31 1 TTTTTTTTAT 0.915346 -128 CTAGGGCAATTTTCTGGTTTTATATTTTTAATTATTGAT 40 114 1 TTTTTTTATT 0.443342 -45 *** * ** ** ** Masking position 10 Map Score: 34.8296 Number of sites scoring better than the average of aligned sites = 375 Number in coding regions = 236 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 3 CTATAAAAGTGCGGTTTGTTTTTATTTCATTT 3 24 0 GCGGTTTTTT 0.835851 -79 ACGCACGCAAGCGGTTAATTTTGTTAGAGAAT 4 60 0 GCGGTATTTT 0.981038 -157 TCTTTATGTAGGGGCGAATTACATTCGCCCTA 5 25 1 GGGGCATTAC 0.851805 -248 TCTTTATGTAGGGGCGAATTACATTCGCCCTA 5 161 1 GGGGCATTAC 0.851805 -112 AAAACAGGGGGAGGTAAGTTTTTTCTAATTTA 6 16 0 GAGGTATTTT 0.803013 -270 AGGGCGGAAGGGGGCAACTTCTATTGCTCTGT 6 118 1 GGGGCATTCT 0.787544 -168 CATTATAAGTGCGGCAATTTTCTATCTTGTTT 6 184 0 GCGGCATTTC 0.982815 -102 TATAAAAAGTGCGGTAATTTTCAGCGACAAAA 9 57 0 GCGGTATTTC 0.979191 -166 TGAATAAAGTGCGGTCATTTTTTACCGCACTT 11 30 0 GCGGTATTTT 0.981038 -54 TTATGAAAAGTCGGCGAATTTTCACCGCACTT 12 22 0 TCGGCATTTT 0.792852 -77 TCCTAAAAGTGCGGTCAATTTTTTGTGAGTTT 15 80 0 GCGGTATTTT 0.981038 -118 TAAAAAGTGCGGTTAGTTTTCTGGTATTTT 19 9 1 GCGGTATTTT 0.981038 -292 CTGATAAAATGCGGCAAATTATAAAGCCTTTC 24 220 0 GCGGCATTAT 0.9528 -41 TAAATTGAAAGCGGTTACTTTCATAAGTATGA 27 68 1 GCGGTATTTC 0.979191 -140 ***** * **** Masking position 9 Map Score: 19.3383 Number of sites scoring better than the average of aligned sites = 430 Number in coding regions = 266 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 4 TCATAGTTAAACATAACAAGTAATTTTATTCTGTCAA 1 32 0 AAAAAATTTT 0.89026 -78 AATGAAATAAAAACAAACCGCACTTTTATAGCACTTT 3 25 1 AAACACTTTT 0.932913 -78 TTGTGGAATAATACAACCCTTAATTTTTTAGAGGGAA 3 70 1 AAACAATTTT 0.977567 -33 TATTGGCATAACATAATACTCAAATTTAGTTGGAGCG 9 143 1 AAACAAATTT 0.757152 -80 GAAAACAAGTAGAATAAGCCGAATTTTATTAACTTAA 12 54 1 AAACAATTTT 0.977501 -45 GAAAGATGCAAAAACAGAAATAATTTTGTCAGTTCAT 13 47 1 AAAAAATTTT 0.890249 -166 CGCAATGGTAACAAAATAGACAATTTTGAAAACGTGA 13 154 0 AAAGAATTTT 0.785143 -59 TTCTGCCGATATAAAAATCTATATTTTCTATTATTAG 14 85 0 AAACTATTTT 0.757091 -216 AATTTTTCGAAAAATACTATAAATTTTACCTATCAAC 14 189 0 AAAAAATTTT 0.889664 -112 AAAAAATGTGACATAAATCACAATTTTTCGAAAAATA 14 210 0 AAACAATTTT 0.977567 -91 AAATACCAGAAAACTAACCGCACTTTTTA 19 3 0 AAACACTTTT 0.932848 -298 GGTATTTTTCAAAATACGCTAAATTTTACCCGCACTT 19 33 1 AAACAATTTT 0.973498 -268 AAAAATGAAAAAATTACTATTAATTTTAGTACTTAGT 24 142 0 AAAAAATTTT 0.890217 -119 GCAAGTACGGAATTTAAGCATAATTTTTTTGAAAGAT 25 70 0 ATACAATTTT 0.757148 -156 ACAAAATAAGAAAATAAGCAAAATTTTTTATGATTTA 27 102 0 AAACAATTTT 0.973498 -106 TTGACATCAAAAATAAAACGGAATTTTTGAAACAGGA 31 25 1 AAACAATTTT 0.977562 -42 TTTTTGTAAATTATGAAACGTAATTTTACTATATAAA 35 133 1 TAACAATTTT 0.757152 -43 TTTTTATAGGATAATAAGCGCACTTTTGAACGTTCCT 37 108 1 AAACACTTTT 0.932851 -193 AGTGCGGTCAATAAAATCCCCAATTTTTGAATATTGC 39 252 1 AAACAATTTT 0.977566 -49 * * * * ****** Masking position 15 Map Score: 31.2446 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 26 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 ATATTTAAATTAGAAAAAACTTACCT 6 3 1 ATAATTAAAA 0.717503 -283 AAATTTGGCGAACTATATCATAAAAGCATTCTCA 8 21 0 ATAATCAAAA 0.968591 -76 AAAAAATTTTAACTTGATCACAATTTTAGAATTT 9 89 1 ATTATCAAAT 0.762962 -134 TTGTCAGTTCATTTATATCAAAAACATATTTATT 13 72 1 ATAATCAAAA 0.968582 -141 AAAAAATGTGACATAAATCACAATTTTTCGAAAA 14 213 0 ATAATCAAAT 0.919633 -88 AGTTTTATCAATGTAAATCAGAAAGAGAATAATT 15 11 0 ATAATCAAAA 0.968591 -187 AAGAAAGTAAAAAAAATCAAAAATGTGAAGTGT 20 10 1 AAAATCAAAA 0.823098 -191 CGATTTTGTGATATTGATCACAATAATTTTCGCA 20 73 0 ATTATCAAAT 0.754149 -128 ACTCTAACAGAGTAACATCATAATCAATCTAGGT 23 81 1 AAAATCAAAT 0.633233 -149 TCTACTGATTAAGTACGTCAAAATAGGGCTCAAG 25 18 1 ATAGTCAAAT 0.702564 -208 AAATTATGTGATCGAGATCATAAATTTGTTTTTC 25 132 1 AGAATCAAAA 0.878004 -94 TAAATCTTATATTTTGATCATAAATAATTTACGA 27 34 1 ATTATCAAAA 0.889825 -174 CATAAGTATGAACTAAATCATAAAAAATTTTGCT 27 89 1 ATAATCAAAA 0.968591 -119 ATAAACCGTGATCTTTGTCACAAAATAAGAAAAT 27 124 0 ATTGTCAAAA 0.641835 -84 ACATGAATCCATTGACATCAAAAATAAAACGGAA 31 14 1 AGAATCAAAA 0.877998 -53 AGAAAATAGGATCTAGATCACAAAATCAGTAAAA 35 35 1 ATAATCAAAA 0.968588 -141 TTGCTACAATAGGTAAAACATAAATAAAAGGAGG 36 81 1 ATAAACAAAA 0.688115 -30 TTTTAATTAAAGCTACATTATAAACAGTCACTTA 37 217 0 ATAATTAAAA 0.717504 -84 AAAAAGCCTGAATTAAATCATAAAAATAAGCTAA 40 42 0 ATAATCAAAA 0.968591 -117 * ** **** *** Masking position 10 Map Score: 21.7169 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 92 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 6 GCGGTTTGTTTTTATTTCATTTTACGAGCTTA 3 14 0 TTTATTCTTT 0.951573 -89 CTCCCCCTGTTTTATTCCGTTACAAACAGAAC 6 35 1 TTTATTCTTA 0.771072 -251 TTTCCTTTTTTATATTAAATTTAATCTATTGA 8 70 0 TATATTATTT 0.536717 -27 TTTTATTTCCTTTTTTATATTAA 8 84 0 TTTATTCTTT 0.951573 -13 ATGACCGCACTTTATTCATTTTTATTCATTAT 11 44 1 TTTATTATTT 0.910601 -40 TAAGCCGAATTTTATTAACTTAACTAATCTAG 12 68 1 TTTATTATTA 0.635828 -31 ATTTATTACCTTTTATATTCCGT 13 2 1 TTTATTCTTT 0.951573 -211 TATTACCTTTTATATTCCGTTTTATCATAAAA 13 14 1 TATATTCTTT 0.690869 -199 AGTACCTAGTTTTATTGCGTAAATAGCTTAAT 14 121 0 TTTATTCTAA 0.442226 -180 TATGTCACATTTTTTTGCATTTATACTCCCTA 14 232 1 TTTTTTCTTT 0.799508 -69 TAATTTATTCTTTCTTCAATTTAAAGTGCGGG 19 61 0 TTTCTTATTT 0.690546 -240 AATTTCTTCTTTTATTTAATATCGGGTTTCGC 19 279 0 TTTATTATAT 0.70568 -22 CATTTTTGATTTTTTTTACTTTCTT 20 4 0 TTTTTTATTT 0.673965 -197 TATATTATTTTTTCTTACATTTTGGGAATCGG 20 170 1 TTTCTTCTTT 0.81149 -31 TTAATAGTAATTTTTTCATTTTTTCTTTCTCA 24 156 1 TTTTTTATTT 0.673964 -105 TTATAAATAATTTATTTATTTTACATTTATTG 35 87 1 TTTATTATTT 0.910601 -89 TTTATTTATTCCTTATCTTGTTGAGA 36 5 1 TTTATTCTAT 0.822232 -106 TTTTGAATTTTTTGTTTAGTTTTTATCCAAAA 37 59 0 TTTGTTATTT 0.548033 -242 TTTGCCCTACTTTATTACCTTTTGACAAATTC 37 171 0 TTTATTCTTT 0.951573 -130 AAGGACACTTTTTATTACTATTCGATCACTAA 37 264 1 TTTATTCATT 0.690868 -37 ATAGCTTCTATTTATTACAATTTCTTAACAAA 38 133 0 TTTATTCATT 0.690869 -141 AGCTAAATAGTTTATTTATTATTCACAATCTC 40 16 0 TTTATTATAT 0.705679 -143 ****** * *** Masking position 6 Map Score: 19.6025 Number of sites scoring better than the average of aligned sites = 359 Number in coding regions = 245 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 7 CTAAAAGTGAAAACCGTGAAATATTTTACTGAATTAG 5 72 1 AAAGTGATTT 0.967493 -201 ATTTTTTTATAAAAAGTGCGGTAATTTTCAGCGACAA 9 59 0 AAAGTGCTTT 0.919619 -164 TTACCACACAAAATAGTGATATAATTTTTTAGTCTCA 10 125 1 AAAGTGATTT 0.967493 -48 TTATTTTCTAAAACTGTGATCTTCCTCACGTTTTCAA 13 129 1 AAAGTGATTC 0.976295 -84 CACGTTTTCAAAATTGTCTATTTTGTTACCATTGCGT 13 155 1 AAAGTCTTTT 0.655654 -58 CTCTTAGGTAAAAAAGTCATTTTGATTGTTGATAGGT 14 162 1 AAAGTCATTT 0.842656 -139 TAAATGCAAAAAAATGTGACATAAATCACAATTTTTC 14 218 0 AAAGTGATTC 0.976294 -83 TAAAAAGTGCGGTTAGTTTTCTGGTATT 19 2 1 AAAGTGCTTT 0.91962 -299 AAAAAAATCAAAAATGTGAAGTGTTTCACAAATCTTT 20 20 1 AAAGTGATTC 0.976295 -181 AAAATAATATAAAAAGTGTAATCATTGTAGGGAAGTG 20 144 0 AAAGTGTTTG 0.737873 -57 TATTGTAAATAAACCGTGATCTTTGTCACAAAATAAG 27 129 0 AAAGTGATTC 0.976295 -79 GAATAGTAATAAAAAGTGTCCTTGTTTATACTGAACT 37 250 0 AAAGTGTTTT 0.913597 -51 ATATTCATTAAAACTGTGATCTTGATCACTTATTTGA 38 164 0 AAAGTGATTC 0.976295 -110 TAAACACTAAAAAGCCTGAATTAAATCATAAAAATAA 40 47 0 AAACTGATTC 0.787944 -112 *** **** * ** Masking position 3 Map Score: 15.2517 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 42 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 GTAATTCGCCCCTACATAAAGATGAAGAATAGATCT 5 7 0 CTAAAGGAAT 0.976136 -266 GTAATTCGCCCCTACATAAAGATGAAGAATAGATCTCTAT 5 143 0 CTAAAGGAAT 0.976136 -130 GATTATAAGGCTTATCCAAATTTGGCGAACTATATCATAA 8 32 0 CTAAAGGAAC 0.934057 -65 CCTTATTTTTAATAATGAATAAAAATGAATAAAGTGCGGT 11 47 0 ATAAAAGAAT 0.647111 -37 TACTTGTTTTCTTATGAAAAGTCGGCGAATTTTCACCGCA 12 25 0 CTAAAGGAAT 0.976136 -74 ATTTTATTAACTTAACTAATCTAGGGGAATCAA 12 76 1 CTAAAGGAAT 0.976133 -23 TGCTAACGCCCTTAATAAAACCAATTGAACCAGATATTTA 22 48 0 CTAAAAGAAC 0.898552 -47 AGTGTTTTCCCTAAGTAAAGGGAAGAGAATTTATTAAAAA 23 167 0 CAAAAAGAAT 0.747485 -63 AATCCATTGACATCAAAAATAAAACGGAATTTTTGAAACA 31 19 1 CTCAAAGAAT 0.814379 -48 AAATCCAGCCCATAAAAAACTAAGGAGAATAT 32 37 1 CTAAAGGAAT 0.976136 -22 AGCGTAAAACCATAGTCAAAAATAAAGAATTTTTGCTACA 36 49 1 CTAAAAGAAT 0.962345 -62 TTGGGGTAAACATAAGCAAAGGAATTGAATTTGTCAAAAG 37 145 1 CTAAAAGAAT 0.962345 -156 * ** ** * **** Masking position 9 Map Score: 13.1038 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 11 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 TTCATCTTTATGTAGGGGCGAATTACATTCGC 5 21 1 TAGGGGCGAA 0.914038 -252 CTTGTTGAGATTATAGGGCGAATGTAATTCGC 5 38 0 TTAGGGCGAA 0.937397 -235 TTCATCTTTATGTAGGGGCGAATTACATTCGC 5 157 1 TAGGGGCGAA 0.914038 -116 TTGTTTGTGATTATAGGGCGAATGTAATTCGC 5 174 0 TTAGGGCGAA 0.937397 -99 TCACAAACAATCATAGGGCAAATTGTCCTTAC 5 196 1 TTAGGGCAAA 0.953253 -77 TGTCCTTACGTTTAAGAGCAATATAGTTGCTA 5 219 1 TAAGAGCAAT 0.691893 -54 TGTCGTAAATTATTGGAGCAAAAGAATTTCTT 6 147 1 TTGGAGCAAA 0.869557 -139 ATAGAGAATCTCAAAGAGCAAATTCTAAAATT 9 110 0 TAAGAGCAAA 0.874917 -113 ATTTGTCAATTTGTAGAGCAAAATCCGCTCCA 9 173 0 TTAGAGCAAA 0.890148 -50 ACTTTTGCTTTGCACGAGCAAAGAAAAAGTAG 19 237 1 TACGAGCAAA 0.620387 -64 AAAGGTAATAAAGTAGGGCAAATTCAAAACCC 37 181 1 ATAGGGCAAA 0.684546 -120 CGGCGCGTAGTATAGGGGCAATCACTAGTGCG 39 226 1 TAGGGGCAAT 0.822976 -75 TGAAAAAGGATACTAGGGCAATTTTCTGGTTT 40 102 1 TTAGGGCAAT 0.867492 -57 * ********* Masking position 11 Map Score: 9.9782 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 63 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 TTATAATCAATAGATTAAATTTAATATAAAA 8 64 1 TAGTTAAATT 0.472681 -33 AATTGTGATCAAGTTAAAATTTTTTTATAAA 9 83 0 AAGTAAAATT 0.788543 -140 GTTTGCTCCAAAGCATAAATTACTTAAATTT 9 201 0 AAGATAAATT 0.895627 -22 TATTAAAAATAAGGAAAAATT 11 73 1 AAGAAAAATT 0.929955 -11 TGATTGTTGATAGGTAAAATTTATAGTATTT 14 184 1 TAGTAAAATT 0.581044 -117 TTGAAAATCCAAGGATAAATTATATTGGGGT 15 123 0 AAGATAAATT 0.895627 -75 AAATTGAAGAAAGAATAAATTAGCTCCCTTC 19 71 1 AAGATAAATT 0.895627 -230 TATTAAATAAAAGAAGAAATT 19 290 1 AAGAGAAATT 0.695045 -11 CCCAAAATGTAAGAAAAAATAATATAAAAAG 20 165 0 AAGAAAAATA 0.501185 -36 ATAAGTGAGAAAGAAAAAATGAAAAAATTAC 24 162 0 AAGAAAAATG 0.598258 -99 TACGGAATTTAAGCATAATTTTTTTGAAAGA 25 71 0 AAGATAATTT 0.533827 -155 AGATTATAACAAGGAAAAAGTT 27 2 0 AAGAAAAAGT 0.80904 -206 ATAAGAAAATAAGCAAAATTTTTTATGATTT 27 103 0 AAGAAAATTT 0.639215 -105 TACAATAATTTAGTATAAATTAATGTAATCG 27 159 1 TAGATAAATT 0.761002 -49 AATTCATTTTTAGGTAAAAGTACGGTTGGAA 29 11 0 TAGTAAAAGT 0.306795 -37 TTACCTATTGTAGCAAAAATTCTTTATTTTT 36 66 0 TAGAAAAATT 0.831266 -45 AGAGAGGAGAAAGTAAAAAGTCTGTTTAAGA 37 20 1 AAGAAAAAGT 0.80904 -281 ATAAAAACTAAACAAAAAATTCAAAAGAATT 37 65 1 AACAAAAATT 0.628449 -236 TATCGCGGCTAACAATAAATTTTGATTTAAT 38 211 1 AACATAAATT 0.522267 -63 *** ******* Masking position 7 Map Score: 9.65402 Number of sites scoring better than the average of aligned sites = 354 Number in coding regions = 276 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 11 TTTGTTTTCCCTCTAAAAAATTA 3 90 0 TGTTTTCCCC 0.973813 -13 CTCTTTTCCCTATACGGTGGAT 15 186 0 TCTTTTCCCA 0.932121 -12 TGTTTACCCCCGATTCCCAAA 20 190 0 TGTTTACCCC 0.951236 -11 TTTTACTTTTCCCAAAAATGATACT 21 85 0 ACTTTTCCCA 0.684019 -15 ACCGTGGGTATGTTTACCCACGGTTGTGAGG 23 15 0 TGTTTACCCC 0.951236 -215 AAATGAAGAGTGTTTTCCCTAAGTAAAGGGA 23 184 0 TGTTTTCCCA 0.9783 -46 TGTTTTCTCTACTGATTAAGT 25 1 1 TGTTTTCTCA 0.815491 -225 CTTTTATTTATGTTTTACCTATTGTAGCAAA 36 80 0 TGTTTTACCA 0.815491 -31 CCTTTGCTTATGTTTACCCCAAAGGAACGTT 37 136 0 TGTTTACCCA 0.959431 -165 ********* * Masking position 5 Map Score: 6.33298 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 31 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 12 GAATTTGCTCTTTGAGATTCTCTATTTATTGGCATA 9 117 1 TTTGCTCATT 0.951376 -106 TATTTCTGTTTTTGCATCTTTCCTTTTATGATAAAA 13 33 0 TTTGTTCTTT 0.935814 -180 ACAGAAATAATTTTGTCAGTTCATTTATATCAAAAA 13 60 1 TTTTTTCTTT 0.628718 -153 CGGTCAATTTTTTGTGAGTTTCTTTTCAAGAGTATG 15 65 0 TTTGTTCTTT 0.935814 -133 GACTAAGCAATTTGCCCACCGCCTTTTTTAAGCTAA 21 11 0 TTTGCGCTTT 0.684265 -89 ATTAAGGGCGTTAGCAATTCTCCATTTAAGTTT 22 72 1 TTAGCTCATT 0.658202 -23 ACGAATCACATTTGTGATAATCAATTGGAGGTGTA 34 47 1 TTTGATCATT 0.751668 -25 ATCAAATTCTTTTGAATTTTTTGTTTAGTTTTTATC 37 64 0 TTTGTTTTTT 0.628718 -237 TTCAAAAGAATTTGATCTTTTCAATTTTTATAGGAT 37 84 1 TTTGTTCATT 0.950497 -217 ATAAGCGCACTTTTGAACGTTCCTTTGGGGTAAACA 37 121 1 TTTTTTCTTT 0.628717 -180 TTTATTACCTTTTGACAAATTCAATTCCTTTGCTTA 37 157 0 TTTGTTCATT 0.950497 -144 GGGTTTTGAATTTGCCCTACTTTATTACCTTTTGAC 37 177 0 TTTGCTTATT 0.69442 -124 TTTGATGTCCTCTATTTAGTGATCGA 37 285 0 TTTGCTCATT 0.951376 -16 TGATCACTTATTTGATAGCTTCTATTTATTACAATT 38 143 0 TTTGTTCATT 0.950497 -131 **** *** *** Masking position 2 Map Score: 7.84506 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 84 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 13 TAACGGAATAAAACAGGGGGAGGTAAGTTTTTT 6 24 0 AAAAGGGGAG 0.740816 -262 CTTCCCCCGTAAACAGGGGAAGGAAAGTGCTTG 6 77 0 AAAAGGGGAG 0.740816 -209 AATTTAATATAAAAAAGGAAATAAAA 8 81 1 AAAAAGGAAA 0.775926 -16 TCATTATTAAAAATAAGGAAAAATT 11 69 1 AAAAAGGAAA 0.775926 -15 TTCAGGCGGCAAAGAAGGGAGCTAATTTATTCT 19 82 0 AAAAAGGGGT 0.761954 -219 ATTTTTCAGGAAATAAGGCAAAGTAGGGCGTGT 19 191 1 AAAAAGGCAG 0.893705 -110 TTAGCTTAAAAAAGGCGGTGGGCAAATTGC 21 8 1 AAAAAGGCGG 0.789663 -92 TGATAGTTACAAAAAAGGCGACTAAGCAATTTG 21 33 0 AAAAAGGCAT 0.903989 -67 CCTAGAATTCAAATAAGGAGGCTATTTCAAAAC 23 122 1 AAAAAGGAGT 0.883321 -108 AGAATTTATTAAAAAAGAATACGGAGTGTTTTG 23 149 0 AAAAAGAAAG 0.654826 -81 TATCAGATTTAAACAGGAAAATTTT 24 246 1 AAAAGGAAAT 0.48682 -15 TGCTAAAGCTAAAGAGGGAGACTGACTATA 26 8 0 AAAAGGGAAT 0.883321 -30 GACTTTCTTAACACAAGGAGACTTTT 33 15 1 ACAAAGGAAT 0.642579 -16 TAATTTACAAAAATAAGAAAGCTCAGTCAATAA 35 113 0 AAAAAGAAGT 0.48682 -63 AACATAAATAAAAGGAGGAAAATA 36 97 1 AAAGAGGAAT 0.642579 -14 AGTTCAGTATAAACAAGGACACTTTTTATTACT 37 250 1 AAAAAGGAAT 0.944303 -51 TATTCAACTAGAAAAAGGAAATTATT 38 4 0 GAAAAGGAAT 0.777764 -270 ATTTCTTAACAAACAAGGCTAAGACTATCAATT 38 113 0 AAAAAGGCAG 0.893705 -161 ATTTTGCTTTGAAAAAGGATACTAGGGCAATTT 40 93 1 GAAAAGGAAT 0.777764 -66 *** ***** * * Masking position 3 Map Score: 9.29438 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 162 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 14 TGCTCTGTCGTAAATTATTGGAGCAAAAGA 6 142 1 TAAATTATTG 0.9247 -144 TTAGCCTTCCTTTATTATTGACCGTGATGA 6 265 0 TTTATTATTG 0.534931 -21 GATTTCCTTGTTAATTATTGAGACTAAAAA 10 150 0 TTAATTATTG 0.836965 -23 ATGAACTGACAAAATTATTTCTGTTTTTGC 13 54 0 AAAATTATTT 0.629233 -159 AGCGAATGCGAAAATTATTGTGATCAATAT 20 67 1 AAAATTATTG 0.782323 -134 TTACACTTTTTATATTATTTTTTCTTACAT 20 160 1 TATATTATTT 0.565079 -41 TATTAGATAATAGATTATTGAGTTTGTTGA 24 44 1 TAGATTATTG 0.809741 -217 CAATTTATCGTAAATTATTTATGATCAAAA 27 45 0 TAAATTATTT 0.852917 -163 TAATTTATACTAAATTATTGTAAATAAACC 27 151 0 TAAATTATTG 0.9247 -57 TAATTTAGTATAAATTAATGTAATCGTTTA 27 164 1 TAAATTAATG 0.547235 -44 CAAAATCAGTAAAATTATTTTAACATATTG 35 55 1 AAAATTATTT 0.629233 -121 GTAAAATAAATAAATTATTTATAAATCAAT 35 81 0 TAAATTATTT 0.852917 -95 GTGTTTATTCTTGATTATTTTGCTTTGAAA 40 77 1 TTGATTATTT 0.456567 -82 TTTTATATTTTTAATTATTGATTAGTCGAG 40 131 1 TTAATTATTG 0.836965 -28 ********** Masking position 4 Map Score: 7.47977 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 163 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 15 TCTTGTTGAGATTATAGGGCGAATGTAATTC 5 40 0 ATATAGGGCG 0.949587 -233 ATTGTTTGTGATTATAGGGCGAATGTAATTC 5 176 0 ATATAGGGCG 0.949587 -97 ATCACAAACAATCATAGGGCAAATTGTCCTT 5 195 1 ATATAGGGCA 0.936023 -78 GAAATAAGGCAAAGTAGGGCGTGTTTTCTTT 19 200 1 AAGTAGGGCG 0.973689 -101 GAGCAAAGAAAAAGTAGGTCGCCATCGGCGA 19 252 1 AAGTAGGTCG 0.763774 -49 AAGTGTAATCATTGTAGGGAAGTGCGGCCAA 20 137 0 ATGTAGGGAA 0.71521 -64 TAAGTACGTCAAAATAGGGCTCAAGTATAAC 25 27 1 AAATAGGGCT 0.783054 -199 AAAAGGTAATAAAGTAGGGCAAATTCAAAAC 37 180 1 AAGTAGGGCA 0.966381 -121 ACCCATATCAAAGGGAGGGCATTAGCTCAAT 38 37 0 AAGGAGGGCA 0.857034 -237 TTGAAAAAGGATACTAGGGCAATTTTCTGGT 40 101 1 ATCTAGGGCA 0.868262 -58 ** ******** Masking position 6 Map Score: 5.31906 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 28 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987