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_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 HI0054 109 uxu operon regulator (uxuR) #2 HI0055 27 mannonate dehydratase (uxuA) #3 HI0079 102 peptidyl-prolyl cis-trans isomerase B (ppiB) #4 HI0096 300 H. influenzae predicted coding region HI0096 #5 HI0097 272 iron(III) ABC transporter, periplasmic-binding protein (hitA) #6 HI0098 216 iron(III) ABC transporter, permease protein (hitB) #7 HI0140 272 N-acetylglucosamine-6-phosphate deacetylase (nagA) #8 HI0141 285 glucosamine-6-phosphate isomerase (nagB) #9 HI0144 45 glucose kinase, putative #10 HI0145 300 conserved hypothetical protein #11 HI0190 28 ferric uptake regulation protein (fur) #12 HI0191 96 flavodoxin (fldA) #13 HI0289 222 serine transporter (sdaC) #14 HI0291 74 H. influenzae predicted coding region HI0291 #15 HI0292 76 mercuric ion scavenger protein (merP) #16 HI0351 172 UDP-glucose 4-epimerase (galE) #17 HI0352 300 conserved hypothetical protein #18 HI0518 83 purine-nucleoside phosphorylase (deoD) #19 HI0519 98 transport protein, putative #20 HI0521 212 conserved hypothetical protein #21 HI0604 300 adenylate cyclase (cyaA) #22 HI0615_HI0616 197 HI0615: L-fucose operon activator (fucR), HI0616: ATP-dependent helicase (hepA) #23 HI0618 26 glp protein, putative #24 HI0619 29 glycerol-3-phosphate regulon repressor (glpR) #25 HI0680 31 rarD protein, putative #26 HI0681 300 transcriptional activator (ilvY) #27 HI0685_HI0686 292 HI0685: anaerobic glycerol-3-phosphate dehydrogenase, subunit A (glpA), HI0686: glycerol-3-phosphatase transporter (glpT) #28 HI0687 99 conserved hypothetical protein #29 HI0688 94 H. influenzae predicted coding region HI0688 #30 HI0690 229 glycerol uptake facilitator protein (glpF) #31 HI0727.1 260 cyaY protein (cyaY) #32 HI0745 225 L-asparaginase II (ansB) #33 HI0819 37 galactokinase (galK) #34 HI0820 207 galactose-1-phosphate uridylyltransferase (galT) #35 HI0953 124 DNA/pantothenate metabolism flavoprotein (dfp) #36 HI0954 47 deoxyuridinetriphosphatase (dut) #37 HI0956 21 conserved hypothetical protein #38 HI0957 66 catabolite gene activator (crp) #39 HI1027 58 L-xylulose kinase (lyx) #40 HI1028 30 conserved hypothetical protein #41 HI1030 71 conserved hypothetical transmembrane protein #42 HI1031 175 conserved hypothetical protein #43 HI1116 110 deoxyribose-phosphate aldolase (deoC) #44 HI1164 300 outer membrane protein P5 (ompA) #45 HI1350 273 cytidine deaminase (cdd) #46 HI1678 300 kpsF protein (kpsF) #47 HI1713 158 phosphocarrier protein HPr (ptsH) #48 HI1714 70 conserved hypothetical protein Motif number 1 AAATAAAAACAAACCGCACTTTTATAGCACT 3 29 1 AACCGCACTT 0.958219 -74 TCCGCAGAATTGACCGCACTTTGTGTTGAAA 4 234 1 TACCGCACTT 0.996283 -67 AGATAGAAAATTGCCGCACTTATAATGATCC 8 189 1 TGCCGCACTT 0.989145 -97 TCGCTGAAAATTACCGCACTTTTTATAAAAA 13 62 1 TACCGCACTT 0.996283 -161 CGGTCATTTTTTACCGCACTTTTTAATTGAT 18 20 0 TACCGCACTT 0.996283 -64 CGGTAAAAAATGACCGCACTTTATTCATTTT 18 35 1 TACCGCACTT 0.996283 -49 CGGCGAATTTTCACCGCACTTTTTGTAAACG 19 12 0 TACCGCACTT 0.996283 -87 CACAAAAAATTGACCGCACTTTTAGGAAGAT 22 85 1 TACCGCACTT 0.996283 -113 ACCAGAAAACTAACCGCACTTTTTA 26 5 0 TACCGCACTT 0.996283 -296 CGCTAAATTTTACCCGCACTTTAAATTGAAG 26 49 1 TCCCGCACTT 0.971422 -252 TTGTTAATTTTGGCCGCACTTCCCTACAATG 27 220 1 TGCCGCACTT 0.989145 -73 CTCTTCATTTCAACCGCACTTCTAAGGAGTG 30 205 1 CACCGCACTT 0.989145 -25 GCTTTATAATTTGCCGCATTTTATCAGATTT 31 225 1 TGCCGCATTT 0.882421 -36 GGCTCAAGTATAACCGCACTTGGGTTATCTT 32 44 1 TACCGCACTT 0.996283 -182 TTCCAACCGTACTTTTACCTAAAA 36 4 1 CACCGTACTT 0.882421 -44 TATAGGATAATAAGCGCACTTTTGAACGTTC 44 112 1 TAGCGCACTT 0.946048 -189 TTGAAGCCCTTAACCGTATTTATACGACCTA 46 170 0 TACCGTATTT 0.645168 -131 GGGATTTTATTGACCGCACTAGTGATTGCCC 46 241 0 TACCGCACTA 0.950438 -60 AGGGAAAAAACGACCGCACTTTT 48 58 1 CACCGCACTT 0.989145 -13 * ********* Masking position 10 Map Score: 59.4663 Number of sites scoring better than the average of aligned sites = 1344 Number in coding regions = 909 Number in noncoding regions = 435 Number of orfs with sites within 600 bp upstream = 292 Fraction of orfs with sites within 600 bp upstream = 0.0469001 Motif number 2 ATCGCATTCATCAATAAAACAACTAACAAGGA 14 47 1 TCAATAACAA 0.990904 -28 AGTTTAACCATCAATAAAACAACTAACAAGGA 15 49 1 TCAATAACAA 0.990904 -28 ATGGTGATTTTCAATAAAATAAAAAACCTGTT 16 91 0 TCAATAATAA 0.877685 -82 AATCAATCAATCAATCAATCAATC 17 3 1 TCAATAACAA 0.990903 -298 AATCAATCAATCAATCAATCAATCAATCAATC 17 15 1 TCAATAACAA 0.990903 -286 AATCAATCAATCAATCAATCAATCAATCAATC 17 35 1 TCAATAACAA 0.990903 -266 AATCAATCAATCAATCAATCAATCAATCAATC 17 47 1 TCAATAACAA 0.990903 -254 AATCAATCAATCAATCAATCAATCAATCAATC 17 67 1 TCAATAACAA 0.990903 -234 AATCAATCAATCAATCAATCAATCAATCAATC 17 79 1 TCAATAACAA 0.990903 -222 AATCAATCAATCAATCAATCAATCAATCAATC 17 91 1 TCAATAACAA 0.990903 -210 AATCAATCAATCAATCAATCAATCAAAGTCTG 17 103 1 TCAATAACAA 0.990903 -198 GGGCATTAGCTCAATTATTCAACTAGAAAAAG 45 20 0 TCAATATCAA 0.920593 -254 GTTAAGGGCTTCAATAAACCAGCGATTGTCTA 46 187 1 TCAATAACAG 0.945004 -114 ***** ** *** Masking position 7 Map Score: 33.5438 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 41 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 3 TGCTATAAAAGTGCGGTTTGTTTTTATTTCA 3 27 0 GTGCGGTTGT 0.892792 -76 TCAACACAAAGTGCGGTCAATTCTGCGGAAG 4 232 0 GTGCGGTAAT 0.991618 -69 ATCATTATAAGTGCGGCAATTTTCTATCTTG 8 187 0 GTGCGGCATT 0.954475 -99 TTTATAAAAAGTGCGGTAATTTTCAGCGACA 13 60 0 GTGCGGTATT 0.988991 -163 TCACTATTTTGTGTGGTAAGAATGGTGATTT 16 113 0 GTGTGGTAGA 0.785593 -60 CAATTAAAAAGTGCGGTAAAAAATGACCGCA 18 22 1 GTGCGGTAAA 0.989622 -62 AATGAATAAAGTGCGGTCATTTTTTACCGCA 18 33 0 GTGCGGTATT 0.988991 -51 TTTACAAAAAGTGCGGTGAAAATTCGCCGAC 19 14 1 GTGCGGTAAA 0.989622 -85 CTTCCTAAAAGTGCGGTCAATTTTTTGTGAG 22 83 0 GTGCGGTAAT 0.991618 -115 TAAAAAGTGCGGTTAGTTTTCTGGTAT 26 7 1 GTGCGGTAGT 0.98983 -294 TCAATTTAAAGTGCGGGTAAAATTTAGCGTA 26 47 0 GTGCGGGAAA 0.923622 -254 TTGTAGGGAAGTGCGGCCAAAATTAACAACA 27 218 0 GTGCGGCAAA 0.956998 -75 CTCCTTAGAAGTGCGGTTGAAATGAAGAGTG 30 203 0 GTGCGGTGAA 0.956998 -27 GATAACCCAAGTGCGGTTATACTTGAGCCCT 32 42 0 GTGCGGTATA 0.986377 -184 ACGTTCAAAAGTGCGCTTATTATCCTATAAA 44 110 0 GTGCGCTATT 0.861473 -191 GGGTGAAAGGGTGCGGTAAGAGCGCACCGTG 46 21 0 GTGCGGTAGA 0.987413 -280 GCAATCACTAGTGCGGTCAATAAAATCCCCA 46 243 1 GTGCGGTAAT 0.991618 -58 AAAAGTGCGGTCGTTTTTTCCCTTG 48 56 0 GTGCGGTGTT 0.954475 -15 ******* *** Masking position 2 Map Score: 38.8954 Number of sites scoring better than the average of aligned sites = 980 Number in coding regions = 604 Number in noncoding regions = 376 Number of orfs with sites within 600 bp upstream = 255 Fraction of orfs with sites within 600 bp upstream = 0.0409573 Motif number 4 TTATAGATAAAAATGATAACTATTAAAATG 4 2 1 TAATAAAAAC 0.737631 -299 TAAATTGATATTTAGATGAAAAACAAAACGGTACATTAA 5 35 0 TTATAAAAAC 0.859811 -238 TCGCCCTATAATCTCAACAAGAGCTAAAAGTGAAAACCG 7 49 1 ATAAAAAAAA 0.843466 -224 GAATTTCTTTTTAAAAACAAGATAGAAAATTGCCGCACT 8 170 1 TTAAAAAAAA 0.952165 -116 TGATCACATTTATGAAAAAACACTTCAAAAATATTCTTT 10 138 1 TAAAAAAAAA 0.90123 -163 TGGATAAGCCTTATAATCAATAGATTAAATTTAATATAA 12 54 1 TTATAAAAAA 0.934018 -43 TACCGCACTTTTTATAAAAAAATTTTAACTTGATCACAA 13 73 1 TTAAAAAAAC 0.896097 -150 GTTTATAGTTTAACCATCAATAAAACAACTAACAAGGAG 15 43 1 TAATAAAAAC 0.737631 -34 AGAATGGTGATTTTCAATAAAATAAAAAACCTGTTGCTA 16 87 0 TTAAAAAAAA 0.952143 -86 CATTATTTTCTTGGCAAGAAAATAAAAAAAGTATTTTTT 17 236 1 TTAAAAAAAA 0.952165 -65 TTTTTATTCATTATTAAAAATAAGGAAAAATT 18 62 1 TTAAAAAAAA 0.952165 -22 CTATAAATTTTACCTATCAACAATCAAAATGACTTTTTT 21 171 0 TAATAAAAAA 0.866469 -130 AATCACAATTTTTCGAAAAATACTATAAATTTTACCTAT 21 193 0 TTAAAAAAAA 0.952127 -108 ATTTAGCGTATTTTGAAAAATACCAGAAAACTAACCGCA 26 18 0 TTAAAAAAAA 0.952165 -283 CGAAACCCGATATTAAATAAAAGAAGAAATT 26 280 1 TAAAAAAAAA 0.90123 -21 TAAAAGAAAATAAAAAATAAGAAAGTAAAAAAAATCAAA 27 85 1 TAAAAAAAAA 0.90123 -208 GCGAAAATTATTGTGATCAATATCACAAAATCGCTTTCT 27 166 1 TTATAAAAAA 0.934018 -127 TCCCAAAATGTAAGAAAAAATAATATAAAAAGTGTAATC 27 250 0 TAAAAAAAAA 0.90123 -43 TTTTGTAACTATCATAAGAATAATAAAAAGATAAGTATC 28 52 1 ATAAAAAAAA 0.843465 -48 CATAAAGGTTATACAATCAACAAAAAAAATTATGTGATC 32 106 1 ATATAAAAAA 0.793044 -120 TAAATTAAGTTATTTATAAACAATGGAAAAACAAATTTA 32 152 0 TAATAAAAAA 0.866469 -74 CATGAATCCATTGACATCAAAAATAAAACGGAATTTTTG 38 15 1 TTATAAAAAC 0.859811 -52 ATAAATTATTTATAAATCAATATGTTAAAATAATTTTAC 42 63 0 TAATAAAAAA 0.866469 -113 ATTTTACTATATAAAATTAAGAGAGGAAAAA 42 155 1 ATATAAAAAA 0.793044 -21 TGCGCTTATTATCCTATAAAAATTGAAAAGATCAAATTC 44 91 0 ATATAAAAAA 0.793044 -210 AACATATCCTTAGGAAAAATATTAAAAATTATAACTGT 45 246 0 TTAAAAAAAA 0.952143 -28 CGATTGAGATTGTGAATAATAAATAAACTATTTAGCTT 47 10 1 TTAAAAAAAC 0.896097 -149 CCTGAATTAAATCATAAAAATAAGCTAAATAGTTTATTT 47 31 0 ATAAAAAAAA 0.843466 -128 TTTTTTCATTTTACCAAAAACAAGGGAAAAAACGACCGC 48 36 1 TTAAAAAAAA 0.952165 -35 ** ** ** * *** Masking position 10 Map Score: 42.6286 Number of sites scoring better than the average of aligned sites = 283 Number in coding regions = 182 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 5 AATTTAAATTGATATTTAGATGAAAAACAAA 5 47 0 GATATTAGAT 0.502739 -226 CTTGTTAGTTGTTTTATTGATGAATGCGATT 14 46 0 GTTTTTTGAT 0.813811 -29 CTTGTTAGTTGTTTTATTGATGGTTAAACTA 15 48 0 GTTTTTTGAT 0.813811 -29 TTGATTGATTGATTGATTGATT 17 2 0 GATTGTTGAT 0.98821 -299 TTGATTGATTGATTGATTGATTGATTGATTG 17 14 0 GATTGTTGAT 0.98821 -287 TTGATTGATTGATTGATTGATTGATTGATTG 17 26 0 GATTGTTGAT 0.98821 -275 TTGATTGATTGATTGATTGATTGATTGATTG 17 38 0 GATTGTTGAT 0.98821 -263 TTGATTGATTGATTGATTGATTGATTGATTG 17 50 0 GATTGTTGAT 0.98821 -251 TTGATTGATTGATTGATTGATTGATTGATTG 17 70 0 GATTGTTGAT 0.98821 -231 TTGATTGATTGATTGATTGATTGATTGATTG 17 82 0 GATTGTTGAT 0.98821 -219 TTGATTGATTGATTGATTGATTGATTGATTG 17 94 0 GATTGTTGAT 0.98821 -207 GACAGACTTTGATTGATTGATTGATTGATTG 17 106 0 GATTGTTGAT 0.98821 -195 ATTATTAGTGGATAGCTTGATATTTTTCTTA 21 62 0 GATAGTTGAT 0.950951 -239 AAAAGAAAGCGATTTTGTGATATTGATCACA 27 177 0 GATTTGTGAT 0.87115 -116 CAAAATATAAGATTTATAGATTATAACAAGG 34 19 0 GATTTTAGAT 0.813811 -189 TAATTTTACTGATTTTGTGATCTAGATCCTA 42 41 0 GATTTGTGAT 0.87115 -135 TGTTAGCCGCGATAGTTTGATTAAATATTCA 45 194 0 GATAGTTGAT 0.950951 -80 ***** ***** Masking position 3 Map Score: 35.6605 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 28 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 ATCATAGTTAAACATAACAAGTAATTTTATTCTGTCA 1 33 0 AATAAAATTT 0.8831 -77 ATGATTATGAAACATAAAAACTCTTTTTGGAATACCA 1 70 1 AATAACTTTT 0.805827 -40 ATATCAATTTAAATTGAGAACTATTTGCATTTAAATA 5 63 1 AATAAATTTG 0.894456 -210 ATTGCTCTTAAACGTAAGGACAATTTGCCCTATGATT 7 204 0 AATAAATTTG 0.894465 -69 TTCTGTTCCTAATATCAACATCAGTTTAACATAGCAA 7 245 0 AATAAAGTTT 0.586391 -28 TAATATGAGAATCAATTTAGGCCAAAAA 10 2 1 AATAAAATTT 0.88181 -299 GTAGTTTAAGTGAGAATGCTTTTATGATATAGT 12 7 1 TATAACTTTT 0.465434 -90 AAAAAATTTTAACTTGATCACAATTTTAGAATTTGCT 13 89 1 AATAAATTTT 0.933259 -134 ACATAAGGTTAAGGTCAAGAAGTTTTTT 15 2 0 AATAATTTTT 0.667705 -75 GAGACTAAAAAATTATATCACTATTTTGTGTGGTAAG 16 124 0 AAAAAATTTT 0.698544 -49 GTAATGGAACAAGTTTAAAATCAATTGACTATAGTTT 17 147 1 AATAAAATTG 0.819005 -154 TTGGCAAGAAAATAAAAAAAGTATTTTTTAATTGTTC 17 246 1 AAAAAATTTT 0.698621 -55 GGAAAGATGCAAAAACAGAAATAATTTTGTCAGTTCA 20 46 1 AAAAAAATTT 0.552992 -167 ACGGTTACTCAAAATAAATATGTTTTTGATATAAATG 20 81 0 AATAATTTTT 0.652759 -132 TTGAGTAAGGTATTTTATAATACTTTGCGTTGATAAG 21 29 1 TATAACTTTG 0.342751 -272 CAATTTTTCGAAAAATACTATAAATTTTACCTATCAA 21 190 0 AAAAAAATTT 0.542361 -111 TCTTGAAAAGAAACTCACAAAAAATTGACCGCACTTT 22 70 1 AATAAAATTG 0.819012 -128 AAGTGCGGCCAAAATTAACAACATTTTGAGTGTAAAA 27 204 0 AATAAATTTT 0.932618 -89 GAATAATAAAAAGATAAGTATCATTTTTGGGAAAAGT 28 69 1 AATAAATTTT 0.932618 -31 TTTTCAGGAAAATATAAAGAACCTTTTACGCCACATC 31 83 1 AATAACTTTT 0.805827 -178 AAAAAATGAAAAAATTACTATTAATTTTAGTACTTAG 31 143 0 AATAAAATTT 0.785444 -118 GCAAGTACGGAATTTAAGCATAATTTTTTTGAAAGAT 32 70 0 AATAAATTTT 0.933259 -156 GATTTCTCCTAAGATGAATAAAAATTTCTCCAAAGTA 32 198 0 AATAAAATTT 0.8831 -28 TGATCATAAATAATTTACGATAAATTGAAAGCGGTTA 34 48 1 TATAAAATTG 0.487013 -160 ACAAAATAAGAAAATAAGCAAAATTTTTTATGATTTA 34 102 0 AATAAATTTT 0.932618 -106 ACCGTACTTTTACCTAAAAATGAATTTCAAACGGAGT 36 16 1 TATAAAATTT 0.613165 -32 TATAAATCAATATGTTAAAATAATTTTACTGATTTTG 42 55 0 TATAAATTTT 0.748033 -121 ACCATAGTCAAAAATAAAGAATTTTTGCTACAATAGG 43 57 1 AATAATTTTG 0.546179 -54 ACTAAACAAAAAATTCAAAAGAATTTGATCTTTTCAA 44 71 1 AATAAATTTG 0.894456 -230 TGTTTTTGGTAAAATGAAAAAAATTTTTGCATAGGAT 48 21 0 AATAAATTTT 0.932618 -50 ** * * * ***** Masking position 10 Map Score: 30.6448 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 141 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 7 CTATAAAAGTGCGGTTTGTTTTTATTTCATTT 3 24 0 GCGGTTTTTT 0.900206 -79 AACACAAAGTGCGGTCAATTCTGCGGAAGTTT 4 229 0 GCGGTATTCT 0.946394 -72 AATCTCTCAAGCGGTTTATTATCCAGATACGA 4 268 1 GCGGTTTTAT 0.774652 -33 ACGCACGCAAGCGGTTAATTTTGTTAGAGAAT 6 60 0 GCGGTATTTT 0.98242 -157 TCTTTATGTAGGGGCGAATTACATTCGCCCTA 7 25 1 GGGGCATTAC 0.759823 -248 TCTTTATGTAGGGGCGAATTACATTCGCCCTA 7 161 1 GGGGCATTAC 0.759823 -112 AAAACAGGGGGAGGTAAGTTTTTTCTAATTTA 8 16 0 GAGGTATTTT 0.772811 -270 AGGGCGGAAGGGGGCAACTTCTATTGCTCTGT 8 118 1 GGGGCATTCT 0.792219 -168 CATTATAAGTGCGGCAATTTTCTATCTTGTTT 8 184 0 GCGGCATTTC 0.971692 -102 TATAAAAAGTGCGGTAATTTTCAGCGACAAAA 13 57 0 GCGGTATTTC 0.974645 -166 TGAATAAAGTGCGGTCATTTTTTACCGCACTT 18 30 0 GCGGTATTTT 0.98242 -54 TTATGAAAAGTCGGCGAATTTTCACCGCACTT 19 22 0 TCGGCATTTT 0.712204 -77 TCCTAAAAGTGCGGTCAATTTTTTGTGAGTTT 22 80 0 GCGGTATTTT 0.98242 -118 TAAAAAGTGCGGTTAGTTTTCTGGTATTTT 26 9 1 GCGGTATTTT 0.98242 -292 CTGATAAAATGCGGCAAATTATAAAGCCTTTC 31 220 0 GCGGCATTAT 0.95004 -41 TAAATTGAAAGCGGTTACTTTCATAAGTATGA 34 68 1 GCGGTATTTC 0.974645 -140 AAAAGTGCGGTCGTTTTTTCCCTTGTTT 48 53 0 GCGGTGTTTT 0.883477 -18 ***** * **** Masking position 9 Map Score: 22.0244 Number of sites scoring better than the average of aligned sites = 503 Number in coding regions = 326 Number in noncoding regions = 177 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 8 TTAAATTGATATTTAGATGAAAAACAAAACGGTA 5 41 0 ATAATGAAAA 0.686104 -232 ATATTTAAATTAGAAAAAACTTACCT 8 3 1 ATAATTAAAA 0.788521 -283 AAATTTGGCGAACTATATCATAAAAGCATTCTCA 12 21 0 ATAATCAAAA 0.96542 -76 AAAAAATTTTAACTTGATCACAATTTTAGAATTT 13 89 1 ATTATCAAAT 0.430531 -134 TTGTCAGTTCATTTATATCAAAAACATATTTATT 20 72 1 ATAATCAAAA 0.965417 -141 AAAAAATGTGACATAAATCACAATTTTTCGAAAA 21 213 0 ATAATCAAAT 0.84998 -88 AGTTTTATCAATGTAAATCAGAAAGAGAATAATT 22 11 0 ATAATCAAAA 0.96542 -187 TAAGAAAGTAAAAAAAATCAAAAATGTGAAGTGT 27 102 1 AAAATCAAAA 0.900402 -191 AATTATTGTGATCAATATCACAAAATCGCTTTCT 27 171 1 AAAATCAAAA 0.900402 -122 ACTCTAACAGAGTAACATCATAATCAATCTAGGT 30 81 1 AAAATCAAAT 0.647222 -149 AAATTATGTGATCGAGATCATAAATTTGTTTTTC 32 132 1 AGAATCAAAA 0.88228 -94 TAAATCTTATATTTTGATCATAAATAATTTACGA 34 34 1 ATTATCAAAA 0.785317 -174 CATAAGTATGAACTAAATCATAAAAAATTTTGCT 34 89 1 ATAATCAAAA 0.96542 -119 ACATGAATCCATTGACATCAAAAATAAAACGGAA 38 14 1 AGAATCAAAA 0.882267 -53 AGAAAATAGGATCTAGATCACAAAATCAGTAAAA 42 35 1 ATAATCAAAA 0.965419 -141 TTGCTACAATAGGTAAAACATAAATAAAAGGAGG 43 81 1 ATAAACAAAA 0.666379 -30 TTTTAATTAAAGCTACATTATAAACAGTCACTTA 44 217 0 ATAATTAAAA 0.788521 -84 TATCCTTAGGAAAAATATTAAAAATTATAACTGT 45 246 0 AAAATTAAAA 0.546976 -28 AAAAAGCCTGAATTAAATCATAAAAATAAGCTAA 47 42 0 ATAATCAAAA 0.965419 -117 * ** **** *** Masking position 7 Map Score: 19.6876 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 62 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 9 AAAGTGCGGTTTGTTTTTATTTCATTTTACGAGCTT 3 15 0 TTTTTTCATT 0.33656 -88 GGAACAATTATTCCGCCTTATTTATTTGATCTGACA 4 39 0 TTCTTTTATT 0.887428 -262 TGTTCCGCCTTTTCCTATTATTTCTTCAATGCTTTT 4 69 1 TTTTTTTCTT 0.856752 -232 GTGGCTATTCTATGCCTAATTTTATTTAAATGCAAA 5 86 0 TACATTTATT 0.552625 -187 ATTAGCCTTCCTTTATTATTGACCGTG 8 269 0 TTCTTTTATT 0.887428 -17 TAAAACTATTTTAAATTTGTTTTTTTACTCTTAGAA 10 76 0 TTTTTTTTTT 0.654876 -225 TTTAAAATAGTTTTACGAGTTTTATTTCCAAAATGA 10 97 1 TTCATTTATT 0.783251 -204 TTTTATTTCCTTTTTTATATTAAATT 12 81 0 TTTTTTTTTT 0.654876 -16 TTAAAATCAATTGACTATAGTTTATTACCTAAAGAT 17 161 1 TTTTTTTATT 0.811436 -140 ATGACCGCACTTTATTCATTTTTATTCATTATTAAA 18 44 1 TTTATTTATT 0.663592 -40 ATTCGGCTTATTCTACTTGTTTTCTTATGAAAAGTC 19 42 0 TTCTTTTCTT 0.916364 -57 ACAAGTAGAATAAGCCGAATTTTATTAACTTAACTA 19 58 1 TACATTTATT 0.552625 -41 TTATTTCTGTTTTTGCATCTTTCCTTTTATGATAAA 20 34 0 TTCTTTCCTT 0.563631 -179 GAGTAACCGTTTGCATAATGTTTATTTTCTAAAACT 20 108 1 TTTATTTATT 0.663592 -105 AAATTGTGATTTATGTCACATTTTTTTGCATTTATA 21 221 1 TTTATTTTTT 0.465186 -80 ATCCTTATTTTAAACCATTATTTATT 25 1 0 TACTTTTATT 0.729346 -31 AGAAGGGAGCTAATTTATTCTTTCTTCAATTTAAAG 26 67 0 TATTTTTCTT 0.671536 -234 TAAGGCAAAGTAGGGCGTGTTTTCTTTTTGCCTACT 26 204 1 TACTTTTCTT 0.789267 -97 ACATTTTTGATTTTTTTTACTTTCTTATTTTTTATT 27 93 0 TTTTTTTCTT 0.856752 -200 TTACACTTTTTATATTATTTTTTCTTACATTTTGGG 27 252 1 TATTTTTCTT 0.671536 -41 TAATAGTAATTTTTTCATTTTTTCTTTCTCACTTAT 31 157 1 TTCTTTTCTT 0.916364 -104 AGTACGGAATTTAAGCATAATTTTTTTGAAAGATAA 32 68 0 TTCTTTTTTT 0.776591 -158 TCATAAAAAATTTTGCTTATTTTCTTATTTTGTGAC 34 106 1 TTCTTTTCTT 0.916364 -102 TTTGACTCCTGTTTTTTATCAATGTAA 34 191 0 TTTCTTTTTT 0.327172 -17 TTTCGTTATTTTACTTTAATTTTATTGAATGCCCAA 35 69 0 TTTATTTATT 0.663592 -56 ATATTCTCCTTAGTTTTTTATGGGCTGGA 39 40 0 TTCTTTTTTT 0.776591 -19 TTTTGTGATCTAGATCCTATTTTCTTGTGATAATAT 42 24 0 TACTTTTCTT 0.789267 -152 TTTACATTTATTGACTGAGCTTTCTTATTTTTGTAA 42 106 1 TTTATTTCTT 0.732736 -70 TATTTTCCTCCTTTTATTTATGTTTTAC 43 93 0 TTCCTTTATT 0.668895 -18 GGGTTTTGAATTTGCCCTACTTTATTACCTTTTGAC 44 177 0 TTCTTTTATT 0.887428 -124 ATAGCTTCTATTTATTACAATTTCTTAACAAACAAG 45 129 0 TTTCTTTCTT 0.605163 -145 CTGTACTTATTAAATCAAAATTTATTGTTAGCCGCG 45 214 0 TACATTTATT 0.552625 -60 ** * * ****** Masking position 11 Map Score: 28.6975 Number of sites scoring better than the average of aligned sites = 455 Number in coding regions = 328 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 10 CTGTCAATGGCATATAAGGAGTCTAAAA 1 4 0 CATAAAGGCA 0.822743 -106 GCATTTAAATAAAATTAGGCATAGAATAGCCACAA 5 89 1 AAAATAGGAA 0.850327 -184 ATATGAGAATCAATTTAGGCCAAAAATGTATGTTT 10 13 1 CAATTAGGAA 0.525145 -288 TTTTCTCCCCCAAAATAGGATTCGAGAGCAATTCT 10 45 1 CAAATAGGCA 0.957411 -256 AATAAAACAACTAACAAGGAGTAAAA 14 59 1 CTAAAAGGAA 0.761422 -16 AATAAAACAACTAACAAGGAGTAAAA 15 61 1 CTAAAAGGAA 0.761422 -16 TCTTACCACACAAAATAGTGATATAATTTTTTAGT 16 123 1 CAAATAGTAA 0.659506 -50 TTTTCATAAGAAAACAAGTAGAATAAGCCGAATTT 19 45 1 AAAAAAGTAA 0.524135 -54 TTTCAGGCGGCAAAGAAGGGAGCTAATTTATTCTT 26 81 0 CAAAAAGGCA 0.972052 -220 CGTGCAAAGCAAAAGTAGGCAAAAAGAAAACACGC 26 218 0 AAAATAGGAA 0.850327 -83 CGAGCAAAGAAAAAGTAGGTCGCCATCGGCGAAAC 26 251 1 AAAATAGGCA 0.892037 -50 ATGATAGTTACAAAAAAGGCGACTAAGCAATTTGC 28 32 0 CAAAAAGGCA 0.972052 -68 ACCTAGAATTCAAATAAGGAGGCTATTTCAAAACA 30 121 1 CAAAAAGGCA 0.972052 -109 TTAAGTACGTCAAAATAGGGCTCAAGTATAACCGC 32 26 1 CAAATAGGCA 0.957411 -200 TACATTGATAAAAAACAGGAGTCAAA 34 192 1 AAAACAGGCA 0.686966 -16 GTAAAACATAAATAAAAGGAGGAAAATA 43 93 1 AATAAAGGAA 0.539808 -18 AATTTCTTAACAAACAAGGCTAAGACTATCAATTA 45 112 0 CAAAAAGGAA 0.959864 -162 TAGAAGCTATCAAATAAGTGATCAAGATCACAGTT 45 155 1 CAAAAAGTCA 0.813374 -119 CATTTTACCAAAAACAAGGGAAAAAACGACCGCAC 48 42 1 AAAAAAGGAA 0.897854 -29 **** **** * * Masking position 7 Map Score: 15.1808 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 72 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 11 TTTTGGAAATAAAACTCGTAAAACTATTTTAA 10 98 0 AAAATCGTAA 0.450937 -203 AAGGCTTATCCAAATTTGGCGAACTATATCAT 12 34 0 CAAATTGGGA 0.833973 -63 TCAGCGACAAAAAAATCGGTGCGATGACGACA 13 37 0 AAAATCGGGC 0.775343 -186 AGTATTGCTCAAAAATTGTAGAACAATTAAAA 17 271 0 AAAATTGTGA 0.802585 -30 TTTTCTTATGAAAAGTCGGCGAATTTTCACCG 19 27 0 AAAATCGGGA 0.948257 -72 CCAGAACAACAAAAATTGGCGAACAATTTACC 21 267 0 AAAATTGGGA 0.966954 -34 TTACATTGATAAAACTTGGGGGCGTATTGTAG 22 29 1 AAAATTGGGG 0.846398 -169 TTGCCGCCTGAAAAATTGGAAATTTGTAGGAA 26 103 1 AAAATTGGAA 0.904193 -198 TTATTTCCTGAAAAATTGGAAATTTGCTTAAC 26 175 0 AAAATTGGAA 0.904193 -126 CGTGCAAAGCAAAAGTAGGCAAAAAGAAAACA 26 221 0 AAAATAGGAA 0.598034 -80 CACATAATTAAAAAGTTGGAGAAAAAATT 27 8 0 AAAATTGGGA 0.966954 -285 AGCAATATTCAAAAATTGGGGATTTTATTGAC 46 258 0 AAAATTGGGA 0.966954 -43 **** **** ** Masking position 4 Map Score: 7.78874 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 88 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 12 TGAACTGAATAATTTGCACTCAACATAAGG 5 131 1 AATTTGCACT 0.813719 -142 GGGCGAATGTAATTCGCCCCTACATAAAGA 7 25 0 AATTCGCCCC 0.952619 -248 GGGCGAATTACATTCGCCCTATAATCTCAA 7 36 1 CATTCGCCCT 0.947218 -237 GGGCGAATGTAATTCGCCCCTACATAAAGA 7 161 0 AATTCGCCCC 0.952619 -112 GGGCGAATTACATTCGCCCTATAATCACAA 7 172 1 CATTCGCCCT 0.947218 -101 ACGTAAGGACAATTTGCCCTATGATTGTTT 7 200 0 AATTTGCCCT 0.980392 -73 ACAATTTTAGAATTTGCTCTTTGAGATTCT 13 108 1 AATTTGCTCT 0.813719 -115 GTGTCATCTAAATTTACCCTTTTGAAACAG 27 37 1 AATTTACCCT 0.797552 -256 GCGACTAAGCAATTTGCCCACCGCCTTTTT 28 19 0 AATTTGCCCA 0.887411 -81 TAGGGTTTTGAATTTGCCCTACTTTATTAC 44 185 0 AATTTGCCCT 0.980392 -116 TAAAACCAGAAAATTGCCCTAGTATCCTTT 47 106 0 AAATTGCCCT 0.863999 -53 ********** Masking position 2 Map Score: 11.6584 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 54 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 13 TTTGTTTTCCCTCTAAAAAATT 3 91 0 TGTTTTCCCT 0.967446 -12 GCTTCCGTTATGTTTGCCGTTTCTGTATGT 6 178 1 TGTTTGCCGT 0.841426 -39 CAAAAATGTATGTTTTCTCCCCCAAAATAG 10 33 1 TGTTTTCTCC 0.778625 -268 AAGATTATGATGTTTTCCGTTGCAATCAAT 17 192 1 TGTTTTCCGT 0.894426 -109 CTCTTTTCCCTATACGGTGGA 22 187 0 TCTTTTCCCT 0.853291 -11 TTAGCTCCCTTCTTTGCCGCCTGAAAAATT 26 90 1 TCTTTGCCGC 0.514142 -211 TGTTTACCCCCGATTCCCAA 27 283 0 TGTTTACCCC 0.923443 -10 ACCGTGGGTATGTTTACCCACGGTTGTGAG 30 16 0 TGTTTACCCA 0.651087 -214 AAATGAAGAGTGTTTTCCCTAAGTAAAGGG 30 185 0 TGTTTTCCCT 0.967446 -45 TGTTTTCTCTACTGATTAAG 32 1 1 TGTTTTCTCT 0.775364 -225 CTTTTATTTATGTTTTACCTATTGTAGCAA 43 81 0 TGTTTTACCT 0.644005 -30 CCTTTGCTTATGTTTACCCCAAAGGAACGT 44 137 0 TGTTTACCCC 0.923443 -164 ACCGCACTAGTGATTGCCCCTATACTACGC 46 230 0 TGATTGCCCC 0.651176 -71 AGTGCGGTCGTTTTTTCCCTTGTTTTTGGT 48 48 0 TTTTTTCCCT 0.680751 -23 ********** Masking position 5 Map Score: 8.07233 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 85 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 14 AGTAATTCACGACGTAACTGTTTCAATTCGCTT 4 114 1 GAGTACGTTT 0.62534 -187 TGGTTCGTTTAATGTACCGTTTTGTTTTTCATC 5 27 1 AAGTCCTTTT 0.757507 -246 TAGTTTTGCTGATATTACCGTTTATAATGGTCA 5 228 1 GAATACGTTT 0.715682 -45 TTCAGTAAAATATTTCACGGTTTTCACTTTTAG 7 72 0 TATTACGTTT 0.68282 -201 ATATGAAAAATAAATGCCATTTTAAAGAATATT 10 167 0 TAATCCTTTT 0.785741 -134 TATTACCTTTTATATTCCGTTTTATCATAAAAG 20 14 1 TAATCCTTTT 0.787192 -199 AAACGTGAGGAAGATCACAGTTTTAGAAAATAA 20 129 0 AAATACGTTT 0.867701 -84 ATCAACAATCAAAATGACTTTTTTACCTAAGAG 21 162 0 AAATACTTTT 0.7828 -139 AATTGTGATTTATGTCACATTTTTTTGCATTTA 21 222 1 TAGTACTTTT 0.654271 -79 GTGTCATCTAAATTTACCCTTTTGAAACAGTAA 27 37 1 AATTCCTTTT 0.663236 -256 AAAATTTTCCTGTTTAAATCTGATA 31 246 0 AATTCCGTTT 0.780392 -15 TTTTGTGACAAAGATCACGGTTTATTTACAATA 34 133 1 AAATACGTTT 0.867701 -75 TCCTGTTTCAAAAATTCCGTTTTATTTTTGATG 38 29 0 AAATCCTTTT 0.824887 -38 TCTTGCTCCTTACATTCCTGTTTCAAAAATTCC 38 44 0 TAATCCGTTT 0.869697 -23 GTTTTTATCCAAAATAACACTTTCTTAAACAGA 44 40 0 AAATACCTTT 0.458899 -261 AAACCCTAGTTAAGTGACTGTTTATAATGTAGC 44 207 1 TAGTACGTTT 0.773481 -94 AATAATTTCCTTTTTCTAGTTGAAT 45 3 1 TATTCCTTTT 0.607283 -271 ATAAGTGATCAAGATCACAGTTTTAATGAATAT 45 168 1 AAATACGTTT 0.867701 -106 ** ** ** **** Masking position 5 Map Score: 7.82926 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 135 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 15 CTTCATCTTTATGTAGGGGCGAATTACATTCG 7 20 1 ATAGGGGCGA 0.955024 -253 TCTTGTTGAGATTATAGGGCGAATGTAATTCG 7 39 0 ATTAGGGCGA 0.969176 -234 CTTCATCTTTATGTAGGGGCGAATTACATTCG 7 156 1 ATAGGGGCGA 0.955024 -117 ATTGTTTGTGATTATAGGGCGAATGTAATTCG 7 175 0 ATTAGGGCGA 0.969176 -98 ATCACAAACAATCATAGGGCAAATTGTCCTTA 7 195 1 ATTAGGGCAA 0.941188 -78 AGGATAAATTATATTGGGGTGACGTATATCTT 22 111 0 ATTGGGGTGA 0.798727 -87 AAAAGGTAATAAAGTAGGGCAAATTCAAAACC 44 180 1 AATAGGGCAA 0.716133 -121 TCGGCGCGTAGTATAGGGGCAATCACTAGTGC 46 225 1 GTAGGGGCAA 0.716325 -76 TTGAAAAAGGATACTAGGGCAATTTTCTGGTT 47 101 1 ATTAGGGCAA 0.941188 -58 ** ******** Masking position 12 Map Score: 3.95019 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 31 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