AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -ipurR_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 HI0221 129 inosine-5'-monophosphate dehydrogenase (guaB) #2 HI0221.1 109 H. influenzae predicted coding region HI0221.1 #3 HI0222 109 GMP synthase (guaA) #4 HI0329 37 conserved hypothetical protein #5 HI0330 98 opacity associated protein (oapA) #6 HI0331 59 opacity associated protein (oapB) #7 HI0334 77 GTP pyrophosphokinase (relA) #8 HI0336 82 molybdopeterin biosynthesis protein (mog) #9 HI0500 300 conserved hypothetical protein #10 HI0501 167 high affinity ribose transport protein (rbsD) #11 HI0505 97 ribokinase (rbsK) #12 HI0506 27 rbs repressor (rbsR) #13 HI0638 128 conserved hypothetical protein #14 HI0639 22 adenylosuccinate lyase (purB) #15 HI0752 300 phosphoribosylformylglycinamidine synthase (purL) #16 HI0840 116 conserved hypothetical protein #17 HI0842 197 H. influenzae predicted coding region HI0842 #18 HI0885 191 thiol:disulfide interchange protein (dsbD) #19 HI0886 111 H. influenzae predicted coding region HI0886 #20 HI0887 187 phosphoribosylaminoimidazolecarboxamide formyltransferase (purH) #21 HI0888 95 phosphoribosylamine--glycine ligase (purD) #22 HI0889 123 serine hydroxymethyltransferase (serine methylase) (glyA) #23 HI1205 214 conserved hypothetical protein #24 HI1206 86 colicin V production protein (cvpA) #25 HI1401 229 dihydroorotate dehydrogenase (pyrD) #26 HI1402 32 H. influenzae predicted coding region HI1402 #27 HI1403 32 H. influenzae predicted coding region HI1403 #28 HI1404 300 H. influenzae predicted coding region HI1404 #29 HI1429 179 phosphoribosylaminoimidazole synthetase (purM) #30 HI1603 207 conserved hypothetical protein #31 HI1604 24 phosphate permease, putative #32 HI1605 65 conserved hypothetical protein #33 HI1607 62 hemM protein (hemM) #34 HI1615 160 phosphoribosylaminoimidazole carboxylase, catalytic subunit (purE) #35 HI1616 69 phosphoribosylaminoimidazole carboxylase, ATPase subunit (purK) #36 HI1632 300 H. influenzae predicted coding region HI1632 #37 HI1633 128 adenylosuccinate synthetase (purA) #38 HI1635 274 purine nucleotide synthesis repressor (purR) #39 HI1723 135 conserved hypothetical protein #40 HI1726 124 phosphoribosylaminoimidazole-succinocarboxamide synthase (purC) Motif number 1 TTTGCTGTTTAAAGTGCGGTTGGTTTTTGC 2 37 1 AAAGTGCGGT 0.998123 -73 TTTGCTGTTTAAAGTGCGGTTGGTTTTTGC 3 37 1 AAAGTGCGGT 0.998123 -73 GAGAAGCTCAAAAGTGCGGCGAAAAAATTA 5 29 0 AAAGTGCGGC 0.990455 -70 CCCTCCAAAAGTGCGGTAAGTTTTTAC 8 8 1 AAAGTGCGGT 0.998123 -75 GGATAAATCAAAAATGCGGTAAAAACTTAC 8 26 0 AAAATGCGGT 0.959135 -57 AATTCTTGAGAAAGTGCGGTCAATTTTTCA 9 193 0 AAAGTGCGGT 0.998123 -108 TCTTGCTGAAAAAGTGCGGTTATAATTTGC 16 27 0 AAAGTGCGGT 0.998123 -90 TAACAATAAAAAAGTGCGGTGATTTTTTAC 18 78 1 AAAGTGCGGT 0.998123 -114 ATAATTTCTTAAAGTGCGGTAAAAATACGA 20 84 0 AAAGTGCGGT 0.998123 -104 TAATTTAAAAAAAGTACGGCTATTTTTTAC 21 55 0 AAAGTACGGC 0.81279 -41 TAGCGTATGATAAGTGCGGTCAATTTTTGA 23 186 1 TAAGTGCGGT 0.973026 -29 CCTTACCTTTAAAGTGCGGTGAAAATTGAC 25 169 1 AAAGTGCGGT 0.998123 -61 TTACTGTAAGAAAGTGCGGTCAATTTTCAC 25 187 0 AAAGTGCGGT 0.998123 -43 ATCTCAATAAAAAGTGCGGTTAATTTTAAC 32 14 1 AAAGTGCGGT 0.998123 -52 CATCACAACAAAAGTGCGGTTAAAATTAAC 32 32 0 AAAGTGCGGT 0.998123 -34 CCGCACTTTAAAAGTGCGGTCAGATCTAAA 35 18 0 AAAGTGCGGT 0.998123 -52 CCGCACTTTTAAAGTGCGGTTGTTTTTTTC 35 29 1 AAAGTGCGGT 0.998123 -41 ATTTAAACCTAAAGTGCGGTGAAAAATCAC 37 12 1 AAAGTGCGGT 0.998123 -117 TATAAAAGAAAAAGTGTGGTGATTTTTCAC 37 30 0 AAAGTGTGGT 0.956985 -99 TGTAGAAACAAAACTGCGGTGATAATAAAA 38 18 1 AAACTGCGGT 0.972057 -257 ********** Masking position 5 Map Score: 93.8902 Number of sites scoring better than the average of aligned sites = 1115 Number in coding regions = 700 Number in noncoding regions = 415 Number of orfs with sites within 600 bp upstream = 285 Fraction of orfs with sites within 600 bp upstream = 0.0457758 Motif number 2 AAACTTTGCAAAAACCAACCGCACTTTAAACA 2 42 0 AAAACACCGC 0.992533 -68 AGTTTTAAATAATATGAACCGCTTACACTATC 2 69 1 AATAGACCGC 0.888193 -41 AAACTTTGCAAAAACCAACCGCACTTTAAACA 3 42 0 AAAACACCGC 0.992533 -68 AGTTTTAAATAATATGAACCGCTTACACTATC 3 69 1 AATAGACCGC 0.888193 -41 AAATGCGGTAAAAACTTACCGCACTTTTGGAG 8 13 0 AAAATACCGC 0.994399 -70 ATTTGACTGAAAAATTGACCGCACTTTCTCAA 9 186 1 AAAATACCGC 0.994399 -115 AAACACCCTAAAAATTCACCGCACT 12 4 0 AAAATACCGC 0.994399 -24 CTTTGAAAAATTTGCCGCAAATTATAAC 16 7 1 AAAATGCCGC 0.988347 -110 AAATCAGGTAAAAAATCACCGCACTTTTTTAT 18 83 0 AAAATACCGC 0.994399 -109 ATTGCAGGTAAAAAATAGCCGTACTTTTTTTA 21 48 1 AAAATGCCGT 0.940438 -48 AAACACCTCAAAAATTGACCGCACTTATCATA 23 191 0 AAAATACCGC 0.994399 -24 TCTCTCAATGAAAAACGGCCGTTTAAAACGAC 24 58 0 AAAACGCCGT 0.922006 -29 CCATAAAAATAAAACTAGCCGTTTTTTATACA 25 29 1 AAAATGCCGT 0.940438 -201 AAGTGCGGTGAAAATTGACCGCACTTTCTTAC 25 180 1 AAAATACCGC 0.994399 -50 AAGTGCGGTTAAAATTAACCGCACTTTTTATT 32 19 0 AAAATACCGC 0.994399 -47 AATTTACGAAAAAAACAACCGCACTTTAAAAG 35 34 0 AAAACACCGC 0.992533 -36 AAGTGCGGTGAAAAATCACCACACTTTTTCTT 37 23 1 AAAATACCAC 0.939488 -106 CAGACATACTAAAAACAACCATAATCATTGCA 38 91 1 AAAACACCAT 0.683939 -184 **** * ***** Masking position 4 Map Score: 46.6982 Number of sites scoring better than the average of aligned sites = 555 Number in coding regions = 355 Number in noncoding regions = 200 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 3 TGCGGTTGGTTTTTGCAAAGTTTTAAATAATATG 2 51 1 TGCAAAGTTT 0.98238 -59 TGCGGTTGGTTTTTGCAAAGTTTTAAATAATATG 3 51 1 TGCAAAGTTT 0.98238 -59 TATATTTGTCTTATCGAAACGTTTCGATAACAAA 10 131 1 TCGAAACTTT 0.823055 -37 ATGCTATATTTAACGGAAACGTTTTCCTGATATT 13 100 1 TGGAAACTTT 0.965535 -29 TACAATTCTGGAGCAAACATTT 14 9 1 TGCAAACTTT 0.993063 -14 GGTTATAATTTGCGGCAAATTTTTCAAAG 16 6 0 TGCAAATTTT 0.9788 -111 TCGGGTATCATAAGCCAAATTTTTTTTATTTTTA 16 88 1 TCCAAATTTT 0.884605 -29 ATGAGAATTATAACGCAAACGTTTGCTTAAATAT 20 128 0 TGCAAACTTT 0.993063 -60 TTTACGCAAACGTTTTCTTTTTGGC 24 2 1 TGCAAACTTT 0.993063 -85 TGGCTATCAATTACGTAAATTTTTTGGTTTCCGC 28 53 1 TGTAAATTTT 0.853837 -248 AATTTAACAATATCGCAAACGTTTGCTTGATGAT 29 115 1 TGCAAACTTT 0.993063 -65 CTTACATATATCAGGCAAACGTTTGCTAAATGGC 34 89 0 TGCAAACTTT 0.993063 -72 TAGTCATCTTTATTGCAAATTTTTTATAAAAAGA 38 201 0 TGCAAATTTT 0.9788 -74 CGTGCTATAATCTCGTAAAGTTTTTTCAAAAAAG 39 21 0 TGTAAAGTTT 0.875844 -115 TTAAATCAAATAAAGCAAACGTTTGCTATTTTTT 40 99 0 TGCAAACTTT 0.993063 -26 * ****** *** Masking position 7 Map Score: 27.3019 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 42 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 4 GTAATCGCCCCTTTTTCTTTTTAAGTTCTT 6 23 1 CTTTTTCTTT 0.716973 -37 ATTTTTCCTTATTTTTATAA 8 73 0 ATTTTTCCTT 0.918506 -10 GCAGAAAAATATTTTTCTTTCTCTGTTAAG 9 241 0 ATTTTTCTTT 0.754371 -60 TCGGAGAATTTTTTATCCTATCTAGAAATT 10 45 1 TTTTATCCTA 0.910223 -123 TATTGTTATATTTTTTCTTTCTACACAATG 11 66 0 TTTTTTCTTT 0.92207 -32 TATTTTATCCTGTATTGTTATA 11 86 0 TTTTATCCTG 0.849182 -12 AATATAGCATTTTTAACCTAGCTTTTGAAC 13 80 0 TTTTAACCTA 0.598536 -49 ACTCGGAAATTTTTATACTTTTAATTAATT 15 51 0 TTTTATACTT 0.563356 -250 AAATAATTTCTTTTTTCTTGCTGAAAAAGT 16 42 0 TTTTTTCTTG 0.823723 -75 AAGCCAAATTTTTTTTATTTTTAACATT 16 99 1 TTTTTTATTT 0.517088 -18 ATTCTCGTCTTTTTATCCTTTCTTTTTTAC 17 169 1 TTTTATCCTT 0.934455 -29 GTGCGGTGATTTTTTACCTGATTTTCCTTT 18 91 1 TTTTTACCTG 0.716049 -101 TTATTTTTTACTTTTGGTAAAAA 19 4 1 TTTTTTACTT 0.797143 -108 AGTTTCATAATTTTATCCTTATTTTTGCCC 20 20 1 TTTTATCCTT 0.934455 -168 TGTATTTTCCTTTCATTAAATA 20 176 0 TATTTTCCTT 0.76211 -12 GTACGGCTATTTTTTACCTGCAATTCCCCC 21 42 0 TTTTTACCTG 0.716049 -54 AAAGTTTGTATTTTTTCCTTACCGATGAAT 23 106 0 TTTTTTCCTT 0.977489 -109 AAATTAAACTATTTTTACTAAAAATAGACT 23 151 1 ATTTTTACTA 0.42041 -64 TTTCCATTAATTATTTCTTTATTATTTGCA 25 107 1 TTATTTCTTT 0.689374 -123 TTTTTTACCTTTCAAATTTTC 30 2 1 TTTTTACCTT 0.864594 -206 CAACTGGGTAATATTTCCTAGTGTGGTAAG 30 68 0 ATATTTCCTA 0.600542 -140 AAGATAAACCTTTTTTCTTACAAATTTTTT 30 110 1 TTTTTTCTTA 0.89378 -98 AGTTTATTTCCTATGTTTTGTTG 31 12 0 TTATTTCCTA 0.852768 -13 AAGGATAAAATTTTATCCTAAGCACAATTT 34 31 0 TTTTATCCTA 0.910223 -130 TAGGATAAAATTTTATCCTTAAAGTTGCAA 34 41 1 TTTTATCCTT 0.934455 -120 GTTGCAATGGTATTTTCCTATAAAAGCCAT 34 64 1 TATTTTCCTA 0.69496 -97 CAACAGCCAAATTTTTCCTAATCCTATTTT 36 171 1 ATTTTTCCTA 0.889077 -130 CCTAATCCTATTTTTTCTTTTATGCGTTCA 36 187 1 TTTTTTCTTT 0.92207 -114 AATCACCACACTTTTTCTTTTATATCATTG 37 36 1 CTTTTTCTTT 0.716973 -93 ATCCCTAAAAATTTTTCCTATTATAAAGGT 38 247 0 ATTTTTCCTA 0.889077 -28 TGCAATCCAGTTTTTTCCTAGAAATCGTGC 39 50 0 TTTTTTCCTA 0.968632 -86 AACTATTTCCTACTTTCCTAAA 39 124 0 CTATTTCCTA 0.553583 -12 CAGAGGATTTTTATTTCTTTTTAAAAAATA 40 77 1 TTATTTCTTT 0.689374 -48 ********** Masking position 4 Map Score: 30.0166 Number of sites scoring better than the average of aligned sites = 796 Number in coding regions = 540 Number in noncoding regions = 256 Number of orfs with sites within 600 bp upstream = 258 Fraction of orfs with sites within 600 bp upstream = 0.0414391 Motif number 5 CTAAAATTTCGTTTTCAAAATAAAGTGAAATCTGTATA 1 53 1 GTTTATAATA 0.675255 -77 CGTCGCAATATTTTTTAACTTCAACTTATTAGCGAGAA 1 95 1 TTTTCTAATA 0.903748 -35 TAAAAGCTCCTTTTTGTTATCGAAACGTTTCGATAAGA 10 139 0 TTTTACAACT 0.276496 -29 ACTCGGAAATTTTTATACTTTTAATTAATTTAAGGACA 15 43 0 TTTTTTAATA 0.725976 -258 AAAGAATGGATTTTTTGCCCTTAAGTCTTTATACTCAC 17 25 1 TTTTCTAATT 0.804003 -173 TTAATAACATTTTTCAGTCTTAAACTGAGGCGTGAGTA 17 56 0 TTTTCTAATA 0.903749 -142 CTGATTTTCCTTTTTGTGATCTAAATCATAGTTTTAGG 18 108 1 TTTTACAATA 0.723341 -84 TAAATCATAGTTTTAGGTATTCAAATTTCTTTGTGATA 18 129 1 TTTTATAATT 0.88168 -63 GTAAAAAGTATTTTTCAATTTTAATTATTGTTTAACTA 19 27 1 TTTTTTAATT 0.536488 -85 TATGTGGGCTTTTTTATGCCTGAAATTTATCGTATTTT 20 55 1 TTTTCTAATT 0.804003 -133 ATATTTAATCTTTTCTATATTTAAGCAAACGTTTGCGT 20 112 1 TTTTATAACA 0.850891 -76 CATCGCTTATTTTTAACTATTTAATGAAAGGAAAATAC 20 159 1 TTTTATAAGA 0.566806 -29 CATTCCTAAATTTTCATCACTTAAATGAAATTAATTCA 22 26 0 TTTTATAATA 0.944618 -98 AGAATACACCTTTTGATGAATAAAATAAATTCATCGGT 23 78 1 TTTTATAATA 0.944618 -137 TTATCGTATTTTTTGAAAAATTAAACTATTTTTACTAA 23 134 1 TTTTATAACA 0.850891 -81 AAACTAGCCGTTTTTTATACATAATTAAAATGTATTAA 25 40 1 TTTTAAAATA 0.821974 -190 TTTAATGACATTTTTAAAATTAAAATGAAATTGCTTGC 29 71 0 TTTTATAATA 0.944618 -109 ACGTTTGCGATATTGTTAAATTAATTCATTTAATGACA 29 99 0 TATTATAATA 0.424354 -81 TTTTTTACCTTTCAAATTTTCTCGCTTTT 30 2 1 TTTTTTAATT 0.536488 -206 ATTTTCTCGCTTTTAAAGCGAAAAGTGTATTGAGTTAC 30 26 1 TTTTCAAATT 0.526165 -182 GCGCACGAATTTTTAACCCCTTAATTTGGAGTAAATCA 30 177 1 TTTTCTAATG 0.461058 -31 TAAAAGTAACTTTACTCAATTAAACTAAATCCTTAAAA 33 15 1 TTTAATAATA 0.573427 -48 TACGCCACGTTTTTAATTAGAAAATTGAGAAAATAGC 34 134 1 TTTTAAAATA 0.821974 -27 AAGTGCGGTTGTTTTTTTCGTAAATTTAACGAGAAATA 35 40 1 GTTTCTAATA 0.533727 -30 GTCAAATACTTTTTTACAAAAAAAGTAATTTTATGTTT 36 62 1 TTTTAAAATA 0.821974 -239 ATCACTTATTTTTTATTCATTTAAACAACTTATATGTT 36 121 1 TTTTATAACA 0.850891 -180 TTTAGGCATTTTTTGTCAAATAAATTTTAATTACAAT 36 220 0 TTTTATAATT 0.88168 -81 CGGCTGTTCATTTAACTAATTTAACCGAATAAAAGGCG 37 95 1 TTTAATAACA 0.310224 -34 ATTGCAAATTTTTTATAAAAAGAAGTGATTTTTTCGTA 38 186 0 TTTTAAAATA 0.821974 -89 TAGGAAAAATTTTTAGGGATTTAAATAT 38 257 1 TTTTATAATT 0.88168 -18 ACGTTTGCTATTTTTTAAAAAGAAATAAAAATCCTCTG 40 77 0 TTTTAAAATA 0.82171 -48 **** * * ** * * Masking position 13 Map Score: 25.1323 Number of sites scoring better than the average of aligned sites = 475 Number in coding regions = 323 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 6 TTATGGCAAATAGTATGAAAATCATAGCATA 1 18 1 TGTATGAAAA 0.879889 -112 GATTTCACTTTATTTTGAAAACGAAATTTTA 1 54 0 TTTTTGAAAA 0.969458 -76 AAATGAGAGATGGTTTGAAAA 4 27 1 TGTTTGAAAA 0.950551 -11 TGAAGTATTTTTGTTTGATAATGTGATATAA 15 108 0 TGTTTGATAA 0.637653 -193 ACAAAATCTTTTTTTTGAAAATAGGGAGTAT 15 248 1 TTTTTGAAAA 0.966684 -53 ATTATGATAATGTTATGAAAAACTCACGGAT 17 99 0 TTTATGAAAA 0.923773 -99 CAATTCCCCCTCTTTTGTAAAGAGGGGGATA 21 21 0 TTTTTGTAAA 0.846614 -75 TCATCTAAGATGGTTTGAAAAATCAGACATA 23 48 1 TGTTTGAAAA 0.950551 -167 CTTTATCGTATTTTTTGAAAAATTAAACTAT 23 132 1 TTTTTGAAAA 0.966684 -83 TCTTACAAATTTTTTTGAAAAATTTTAACTA 30 125 1 TTTTTGAAAA 0.966684 -83 TTTGACCTATTCTTATAAAAATTGTGCTTAG 34 13 1 TTTATAAAAA 0.668407 -148 TAAAATTACTTTTTTTGTAAAAAAGTATTTG 36 64 0 TTTTTGTAAA 0.846565 -237 AATCACTTCTTTTTATAAAAAATTTGCAATA 38 194 1 TTTATAAAAA 0.661996 -81 TTTATCTCACTTTTTTGAAAAAACTTTACGA 39 12 1 TTTTTGAAAA 0.966684 -124 ACGTTTGCTATTTTTTAAAAAGAAATAAAAA 40 84 0 TTTTTAAAAA 0.768077 -41 * ********* Masking position 10 Map Score: 20.4169 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 73 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 7 CAGATTTCACTTTATTTTGAAAACGAAATT 1 57 0 TTTATTTTGA 0.585001 -73 TTATAATGCTCTTATTATTGATAGTGTAAG 2 90 0 CTTATTATTG 0.862528 -20 TTATAATGCTCTTATTATTGATAGTGTAAG 3 90 0 CTTATTATTG 0.862528 -20 TCCTGTCGCTTTTATTTTGGGTGGATATTG 7 26 0 TTTATTTTGG 0.755922 -52 ATTTTTCCTTATTTTTATAAATGATTT 8 66 0 CTTATTTTTA 0.848264 -17 TAACAATGAGCTTATTTTCAGAACCATCTA 15 13 0 CTTATTTTCA 0.566109 -288 ATTACAAAATCTTTTTTTTGAAAATAGGGA 15 245 1 CTTTTTTTTG 0.753583 -56 ATCTTATTGTTTTATTTTGA 15 291 1 TTTATTTTGA 0.585001 -10 CCAAATTTTTTTTATTTTTAACATT 16 102 1 TTTATTTTTA 0.759437 -15 CATCCTTATACTTATTTTGGCGTATGCTAT 18 15 1 CTTATTTTGG 0.845783 -177 ATCACCGCACTTTTTTATTGTTACAATAAT 18 71 0 TTTTTTATTG 0.468702 -121 TAATTTTATCCTTATTTTTGCCCACATTTA 20 27 1 CTTATTTTTG 0.924712 -161 ATTCTCATCGCTTATTTTTAACTATTTAAT 20 154 1 CTTATTTTTA 0.848264 -34 TCTTTTTGGCTTTATTTTTGTAGAATAGCT 24 26 1 TTTATTTTTG 0.87399 -61 AACGGCTAGTTTTATTTTTATGGTGCCTAG 25 22 0 TTTATTTTTA 0.759437 -208 TAATTATTTCTTTATTATTTGCACATCATT 25 114 1 TTTATTATTT 0.309527 -116 GGCATGCCTATTTATTTTCGGAGAAGGTTG 28 259 1 TTTATTTTCG 0.618137 -42 ATTAACCGCACTTTTTATTGAGATCAA 32 8 0 CTTTTTATTG 0.609711 -58 AAGCATATCACTTATTTTTTATTCATTTAA 36 115 1 CTTATTTTTT 0.608459 -186 ATCAAACCAACTTTTTATTATCACCGCAGT 38 30 0 CTTTTTATTA 0.415564 -245 GGGGAAAATGTTTATTATTGGAAATTTAGT 40 27 0 TTTATTATTG 0.779884 -98 ********** Masking position 5 Map Score: 17.7525 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 199 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 8 GCGGTAAGTTTTTACCGCATTTTTGATTTATCCA 8 23 1 TTACATTTTT 0.693643 -60 CGGTCAATTTTTCAGTCAAATTTTGTCGTTCTTG 9 173 0 TTAGAATTTT 0.790809 -128 TCTTTCTCTGTTAAGGTTGTTTGTAACCCCGTTA 9 222 0 TTAGGTTTGT 0.526495 -79 GCGGTGAATTTTTAGGGTGTTTTT 12 14 1 TTAGGTTTTT 0.835402 -14 GATAAAGTAATTGATTGATTTTTTAGCGGTTGTA 15 192 1 TTATTTTTTT 0.772361 -109 CGGATTTTCATTAATAACATTTTTCAGTCTTAAA 17 70 0 TTATATTTTT 0.906461 -128 GTTTCATAATTTTATCCTTATTTTTGCCCACATT 20 21 1 TTATTATTTT 0.423147 -167 ATGCCTGAAATTTATCGTATTTTTACCGCACTTT 20 70 1 TTATATTTTT 0.906461 -118 GAATGAAATTTTAATTAAATTTTTATCCATAAAC 22 59 1 TTATATTTTT 0.906461 -65 AAATACAAACTTTATCGTATTTTTTGAAAAATTA 23 123 1 TTATATTTTT 0.906461 -92 ATACGCTATTTTAAGTCTATTTTTAGTAAAAATA 23 160 0 TTAGATTTTT 0.945903 -55 CCGTTTTTCATTGAGAGATTTTTTA 24 72 1 TTAGTTTTTT 0.859591 -15 TGGCTATCAATTACGTAAATTTTTTGGTTTCCGC 28 53 1 TTCGATTTTT 0.662306 -248 CTCCTAAATCTTGAGCTTATTTGTACTATTAAAG 29 16 1 TTAGATTTGT 0.792989 -164 TGCAAGCAATTTCATTTTAATTTTAAAAATGTCA 29 70 1 TTATAATTTT 0.67691 -110 ATTAATTCATTTAATGACATTTTTAAAATTAAAA 29 84 0 TTATATTTTT 0.906461 -96 GAAATAACGATTTAGGCATTTTTTGTCAAATAAA 36 234 0 TTAGTTTTTT 0.859591 -67 CCCCTAACATTTCAGAGGATTTTTATTTCTTTTT 40 65 1 TTAGATTTTT 0.945903 -60 ** ** ****** Masking position 11 Map Score: 15.3367 Number of sites scoring better than the average of aligned sites = 284 Number in coding regions = 206 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 9 GTAAATATCAGGAAAACGTTTCCGTTAAAT 13 107 0 GGAAAACGTT 0.932289 -22 ACAATTCTGGAGCAAACATTT 14 12 1 AGCAAACATT 0.874155 -11 TCTATATTTAAGCAAACGTTTGCGTTATAA 20 125 1 AGCAAACGTT 0.984178 -63 AAAGCCAAAAAGAAAACGTTTGCGTAAA 24 9 0 AGAAAACGTT 0.960497 -78 TATATCATCAAGCAAACGTTTGCGATATTG 29 122 0 AGCAAACGTT 0.984178 -58 AAAGCCATTTAGCAAACGTTTGCCTGATAT 34 86 1 AGCAAACGTT 0.984178 -75 AAGTATAGGGGGAAAATGTTTATTATTGGA 40 35 0 GGAAAATGTT 0.605918 -90 TTTAAAAAATAGCAAACGTTTGCTTTATTT 40 96 1 AGCAAACGTT 0.984178 -29 ********** Masking position 5 Map Score: 11.7704 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 17 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 CCCTTGTTGATGAAGAGCAAGCAACTTCCTGTCGCT 7 46 0 TGAACACAAT 0.956376 -32 AAAACCAGTTTGAACAACAAACAATTAAAGTACAGA 9 75 1 TGAACACAAT 0.956376 -226 AAGAAATTATTTAGGTTCTACCAAATAATCGGGTAT 16 60 1 TTAGCACAAT 0.912885 -57 TGGATTTCTATTAACCTCAATCAAATATAGGGTTCC 23 12 0 TTAACACAAT 0.97819 -203 TTTCGGGTTATTAATGGCTATCAATTACGTAAATTT 28 39 1 TTAACACAAT 0.97819 -262 TGCAGAATCCTTAAAAACTACCAAATAGGCACGCTA 28 209 1 TTAACACAAT 0.97819 -92 CAAATAAATTTTGATTGCAAGCAATTTCATTTTAAT 29 55 1 TTGACACAAT 0.912885 -125 GATTAACCTCGATCAATTGAAATAAAAA 29 162 0 TTAACACAAT 0.97819 -18 ACTTTTCGCTTTAAAAGCGAGAAAATTTGAAAGGTA 30 16 0 TTAACAAAAT 0.814708 -192 **** * * *** * Masking position 10 Map Score: 7.12942 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 5 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 11 TTTGAAAACGAAATTTTAGGATTTATGCTAT 1 41 0 AATTTTAGGA 0.930011 -89 AACCATCTCTCATTTTTAGGATATTTCAAAT 4 11 0 CATTTTAGGA 0.794112 -27 AATCATTTATAAAAATAAGGAAAAAT 8 67 1 AAAATAAGGA 0.721806 -16 GTACAGACTGAAAATCAAGGACTGCAATATC 9 104 1 AAATCAAGGA 0.72262 -197 AGTGCGGTGAATTTTTAGGGTGTTTTT 12 10 1 AATTTTAGGG 0.838608 -18 TACTTTTAATTAATTTAAGGACATAACAATG 15 35 0 TATTTAAGGA 0.713754 -266 ACGCCAAAATAAGTATAAGGATGGAAA 18 7 0 AATATAAGGA 0.767685 -185 AAATGTGGGCAAAAATAAGGATAAAATTATG 20 25 0 AAAATAAGGA 0.721806 -163 TTAAGTGATGAAAATTTAGGAATGAAATTTT 22 40 1 AAATTTAGGA 0.912536 -84 AAATAAGCTCAAGATTTAGGAGAAAAA 29 7 0 AAATTTAGGA 0.912536 -173 TGATTTACTCCAAATTAAGGGGTTAAAAATT 30 184 0 CAATTAAGGG 0.542174 -24 TAAGCTCGCATATTTTAAGGATTTAGTTTAA 33 34 0 TATTTAAGGA 0.713754 -29 ATACCATTGCAACTTTAAGGATAAAATTTTA 34 46 0 AATTTAAGGA 0.93001 -115 AAAAAAACACAACATCTAGGAGTATCTT 36 283 1 AAATCTAGGA 0.72262 -18 TAATAGGAAAAATTTTTAGGGATTTAAATAT 38 254 1 AATTTTAGGG 0.838608 -21 GGCGGGATTGAAATTTTAGGAAAGTAGGAAA 39 110 1 AATTTTAGGA 0.930011 -26 ** ******** Masking position 8 Map Score: 13.1902 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 19 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 12 GGCAGGCTAAAGCCCACCTTAAAGA 2 6 0 AGCCCACCTT 0.982376 -104 GGTGGGCTTTAGCCTGCCTTTTGCTGTTTA 2 18 1 AGCCTGCCTT 0.982376 -92 GGCAGGCTAAAGCCCACCTTAAAGA 3 6 0 AGCCCACCTT 0.982376 -104 GGTGGGCTTTAGCCTGCCTTTTGCTGTTTA 3 18 1 AGCCTGCCTT 0.982376 -92 AAATCCTACCTTGAGAAAAGAA 6 48 0 ATCCTACCTT 0.922946 -12 TAAAATTTCAATCCCGCCATTATCTAATAA 39 98 0 ATCCCGCCAT 0.879605 -38 ********** Masking position 1 Map Score: 4.95942 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 4 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 13 GTGGGCTTTAGCCTGCCTTTTGCTGTTTAAA 2 19 1 GCTGCCTTTT 0.988626 -91 GTGGGCTTTAGCCTGCCTTTTGCTGTTTAAA 3 19 1 GCTGCCTTTT 0.988626 -91 TTGCTTTCCTTTTGTTTAAAGAT 19 99 0 GCTTCCTTTT 0.943361 -13 AAGTTTGGTAGCGTGCCTATTTGGTAGTTTT 28 222 0 GCTGCCTATT 0.983782 -79 CTTAATTGAGGCATGCCTATTTATTTTCGGA 28 250 1 GCTGCCTATT 0.983782 -51 ** ******** Masking position 4 Map Score: 4.57239 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 7 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 14 GTTCAAACTGGTTTTTAATGCTACTAAGTT 9 60 0 GTTTTTAATG 0.92801 -241 ACAGTTTTAAGGTATTAAGGATTGATT 13 8 0 GGTATTAAGG 0.791434 -121 AACTCTAGGCTTTTTTAATGTTCGAGTTCA 13 55 1 TTTTTTAATG 0.717386 -74 ACTGAAAAATGTTATTAATGAAAATCCGTG 17 76 1 GTTATTAATG 0.940765 -122 ATAATTAAAATGTATTAATGATCGTGTAGA 25 60 1 TGTATTAATG 0.604533 -170 GCAATTTCGGGTTATTAATGGCTATCAATT 28 35 1 GTTATTAATG 0.940765 -266 CTATTTGGTAGTTTTTAAGGATTCTGCATT 28 207 0 GTTTTTAAGG 0.863035 -94 TCTACGCCACGTTTTTAATTAGAAAATTGA 34 132 1 GTTTTTAATT 0.558256 -29 TGTTTGTTTGGTTATTAATGAAGCATATCA 36 95 1 GTTATTAATG 0.940765 -206 ********** Masking position 5 Map Score: 4.21681 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 64 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 15 TATCTAGAAATTTTGTGATCAATATCCCAA 10 63 1 TTTTGTGATC 0.95737 -105 GTTTTTCTATTTTTGTTATCTATATTTGTC 10 111 1 TTTTGTTATC 0.948972 -57 AAAAGCTCCTTTTTGTTATCGAAACGTTTC 10 146 0 TTTTGTTATC 0.948972 -22 AAATCCATTCTTTTGTGCACTTATAGA 17 8 0 TTTTGTGCAC 0.7583 -190 TGATTTTCCTTTTTGTGATCTAAATCATAG 18 109 1 TTTTGTGATC 0.95737 -83 CAAACCAACTTTTTATTATCACCGCAGTTT 38 28 0 TTTTATTATC 0.706935 -247 AAATCGCTCATTTTGTTCTCCTCATAAAAA 38 129 1 TTTTGTTCTC 0.926003 -146 ********** Masking position 6 Map Score: 3.84359 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 32 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548