AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00030_hinf_reg_300.orf -o00030_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: HI0052 26 conserved hypothetical protein HI1604 24 phosphate permease, putative Input sequences: #1 HI0050 74 conserved hypothetical transmembrane protein #2 HI0051 38 conserved hypothetical transmembrane protein #3 HI0053 109 zinc-type alcohol dehydrogenase #4 HI0462 192 ATP-dependent proteinase (lon) #5 HI0463 115 oxygen-independent coproporphyrinogen III oxidase, putative #6 HI0464 132 ribose 5-phosphate isomerase A (rpiA) #7 HI0500 300 conserved hypothetical protein #8 HI0501 167 high affinity ribose transport protein (rbsD) #9 HI0505 97 ribokinase (rbsK) #10 HI0524 110 fructose-bisphosphate aldolase (fba) #11 HI0525 101 phosphoglycerate kinase (pgk) #12 HI0526 77 H. influenzae predicted coding region HI0526 #13 HI0553 300 6-phosphogluconate dehydrogenase, decarboxylating (gnd) #14 HI0558 75 glucose-6-phosphate 1-dehydrogenase (zwf) #15 HI0559 194 sulfite synthesis pathway protein (cysQ) #16 HI0559.1 56 H. influenzae predicted coding region HI0559.1 #17 HI0561 300 conserved hypothetical protein #18 HI0566 116 ribulose-phosphate 3-epimerase (dod) #19 HI0567 150 DNA gyrase, subunit B (gyrB) #20 HI0568 95 transcription accessory protein (tex) #21 HI0982 95 6-phosphofructokinase (pfkA) #22 HI0985 300 DNA processing chain A (dprA) #23 HI1023 128 transketolase 1 (tktA) #24 HI1024 49 hexulose-6-phosphate synthase, putative #25 HI1027 58 L-xylulose kinase (lyx) #26 HI1028 30 conserved hypothetical protein #27 HI1030 71 conserved hypothetical transmembrane protein #28 HI1031 175 conserved hypothetical protein #29 HI1116 110 deoxyribose-phosphate aldolase (deoC) #30 HI1125 295 transaldolase B (talB) #31 HI1573 300 pyruvate kinase, type II (pykA) #32 HI1574 33 replicative DNA helicase (dnaB) #33 HI1576 54 glucose-6-phosphate isomerase (pgi) #34 HI1603 207 conserved hypothetical protein #35 HI1605 65 conserved hypothetical protein #36 HI1607 62 hemM protein (hemM) #37 HI1645 233 fructose-1,6-bisphosphatase (fbp) Motif number 1 TTTTAGACTCCTTATATGCCATTGACA 3 93 0 TTTTTTATAT 0.889435 -17 AACTCAATATTTTGTGAAATTTAATAAAATTTTTCA 4 10 1 TTTTTTAATA 0.773785 -183 CTTTTATTGATTTTAGAGATGATAATTTCATCTTTAC 5 41 1 TTTTATAATT 0.702375 -75 TTCTTTTCCTTATCTTAATAAGTAAACGAT 6 113 0 TTTTTTAATA 0.773887 -20 GTTTTTCTATTTTTGTTATCTATATTTGTCTTATCGA 8 111 1 TTTTATATTT 0.811688 -57 TCAATCAAGTTTTTGTCGGCTATAATTCGCCGCTTTC 12 32 0 TTTTATAATT 0.702376 -46 ACATTCGCCCTTTTAATCTACATATAATTGAT 13 6 0 TTTTATATAA 0.612559 -295 ACATTCGCCCTTTTAATCTACATATAATTAATCTTGT 13 171 0 TTTTATATAA 0.612559 -130 TGTTTTTATTTTTTTTTCATTTAATAAAAATCCTATT 17 76 0 TTTTTAATAA 0.830574 -225 ATTTTTCAAGTTTTTTTAACATAAAATTTGTTTTATT 17 133 0 TTTTTAAAAT 0.830574 -168 ATTTTCGTCTATTTATATTCATGACTGA 18 2 1 TTTTTTATAT 0.889436 -115 TATCTCATTCTTTTGTAAATAAAAATTGGGCGAGATT 19 120 0 TTTTAAAATT 0.734674 -31 TAAAAGAAAGTTTTTTGAATTATATTTGAGCCATCCC 20 19 1 TTTTATATTT 0.811687 -77 TCTATCTTCGTTTTTTTATAATAAAGAAGTACGACA 20 70 1 TTTTTAAAGA 0.502787 -26 GTCAAACTATTTTTTGGCATTTTATATTAAAAATAAA 22 27 1 TTTTTTATAT 0.889434 -274 AATATGCTAATTTTATTAAGTTTATTAGTTAAATGTA 22 86 0 TTTTTTATTA 0.862038 -215 ATTTTTCTTATTTTGAAAATGTAAAAAATCCAATAAG 22 154 0 TTTTTAAAAA 0.7099 -147 GCAAAAATTCTTTTTAATGAATAAAAAATTGCAAAAT 22 189 0 TTTTTAAAAA 0.465904 -112 ATTTTTTCCTTTTTATTTGAAAATCTAG 22 283 0 TTTTTTATTT 0.919468 -18 CGTTTTTCCTTAAATAATATGAGGAAGGCA 24 30 0 TTTTTAATAT 0.904203 -20 ATGGGCTGGATTTTTATTATGTAAAATCCAGCCTATT 25 13 0 TTTTTAAAAT 0.819137 -46 CTAGATCCTATTTTCTTGTGATAATATTTCATATTGT 28 14 0 TTTTTAATAT 0.904202 -162 TTTTTCCTCTCTTAATTTTATATAGTAA 28 158 0 TTTTTAATTT 0.930538 -18 TATTTTCCTCCTTTTATTTATGTTTTACC 29 92 0 TTTTTTATTT 0.919469 -19 AAAAATGAATTTTTGAGCTAATAAATAGAAGACTTTT 30 45 0 TTTTTAAATA 0.800343 -251 AAAACTCAATTTTTCTTCAAATAATTTCCTGACAAAT 30 88 0 TTTTTAATTT 0.930538 -208 TTTAGCAATTTTTTTAGCGATTTATTAGACACAACTC 30 127 0 TTTTTTATTA 0.861924 -169 ATGTATTGATTTTTCCTATTGTAAATATTTTCCTACA 30 194 1 TTTTTAAATA 0.800627 -102 ATTGTAAATATTTTCCTACATAAATTACCCTTTTAAT 30 211 1 TTTTAAATTA 0.734674 -85 TTTTGTTTACTTTTTTGCCAGTTATATCGGGTTTTAA 31 139 0 TTTTTTATAT 0.889371 -162 TTTCCAAAAGTTTTAAGCGTATAATGTGCACCGATTT 31 204 1 TTTTTAATGT 0.774418 -97 TGCACCGATTTTTTATCTGGCTAATATGTAGCGAAGT 31 230 1 TTTTTAATAT 0.904146 -71 AATTACAAAATTTTAAAGGTGTTATTTTACTTCGCTA 31 258 0 TTTTTTATTT 0.919468 -43 TTTTTTACCTTTCAAATTTTCTCGCTTTT 34 3 1 TTTTAAATTT 0.834911 -205 AAGATAAACCTTTTTTCTTACAAATTTTTTTGAAAAA 34 110 1 TTTTAAATTT 0.834911 -98 GCGCACGAATTTTTAACCCCTTAATTTGGAGTAAATC 34 177 1 TTTTTAATTT 0.930537 -31 TTTTTACCTTTTGGCTTAATAAAGTGCGGTTATGG 37 9 1 TTTTTAAAGT 0.652731 -225 **** ****** Masking position 4 Map Score: 37.3677 Number of sites scoring better than the average of aligned sites = 858 Number in coding regions = 588 Number in noncoding regions = 270 Number of orfs with sites within 600 bp upstream = 207 Fraction of orfs with sites within 600 bp upstream = 0.0332477 Motif number 2 GAGCTTATAATGTTACTATTATTTTGTGTAGTTT 1 10 1 ATTATTTTTT 0.521466 -65 AATTTAATAAAATTTTTCATTATTTTAGCCATTAT 4 28 1 AATTCTTTTT 0.706698 -165 TTCATTTGCCAAAATTCTTTTTTGTTTAAAACCCA 4 66 1 AATTTTTTGT 0.842534 -127 CGCCTGTTAAAAATTACACTTGTTTATTAAATACT 6 59 1 AATAATTTTT 0.642314 -74 GTTGTGCAGAAAAATATTTTTCTTTCTCTGTTAAG 7 241 0 AATATTTTTT 0.846812 -60 TGGATTGTTCAAAGTTCTGTTGTTGTGCAGAAAAA 7 262 0 AATTTTTTTG 0.880138 -39 TTTATCCTGTATTGTTATATTTTTTCTTTCTACAC 9 70 0 ATTTTTTTTT 0.822361 -28 AAATTTTGTTTAGTTTTTGTCAATCA 12 62 0 AATTTTATTT 0.772747 -16 TCAGCATAAAATTATTCTCTTGTTTTTGGCAGCAA 15 55 0 ATTTTTTTTT 0.822361 -140 ACTGTTATTAAAAATTTTATTCTTTAATAGGATTT 17 51 1 AATTTTTTTT 0.959906 -250 TGTTTAAATTAACCTGTTTTTATTTTTTTTTCATT 17 92 0 AATGTTTTTT 0.899467 -209 TTTTAACATAAAATTTGTTTTATTGAAAAATGTTT 17 122 0 AATTTTTTTG 0.880138 -179 ACCTTGTCAAAAATTTGACTATTTTTCAAGTTTTT 17 155 0 AATTATATTT 0.521664 -146 TTCGCCCCATAACTTGTTATTTTTTCCAATTTTTT 19 17 0 AATGTTTTTT 0.899467 -134 TAATTCAAAAAACTTTCTTTTATTTTTATT 20 6 0 AATTTTTTTT 0.959941 -90 CCTAATCAACAAATTTTTCTTATTGGATTTTTTAC 22 136 1 AATTTTTTTG 0.880138 -165 AAAAATTGCAAAATTTTTCTTATTTTGAAAATGTA 22 168 0 AATTTTTTTT 0.959906 -133 AAAATTTTGCAATTTTTTATTCATTAAAAAGAATT 22 186 1 AATTTTTATT 0.55363 -115 TTCTCCTGTGAATATTTTGTTATTTTCCTAATCTT 23 100 0 AATTTTTTTT 0.959939 -29 TGATTTATAAATAATTTATTTATTTTACATTTATT 28 83 1 ATTTATTTTT 0.602031 -93 TATTGTAGCAAAAATTCTTTATTTTTGACTATGGT 29 57 0 AATTTTATTT 0.770504 -54 TATTAGCTCAAAAATTCATTTTTGTAAAGATTTGT 30 59 1 AATTATTTGT 0.636156 -237 TATTTGAAGAAAAATTGAGTTTTGTGAGTTGTGTC 30 102 1 AATTATTTGT 0.636156 -194 TCAGTTATTTAAGCTGGTTTTGTTTACTTTTTTGC 31 158 0 AATGTTTTTT 0.899467 -143 TAATTGAGTAAAGTTACTTTTATTTG 36 2 0 AATATTTTTT 0.849382 -61 TGCAGTAATAAATGTGAATTTTTTGTGATAAAGAT 37 125 1 AATGATTTTG 0.472541 -109 ** ** * ** *** Masking position 10 Map Score: 21.8454 Number of sites scoring better than the average of aligned sites = 438 Number in coding regions = 309 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 3 GACAAATATAATTTGCCCCATAATGTGATAT 9 34 0 ATTTGCCCCT 0.980607 -64 GGCAAATTATATTTGTCCCATTGTGTAGAAA 9 48 1 ATTTGTCCCT 0.79938 -50 GTCGGCTATAATTCGCCGCTTTCAACTCTCT 12 24 0 ATTCGCCGCT 0.95584 -54 AGGGAATTACATTCGCCCTTTTAATCTACAT 13 20 0 ATTCGCCCTT 0.978686 -281 GGCTAATATAATTAGCCCCTACATGTTTGTC 13 73 0 ATTAGCCCCA 0.974082 -228 GGCTAATTATATTAGCCCCCACCATAAACAA 13 87 1 ATTAGCCCCA 0.974082 -214 AGGGAATTACATTCGCCCTTTTAATCTACAT 13 185 0 ATTCGCCCTT 0.978686 -116 GGCTAATATAATTAGCCCCTACATGTTTTGT 13 239 0 ATTAGCCCCA 0.974082 -62 GGCTAATTATATTAGCCCCATCATAAACAAA 13 253 1 ATTAGCCCCT 0.989511 -48 GGGCGAATAATTTCGCCCCATAACTTGTTAT 19 32 0 TTTCGCCCCT 0.95927 -119 GGGCGAAATTATTCGCCCTTTTTTTATCGTT 19 45 1 ATTCGCCCTT 0.978686 -106 ********* * Masking position 3 Map Score: 16.8666 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 43 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 TTTGTGAAATTTAATAAAATTTTTCATTATTTT 4 21 1 TTAAAATTTT 0.699601 -172 ACCCCAATATTTACCCAAATTATCGGAACGAAA 4 152 1 TTCAAATTAT 0.611307 -41 GGTCAATTTTTCAGTCAAATTTTGTCGTTCTTG 7 173 0 TCCAAATTTT 0.942635 -128 GTAAATTTGGTCGGAGAATTTTTTATCCTATCT 8 35 1 TCGAATTTTT 0.723439 -133 TTAGTTTTTGTCAATCAAGTTTTTGTCGGCTAT 12 46 0 TCCAAGTTTT 0.883204 -32 TGTAATTCCCTCCTACAATTTATCTACATCATA 13 40 1 TCCAATTTAT 0.821513 -261 TGTAATTCCCTCCTACAATTTATCTACATCATA 13 205 1 TCCAATTTAT 0.821513 -96 TTAATCCTTAAATTTATTTTAGAATAG 16 5 1 TCAAATTTAT 0.61864 -52 AATGAACTGTTATTAAAAATTTTATTCTTTAAT 17 46 1 TAAAAATTTT 0.518803 -255 CATTTTTCAATAAAACAAATTTTATGTTAAAAA 17 125 1 TACAAATTTT 0.753636 -176 AATTTGACTATTTTTCAAGTTTTTTTAACATAA 17 146 0 TTCAAGTTTT 0.752527 -155 ACTTGAAAAATAGTCAAATTTTTGACAAGGTTG 17 159 1 TAAAATTTTT 0.55924 -142 ACTTGTTATTTTTTCCAATTTTTTAGTGCA 19 8 0 TTCAATTTTT 0.886057 -143 TGCTATAATCTCGCCCAATTTTTATTTACAAAA 19 114 1 TCCAATTTTT 0.950831 -37 AGATCAAAATCCCGTCAAATTTTGCTAGAGCAG 21 14 1 CCCAAATTTT 0.77867 -82 AAACTGGCTGTCAAACTATTTTTTGGCATTTTA 22 18 1 TCCTATTTTT 0.49054 -283 ACAACCCTAATCAACAAATTTTTCTTATTGGAT 22 131 1 TCAAATTTTT 0.872052 -170 ATAAGAAAAATTTTGCAATTTTTTATTCATTAA 22 180 1 TTCAATTTTT 0.886057 -121 GATCACAAAATCAGTAAAATTATTTTAACATAT 28 50 1 TCAAAATTAT 0.579557 -126 TATCATCACTTTTAGCAATTTTTTTAGCGATTT 30 141 0 TTCAATTTTT 0.886057 -155 CGTTTTTGATTTCCAAAAGTTTTAAGCGTATAA 31 195 1 TTAAAGTTTT 0.517313 -106 TAAAATAACACCTTTAAAATTTTGTAATTATTG 31 266 1 CCAAAATTTT 0.553563 -35 TTTCTGGAATTTTTATTAGGGAGA 33 41 0 TTGAATTTTT 0.512644 -14 TTTTTTACCTTTCAAATTTTCTCGCTTTTA 34 8 1 CCCAAATTTT 0.77867 -200 AAACCTTTTTTCTTACAAATTTTTTTGAAAAAT 34 115 1 TCCAAATTTT 0.942635 -93 TACAAATTTTTTTGAAAAATTTTAACTATCAAC 34 128 1 TTAAAATTTT 0.699601 -80 TCACATTTATTACTGCAATTTTTAGAAACTATC 37 109 0 TACAATTTTT 0.782608 -125 ** ******** Masking position 8 Map Score: 22.3342 Number of sites scoring better than the average of aligned sites = 533 Number in coding regions = 418 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 5 TTAACAGGCGTTTTTCTCAAGCAATGTTATTTCAC 6 34 0 TTTTCTACAT 0.583459 -99 AAGAAAAATATTTTTCTGCACAACAACAGAACTTT 7 252 1 TTTTCTAAAA 0.952123 -49 CCGCACTTTTCCTCTATAACATATTGATGGT 10 7 1 TTTTCTAAAA 0.952092 -104 TAATTTTAATTTTAACTTAACAAGAGGATAGATT 11 78 1 TTTACTAAAA 0.943362 -24 CCTCCTACAATTTATCTACATCATAGACAAACATG 13 48 1 TTTACTACAA 0.91162 -253 CCTCCTACAATTTATCTACATCATAGACAAAACAT 13 213 1 TTTACTACAA 0.91162 -88 TCGATTGGTTTTTTTCTCTAGAATACGGCATTATT 14 16 1 TTTTCTAAAA 0.952092 -60 AATTTAAACATTTTTCAATAAAACAAATTTTATGT 17 117 1 TTTTCAAAAA 0.693425 -184 TAAAACAAATTTTATGTTAAAAAAACTTGAAAAAT 17 135 1 TTTAGTAAAA 0.534057 -166 AAATTGTTCCTTGAGCTTAAAAAAAGAAAACCGCG 17 192 0 TTGACTAAAA 0.745581 -109 TCGCCCAATTTTTATTTACAAAAGAATGAGATAAA 19 124 1 TTTATTAAAA 0.578405 -27 TCCCGTCAAATTTTGCTAGAGCAGATTCTTTGAAT 21 23 1 TTTTCTACAA 0.924901 -73 TTTTTGGCATTTTATATTAAAAATAAACCTACTTA 22 37 1 TTTAATAAAA 0.578405 -264 CAAAAATTCTTTTTAATGAATAAAAAATTGCAAAA 22 190 0 TTTTATAAAA 0.60701 -111 ATAGGCTGGATTTTACATAATAAAAATCCAGCCCA 25 14 1 TTTTCAAAAA 0.677835 -45 TGAAACGTAATTTTACTATATAAAATTAAGAGAGG 28 146 1 TTTTCTAAAA 0.949562 -30 CAAAACTCAATTTTTCTTCAAATAATTTCCTGACA 30 91 0 TTTTCTAATA 0.550084 -205 ATTGTAAATATTTTCCTACATAAATTACCCTTTTA 30 211 1 TTTTCTAAAT 0.693448 -85 TATAGATATTTTTAACTTGAACACAAGTATTTTTC 31 104 1 TTTACTACAA 0.91162 -197 GCACCGATTTTTTATCTGGCTAATATGTAGCGAAG 31 231 1 TTTACTCAAA 0.602812 -70 CGCTCTTTTATTTTAACATATTTAGATTGT 32 14 0 TTTTTTACAA 0.503529 -20 TTGATCTCAATAAAAAGTGCGGTTA 35 1 1 TTGACTAAAA 0.745581 -65 **** ** * ** * Masking position 2 Map Score: 17.9684 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 153 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 6 AATTCTTGAGAAAGTGCGGTCAATTTTTCAGT 7 191 0 AAAGTGCGTA 0.973761 -110 GGTGGCATCAAAAATGCCATCATCAATACAAA 10 39 1 AAAATGCATA 0.953314 -72 TCATTTAATAAAAATCCTATTAAAGAATAAAA 17 65 0 AAAATCCATA 0.864726 -236 TGTAGATCAAAATCCCGTCAAATTTTGCTA 21 9 1 AAAATCCGTA 0.933873 -87 TTTTTAATATAAAATGCCAAAAAATAGTTTGA 22 28 0 AAAATGCAAA 0.684843 -273 GAAAATGTAAAAAATCCAATAAGAAAAATTTG 22 145 0 AAAATCCATA 0.864726 -156 TCTGCATCGCAAAATGCTTTTAAATTAATCGT 22 228 1 AAAATGCTTA 0.834315 -73 TGTTTCCAGTAAAACGCCATAATATAAAACGA 27 19 1 AAAACGCATA 0.763071 -53 CTCTGTTCAAAAAATGCAGTGA 33 1 0 AAAATGCGTA 0.978311 -54 ATCTCAATAAAAAGTGCGGTTAATTTTAACCG 35 14 1 AAAGTGCGTA 0.973758 -52 CATCACAACAAAAGTGCGGTTAAAATTAACCG 35 30 0 AAAGTGCGTA 0.973758 -36 TTGGCTTAATAAAGTGCGGTTATGGTAGCCCA 37 21 1 AAAGTGCGTA 0.973758 -213 TAGTTTCTAAAAATTGCAGTAATAAATGTGAA 37 111 1 AAATTGCGTA 0.87671 -123 ******* ** * Masking position 3 Map Score: 14.9915 Number of sites scoring better than the average of aligned sites = 873 Number in coding regions = 522 Number in noncoding regions = 351 Number of orfs with sites within 600 bp upstream = 242 Fraction of orfs with sites within 600 bp upstream = 0.0388693 Motif number 7 AGATGATGTATTTGTTCATCACGTTCAGTTAAA 7 136 0 TTTGTATACG 0.863323 -165 TCAGTCAAATTTTGTCGTTCTTGCGTGAGATGA 7 163 0 TTTGTTTTTG 0.772875 -138 TTGTTTAGTTTTTGTCAATCAAGTTTTTGTCGG 12 50 0 TTTGTATAAG 0.809951 -28 CCCCTACATGTTTGTCTATGATGTAGATAAATT 13 56 0 TTTGTATATG 0.971049 -245 ATACTGAATCTTTGTTTATGGTGGGGGCTAATA 13 96 0 TTTGTATGTG 0.95981 -205 CCCTACATGTTTTGTCTATGATGTAGATAAATT 13 221 0 TTTGTATATG 0.971049 -80 TTACTAAATCTTTGTTTATGATGGGGCTAATAT 13 261 0 TTTGTATATG 0.971049 -40 GAGCCCTTTCTTTGTTTATCTTGTTATTTCATA 18 51 1 TTTGTATTTG 0.938225 -66 ATAAGAAAAATTTGTTGATTAGGGTTGTATTGG 22 126 0 TTTGTATAGG 0.863323 -175 CTTTCTTATTTTTGTAAATTATGAAACGTAATT 28 125 1 TTTGTATATG 0.971049 -51 AAAATTGAGTTTTGTGAGTTGTGTCTAATAAAT 30 112 1 TTTGTGTGTG 0.818095 -184 CCTTTAAAATTTTGTAATTATTGACGGAGTAAA 31 276 1 TTTGTTTTTG 0.772875 -25 TTACCCGATTTTTGTTGATAGTTAAAATTTTTC 34 141 0 TTTGTATGTT 0.611345 -67 ***** ** *** Masking position 5 Map Score: 11.7856 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 45 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 AAAATTCTTTTTTGTTTAAAACCCACTTTA 4 76 1 TTTGTTTAAA 0.518442 -117 TAACTCAGATTTTGTTATAATCTTTTCCTT 4 106 1 TTTGTTATAA 0.661233 -87 TGTTTTAGGGCTTGTGAAAACAAGCCTTTT 5 16 1 CTTGTGAAAA 0.950512 -100 ATAAATTAACCTTGTGTAAAGATGAAATTA 5 63 0 CTTGTGTAAA 0.924659 -53 AATAACATTGCTTGAGAAAAACGCCTGTTA 6 38 1 CTTGAGAAAA 0.67148 -95 ATCTAGAAATTTTGTGATCAATATCCCAAA 8 64 1 TTTGTGATCA 0.736387 -104 ACCGCGCAACCTTGTCAAAAATTTGACTAT 17 168 0 CTTGTCAAAA 0.713228 -133 AAAAGTCTCCTTGTGTTAAGAAAGTCTGT 26 12 0 CTTGTGTTAA 0.934289 -19 ACGAATCACATTTGTGATAATCAATTGGAG 27 47 1 TTTGTGATAA 0.898395 -25 ATCCTATTTTCTTGTGATAATATTTCATAT 28 17 0 CTTGTGATAA 0.956991 -159 CTTGAATGGACTTGTTTAAATCTAATCAGG 30 267 0 CTTGTTTAAA 0.730407 -29 AAGAAAAATACTTGTGTTCAAGTTAAAAAT 31 111 0 CTTGTGTTCA 0.817914 -190 ATGTGAATTTTTTGTGATAAAGATCTCATT 37 136 1 TTTGTGATAA 0.898395 -98 ********** Masking position 10 Map Score: 7.76186 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 121 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 9 CATCTCTAAAATCAATAAAAGGCTTGTTTTCA 5 30 0 ACATAAAAGG 0.928199 -86 CACTTTCTCAAGAATTAACGGGGTTACAAACA 7 207 1 AAATAACGGG 0.739583 -94 AAACGTTTCGATAACAAAAAGGAGCTTTTAG 8 147 1 AAAAAAAAGG 0.945842 -21 TATCCCGCTAAACATAAAAAGGAAACACAAGT 10 89 1 ACAAAAAAGG 0.952899 -22 CAACAGTTTTATCAAAAACAGGTTCATGTTGA 15 151 1 ACAAAACAGG 0.936931 -44 ATGAAAAAAAAATAAAAACAGGTTAATTTAAA 17 93 1 ATAAAACAGG 0.696803 -208 TAACAAGATAAACAAAGAAAGGGCTCTTTGGT 18 45 0 ACAAGAAAGG 0.761388 -72 AAGGAAAACGATAAAAAAAGGGCGAATAATTT 19 50 0 AAAAAAAGGG 0.858211 -101 GAATAAAAAACTGGCTGTCAAACT 22 3 1 AAAAAACTGG 0.619693 -298 ACTAGATTTTCAAATAAAAAGGAAAAAAT 22 282 1 CAAAAAAAGG 0.733658 -19 TAGGTAAAACATAAATAAAAGGAGGAAAATA 29 90 1 AAATAAAAGG 0.917761 -21 TAGCACAATTAGCATTAAAAGGGTAATTTATG 30 229 0 ACATAAAAGG 0.928199 -67 CGTATTATGAAAAACTAAAAGGAAATT 37 217 1 AAATAAAAGG 0.917761 -17 * ** ******* Masking position 8 Map Score: 7.31116 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 92 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 10 CGTTATATCACATTATGGGGCAAATTATATT 9 30 1 CATTTGGGGC 0.957769 -68 CATAGACAAACATGTAGGGGCTAATTATATT 13 69 1 CATGAGGGGC 0.987433 -232 AATCTTTGTTTATGGTGGGGGCTAATATAAT 13 92 0 TATGTGGGGG 0.962813 -209 ATAGACAAAACATGTAGGGGCTAATTATATT 13 235 1 CATGAGGGGC 0.987433 -66 AATCTTTGTTTATGATGGGGCTAATATAATT 13 257 0 TATGTGGGGC 0.980212 -44 ACCACCTTGACATGGTGGGGGTCACTGGTTC 31 26 0 CATGTGGGGG 0.987117 -275 **** ****** Masking position 3 Map Score: 5.6477 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 2 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 11 TTATTTTGTGTAGTTTATTCTTATTGTTATT 1 29 1 TAGTTTATCT 0.82867 -46 CATAACAAGTAATTTTATTCTGTCAATGGCA 3 73 1 AATTTTATCT 0.933949 -37 TACACAAGGTTAATTTATACTTTTCCAAATT 5 75 1 TAATTTATCT 0.765443 -41 GGTCGGAGAATTTTTTATCCTATCTAGAAAT 8 43 1 TTTTTTATCT 0.744431 -125 TATTTTATCCTGTATTGTTAT 9 87 0 TATTTTATCT 0.95392 -11 TGCGGAATGGTATTTTATGCTCTATTTGTAA 15 16 1 TATTTTATCT 0.95392 -179 ACAAGAGAATAATTTTATGCTGACGCTAACG 15 67 1 AATTTTATCT 0.933949 -128 TGTTATTAAAAATTTTATTCTTTAATAGGAT 17 53 1 AATTTTATCT 0.933949 -248 CAATAAAACAAATTTTATGTTAAAAAAACTT 17 132 1 AATTTTATTT 0.552643 -169 AGGTGGCAGCTATTTTATACTATTCTGCCT 23 10 0 TATTTTATCT 0.95392 -119 ******** ** Masking position 6 Map Score: 8.71896 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 31 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 12 AAAATTTTATTAAATTTCACAAAATATTGA 4 14 0 TAAATTTCAC 0.700951 -179 ATTTTAATTTTAATTTTAACTTAACAAGAG 11 74 1 TAATTTTAAC 0.949591 -28 CTGGATAGCCTATTTTTCACT 16 46 1 TATTTTTCAC 0.816207 -11 AAAAACAGGTTAATTTAAACATTTTTCAAT 17 106 1 TAATTTAAAC 0.649621 -195 ATTTTTCAAGTTTTTTTAACATAAAATTTG 17 140 0 TTTTTTTAAC 0.66217 -161 TTGATTACGGTAATTTTCACTGCATCCAAT 17 281 1 TAATTTTCAC 0.925876 -20 AATTTACCTACTTTTAACCATAATTGAA 21 78 0 TACTTTTAAC 0.878492 -18 TCATCAAATATACATTTAACTAATAAACTT 22 76 1 TACATTTAAC 0.575678 -225 AGCTGCCACCTAATTTTCACATAGTAACCT 23 30 1 TAATTTTCAC 0.925876 -99 ATCAGTAAAATTATTTTAACATATTGATTT 28 59 1 TTATTTTAAC 0.846463 -117 TGATTATAGATATTTTTAACTTGAACACAA 31 100 1 TATTTTTAAC 0.870086 -201 CGCTCTTTTATTTTAACATATTTAGAT 32 17 0 TTATTTTAAC 0.846463 -17 TTTTTTTGAAAAATTTTAACTATCAACAAA 34 134 1 AAATTTTAAC 0.649621 -74 AAAGTGCGGTTAATTTTAACCGCACTTTTG 35 24 1 TAATTTTAAC 0.949591 -42 ********** Masking position 9 Map Score: 12.6089 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 61 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 13 AACTCAATATTTTGTGAAATTTAATAAAA 4 10 1 TTTTGTGAAA 0.611615 -183 ATAACTCAGATTTTGTTATAATCTTTTCCT 4 105 1 TTTTGTTATA 0.854661 -88 TATCTAGAAATTTTGTGATCAATATCCCAA 8 63 1 TTTTGTGATC 0.952059 -105 GTTTTTCTATTTTTGTTATCTATATTTGTC 8 111 1 TTTTGTTATC 0.887532 -57 AAAAGCTCCTTTTTGTTATCGAAACGTTTC 8 146 0 TTTTGTTATC 0.887532 -22 AACGGCGATTTTTTGCTATAATCTCGCCCA 19 101 1 TTTTGCTATA 0.748014 -50 TAAAAAGAATTTTTGCGATCTGCATCGCAA 22 210 1 TTTTGCGATC 0.909299 -91 TTTAAAAGCATTTTGCGATGCAGATCGCAA 22 222 0 TTTTGCGATG 0.696846 -79 CCTGTGAATATTTTGTTATTTTCCTAATCT 23 101 0 TTTTGTTATT 0.549717 -28 AACGAATCACATTTGTGATAATCAATTGGA 27 46 1 ATTTGTGATA 0.611618 -26 GATCCTATTTTCTTGTGATAATATTTCATA 28 18 0 TCTTGTGATA 0.700062 -158 ATTTTACTGATTTTGTGATCTAGATCCTAT 28 40 0 TTTTGTGATC 0.952059 -136 AATGTGAATTTTTTGTGATAAAGATCTCAT 37 135 1 TTTTGTGATA 0.936701 -99 ********** Masking position 8 Map Score: 11.3591 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 105 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 14 CAGGTACACCAAGAAATAACAATAAGAATA 1 44 0 AAGAAATAAC 0.686805 -31 CCTAATCGTGAAATAACCTAGTCGTGA 6 8 1 GTGAAATAAC 0.960807 -125 TAACCTAGTCGTGAAATAACATTGCTTGAG 6 24 1 GTGAAATAAC 0.960807 -109 GCCCCATAATGTGATATAACGAGCTTATTT 9 21 0 GTGATATAAC 0.772575 -77 TAATCCTTATATGAAATAACAAGATAAACA 18 63 0 ATGAAATAAC 0.874044 -54 AAAAAATTGGAAAAAATAACAAGTTATGGG 19 17 1 AAAAAATAAC 0.578967 -134 GTCAAGATTAGGAAAATAACAAAATATTCA 23 97 1 GGAAAATAAC 0.803766 -32 GTCAATAAATGTAAAATAAATAAATTATTT 28 91 0 GTAAAATAAA 0.573991 -85 ATTTTATATAGTAAAATTACGTTTCATAAT 28 142 0 GTAAAATTAC 0.678404 -34 ATGTAGCGAAGTAAAATAACACCTTTAAAA 31 255 1 GTAAAATAAC 0.938605 -46 ********** Masking position 6 Map Score: 3.52991 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 95 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 15 TATGAAACATAAAAACTCTTTTTGGAATAC 3 26 0 AAAAACTCTT 0.821615 -84 CTTCATTTGCCAAAATTCTTTTTTGTTTAA 4 65 1 CAAAATTCTT 0.804346 -128 AGATAGGATAAAAAATTCTCCGACCAAATT 8 38 0 AAAAATTCTC 0.804346 -130 CATCATCAATACAAATTCTTCAAATTGTGG 10 56 1 ACAAATTCTT 0.802572 -55 TGCAGATCGCAAAAATTCTTTTTAATGAAT 22 204 0 AAAAATTCTT 0.941502 -97 CTATTGTAGCAAAAATTCTTTATTTTTGAC 29 63 0 AAAAATTCTT 0.941502 -48 ATATTTTTATAAAAAGTCTTCTATTTATTA 30 34 1 AAAAAGTCTT 0.821615 -262 TTATTAGCTCAAAAATTCATTTTTGTAAAG 30 58 1 AAAAATTCAT 0.756614 -238 GGGTTTTAAGAAAAATACTTGTGTTCAAGT 31 118 0 AAAAATACTT 0.735135 -183 TTAAGGGGTTAAAAATTCGTGCGCATATTA 34 171 0 AAAAATTCGT 0.82 -37 ********** Masking position 5 Map Score: 4.8655 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 41 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802