AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00530_hinf_reg_100.orf -o00530_hinf_100.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 Input sequences: #1 HI0059 72 conserved hypothetical protein #2 HI0060 40 ABC transporter, ATP-binding protein (msbA) #3 HI0061 258 recombination protein (rec2) #4 HI0140 272 N-acetylglucosamine-6-phosphate deacetylase (nagA) #5 HI0141 285 glucosamine-6-phosphate isomerase (nagB) #6 HI0144 45 glucose kinase, putative #7 HI0145 300 conserved hypothetical protein #8 HI0195.1 26 conserved hypothetical transmembrane protein (aefA) #9 HI0197 84 penicillin-insensitive murein endopeptidase (mepA) #10 HI0199 46 lipid A biosynthesis (kdo)2-(lauroyl)-lipid IVA acyltransferase (msbB) #11 HI0266 82 conserved hypothetical protein #12 HI0267 41 nitrate/nitrite sensor protein (narQ) #13 HI0301 300 hemolysin, putative #14 HI0413 300 ribonuclease E (rne) #15 HI0429 111 glucosamine--fructose-6-phosphate aminotransferase (glmS) #16 HI0448 71 PTS system, fructose-specific IIA/FPr component (fruB) #17 HI0449 86 H. influenzae predicted coding region HI0449 #18 HI0451 71 conserved hypothetical protein #19 HI0452 50 conserved hypothetical protein #20 HI0453 26 conserved hypothetical protein #21 HI0454 54 conserved hypothetical protein #22 HI0457 69 conserved hypothetical protein #23 HI0458 70 stationary phase survival protein SurA, putative #24 HI0459 131 pyrimidine operon regulatory protein (pyrR) #25 HI0642 159 UDP-N-acetylglucosamine pyrophosphorylase (glmU) #26 HI0652 62 3-deoxy-d-manno-octulosonic-acid transferase (kdtA) #27 HI0759 176 A/G-specific adenine glycosylase (mutY) #28 HI0825 145 H. influenzae predicted coding region HI0825 #29 HI0867 237 lipopolysaccharide biosynthesis protein, putative #30 HI0870.1 300 H. influenzae predicted coding region HI0870.1 #31 HI0916 107 outer membrane protein, putative #32 HI1060 66 lipid-A-disaccharide synthetase (lpxB) #33 HI1062 85 (3R)-hydroxymyristol (acyl carrier protein) dehydrase (fabZ) #34 HI1064 56 conserved hypothetical protein #35 HI1084 29 conserved hypothetical protein #36 HI1087 300 ABC transporter, ATP-binding protein #37 HI1139 137 UDP-N-acetylmuramate--alanine ligase (murC) #38 HI1140 71 D-alanine--D-alanine ligase (ddlB) #39 HI1143 83 cell division protein (ftsZ) #40 HI1144 38 UDP-3-0-(3-hydroxymyristoyl) N-acetylglucosamine deacetylase (lpxC) #41 HI1279 104 acylneuraminate cytidylyltransferase (neuA) #42 HI1336 111 dihydropteroate synthase (folP-1) #43 HI1337 37 mrsA protein (mrsA) #44 HI1338 58 conserved hypothetical protein #45 HI1354 300 glutaminyl-tRNA synthetase (glnS) #46 HI1355 65 conserved hypothetical protein #47 HI1356 61 4-alpha-glucanotransferase (malQ) #48 HI1358 95 glycogen operon protein (glgX) #49 HI1527 84 lipid A biosynthesis lauroyl acyltransferase (htrB) #50 HI1578 300 glycosyl transferase, putative #51 HI1711 59 PTS system, glucose-specific IIA component (crr) #52 HI1712 79 phosphoenolpyruvate-protein phosphotransferase (ptsI) #53 HI1713 158 phosphocarrier protein HPr (ptsH) Motif number 1 CGCGTTATTTTATCCGCACTTATTAGAAAGG 1 45 1 TTCCGCACTT 0.981317 -28 AGATAGAAAATTGCCGCACTTATAATGATCC 5 189 1 TGCCGCACTT 0.987318 -97 TAATTAATTTTAACCGCACTTTTGCGCGCTT 10 17 0 TACCGCACTT 0.998473 -30 AAATTTTACCGCACTTTTCTAAATTT 12 6 1 TACCGCACTT 0.998473 -36 TGTGTATTTTTAACCGCACTTTAGGTTTAAA 13 173 1 TACCGCACTT 0.998473 -128 CAATAAAAAATAACCGCACATTGGGTTTAAA 13 198 0 TACCGCACAT 0.980194 -103 GGATAAAAATTTACCGCACTT 18 1 0 TACCGCACTT 0.998473 -71 TAAAAGAAAACGACCGCACTTTGCGACCGTT 19 18 0 CACCGCACTT 0.993491 -33 TCAGCATTTTTAACCGCACTTTTCTTTTT 27 158 1 TACCGCACTT 0.998473 -19 TCTTCATTTTCAACCGCACTTTACACACCAA 32 18 1 CACCGCACTT 0.993491 -49 TCCTAAAAAATAACCGCACTTTGGTGTGTAA 32 38 0 TACCGCACTT 0.998473 -29 TTGCGAATTTTAACCGCACTTTTAGTTGAGT 37 89 1 TACCGCACTT 0.998473 -49 CTCTAAAAATTAACCGCATTTT 42 100 1 TACCGCATTT 0.968299 -12 TTTTTGACCGCACTTAGTAAAGTGC 44 5 1 TACCGCACTT 0.998473 -54 TTATAAAAATAAACCGCACTTTACTAAGTGC 44 20 0 AACCGCACTT 0.982443 -39 TTCAAAAAACTTACCGCACTTTGTGCATTTA 45 122 1 TACCGCACTT 0.998473 -179 ACGTTTGTTTTGACCGCACTTGGTTGATTAA 46 13 0 TACCGCACTT 0.998473 -53 AACGTGATTTTGACCGCACTTTTTATTTGTA 46 39 1 TACCGCACTT 0.998473 -27 * ********* Masking position 11 Map Score: 75.6527 Number of sites scoring better than the average of aligned sites = 961 Number in coding regions = 606 Number in noncoding regions = 355 Number of orfs with sites within 600 bp upstream = 247 Fraction of orfs with sites within 600 bp upstream = 0.0396723 Motif number 2 TCGCGTTATTTTATCCGCACTTATTAGAAAG 1 44 1 TTTCCGCACT 0.968596 -29 AAGATAGAAAATTGCCGCACTTATAATGATC 5 188 1 ATGCCGCACT 0.932262 -98 GTAATTAATTTTAACCGCACTTTTGCGCGCT 10 18 0 TTACCGCACT 0.997552 -29 AAATTTTACCGCACTTTTCTAAATT 12 5 1 TTACCGCACT 0.997552 -37 TTGTGTATTTTTAACCGCACTTTAGGTTTAA 13 172 1 TTACCGCACT 0.997552 -129 TCAATAAAAAATAACCGCACATTGGGTTTAA 13 199 0 ATACCGCACA 0.897773 -102 TGGATAAAAATTTACCGCACTT 18 2 0 TTACCGCACT 0.997552 -70 ATAAAAGAAAACGACCGCACTTTGCGACCGT 19 19 0 ACACCGCACT 0.964147 -32 ATCAGCATTTTTAACCGCACTTTTCTTTTT 27 157 1 TTACCGCACT 0.997552 -20 TTCTTCATTTTCAACCGCACTTTACACACCA 32 17 1 TCACCGCACT 0.988924 -50 ATCCTAAAAAATAACCGCACTTTGGTGTGTA 32 39 0 ATACCGCACT 0.991919 -28 AACATTCTTTTTGACCTCACTAAAGAAGCTT 36 92 0 TTACCTCACT 0.947338 -209 GTTGCGAATTTTAACCGCACTTTTAGTTGAG 37 88 1 TTACCGCACT 0.997552 -50 ACTCTAAAAATTAACCGCATTTT 42 99 1 TTACCGCATT 0.947338 -13 TTTTTGACCGCACTTAGTAAAGTG 44 4 1 TTACCGCACT 0.997552 -55 TTTATAAAAATAAACCGCACTTTACTAAGTG 44 21 0 TAACCGCACT 0.970356 -38 ATTCAAAAAACTTACCGCACTTTGTGCATTT 45 121 1 CTACCGCACT 0.982237 -180 CACGTTTGTTTTGACCGCACTTGGTTGATTA 46 14 0 TTACCGCACT 0.997552 -52 AAACGTGATTTTGACCGCACTTTTTATTTGT 46 38 1 TTACCGCACT 0.997552 -28 ** ******** Masking position 9 Map Score: 64.2291 Number of sites scoring better than the average of aligned sites = 842 Number in coding regions = 496 Number in noncoding regions = 346 Number of orfs with sites within 600 bp upstream = 239 Fraction of orfs with sites within 600 bp upstream = 0.0383874 Motif number 3 AAGGTACAATGCGTGCAATTTTTACTATTAGATA 2 11 1 GCGTTTTTTA 0.951856 -30 AAAACAGGGGGAGGTAAGTTTTTTCTAATTTAAA 5 14 0 GAGGTTTTTT 0.817286 -272 CATTATAAGTGCGGCAATTTTCTATCTTGTTTTT 5 182 0 GCGGTTTCTA 0.981401 -104 AACCCAATGTGCGGTTATTTTTTATTGATTTTCC 13 202 1 GCGGTTTTTA 0.995596 -99 TGTCGATTGCGCAGGGGTTTTTTATTGTGTAAAC 15 37 1 GCAGTTTTTA 0.927496 -75 CAGTATAATGGCGGCGTTTTATTAACTTTAATCG 17 60 1 GCGGTTATTA 0.944781 -27 AAGTGCGGTAAATTTTTATCCATTTCTC 18 5 1 GCGGTTTTTA 0.995596 -67 GTCGCAAAGTGCGGTCGTTTTCTTTTATATTTTT 19 22 1 GCGGTTTCTT 0.95465 -29 TGGTGCAAATGCCGTCGCTTTTTAGGCGTATTTT 24 63 1 GCCGTTTTTA 0.980704 -69 TGCTATACTAGCCGAAATTTTTTTAAGTATAACC 26 28 1 GCCGTTTTTT 0.953 -35 ACACCAAAGTGCGGTTATTTTTTAGGATAAATTT 32 42 1 GCGGTTTTTA 0.995596 -25 TATATTGAGTGCGTTTTATTTTTAGCTATAAATA 33 13 1 GCGTTTTTTA 0.951856 -73 TCTTGAGCGGTTATTTTATAGAATAAGCCA 34 37 0 GCGGTTTATA 0.950848 -20 AAAATGCGGTTAATTTTTAGAGTGATTTT 42 93 0 GCGGTTTTTA 0.995596 -19 TTAGTAAAGTGCGGTTTATTTTTATAAAGTTTTT 44 24 1 GCGGTTTTTA 0.995596 -35 TGCACAAAGTGCGGTAAGTTTTTTGAATGTTTAG 45 115 0 GCGGTTTTTT 0.989035 -186 CGATAATTTCGTGGCGGTTTTTTATGGCAAGTTT 45 163 1 GTGGTTTTTA 0.918114 -138 GTATAGAATAGCCGAATATTTTTTTATTTTAACG 45 270 1 GCCGTTTTTT 0.953 -31 **** ****** Masking position 9 Map Score: 35.8251 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 172 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 4 ACTCGCGTTATTTTATCCGCACTTATTAGA 1 42 1 TTTTATCCGC 0.980843 -31 ATGTAATTAATTTTAACCGCACTTTTGCGC 10 21 0 TTTTAACCGC 0.993769 -26 AATTGTGTATTTTTAACCGCACTTTAGGTT 13 170 1 TTTTAACCGC 0.993769 -131 GGTCGATTTGTTTCATCCGCAGCTTTCTTT 16 31 1 TTTCATCCGC 0.941779 -41 TTTCTATTTTAACCACTTTAAAATTC 25 7 1 TTTTAACCAC 0.919634 -153 TCATCAGCATTTTTAACCGCACTTTTCTTT 27 155 1 TTTTAACCGC 0.993769 -22 ATTTTATCTCTCTTATCCGCTATTTTAGTA 30 129 1 TCTTATCCGC 0.889815 -172 ACTTCTTCATTTTCAACCGCACTTTACACA 32 15 1 TTTCAACCGC 0.980539 -52 GTAACATTCTTTTTGACCTCACTAAAGAAG 36 95 0 TTTTGACCTC 0.893647 -206 ACGTTGCGAATTTTAACCGCACTTTTAGTT 37 86 1 TTTTAACCGC 0.993769 -52 TTTTTGACCGCACTTAGTAAA 44 2 1 TTTTGACCGC 0.991533 -57 ATCACGTTTGTTTTGACCGCACTTGGTTGA 46 17 0 TTTTGACCGC 0.991533 -49 ACAAACGTGATTTTGACCGCACTTTTTATT 46 36 1 TTTTGACCGC 0.991533 -30 ********** Masking position 3 Map Score: 30.0329 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 102 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 5 TTCATCTTTATGTAGGGGCGAATTACATTCGCCC 4 21 1 TGGGCGAATT 0.991487 -252 CTTGTTGAGATTATAGGGCGAATGTAATTCGCCC 4 36 0 TGGGCGAATG 0.990649 -237 TTCATCTTTATGTAGGGGCGAATTACATTCGCCC 4 157 1 TGGGCGAATT 0.991487 -116 TTGTTTGTGATTATAGGGCGAATGTAATTCGCCC 4 172 0 TGGGCGAATG 0.990649 -101 TCACAAACAATCATAGGGCAAATTGTCCTTACGT 4 196 1 TGGGCAAATT 0.980006 -77 AACGATTAATTAGCAAGGCGAATTTGCGTTCA 14 9 0 TAGGCGAATT 0.973821 -292 CTGTAAGGCTTATCTAGGCAAATG 17 1 0 TAGGCAAATG 0.934376 -86 ATGCCGTCGCTTTTTAGGCGTATTTTCTTTATAC 24 71 1 TAGGCGTATT 0.773001 -61 AAATGAATGAAAAGTGGGCAAATTTGTCCACTTT 28 30 1 AGGGCAAATT 0.817747 -116 TAGAGTGATTTTGGTGGGCGATTATAGCGAAATA 42 71 0 TGGGCGATTA 0.739872 -41 ATAGATAAATTGTAGGGGCGAATTACATTCGCCT 48 16 1 TGGGCGAATT 0.991487 -80 CATCGGTGGTTTATCAGGCGAATGTAATTCGCCC 48 31 0 TAGGCGAATG 0.971292 -65 ACCACCGATGTTTTTGGGCAAATGTAATTTGCCT 48 55 1 TGGGCAAATG 0.97806 -41 TTTTATCGATTTTGTAGGCAAATTACATTTGCCC 48 70 0 TAGGCAAATT 0.939955 -26 TGAAAAAGGATACTAGGGCAATTTTCTGGTTTTA 53 102 1 TGGGCAATTT 0.894809 -57 * ********* Masking position 13 Map Score: 25.2202 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 56 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 TTTTAGCAAGTAAATTTTCCTGAAAAATTTATTTTTAC 3 141 1 TATTTCAAAT 0.894601 -118 AGAATAGATCTCTATTTATCCTGATAATCCGTACCAGC 4 120 0 TATTTTAAAT 0.839988 -153 GGGGAGGTAAGTTTTTTCTAATTTAAATAT 5 3 0 GTTTTTTAAT 0.675955 -283 TAAAAAGAAATTCTTTTGCTCCAATAATTTACGACAGA 5 145 0 TTTTTCAAAT 0.949243 -141 GGAGAAAACATACATTTTTGGCCTAAATTGATTCTCAT 7 15 0 TATTTTTAAT 0.70436 -286 TTTAAATTTGTTTTTTTACTCTTAGAATTGCTCTCGAA 7 65 0 TTTTTCAAAT 0.949243 -236 ATAGTTTTACGAGTTTTATTTCCAAAATGAGAAGTTGA 7 103 1 GTTTTTAAAT 0.821307 -198 ATCTTTGCCCTCTTTTTACGAGATCAATTCACAATCAA 13 34 1 TTTTTCTAAT 0.894601 -267 TAAAATATGATAATTTTTCGCCGTCAATAAGACATCAA 13 261 1 TTTTTCTAAT 0.894601 -40 TGCTAATTAATCGTTTTCTATGGATAATAGAGCCTCTT 14 28 1 TTTTTTAAAT 0.920424 -273 TAAATTTTTATCCATTTCTCTACAAAATTATGTTATAA 18 19 1 TATTTTAAAT 0.839988 -53 GGAAACCATCGGTTTTTTCTTATATAAAAGTTTGTTAT 25 49 1 GTTTTCAAAA 0.649339 -111 TTGTTTATCTGCATTTTTTCAGTATAATTCGCAACCTA 27 98 0 GTTTTTAAAT 0.821307 -79 ATAAACAAGCTCTATTTTCGTGTAAAATCATCAGCATT 27 128 1 TATTTCAAAT 0.894601 -49 TTGTCCACTTTTGTTTTATCTATTCAATTCTGAATTAA 28 53 1 TTTTTTTAAT 0.839988 -93 TTTAAGGTATTAATTTTCCCTCCAGAATATTGGACAAA 30 245 0 TTTTTCAAAT 0.949243 -56 CAAAGTGCGGTTATTTTTTAGGATAAATTTG 32 46 1 TTTTTTTAAT 0.839988 -21 TTGAGTGCGTTTTATTTTTAGCTATAAATATCGTATAA 33 17 1 TATTTTAAAA 0.566635 -69 TTATCAATGTTTATTTTCCATAAACAAAGTATTATTAA 36 28 1 TTTTTCAAAA 0.822851 -273 TTATTTTAATTTTTCATCTACAATAAAGGGAATT 39 7 1 TTTTTCAAAT 0.949243 -77 TGGTTTTATAACGATAAAAAATTAAAGG 43 1 1 TTTTTTAAAA 0.742411 -37 TTGGGCAAATGTAATTTGCCTACAAAATCGATAAAAAT 48 68 1 GATTTCAAAT 0.771312 -28 TACTACCTTGTTTATTTTCTCGAATAATCGGTAACAGT 50 60 0 TATTTCAAAT 0.894597 -241 TCTATGCATCTCCTTTTGTTATTTAAATAACGTATAAA 50 239 1 TTTTTTTAAT 0.839988 -62 TTATTCTTGATTATTTTGCTTTGAAAAAGGATACTAGG 53 81 1 TTTTTCAAAA 0.823324 -78 GGCAATTTTCTGGTTTTATATTTTTAATTATTGATTAG 53 118 1 TTTTTTTAAT 0.839988 -41 * **** * * *** Masking position 7 Map Score: 28.101 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 195 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 7 AGATCTATTCTTCATCTTTATGTAGGGGCGA 4 6 1 TATTTCTTTT 0.63431 -267 AATAGAGATCTATTCTTCATCTTTATGTAGGGGCGA 4 142 1 TATTTCTTTT 0.63431 -131 GTAAAACTATTTTAAATTTGTTTTTTTACTCTTAGA 7 77 0 TTTATTTTTT 0.917902 -224 TAAAGAATATTTTTGAAGTGTTTTTTCATAAATGTG 7 142 0 TTTTATTTTT 0.86221 -159 AAATTTTACCGCACTTTTCTAAATTTCCAC 12 5 1 TTTAGTTTTT 0.73627 -37 TCTTTTCGCGTTTTGCGATTTTTTCTAAAATATGAT 13 236 1 TTTTGTTTTT 0.706019 -65 TAACCTCAAATTTTTTATGGTTTTATAACATAATTT 18 43 0 TTTTATTTTT 0.86221 -29 TAATTGCCCCTTTTGTTGTTTTTTATTTTCTCTTTC 22 35 1 TTTTTTTTTT 0.90582 -35 GCCGTCGCTTTTTAGGCGTATTTTCTTTATACTTTG 24 73 1 TTTACTTTTT 0.602699 -59 AAGTAAAAACTATAACAAACTTTTATATAAGAAAAA 25 62 0 TATAATTTTT 0.767514 -98 ATTTTCAATCCTTTTTTTGCTATACTA 26 2 1 TTTTATTTTT 0.86221 -61 ATAGAGCTTGTTTATCTGCATTTTTTCAGTATAATT 27 107 0 TTTATTTTTT 0.917902 -70 ATTTGCCCACTTTTCATTCATTTTATTAAGATTGCG 28 17 0 TTTTTTTTTT 0.90582 -129 CTTCCTTGCTTATTACTTTCTTTTTTGATTTTAAGA 30 79 1 TATTTTTTTT 0.813611 -222 GCTATTTTAGTATATTATGATTTTTTCGGGTGGGTA 30 147 1 TATAATTTTT 0.767514 -154 TTTGGTAGGGTTTATTATTATTTTGTCCAATATTCT 30 224 1 TTTAATTTTT 0.87914 -77 TACCTTAAACTATATAAAGGTTTTCTCTATATATGT 30 274 1 TATAATTTTT 0.767514 -27 CGATAGATTTTATTTGTTTATTTTTTGTAAGGTATC 33 57 1 TATTTTTTTT 0.813611 -29 TTTATTGAATTTTAATAATACTTTGTTTATGGAAAA 36 41 0 TTTAACTTTT 0.742961 -260 AGTGATAAATTTTATTTCTATTTTTTATAGATTAAA 36 137 0 TTTATTTTTT 0.917902 -164 TAACCGCACTTTTAGTTGAGTTTTGTCATTGGGAGA 37 99 1 TTTATTTTTT 0.917902 -39 ATATATAAAATATAAATTCCCTTTATTGTAGATGAA 39 23 0 TATATCTTTT 0.668476 -61 TTTATTTCCTCTTTGTTAAACAAAAA 41 1 1 TTTATCTTTT 0.816271 -104 TATGGCAAGTTTTTACAATCTTTTATTTAAATCTAG 45 185 1 TTTTATTTTT 0.86221 -116 ATTTTTATCGATTTTGTAGGCAAATTA 48 79 0 TTTTTTTTTT 0.90582 -17 AAATAAACTATTTAGCTTATTTTTATGATTTAATTC 53 31 1 TTTATTTTTT 0.917902 -128 **** * **** * Masking position 12 Map Score: 26.1472 Number of sites scoring better than the average of aligned sites = 454 Number in coding regions = 308 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 8 TATTTTTCCCTAATCTAAATG 8 16 0 ATTTTTCCCT 0.884607 -11 AATAACGAACAGTTTTTCTTGCTGGAGTGC 11 60 1 AGTTTTTCTT 0.777246 -23 GTTGTCTAGAATTTTCCCCTCTCCGTAAAA 13 141 1 ATTTTCCCCT 0.853305 -160 AAGTTTTCCTTATTTATTCTA 15 101 0 AGTTTTCCTT 0.884607 -11 ACTTTTCCCTTGTTAGAACTG 20 16 0 CTTTTCCCTT 0.777638 -11 AATTATTTTTCCTTATGCCTAAGG 21 41 0 ATTTTTCCTT 0.944959 -14 GTTGTTTTTTATTTTCTCTTTCTTATAGCT 22 49 1 ATTTTCTCTT 0.855686 -21 GAAACCATCGGTTTTTTCTTATATAAAAGT 25 50 1 GTTTTTTCTT 0.677188 -110 AAATTTTCTCTTTATTCATCAA 25 148 0 ATTTTCTCTT 0.855686 -12 AAAAGCATTTAGTTTTCCTTTTATTCTCAC 29 197 0 AGTTTTCCTT 0.884607 -41 TAAGGTATTAATTTTCCCTCCAGAATATTG 30 251 0 ATTTTCCCTC 0.580074 -50 TAAATTGAACTTTTTTCTTCATCAGAACT 31 10 1 CTTTTTTCTT 0.677188 -98 TGTTTTTTCCTTCTGGCTTAAA 34 3 1 TTTTTTCCTT 0.748718 -54 TAAAGATGAAGTTTTTTCTTTTATCGCAAC 36 211 0 GTTTTTTCTT 0.677188 -90 TTATTTTTCCTTTTCTCCCAAT 37 126 0 ATTTTTCCTT 0.944959 -12 TTTCTATCCTGTTTTTCTTCTTACTGATG 38 53 0 TGTTTTTCTT 0.37717 -19 CTATTCTAGAATCTTTCCCTTGTTTTAGCA 41 64 0 ATCTTTCCCT 0.448397 -41 GAAAGGCTTTATTTTTTCCTAATGATTTTG 42 31 1 ATTTTTTCCT 0.777246 -81 ATGAACCTTTATTTTCCCTTAGATTTGTAT 45 244 1 ATTTTCCCTT 0.928709 -57 ********** Masking position 5 Map Score: 14.8654 Number of sites scoring better than the average of aligned sites = 373 Number in coding regions = 271 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 9 TTCATCTTTATGTAGGGGCGAATTACATTCGC 4 21 1 TTAGGGCGAA 0.972983 -252 CTTGTTGAGATTATAGGGCGAATGTAATTCGC 4 38 0 TATGGGCGAA 0.979859 -235 TTCATCTTTATGTAGGGGCGAATTACATTCGC 4 157 1 TTAGGGCGAA 0.972983 -116 TTGTTTGTGATTATAGGGCGAATGTAATTCGC 4 174 0 TATGGGCGAA 0.979859 -99 TCACAAACAATCATAGGGCAAATTGTCCTTAC 4 196 1 TATGGGCAAA 0.950818 -77 CCTTCCCCTGTTTACGGGGGAAGGTGCCCGAA 5 87 1 TTAGGGGGAA 0.895639 -199 TCGAATCCTATTTTGGGGGAGAAAACATACAT 7 38 0 TTTGGGGAGA 0.627719 -263 CTGCCTAATTTAATTGGGCAGAGAAAATATTA 31 55 1 TATGGGCAGA 0.859308 -53 TTGAGTTTTGTCATTGGGAGAAAAGGAAAAAT 37 114 1 TATGGGAGAA 0.882284 -24 TCTATACAAATCTAAGGGAAAATAAAGGTTCA 45 245 0 TTAGGGAAAA 0.687962 -56 ATAGATAAATTGTAGGGGCGAATTACATTCGC 48 16 1 TTAGGGCGAA 0.972983 -80 CATCGGTGGTTTATCAGGCGAATGTAATTCGC 48 33 0 TATAGGCGAA 0.762153 -63 ACCACCGATGTTTTTGGGCAAATGTAATTTGC 48 55 1 TTTGGGCAAA 0.957258 -41 * ** ******* Masking position 12 Map Score: 11.5752 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 96 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 GTGCGGATAAAATAACGCGAGTTTTTCAACTCGC 1 30 0 AATAAAGTTT 0.718854 -43 TTTGGGGGAGAAAACATACATTTTTGGCCTAAAT 7 25 0 AAAACATTTT 0.49295 -276 AAAAAAACAAATTTAAAATAGTTTTACGAGTTTT 7 86 1 ATTTAAGTTT 0.620826 -215 TATATGAAAAATAAATGCCATTTTAAAGAATATT 7 167 0 ATAAAATTTT 0.713969 -134 TTTTGTGTGGATTAAATTAATTTTAAAGTGATTT 7 251 1 ATTAAATTTT 0.852949 -50 TGCGGTTAAAATTAATTACATTTTATT 10 30 1 ATTAAATTTT 0.852949 -17 TTTGGGTAGAATAACGAACAGTTTTTCTTGCTGG 11 51 1 ATAACAGTTT 0.331487 -32 ATATAAACAAAATAAGAATATTTTGTTGTCTAGA 13 117 1 AATAAATTTT 0.843624 -184 GTGCGGTTAAAAATACACAATTTTTACGGAGAGG 13 158 0 AAATAATTTT 0.58033 -143 GACGGCGAAAAATTATCATATTTTAGAAAAAATC 13 252 0 AATTAATTTT 0.762658 -49 ATTTGCGTAAAAAAGGATAAGTTTTGTTGGTGAA 14 79 1 AAAAGAGTTT 0.441782 -222 AAGCGACGGCATTTGCACCATTTTTCTTGTTCGT 24 49 0 ATTTGATTTT 0.713043 -83 AGAAAAAGGCTATTTTTATCAGTACG 29 3 1 AAAAAATTTT 0.698603 -235 TGATTTTAAGATAAGGGATATTTTGATTTTATCT 30 104 1 ATAAGATTTT 0.642264 -197 TATAGCTAACATTAGAGTAATTTTCATACAAATA 30 188 0 ATTAGATTTT 0.806649 -113 GTGCGGTTGAAAATGAAGAAGTTTTA 32 3 0 AAATGAGTTT 0.320366 -64 TATTTTATAGAATAAGCCAATTTTTTAAGCCAGA 34 22 0 AATAAATTTT 0.843624 -35 TTTCTTCATTATTTATTGAATTTTAATAATACTT 36 54 0 ATTTAATTTT 0.775521 -247 GAATGTTACTATTACAAAAATTTTAATCTATAAA 36 116 1 ATTACATTTT 0.708558 -185 ATACTTTTCTAATACTAAGATTTTCAATCAATCC 38 19 0 AATACATTTT 0.693372 -53 CACTCTAAAAATTAACCGCATTTT 42 98 1 ATTAAATTTT 0.852949 -14 ACGATAAAAAATTAAAGGAATTTTATT 43 21 1 ATTAAATTTT 0.852949 -17 TGGTTATTCAAATAGAGAGATTTTAAA 49 4 0 AATAGATTTT 0.795094 -81 AAAACAATTAATTTAGGAGAGTTTTAATTGGTTA 50 205 1 ATTTAAGTTT 0.620826 -96 ACAAAATTATTTGATTTTACGTTAAAAT 51 5 1 AATTAATTTT 0.762658 -55 TTAGCCATAAAATTGTGAAATTTTATGGCTATTG 52 18 1 AATTGATTTT 0.697995 -62 TAAATAAACTATTTAGCTTATTTTTATGATTTAA 53 30 1 ATTTAATTTT 0.775521 -129 ***** ***** Masking position 10 Map Score: 17.0826 Number of sites scoring better than the average of aligned sites = 536 Number in coding regions = 382 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 11 GATCATCACGGTCAATAATAAAGGAAGGCTAAT 5 263 1 GTAAATAAAG 0.73095 -23 ACCTTATTATATGAAAAATAAATGCCATTTTAAA 7 174 0 ATAAATAAAG 0.830852 -127 CGAAAAGAGGAAAATCAATAAAAAATAACCGCAC 13 210 0 AAAAATAAAA 0.61147 -91 TGATAACGTTATTAAGCATAAATATTTGCTTGAT 14 209 0 ATACATAAAA 0.545176 -92 CAAAGTATCAAAAATAAAGGGGCTTAATTG 22 7 1 ATAAATAAAG 0.830852 -63 CCCGTTGTTATTGATGAATAAAGAGAAAATTT 25 138 1 TTAAATAAAA 0.664991 -22 TTTATGATCTGTAAGGAATAAAGA 29 224 1 GTAAATAAAA 0.879176 -14 TTGATACCTTACAAAAAATAAACAAATAAAATCT 33 61 0 ACAAATAAAA 0.569485 -25 TACTTTGTTTATGGAAAATAAACATTGATAAATG 36 25 0 ATGAATAAAA 0.545176 -276 TTAAAATTCAATAAATAATGAAGAAATGTAAAGC 36 62 1 ATAAATGAAA 0.596064 -239 ATTTTAATCTATAAAAAATAGAAATAAAATTTAT 36 135 1 ATAAATAGAA 0.545176 -166 TAATATCTCGTTTATAAATAAAAAGTTCAATCAG 36 277 0 TTAAATAAAA 0.66499 -24 AAGTGCTAATATTAGAAATAAAAACGTTGCGAAT 37 63 1 ATAAATAAAA 0.929358 -75 TTTATTGTAGATGAAAAATTAAAATAA 39 4 0 ATAAATTAAA 0.766119 -80 GAACAAAATCATTAGGAAAAAATAAAGCCTTTCC 42 30 0 ATAAAAAAAA 0.447129 -82 TTTTATAACGATAAAAAATTAAAGGAATTTTATT 43 14 1 ATAAATTAAG 0.550163 -24 AGTTGATACAAATAAAAAGTGCGGTCAA 46 48 0 GAAAATAAAA 0.465374 -18 AGATGCATAGATAACCAATTAAAACTCTCCTAAA 50 216 0 ATAAATTAAA 0.766119 -85 AATTAACAAAGTAATAAATAAACAATAGCCATAA 52 40 0 GTAAATAAAA 0.879176 -40 GATTGAGATTGTGAATAATAAATAAACTATTTAG 53 12 1 GTAAATAAAA 0.879176 -147 AAGCAAAATAATCAAGAATAAACACTAAAAAGCC 53 68 0 ATAAATAAAA 0.929358 -91 ACCTCGACTAATCAATAATTAAAAATATAAAACC 53 129 0 ATAAATTAAA 0.766119 -30 ** * ****** * Masking position 8 Map Score: 10.4523 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 120 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 12 TTCATCTTTATGTAGGGGCGAATTACATTC 4 21 1 TGTAGGGGCG 0.985731 -252 TTCATCTTTATGTAGGGGCGAATTACATTC 4 157 1 TGTAGGGGCG 0.985731 -116 CTTTAGACAGTATAATGGCGGCGTTTTATT 17 53 1 TATAATGGCG 0.646948 -34 AGAAAGTTCCTATAGCGGCGTGGCTTCATT 27 24 0 TATAGCGGCG 0.884648 -153 GGGTTGTGGCGTTTTATAAAT 37 2 1 GGTTGTGGCG 0.805244 -136 TTTAATGTGATGTAGTGGAGGGAGGCGTAT 45 11 0 TGTAGTGGAG 0.824188 -290 GCCACGAAATTATCGTGGCGATGTATAAAT 45 148 0 TATCGTGGCG 0.911129 -153 GCCACGATAATTTCGTGGCGGTTTTTTATG 45 159 1 TTTCGTGGCG 0.877374 -142 ATAGATAAATTGTAGGGGCGAATTACATTC 48 16 1 TGTAGGGGCG 0.985731 -80 GTAAGTTAGGGGCGTAGTTTATCG 49 71 0 GTTAGGGGCG 0.890146 -14 ********** Masking position 3 Map Score: 7.62978 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 42 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 13 CTTGTTGAGATTATAGGGCGAATGTAATTCG 4 39 0 TTATAGGGCA 0.942777 -234 TTGTTTGTGATTATAGGGCGAATGTAATTCG 4 175 0 TTATAGGGCA 0.942777 -98 TCACAAACAATCATAGGGCAAATTGTCCTTA 4 196 1 TCATAGGGCA 0.756256 -77 CTTATTTTGTTTATATGACGAAAAGTATCTA 13 102 0 TTATATGACA 0.730754 -199 TTATCACTATTTTTATGACCACATCAAAGTT 36 165 1 TTTTATGACA 0.798935 -136 AAGTTTTTTCTTTTATCGCAACACATCTCTT 36 202 0 TTTTATCGCA 0.750749 -99 CGTGGCGGTTTTTTATGGCAAGTTTTTACAA 45 172 1 TTTTATGGCA 0.962675 -129 AATCTAGTATTTCTATGGCAAGAACAGGAGA 45 214 1 TTCTATGGCA 0.888095 -87 ACCACCGATGTTTTTGGGCAAATGTAATTTG 48 55 1 TTTTTGGGCA 0.753986 -41 AATTTCACAATTTTATGGCTAAGTAAGAA 52 9 0 TTTTATGGCA 0.962675 -71 AATTGTGAAATTTTATGGCTATTGTTTATTT 52 28 1 TTTTATGGCA 0.962675 -52 ********* * Masking position 11 Map Score: 7.51643 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 41 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 14 AGATCTATTCTTCATCTTTATG 4 3 1 ATCTATTCTT 0.737557 -270 ATAAATAGAGATCTATTCTTCATCTTTATG 4 139 1 ATCTATTCTT 0.737557 -134 AACTTATCCTTATAGTGTAA 6 36 0 AACTTATCCT 0.730307 -10 TCACCAACAAAACTTATCCTTTTTTACGCA 14 82 0 AACTTATCCT 0.730307 -219 ATCTTATCTATTGTGAACCT 23 1 1 ATCTTATCTA 0.692374 -70 TATCTTATCTTATCTTATCTT 30 2 1 ATCTTATCTT 0.946563 -299 ATCTTATCTTATCTTATCTTATCTTATCTT 30 12 1 ATCTTATCTT 0.946563 -289 ATCTTATCTTATCTTATCTTATCTTATCTT 30 22 1 ATCTTATCTT 0.946563 -279 ATCTTATCTTATCTTATCTTTTTCATTGTT 30 32 1 ATCTTATCTT 0.946563 -269 TTTTAGCAAAAACTAATCTTTAATATGGCA 41 42 0 AACTAATCTT 0.737556 -63 AGTTTTTACAATCTTTTATTTAAATCTAGT 45 192 1 ATCTTTTATT 0.357299 -109 ********** Masking position 1 Map Score: 6.45466 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 23 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 15 TAGGCTAGTTTTATTTAAATATGCAAACGGTT 3 203 0 TTTTAAATAT 0.835184 -56 AAGTTTTTTCTAATTTAAATAT 5 1 0 TTTTAAATAT 0.87313 -285 CTCGTAAAACTATTTTAAATTTGTTTTTTTAC 7 84 0 TTTTAAATTT 0.480629 -217 ATAACACCCCTCATTTAAATCTGAATAAATCA 7 279 0 TTTTAAATCT 0.827116 -22 AGGGAGTTAATATTTTAAAGATAATAACCGCT 29 39 0 TTTTAAAGAT 0.856638 -199 ATTGTTCTAGTGCTTTATATCTGCTTCCTTGC 30 56 1 TTTTATATCT 0.647622 -245 CTTGAGCGGTTATTTTATAGAATAAGCCAATT 34 34 0 TTTTATAGAA 0.464869 -23 TTTATTTCTATTTTTTATAGATTAAAATTTTT 36 131 0 TTTTATAGAT 0.695144 -170 TAGATTTGTTTAATTTAAAGATGAAGTTTTTT 36 224 0 TTTTAAAGAT 0.850795 -77 AGGGAATTTATATTTTATATATTTAGTCAGCT 39 37 1 TTTTATATAT 0.735208 -47 TTACAATCTTTTATTTAAATCTAGTATTTCTA 45 197 1 TTTTAAATCT 0.787073 -104 CCATTCATATTCCTTTAAATATAGCTTAAGAA 50 130 0 TTTTAAATAT 0.878099 -171 AAATTTGAGTTTTTTTAAATCACTGTGATTAA 50 166 0 TTTTAAATCA 0.603397 -135 TCTCCTTTTGTTATTTAAATAACGTATAAAAT 50 247 1 TTTTAAATAA 0.464944 -54 ACGTATAAAATAGTTTAAAGAAGAGTGTAAAA 50 268 1 TTTTAAAGAA 0.68798 -33 * ********* Masking position 7 Map Score: 8.34897 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 86 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357