AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00051_hinf_reg_300.orf -o00051_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 Input sequences: #1 HI0058 70 3-deoxy-D-manno-octulosonate cytidylyltransferase (kdsB) #2 HI0059 72 conserved hypothetical protein #3 HI0060 40 ABC transporter, ATP-binding protein (msbA) #4 HI0061 258 recombination protein (rec2) #5 HI0448 71 PTS system, fructose-specific IIA/FPr component (fruB) #6 HI0449 86 H. influenzae predicted coding region HI0449 #7 HI0451 71 conserved hypothetical protein #8 HI0452 50 conserved hypothetical protein #9 HI0453 26 conserved hypothetical protein #10 HI0454 54 conserved hypothetical protein #11 HI0457 69 conserved hypothetical protein #12 HI0458 70 stationary phase survival protein SurA, putative #13 HI0459 131 pyrimidine operon regulatory protein (pyrR) #14 HI0524 110 fructose-bisphosphate aldolase (fba) #15 HI0525 101 phosphoglycerate kinase (pgk) #16 HI0526 77 H. influenzae predicted coding region HI0526 #17 HI0613 72 fuculokinase (fucK) #18 HI0614 181 L-fucose isomerase (fucI) #19 HI0615 197 L-fucose operon activator (fucR) #20 HI0678 165 triosephosphate isomerase (tpiA) #21 HI0740 300 phosphomannomutase (yhxB) #22 HI0982 95 6-phosphofructokinase (pfkA) #23 HI0985 300 DNA processing chain A (dprA) #24 HI1062 85 (3R)-hydroxymyristol (acyl carrier protein) dehydrase (fabZ) #25 HI1064 56 conserved hypothetical protein #26 HI1112 233 xylose isomerase (xylA) #27 HI1126.1 181 H. influenzae predicted coding region HI1126.1 #28 HI1129 201 conserved hypothetical protein #29 HI1130 30 conserved hypothetical protein #30 HI1136 122 UDP-N-acetylmuramoylalanine--D-glutamate ligase (murD) #31 HI1137 21 cell division protein (ftsW) #32 HI1560 22 H. influenzae predicted coding region HI1560 #33 HI1561 106 peptide chain release factor 1 (prfA) #34 HI1562 252 H. influenzae predicted coding region HI1562 #35 HI1563 32 conserved hypothetical protein #36 HI1564 32 H. influenzae predicted coding region HI1564 #37 HI1564.1 284 H. influenzae predicted coding region HI1564.1 #38 HI1645 233 fructose-1,6-bisphosphatase (fbp) #39 HI1711 59 PTS system, glucose-specific IIA component (crr) #40 HI1712 79 phosphoenolpyruvate-protein phosphotransferase (ptsI) #41 HI1713 158 phosphocarrier protein HPr (ptsH) #42 HI1714 70 conserved hypothetical protein #43 HI1716 196 undecaprenyl-phosphate alpha-N-acetylglucosaminyltransferase (rfe), putative #44 HI1717 133 H. influenzae predicted coding region HI1717 #45 HI1718 56 H. influenzae predicted coding region HI1718 #46 HI1719 61 uridylyl transferase (glnD) Motif number 1 ATGCAAACGGTTGCTTCAAATTTTGCGATCCATA 4 181 0 TTGTTATTTT 0.851876 -78 TAACCTCAAATTTTTTATGGTTTTATAACATAAT 7 45 0 TTTTTGTTTT 0.795207 -27 TGCGGTCGTTTTCTTTTATATTTTTGAGTA 8 31 1 TTCTTATTTT 0.779487 -20 AAGCCCCTTTATTTTTGATACTTTG 11 2 0 ATTTTACTTT 0.739893 -68 GCCCCTTTTGTTGTTTTTTATTTTCTCTTTCTTA 11 40 1 TTGTTATTTT 0.851876 -30 TTAGGCGTATTTTCTTTATACTTTGTGCATTGAA 13 84 1 TTTTTACTTT 0.656645 -48 AAATTTTGTTTAGTTTTTGTCAATCAAG 16 60 0 TTTTTTTTTT 0.845048 -18 GCAGTCAAAAATCATTATGTTTTTGACCGCACTT 17 33 0 ATCTTTTTTT 0.654266 -40 TATATGACCGATTCTTTCAATTTTTAGTAATTTT 18 33 0 ATTTTATTTT 0.957515 -149 CAAAATTTCATTTCTTACTGTTTTCCTTATCATT 18 114 1 TTTTTGTTTT 0.795207 -68 TTCTGTGAGAATTTTTTTAATTTTATGATCTTCT 20 75 1 ATTTTATTTT 0.957515 -91 TGTCAAACTATTTTTTGGCATTTTATATTAAAAA 23 26 1 TTTTTATTTT 0.938089 -275 TTCTTATTGGATTTTTTACATTTTCAAAATAAGA 23 152 1 ATTTTATTTT 0.957515 -149 AAATTGCAAAATTTTTCTTATTTTGAAAATGTAA 23 167 0 ATTTTATTTT 0.957515 -134 ATTTTTTCCTTTTTATTTGAAAAT 23 287 0 ATTTTTTTTT 0.890251 -14 ATAGATTTTATTTGTTTATTTTTTGTAAGGTATC 24 59 1 TTTTTTTTTT 0.845048 -27 ATCTTTCTCCATTATTACGTTTTTTCACAACTGT 26 96 1 ATTTTTTTTT 0.890251 -138 AGGTGATGAAATTTTTCGTATTTTTGTGAAAAAC 26 195 0 ATTTTATTTT 0.957515 -39 CAATTACTTATTTATTAGCATTTTAATGGATGTT 27 30 1 TTTTTATTTT 0.938089 -152 ATTTTAATGGATGTTTTAGATTTTACAAATGTGA 27 49 1 ATGTTATTTT 0.895334 -133 AGTGATCAAAATTGCTCACTTTTTTCAGTCTTAA 34 19 1 ATTCTTTTTT 0.678221 -234 TTCTTCTTTAATTGCTTCAATTTTTTCTTGAAGA 34 226 0 ATTCTATTTT 0.854144 -27 ATGTTTGAGAATTATTATTATTTTTTTTATAGGA 37 75 0 ATTTTATTTT 0.957515 -210 AATAGTTTTTATTTCTTGATTTTTATCAAAAATC 37 149 0 ATTCTTTTTT 0.678221 -136 AATAAAAACTATTCTTATTATTTTCTGTATTTAA 37 170 1 ATTTTATTTT 0.957515 -115 ATTCACATTTATTACTGCAATTTTTAGAAACTAT 38 110 0 ATTCTATTTT 0.854144 -124 AATTTCCTTTTAGTTTTTCATAATACG 38 217 0 TTCTTGTTTT 0.475304 -17 TCCATTCAAGATGGTTGCTATTTTAACGTAAAAT 39 24 0 ATGTTATTTT 0.895334 -36 CTATGCAAAAATTTTTTTCATTTTACCAAAAACA 42 24 1 ATTTTATTTT 0.957515 -47 CTTTGTTTTGTTGTTTTATATTTTTAATAAAATA 45 18 0 TTGTTATTTT 0.851876 -39 *** ** ***** Masking position 6 Map Score: 43.4087 Number of sites scoring better than the average of aligned sites = 426 Number in coding regions = 289 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 2 GTTATTTTATCCGCACTTATTAGAAAGGAT 2 48 1 CCGCACTTAT 0.956443 -25 AAGAAAACGACCGCACTTTGCGACCGTTTG 8 16 0 CCGCACTTTG 0.986011 -35 CCGCACTTTTCCTCTATAAC 14 1 1 CCGCACTTTT 0.995538 -110 ATGTTTTTGACCGCACTTTTTTATAAAAAC 17 21 0 CCGCACTTTT 0.995538 -52 AAAAAATTGACCGCACTTTTAGGAAGATAT 19 88 1 CCGCACTTTT 0.995538 -110 GCAGAATTAACCGCACTTTTAGATGCCGCA 21 179 1 CCGCACTTTT 0.995538 -122 CGCTTTATCTCCGCCTTTTGCGGCATCTAA 21 197 0 CCGCCTTTTG 0.893716 -104 GCTACCATAACCGCACTTTATTAAGCCAAA 38 20 0 CCGCACTTTA 0.962744 -214 GAAAAAACGACCGCACTTTT 42 61 1 CCGCACTTTT 0.995538 -10 TCAAAATTGACCGCACTTTTACGCCTATCT 43 62 0 CCGCACTTTT 0.995538 -135 TCAATTTTGACCGCATTTTTTATAAAAATA 43 82 1 CCGCATTTTT 0.983004 -115 ACTTCAACGCCCGTATTTTTATAAAAAATG 43 95 0 CCGTATTTTT 0.778794 -102 TTCTCCTTGTCCGCCTTGTTCGCCTTGTTC 44 39 0 CCGCCTTGTT 0.79519 -95 ATACGCCCTTTTTGTTTTTCTT 46 3 1 ACGCCCTTTT 0.862065 -59 ********** Masking position 7 Map Score: 34.6556 Number of sites scoring better than the average of aligned sites = 1330 Number in coding regions = 862 Number in noncoding regions = 468 Number of orfs with sites within 600 bp upstream = 306 Fraction of orfs with sites within 600 bp upstream = 0.0491487 Motif number 3 TACAATGCGTGCAATTTTTACTATTAGATA 3 15 1 GCAATTTTTA 0.946115 -26 TTTTAGGAACCCAATTTTTGCGGGCGGTAT 4 92 1 CCAATTTTTG 0.808545 -167 CGAAAAGTTTTCAATTTTAATTTTAATTTT 15 61 1 TCAATTTTAA 0.730092 -41 TTTTTGTCAATCAAGTTTTTGTCGGCTATA 16 45 0 TCAAGTTTTT 0.784533 -33 ACCGATTCTTTCAATTTTTAGTAATTTTCG 18 31 0 TCAATTTTTA 0.96931 -151 TTAAATATAGTCAATTTTTGTGATGCTCGC 18 74 1 TCAATTTTTG 0.908985 -108 CAATACGCCCCCAAGTTTTATCAATGTAAA 19 28 0 CCAAGTTTTA 0.733953 -170 AAAAGTGCGGTCAATTTTTTGTGAGTTTCT 19 78 0 TCAATTTTTT 0.94635 -120 CGGCTAATTATCAATTTTTTGATCTACTTA 21 15 0 TCAATTTTTT 0.94635 -286 GAAAAATTTTGCAATTTTTTATTCATTAAA 23 184 1 GCAATTTTTT 0.907373 -117 ATAGAATAAGCCAATTTTTTAAGCCAGAAG 25 20 0 CCAATTTTTT 0.881769 -37 ATCTTTAAATTCAATTTTGATTTGACGTAA 27 106 1 TCAATTTTGA 0.91192 -76 AAAAATAAGTTCAATTTTTAAGGCGTAAT 28 183 1 TCAATTTTTA 0.96931 -19 AAAAAAGTGAGCAATTTTGATCACTTTCTG 34 14 0 GCAATTTTGA 0.856432 -239 ATTAAATAGTTCAATTTTTAATCATTTCAC 34 72 1 TCAATTTTTA 0.96931 -181 TTTAATTGCTTCAATTTTTTCTTGAAGATC 34 224 0 TCAATTTTTT 0.94635 -29 TTATCAAAAATCAATCTTTATTGTTGTGAG 37 131 0 TCAATCTTTA 0.769967 -154 ATTTATTACTGCAATTTTTAGAAACTATCG 38 108 0 GCAATTTTTA 0.946115 -126 AAAAGTGCGGTCAATTTTGACCGCATTTTT 43 72 1 TCAATTTTGA 0.91192 -125 ********** Masking position 7 Map Score: 26.0072 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 154 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 4 TTTCTAATAAGTGCGGATAAAATAACGCGA 2 44 0 GTGCGGATAA 0.932202 -29 AAGTGCGGTAAATTTTTATCCA 7 3 1 GTGCGGTAAA 0.970494 -69 CGGTCGCAAAGTGCGGTCGTTTTCTTTTAT 8 20 1 GTGCGGTCGT 0.982871 -31 TTATAAAAAAGTGCGGTCAAAAACATAATG 17 25 1 GTGCGGTCAA 0.996072 -48 CTTCCTAAAAGTGCGGTCAATTTTTTGTGA 19 84 0 GTGCGGTCAA 0.996072 -114 GCATCTAAAAGTGCGGTTAATTCTGCACGA 21 175 0 GTGCGGTTAA 0.990844 -126 TCTTGAGCGGTTATTTTATAGAAT 25 43 0 GAGCGGTTAT 0.890193 -14 GCTTAATAAAGTGCGGTTATGGTAGCCCAA 38 24 1 GTGCGGTTAT 0.984569 -210 AAAAGTGCGGTCGTTTTTTCCCTT 42 57 0 GTGCGGTCGT 0.982871 -14 AGGCGTAAAAGTGCGGTCAATTTTGACCGC 43 66 1 GTGCGGTCAA 0.996072 -131 TTTATAAAAAATGCGGTCAAAATTGACCGC 43 78 0 ATGCGGTCAA 0.952335 -119 ********** Masking position 4 Map Score: 23.1223 Number of sites scoring better than the average of aligned sites = 578 Number in coding regions = 390 Number in noncoding regions = 188 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 5 TAAAAATAAATTTTTCAGGAAAATTTACTTGCTA 4 144 0 TTTTTAAAAT 0.918036 -115 CATCCGCAGCTTTCTTTTTAAATTATTAAGGAGC 5 44 1 TTTCTAAATT 0.675534 -28 TTTTTATCCATTTCTCTACAAAATTATGTTATAA 7 23 1 TTTCTAAAAT 0.910863 -49 CAAATGACCATTTTGACCGAAAATTACTAAAAAT 18 14 1 TTTTGAAAAT 0.843464 -168 ATGCTCGCAGTTTTGCAACAAAATTTCATTTCTT 18 96 1 TTTTGAAAAT 0.843464 -86 GTAGGTTTATTTTTAATATAAAATGCCAAAAAAT 23 35 0 TTTTAAAAAT 0.91657 -266 ATTTTTTCCTTTTTATTTGAAAATCTAGTATGGA 23 277 0 TTTTAAAAAT 0.91657 -24 TATACGATATTTATAGCTAAAAATAAAACGCACT 24 20 0 TTATAAAAAT 0.523042 -66 AAAAATTGGCTTATTCTATAAAATAACCGCTCAA 25 31 1 TTATTAAAAT 0.709448 -26 GAAAAGTTAGTTTTTCACAAAAATACGAAAAATT 26 186 1 TTTTTAAAAT 0.918036 -48 TTCAAACGGCTTTTTTCATAAAATTTTATTGA 28 9 0 TTTTTAAAAT 0.918036 -193 CGGCTTTTTTATTTTGATAAAAATCAGTTGCTTT 28 56 1 ATTTTAAAAT 0.48019 -146 AATGTAGTACTTTTATCTTAAATTT 29 16 1 TTTTAAAATT 0.691176 -15 TTCGCTGTCAATTTTCCCTAAAATCGGCTAGAAT 33 54 1 ATTTTAAAAT 0.48019 -53 AGGCAAGCACGTTTAATCTAAAATTGGTCATATT 37 38 1 GTTTAAAAAT 0.660258 -247 AGAAAATACCTTTCTTCATATAATATGTTTGAGA 37 99 0 TTTCTATAAT 0.504983 -186 TATTTCTTGATTTTTATCAAAAATCAATCTTTAT 37 140 0 TTTTTAAAAT 0.918036 -145 CTATCGCTTATTTTTGAATAAATTTTGGAGTGTT 38 80 0 TTTTTAAATT 0.832656 -154 AATTATTTGATTTTACGTTAAAATAGCAACCATC 39 15 1 TTTTAAAAAT 0.91657 -45 TAGTATCCTTTTTCAAAGCAAAATAATCAAGAAT 41 83 0 TTTCAAAAAT 0.821861 -76 TTTTTCCCTTGTTTTTGGTAAAATGAAAAAAATT 42 33 0 GTTTTAAAAT 0.776773 -38 AACGCCCGTATTTTTATAAAAAATGCGGTCAAAA 43 86 0 TTTTTAAAAT 0.918036 -111 TAAAAATATATTTCTAGGTAAATTTGCCTTATGT 43 142 1 TTTCTAAATT 0.675534 -55 ATATCTCTATTTTATTAAAAATATAAAACAAC 45 9 1 ATTTTAAAAT 0.48019 -48 GCCCTTTTTGTTTTTCTTTATAATAAAACGACTT 46 15 1 TTTTTATAAT 0.709343 -47 ***** ***** Masking position 2 Map Score: 25.7827 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 230 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 6 TTTTGTAGAGAAATGGATAAAAATTTACCGCACT 7 12 0 AAATTAAAAT 0.695066 -60 ACATTCCATCAAAGGAAACCAAATT 13 2 0 AAAGACAAAT 0.489813 -130 ACGAACAAGAAAAATGGTGCAAATGCCGTCGCTT 13 49 1 AAAATCAAAT 0.817104 -83 TCATCAATACAAATTCTTCAAATTGTGGGCTTAT 14 58 1 AAATTAAATT 0.776525 -53 GTATAATACGAAAAGTTTTCAATTTTAATTTTAA 15 53 1 AAAATCAATT 0.872074 -49 TTTTGACCGAAAATTACTAAAAATTGAAAGAATC 18 24 1 AAATTAAAAT 0.695068 -158 ACATTTCCTTAAATATAGTCAATTTTTGTGATGC 18 66 1 AAATGCAATT 0.839234 -116 GGAACCAATAAAAAATAACCAATT 20 1 0 AAAAACAATT 0.821135 -165 ATCTTGAGCTAAAAAGCTACAATTACCTGTATGG 20 33 0 AAAATCAATT 0.872077 -133 GAAGATCATAAAATTAAAAAAATTCTCACAGAAA 20 74 0 AAATAAAATT 0.700574 -92 TGTAGATCAAAATCCCGTCAAATTTTGCTAGAG 22 10 1 AAATGCAAAT 0.773816 -86 ATTATGGTTAAAAGTAGGTAAATT 22 82 1 AAAGGAAATT 0.524753 -14 TTAACTAATAAACTTAATAAAATTAGCATATTTA 23 91 1 AACTTAAATT 0.373809 -210 TCTTATTTTGAAAATGTAAAAAATCCAATAAGAA 23 152 0 AAAAAAAAAT 0.636304 -149 CAAAATAAGAAAAATTTTGCAATTTTTTATTCAT 23 176 1 AAAATCAATT 0.872075 -125 ATTTTCAAATAAAAAGGAAAAAAT 23 287 1 AAAAAAAAAT 0.636304 -14 ATACCTTACAAAAAATAAACAAATAAAATCTATC 24 58 0 AAAAACAAAT 0.750533 -28 ACACTTTAAAAAAGGCTTTCAATTATAAAATCTT 26 67 1 AAAGTCAATT 0.685082 -167 GTTTTTCACAAAAATACGAAAAATTTCATCACCT 26 195 1 AAAAGAAAAT 0.693962 -39 AAATCTTATAAAAATCTTTAAATTCAATTTTGAT 27 93 1 AAAATAAATT 0.798563 -89 ATTCTATTTCAAATTACGTCAAATCAAAATTGAA 27 115 0 AAATGCAAAT 0.773814 -67 TATTTTTAGAAAATCTCTAAAAATCTCCACAAAA 28 156 0 AAATTAAAAT 0.69507 -46 GATTTTCTAAAAATAAGTTCAATTTTTAAGGCGT 28 175 1 AAATTCAATT 0.856759 -27 TAAGACTGAAAAAAGTGAGCAATTTTGATCACTT 34 18 0 AAAAACAATT 0.821135 -235 ACTGGGTGTGAAATGATTAAAAATTGAACTATTT 34 75 0 AAATTAAAAT 0.695068 -178 CTTCAAGAAAAAATTGAAGCAATTAAAGAAGAAT 34 227 1 AAATACAATT 0.800843 -26 TAGTTACTTGAAAATCTTCAAATTTAAGCT 36 7 0 AAAATAAATT 0.798563 -26 TTATAGGACTAAATATGACCAATTTTAGATTAAA 37 49 0 AAATACAATT 0.801108 -236 ACTTAGCCATAAAATTGTGAAATTTTATGGCTAT 40 16 1 AAAATAAATT 0.798565 -64 TTAAAAATATAAAACCAGAAAATTGCCCTAGTAT 41 111 0 AAAAGAAATT 0.775791 -48 GTTTTTGGTAAAATGAAAAAAATTTTTGCATAGG 42 23 0 AAATAAAATT 0.700407 -48 TGTAAAGGATAACATAAGGCAAATTTACCTAGAA 43 153 0 AACAGCAAAT 0.401047 -44 ACTTCGATCTAACAAAAGGCAATTCAT 46 45 1 AACAGCAATT 0.505373 -17 **** * ***** Masking position 11 Map Score: 33.4073 Number of sites scoring better than the average of aligned sites = 718 Number in coding regions = 551 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 7 TGAAATATTAAAGAATAAGGAATAAATT 1 53 1 AGAAAGATAA 0.701005 -18 AATCGCTATCTAATAGTAAAAATTGCACGCAT 3 19 0 ACATATAAAA 0.689201 -22 AAATTTTGCGATCCATATCGTAAAAATAAATTTTT 4 163 0 ACAATGAAAA 0.809365 -96 TTCAAGCCTTAGGCATAAGGAAAAATAATT 10 35 1 AGAAAGAAAA 0.908761 -20 TGGATAGTATAACGAACAAGAAAAATGGTGCAAAT 13 38 1 ACACAGAAAA 0.779473 -94 TAGTATTTCAATGCACAAAGTATAAAGAAAATACG 13 89 0 AGAAAGATAA 0.701005 -43 ACAACCTAGCACGAAGTAGGTATAATACGAAAAGT 15 34 1 AGATAGATAA 0.604014 -68 GACTAAATCCACCGTATAGGGAAAAGAG 19 180 1 ACTTAGAAAA 0.487835 -18 AGTTAATTTTATCAACTATGGAGAAACAAAA 20 145 1 ACATAGAGAA 0.767846 -21 TATTTATTTCAACGAATAAGGATAACGCTATGACA 21 87 1 ACATAGATAA 0.799581 -214 ACCTACTTTTAACCATAATTGAAAATGGGCATAAG 22 66 0 ACAAATAAAA 0.773163 -30 AATGTAAAAAATCCAATAAGAAAAATTTGTTGATT 23 139 0 ACATAGAAAA 0.944285 -162 GCATTTTGCGATGCAGATCGCAAAAATTCTTTTTA 23 210 0 AGAATGAAAA 0.618794 -91 TTATTTGAAAATCTAGTATGGAAAAAACGAGGGAG 23 264 0 ACATAGAAAA 0.944285 -37 CTAGATTTTCAAATAAAAAGGAAAAAAT 23 283 1 AAAAAGAAAA 0.694949 -18 CAATTTTTTAAGCCAGAAGGAAAAAACA 25 4 0 ACAAAGAAAA 0.963033 -53 GTTGCAAATAATCAACATAGAAAAATTAAATAACA 26 143 1 ACAATGAAAA 0.809365 -91 AAATTTCATCACCTAGAGAGGAAAATGTT 26 215 1 ACAAGGAAAA 0.7135 -19 TAAAATTTATAGCAATTAAGAAGAAAGAAA 30 103 1 ACATAGAGAA 0.767846 -20 TTTGATAAAAATCAAGAAATAAAAACTATTCTTAT 37 153 1 ACAAATAAAA 0.773163 -132 CACTTTATTAAGCCAAAAGGTAAAAA 38 2 0 ACAAAGAAAA 0.963033 -232 TAATTGATCAACGTATTATGAAAAACTAAAAGGAA 38 206 1 AGATAGAAAA 0.866311 -28 ACCTCGACTAATCAATAATTAAAAATATAAAACCA 41 128 0 ACAAATAAAA 0.773163 -31 TCATTTTACCAAAAACAAGGGAAAAAACGACCGCA 42 41 1 AAAAAGAAAA 0.694949 -30 * * * ** * **** Masking position 12 Map Score: 24.9088 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 209 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 8 ATAAGCTGCTGGTCGATTTGTTTCATCCGCAG 5 21 1 GGTCGTTTTT 0.847096 -51 TTGTTTCATCCGCAGCTTTCTTTTTAAATTAT 5 38 1 CGCAGTTTTT 0.707688 -34 AGTATAATGGCGGCGTTTTATTAACTTTAATC 6 61 1 CGGCGTTTTT 0.767864 -26 CGCAAAGTGCGGTCGTTTTCTTTTATATTTTT 8 24 1 GGTCGTTTTT 0.847096 -27 GGGGCAATTAAGCCCCTTTATTTTTGATACTT 11 13 0 AGCCCTTTTT 0.719123 -57 GTGCAAATGCCGTCGCTTTTTAGGCGTATTTT 13 65 1 CGTCGTTTTA 0.589255 -67 GGCTATAATTCGCCGCTTTCAACTCTCTATTA 16 20 0 CGCCGTTTAA 0.646684 -58 CTAAAAGTGCGGTCAATTTTTTGTGAGTTTCT 19 78 0 GGTCATTTTT 0.409753 -120 ATTGATAATTAGCCGTTTTCATTTNGTTAGAT 21 30 1 AGCCGTTTAT 0.938874 -271 GCTAGTCTAACGACGATTTTTTATTTATTTCA 21 66 1 CGACGTTTTT 0.797386 -235 ATAGTTTGACAGCCAGTTTTTTATTC 23 5 0 AGCCATTTTT 0.813599 -296 ATGAAGTGTAAGTAGGTTTATTTTTAATATAA 23 48 0 AGTAGTTTTT 0.483744 -253 TTATAGAATAAGCCAATTTTTTAAGCCAGAAG 25 20 0 AGCCATTTTT 0.813596 -37 AATAGAATACAGCCGCTTGTTTAGGGCATATA 27 141 1 AGCCGTTGTT 0.912842 -41 TTATGAAAAAAGCCGTTTGAATTGTTTATTCA 28 22 1 AGCCGTTGAT 0.822009 -180 AAAATAAAAAAGCCGTTTGAATAAACAATTCA 28 39 0 AGCCGTTGAT 0.822009 -163 TAAGAATCTCAGACGCTTTATTTGTGATTTAC 33 14 0 AGACGTTTTT 0.815061 -93 GGCGTATTCTAGCCGATTTTAGGGAAAATTGA 33 61 0 AGCCGTTTAG 0.632731 -46 GGCTAGAATACGCCGATTTTATTTTCGGTGAC 33 79 1 CGCCGTTTAT 0.932045 -28 GTTAGATCGAAGTCGTTTTATTATAAAGAAAA 46 26 0 AGTCGTTTTT 0.923305 -36 ***** *** ** Masking position 7 Map Score: 13.1793 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 253 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 9 ATAAGAAAGAGAAAATAAAAAACAACAAAAGG 11 43 0 GAAATAAAAA 0.740666 -27 TTTTATCAATGTAAATCAGAAAGAGAATAATT 19 11 0 GAAATCAAAA 0.979131 -187 CTCTTGAAAAGAAACTCACAAAAAATTGACCG 19 69 1 GAACTCAAAA 0.931595 -129 ATTCTTTGCAGAAGATCATAAAATTAAAAAAA 20 86 0 GAGATCAAAA 0.968858 -80 ATGTTAAGTAGATCAAAAAATTGATAATT 21 8 1 GAGATCAAAA 0.968858 -293 TGTAGATCAAAATCCCGTCAAAT 22 2 1 GAGATCAAAT 0.853758 -94 ATTTTGCGATGCAGATCGCAAAAATTCTTTTT 23 211 0 GAGATCGAAA 0.819436 -90 TCAAATTACGTCAAATCAAAATTGAATTTAAA 27 109 0 TAAATCAAAT 0.505583 -73 TTTAGTAACTCACGAAATAAG 31 5 1 GAACTCAGAA 0.665174 -17 TGGGTAAATCACAAATAAAGCGTCT 33 4 1 GAAATCAAAA 0.979131 -103 GGCTGTTTTGGCAAATCAAAAACACACTAAAA 34 191 0 GAAATCAAAA 0.979131 -62 AAAGCCTGAATTAAATCATAAAAATAAGCTAA 41 42 0 TAAATCAAAA 0.844946 -117 GCTAATCAAGGTAAATCAGAAACTGAATTTGT 44 108 1 GAAATCAAAA 0.979131 -26 TTATTATAAAGAAAAACAAAAAGGGCGTAT 46 9 0 GAAAACAAAA 0.821995 -53 * ****** *** Masking position 3 Map Score: 14.1204 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 72 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 10 GCGTTTTCGATAATCAATAAA 2 1 0 TAATCAAAAA 0.926218 -72 TACTCAAAAATATAAAAGAAA 8 40 0 TACTCAAAAT 0.559761 -11 GGTTTATTTTTAATATAAAATGCCAAAAAAT 23 35 0 TAATATAAAT 0.287689 -266 AATACAACCCTAATCAACAAATTTTTCTTAT 23 128 1 TAATCAAAAA 0.926218 -173 AAATTCTTTTTAATGAATAAAAAATTGCAAA 23 191 0 TAATGAAAAA 0.692809 -110 CAGTTGCAAATAATCAACATAGAAAAATTAA 26 141 1 TAATCAAATA 0.626203 -93 CAATAAAATTTTATGAAAAAAGCCGTTTGAA 28 12 1 TTATGAAAAA 0.455597 -190 CAACTGATTTTTATCAAAATAAAAAAGCCGT 28 55 0 TTATCAAATA 0.383338 -147 CAAGCACGTTTAATCTAAAATTGGTCATATT 37 41 1 TAATCTAAAT 0.602032 -244 TTCTTGATTTTTATCAAAAATCAATCTTTAT 37 140 0 TTATCAAAAT 0.807929 -145 TTTTTGATAAAAATCAAGAAATAAAAACTAT 37 151 1 AAATCAAAAA 0.473171 -134 CTACAACTACTAATCAACAATCAACGGCTCG 37 225 0 TAATCAAAAT 0.918936 -60 CTCCAAAATTTATTCAAAAATAAGCGATAGT 38 84 1 TATTCAAAAT 0.461754 -150 ATTAACAAAGTAATAAATAAACAATAGCCAT 40 42 0 TAATAAAAAA 0.770198 -38 AGATTGTGAATAATAAATAAACTATTTAGCT 41 17 1 TAATAAAAAA 0.770198 -142 CAAAGCAAAATAATCAAGAATAAACACTAAA 41 73 0 TAATCAAAAT 0.918936 -86 CTACCTCGACTAATCAATAATTAAAAATATA 41 134 0 TAATCAAAAT 0.918936 -25 GCCCGTATTTTTATAAAAAATGCGGTCAAAA 43 86 0 TTATAAAAAT 0.528976 -111 AGTCGTTTTATTATAAAGAAAAACAAAAAGG 46 17 0 TTATAAAAAA 0.5543 -45 ******* *** Masking position 4 Map Score: 8.8294 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 235 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 11 TCTTTAATATTTCAGCTTTATCGGCAAGCAATCAA 1 32 0 TTCCTTCGGC 0.989457 -39 TCCTTATGCCTAAGGCTTGAACGCCATAGACGATA 10 21 0 TAACTTCGCC 0.804364 -34 CCGCTTTATCTCCGCCTTTTGCGGCATCTAAAAGT 21 193 0 TCCCTTCGGC 0.966528 -108 GCGCATGTAATTCTGCTTCTGCCGCTTTATCTCCG 21 214 0 TTCCTTCCGC 0.939512 -87 AAGCCCTATTTTTCACTTCAACGCCCGTATTTTTA 43 104 0 TTTCTTCGCC 0.951933 -93 GTTCGCCTTGTTCGCCTTGTTCGCCTTTTAAT 44 8 0 TTCCTTCGCC 0.993493 -126 GTCCGCCTTGTTCGCCTTGTTCGCCTTGTTCGCCT 44 26 0 TTCCTTCGCC 0.993493 -108 ATTTTCCTCGTTCTCCTTGTCCGCCTTGTTCGCCT 44 44 0 TTCCTTCGCC 0.993493 -90 *** *** **** Masking position 8 Map Score: 6.91764 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 19 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 12 CAAGTAAATTTTCCTGAAAAATTTATTTTTAC 4 147 1 TTTGAAAAAT 0.633754 -112 TAGGCTAGTTTTATTTAAATATGCAAACGGTT 4 203 0 TTTTAAATAT 0.716482 -56 TTTTATAAAAGATTAATTCCAGC 4 246 0 TTTAAAAGAT 0.456969 -13 TCATATACATTTCCTTAAATATAGTCAATTTT 18 60 1 TTTTAAATAT 0.721237 -122 TACGCTTGAGTATATTGAAAATCCAAGGATAA 19 136 0 TATTGAAAAT 0.72247 -62 TTCGTTGAAATAAATAAAAAATCGTCGTTAGA 21 71 0 TATAAAAAAT 0.488864 -230 ACTTTTAACCATAATTGAAAATGGGCATAAGA 22 65 0 ATTTGAAAAT 0.652877 -31 TTTGGCATTTTATATTAAAAATAAACCTACTT 23 39 1 TATTAAAAAT 0.760503 -262 TAGGGTTGTATTGGTTAAATATGCTAATTTTA 23 108 0 TTTTAAATAT 0.721307 -193 AAATTTTTCTTATTTTGAAAATGTAAAAAATC 23 161 0 TATTGAAAAT 0.722383 -140 TTTTTCCTTTTTATTTGAAAATCTAGTATGGA 23 277 0 TTTTGAAAAT 0.911158 -24 ATTGAACTTATTTTTAGAAAATCTCTAAAAAT 28 166 0 TTTAGAAAAT 0.758839 -36 TGGGTGTGAAATGATTAAAAATTGAACTATTT 34 75 0 ATTTAAAAAT 0.697034 -178 GCTTCAATTTTTTCTTGAAGATCAGGCTGTTT 34 215 0 TTTTGAAGAT 0.69601 -38 AGTAGTTACTTGAAAATCTTCAAATTT 36 16 0 TTTTGAAAAT 0.912681 -17 TTTCTTGATTTTTATCAAAAATCAATCTTTAT 37 140 0 TTTCAAAAAT 0.760721 -145 ACTCCAAAATTTATTCAAAAATAAGCGATAGT 38 83 1 TTTCAAAAAT 0.756833 -151 CGACTAATCAATAATTAAAAATATAAAACCAG 41 127 0 ATTTAAAAAT 0.692808 -32 CGCCCGTATTTTTATAAAAAATGCGGTCAAAA 43 86 0 TTTAAAAAAT 0.793433 -111 AAAATAGGGCTTCGTTAAAAATATATTTCTAG 43 127 1 TTTTAAAAAT 0.927193 -70 ATATCTCTATTTTATTAAAAATATAAAACAAC 45 11 1 TTTTAAAAAT 0.92684 -46 ** ******** Masking position 5 Map Score: 14.2215 Number of sites scoring better than the average of aligned sites = 282 Number in coding regions = 193 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 13 CTCTATAACATATTGATGGTGGCATCAAAAATGC 14 22 1 TTTGTGTGCA 0.98064 -89 GAAGAATTTGTATTGATGATGGCATTTTTGATGC 14 43 0 TTTGTGTGCA 0.98064 -68 TAGTCAATTTTTGTGATGCTCGCAGTTTTGCAAC 18 81 1 TGTGTGTGCA 0.971498 -101 CTTGGGGGCGTATTGTAGCTTGCATACTCTTGAA 19 43 1 TTTGAGTGCA 0.974938 -155 ATGACAACACTTTTGGAGGTTGCACAACATTGGT 21 116 1 TTTGAGTGCA 0.974938 -185 TACATGCGCGTTTTGATGGTCGCTTACAATTTGG 21 240 1 TTTGTGTGCT 0.913165 -61 AATTATTGATTAGTCGAGGTAGCATT 41 143 1 TGTCAGTGCA 0.834229 -16 * *** ** * *** Masking position 10 Map Score: 2.53027 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 38 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 14 CAAAGTATAAAGAAAATACGCCTAAAAAGCGA 13 77 0 AAAATACGCC 0.967306 -55 TTTTTGTCGGCTATAATTCGCCGCTTTCAACT 16 28 0 CAAATTCGCC 0.979135 -50 AGTATGCAAGCTACAATACGCCCCCAAGTTTT 19 39 0 CAAATACGCC 0.988708 -159 CTTACTATACCAAAATTTCGCCCCTATTCTTT 20 111 0 CAATTTCGCC 0.920493 -55 CGGTTATTTTATAGAATAAGCCAATTTTTTAA 25 28 0 AAAATAAGCC 0.820696 -29 CTAAAATCGGCTAGAATACGCCGATTTTATTT 33 71 1 CAAATACGCC 0.988708 -36 * * ******** Masking position 7 Map Score: 1.13044 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 39 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 15 ********** No masking Map Score: 1.28775e-11 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0