AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00400_hinf_reg_100.orf -o00400_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 Purged sequences: HI0195.1 26 conserved hypothetical transmembrane protein (aefA) Input sequences: #1 HI0207 284 shikimic acid kinase I (aroK) #2 HI0468 300 ATP phosphoribosyltransferase (hisG) #3 HI0469 92 histidinol dehydrogenase (hisD) #4 HI0470 68 histidinol-phosphate aminotransferase (hisC) #5 HI0658 160 ABC transporter, ATP-binding protein #6 HI0932 120 enolase (eno) #7 HI0967 25 H. influenzae predicted coding region HI0967 #8 HI0970 57 3-dehydroquinase (aroQ) #9 HI1145 126 chorismate mutase / prephenate dehydratase (pheA) #10 HI1171 41 anthranilate synthase component II (trpG) #11 HI1288 300 ribosome binding factor A (rbfA) #12 HI1290 59 chorismate mutase / prephenate dehydrogenase (tyrA) #13 HI1311 148 phenylalanyl-tRNA synthetase, alpha subunit (pheS) #14 HI1312 33 phenylalanyl-tRNA synthetase, beta subunit (pheT) #15 HI1387 105 anthranilate synthase component I (trpE) #16 HI1388.1 48 H. influenzae predicted coding region HI1388.1 #17 HI1389 52 anthanilate phosphoribosyltransferase (trpD) #18 HI1389.1 36 indole-3-glycerol phosphate synthase / phosphoribosylanthranilate isomerase (trpC) #19 HI1430 179 short chain dehydrogenase/reductase #20 HI1547 217 phospho-2-dehydro-3-deoxyheptonate aldolase (phenylalanine repressible) (aroG) #21 HI1587 300 DNA-binding protein H-NS (hns) #22 HI1588 69 formyltetrahydrofolate deformylase (purU) #23 HI1610 200 tyrosyl tRNA synthetase (tyrS) #24 HI1617 138 aspartate aminotransferase (aspC) Motif number 1 ATACGCGCTATTTTTAGCCTATTTTTCAATT 1 5 0 TTTTTTTTTC 0.817114 -280 AATAGCGCGTATTTAACGCGCTATTTTTGTTATTAGT 1 30 1 ATTTATATTT 0.413196 -255 AAATCACCCTATTTTTCAACCTCTATAGGGAATTTAT 1 138 0 ATTTTTCTTA 0.741621 -147 TCTACCCCATTTTTTGGGAGATCTTTCTATCTTCTGC 1 185 1 TTTTTTCTTC 0.775232 -100 ATCTTCTGCATTTTTACGCAGTTTATTTTCATTAGAA 1 213 1 TTTTTTTTTT 0.943105 -72 AAAAATTGTGTTTTTAGTACATTTTTACTA 2 4 0 TTTTTTTTTA 0.906619 -297 AAAAGCAATTTTTTTGAAAAAAATTGTGTTTTTAGTA 2 22 0 TTTTTAATGT 0.354823 -279 GCTTTTTTTAATTTTAAAGTGTATTTTTAAGGCAATA 2 53 1 ATTTTTATTT 0.752939 -248 TATTTATTGCTTTTACACTGATTTTTATTACACTCGG 2 211 0 TTTTATTTTA 0.691665 -90 GTCTATTCCGATTTTATCGATTTTCTAGTCAAAAAAG 5 75 0 ATTTTTTTTA 0.788054 -86 ATTTGAGGCTATTTTGCAATATTTTTTCTTTTCTCGG 5 116 0 ATTTTTTTTT 0.863912 -45 GATAAAGCTATTTTAGATTTTTTCTTGTAAAAAATG 6 34 0 TTTTTTTTT 0.792959 -87 ATTATACTGGTTTTTTCGATTTTTGGTGGTCGAA 8 8 0 TTTTTTTTGT 0.832163 -50 AAGTATAGCTTTTTTGTTTCATCTCGTGCTTAAATAG 9 47 1 TTTTTTCTGT 0.792854 -80 ACAACAAGCATTTTTAAATGATTAGACGAAAAACTT 11 52 0 TTTTTTTGA 0.401549 -249 TAATGTGTGATTTTTATCGACAATCTTGGTCGTCTCG 11 88 1 TTTTTAATTT 0.647719 -213 TGTAATTAATTTTTTACAATATATGTAAGATAAAAAT 12 28 1 TTTTTTATTA 0.82335 -32 AAGCCAATGATTTTTCGCATTATTCTTTTACTTTTTA 13 59 1 TTTTTATTTT 0.792959 -90 CTGATTTTTATTTTTTATACTTTTTGATTAAAAATTG 15 17 0 TTTTTTTTGA 0.743855 -89 AGTGCGGTAATTTTTAACCGCACTTTAAAGGAGAAAA 16 21 1 TTTTTACTTA 0.633926 -28 AAATTAATTCATTTAATGACATTTTTAAAATTAAAAT 19 81 1 ATTTATTTTA 0.462102 -99 TTTTTCTCCTAAATCTTGAGCTTATTT 19 163 0 TTTTTAATTT 0.647719 -17 AAGTGCGGTATTTTTTTATCTTTTATTTACTTAATTA 20 30 1 TTTTTTTTTT 0.943105 -188 GTTTATAAAATTTTTATAAAATCTGTTGGCATTTTGT 21 130 0 TTTTTTCTTT 0.927516 -171 TTCTTTATATTTTTATTAAAGTTTATAAAATTTTTAT 21 150 0 TTTTATTTTA 0.691665 -151 ACAGATATATTTTTTTGTGTTTATTTTCTTTATATTT 21 175 0 TTTTTTATTT 0.888365 -126 TTTACAATAAATTTTATTTTCTCTATTATTAAATAAA 21 238 1 ATTTTTCTTT 0.830524 -63 ATTTTCCCACATTTAATGTTATTTATTGAGGTTTATT 21 274 1 ATTTATTTTT 0.594609 -27 ACTAGAACCTATTTTATGGGTTCTATTTTTTTATCTA 22 25 1 ATTTTTCTTT 0.830524 -45 TATTTTTTTGAGGAATTATTTTCATTTAAC 23 4 1 TTTTTATTTT 0.792959 -197 CTAAATTATGTTTTAAAAGGTTTTATTATAGGGATTC 23 165 0 TTTTATTTTT 0.792959 -36 ATGACCGCACTTTTTGATGAATATTTAAAAATATCAA 24 19 1 TTTTTTATTA 0.82335 -120 GCGTGGTTAATTTTTATAAAATCTTTCTTGATAAAAT 24 57 1 TTTTTTCTTC 0.775232 -82 ***** *** ** Masking position 4 Map Score: 34.417 Number of sites scoring better than the average of aligned sites = 1429 Number in coding regions = 963 Number in noncoding regions = 466 Number of orfs with sites within 600 bp upstream = 302 Fraction of orfs with sites within 600 bp upstream = 0.0485063 Motif number 2 GGGAATTTATTTTCCACGAGAAAGCATCTAAATA 1 114 0 TTTAAGAAAG 0.902315 -171 ACGCAGTTTATTTTCATTAGAAATGATCGAATTT 1 228 1 TTTAAGAAAT 0.638994 -57 TGATTGTATGTTTGGAAGATAATAAAATATCTTC 2 178 1 TTTAATAATA 0.770403 -123 TTATCTCAACTTTAAAATAGGAAAAACATT 2 281 1 TTTAAGGAAA 0.894568 -20 ATAAAAACTATTTATAATATAACAAGTCAATATA 5 22 0 TTTAATAACA 0.663099 -139 TACGTGGCTTTTTTGACTAGAAAATCGATAAAAT 5 68 1 TTTAAGAAAA 0.967832 -93 GCATACGCATTTTTTACAAGAAAAAATCTYAAAA 6 27 1 TTTAAGAAAA 0.96742 -94 AATATAGCTTTTTCAACAATAAAACAA 9 4 0 TTTAATAAAA 0.95857 -123 TTCGTGGGATTTTTTATAAGGAAGCATT 9 109 1 TTTAAGGAAG 0.724211 -18 AATTCAATGATTTCCAGTAGAATGAGGCGCTTTT 11 260 1 TTTAAGAATG 0.567438 -41 TTTTACAATATATGTAAGATAAAAATTACAG 12 39 1 TATAATAAAA 0.826966 -21 ATCATTGGCTTATCAAAAATAAAAATGGAATAAC 13 36 0 TATAATAAAA 0.826865 -113 TTCTCTTTTCTCTATAAAATAAAAAACCGAGTAA 13 113 0 TCTAATAAAA 0.798474 -36 AAAATACAATTTTTAATCAAAAAGTATAAAAAAT 15 11 1 TTTAAAAAAG 0.538909 -95 AATCAAAAAGTATAAAAAATAAAAATCAGGCTTG 15 25 1 TATAATAAAA 0.826844 -81 TTTGGAAAATTTTGTACTATTAAACTAGTGCAAA 15 69 0 TTTAATTAAA 0.890624 -37 AGTACAAAATTTTCCAAAAGGATAAATAAAT 15 85 1 TTTAAGGATA 0.5488 -21 TTAACCGCACTTTAAAGGAGAAAAA 16 34 1 TTTAAGAAAA 0.966882 -15 TTTAATGACATTTTTAAAATTAAAATGAAATTGC 19 92 1 TTTAATTAAA 0.890194 -88 CTTGAGCTTATTTGTACTATTAAAGTAGTACAAA 19 142 0 TTTAATTAAA 0.890624 -38 TCGATATGTTTTTTTAGAATAAAACCTACAAATT 20 116 0 TTTAATAAAA 0.958928 -102 TACACTTATTTTTGTACTAGTAAACTAGTTCGAT 20 145 0 TTTAAGTAAA 0.912194 -73 TTATTGTAAATATCTATTATTAAATAAATGGTCG 21 214 0 TATAATTAAA 0.622205 -87 AATTTTATTTTCTCTATTATTAAATAAATTTTCC 21 247 1 TCTAATTAAA 0.577246 -54 TAGGTTCTAGTTTCAAATAGAAAAA 22 2 0 TTTAAGAAAA 0.967059 -68 GTGTGCTATGTTTAGATAAAAAAATAGAACCCAT 22 40 0 TTTAAAAAAA 0.792276 -30 AAAATCTTTCTTGATAAAATAAAATGACTGAAGT 24 74 1 TTGAATAAAA 0.635542 -65 *** * ****** Masking position 6 Map Score: 30.5169 Number of sites scoring better than the average of aligned sites = 555 Number in coding regions = 342 Number in noncoding regions = 213 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 3 GAATGTACTAAAAGTGCGGTCAATTTCGTG 9 85 1 AAAGTGCGGT 0.996383 -42 AACAGTTCGGTATTCGTTATA 10 31 0 ACAGTTCGGT 0.917005 -11 GACATCAAAAAGTGCGGTAATTTTTAAC 16 9 1 AAAGTGCGGT 0.996383 -40 TTTCTCCTTTAAAGTGCGGTTAAAAATTAC 16 27 0 AAAGTGCGGT 0.996383 -22 GTACAGCACAAAAGTGCGGTATTTTTTTAT 20 19 1 AAAGTGCGGT 0.996383 -199 TATTCATCAAAAAGTGCGGTCATTTTTTAC 24 12 0 AAAGTGCGGT 0.996383 -127 TAAAAATATCAAAGCGTGGTTAATTTTTAT 24 44 1 AAAGCGTGGT 0.917119 -95 ********** Masking position 3 Map Score: 17.3677 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 4 GATCATTTCTAATGAAAATAAACTGCGTAAAA 1 224 0 AATGAAAAAA 0.76794 -61 TATCTAATTAAATTAAAAGTGAAATAAAATTC 1 256 0 AATTAAAAGA 0.766367 -29 TACACTTTAAAATTAAAAAAAGCAATTTTTTT 2 44 0 AATTAAAAAG 0.893461 -257 TTCCGAGTGTAATAAAAATCAGTGTAAAAGCA 2 209 1 AATAAAAAAG 0.938536 -92 TACGGATACAAAGGAAAATAAACA 3 79 1 AAGGAAAAAA 0.704157 -14 AATAAGACGCAATAAAAACTATTTATAATATA 5 35 0 AATAAAAAAT 0.865336 -126 GTTCCGAGAAAAGAAAAAATATTGCAAAATAG 5 113 1 AAGAAAAAAT 0.822123 -48 CATTTTTTACAAGAAAAAATCTYAAAATAGCT 6 34 1 AAGAAAAACT 0.535761 -87 CAATTAAGTTAATTAAAACGGGTTAGGCGAGC 6 87 0 AATTAAAAGG 0.855464 -34 GTAAAAAATTAATTACAAGGAGATTACTAGAA 12 13 0 AATTACAAAG 0.421909 -47 CAAGAAAAAATGGAATAGCGAAT 13 2 1 AAGAAAAAGG 0.88573 -147 GCTTATCAAAAATAAAAATGGAATAACGTATT 13 31 0 AATAAAAAGA 0.856582 -118 AGTCCTTAAAAAGTAAAAGAATAATGCGAAAA 13 70 0 AAGTAAAAAT 0.717384 -79 TTCTCTATAAAATAAAAAACCGAGTAATGATA 13 108 0 AATAAAAACG 0.792219 -41 CTCGGATTTGAATTAAAAGGATAACAACAA 14 14 1 AATTAAAAAT 0.779209 -20 AAGTATAAAAAATAAAAATCAGGCTTGACTTA 15 32 1 AATAAAAAAG 0.938536 -74 TCCATATACAAAGAAAAACAGGAATAGACT 17 33 1 AAGAAAAAGG 0.88573 -20 GATCAATTGAAATAAAAATTGGGCAGATTATA 19 21 1 AATAAAAAGG 0.915087 -159 ACATTTTTAAAATTAAAATGAAATTGCTTGCA 19 99 1 AATTAAAAAA 0.822939 -81 GATAACGAAGAAGAAAAAAGAAAGGAATAGTT 21 27 0 AAGAAAAAAA 0.858892 -274 TATAAACTTTAATAAAAATATAAAGAAAATAA 21 160 1 AATAAAAATA 0.436526 -141 TCAATAGTTAAATGAAAATAATTCCTCAAAAA 23 15 0 AATGAAAAAT 0.715325 -186 GCAATTTGTGAATAAAAAAAAACGCCTATCTG 23 130 0 AATAAAAAAA 0.894321 -71 ******** ** Masking position 7 Map Score: 21.8314 Number of sites scoring better than the average of aligned sites = 587 Number in coding regions = 414 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 5 TAAGAATTTTAACTATTCCATATTTAGATGCTT 1 94 1 ATATTCCTAT 0.958078 -191 CTCGTGGAAAATAAATTCCCTATAGAGGTTGAA 1 128 1 AAATTCCTAT 0.948508 -157 GTAAGTGCAGATAAAATTCATATTGTATATGCT 2 113 0 AAAATTCTAT 0.689402 -188 AATGTTTTTCCTATTTTAAAGTTG 2 287 0 ATTTTTCTAT 0.711018 -14 ACATATTTCGTATTGTTGTATGA 4 56 0 ATATTTCTAT 0.901481 -13 ATTTGATCCTTATAAAAGTGAGA 7 1 1 ATGATCCTAT 0.744251 -25 AACAGTTCGGTATTCGTTATAAT 10 29 0 AAGTTCGTAT 0.620579 -13 AGTTATTCCTTATTTATAAAAGC 11 288 0 ATATTCCTAT 0.958078 -13 AAATGGAATAACGTATTCGCTATTCCATTTTTT 13 15 0 ATATTCGTAT 0.82757 -134 ATCAGGCTTGACTTATTCCTTTTGCACTAGTTT 15 49 1 ATATTCCTTT 0.901161 -57 ATAGAAAATTAACAAATCCATATACAAAGAAAA 17 17 1 AAAATCCTAT 0.847282 -36 GATATTGTTAAATTAATTCATTTAATGACATTT 19 72 1 ATAATTCTTT 0.523694 -108 TTTGATTGCAAGCAATTTCATTTTAATTTTAAA 19 104 0 AAATTTCTTT 0.746346 -76 TTATTTACTTAATTATTTCGTTTTATTCAGCTT 20 52 1 ATATTTCTTT 0.784971 -166 AATAAAACCTACAAATTCCCTATTAAACTATCT 20 100 0 AAATTCCTAT 0.948508 -118 GTACTAGTAAACTAGTTCGATATGTTTTTTTAG 20 133 0 AAGTTCGTAT 0.620579 -85 TTTTTGAGGAATTATTTTCATTTAACTATTGAC 23 15 1 AATTTTCTTT 0.441704 -186 AGCTTTTCCTTATGTATGTGTTG 24 126 0 ATTTTCCTAT 0.860044 -13 * ****** *** Masking position 7 Map Score: 14.5132 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 189 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 6 ATTGCCTTCCGAGGGGTATTTATTGCTTTTA 2 233 0 GAGGGGTTTT 0.743863 -68 ATGTAGTGCGAGCTTTGACTCGCCAT 3 6 1 GTGCGAGTTT 0.739305 -87 TATATTTCTGGTGGGAAGTATAGCTTTTTTG 9 32 1 GTGGGAATAT 0.661493 -95 TGTACTAAAAGTGCGGTCAATTTCGTGGGAT 9 88 1 GTGCGGTAAT 0.909344 -39 GGTCAATTTCGTGGGATTTTTTATAAGGAAG 9 102 1 GTGGGATTTT 0.912661 -25 ATCAAGTTGTTTGCGGAGTTTATCAGCAGAT 11 16 1 TTGCGGATTT 0.717806 -285 TTGTTGTAATGTGTGATTTTTATCGACAATC 11 82 1 GTGTGATTTT 0.575446 -219 ACATCAAAAAGTGCGGTAATTTTTAACCGCA 16 12 1 GTGCGGTATT 0.971651 -37 CTCCTTTAAAGTGCGGTTAAAAATTACCGCA 16 23 0 GTGCGGTAAA 0.653053 -26 CAGCACAAAAGTGCGGTATTTTTTTATCTTT 20 22 1 GTGCGGTTTT 0.971651 -196 TTTGTAGTGATTGGGGAGATTACCGTAAAAC 21 97 1 TTGGGGAATT 0.686509 -204 AACATTAAATGTGGGAAAATTTATTTAATAA 21 263 0 GTGGGAAATT 0.869744 -38 ACGCCTATCTGTGGGGAAATAGGCGGGAATG 23 110 0 GTGGGGAATA 0.779646 -91 TCATCAAAAAGTGCGGTCATTTTTTACA 24 8 0 GTGCGGTATT 0.971651 -131 ******* *** Masking position 5 Map Score: 9.19124 Number of sites scoring better than the average of aligned sites = 980 Number in coding regions = 667 Number in noncoding regions = 313 Number of orfs with sites within 600 bp upstream = 228 Fraction of orfs with sites within 600 bp upstream = 0.0366206 Motif number 7 CTATAGGGAATTTATTTTCCACGAGAAAGC 1 123 0 TTTATTTTCC 0.868011 -162 TTTTACGCAGTTTATTTTCATTAGAAATGA 1 224 1 TTTATTTTCA 0.504307 -61 TATTTCACTTTTAATTTAATTAGATAAAGA 1 262 1 TTAATTTAAT 0.608376 -23 AAAAAATTGCTTTTTTTAATTTTAAAGTGT 2 45 1 TTTTTTTAAT 0.379798 -256 CGGAAGATATTTTATTATCTTCCAAACATA 2 184 0 TTTATTATCT 0.597771 -117 TTCGAGGGGTTTTCTTTTATCTCAACTTTA 2 265 1 TTTCTTTTAT 0.609025 -36 TGTTTATTTTCCTTTGTATCCG 3 81 0 TTTATTTTCC 0.868011 -12 TGCAATATTTTTTCTTTTCTCGGAACAGTC 5 109 0 TTTCTTTTCT 0.715469 -52 CTAACCCGTTTTAATTAACTTAATTGAGGA 6 93 1 TTAATTAACT 0.199047 -28 TTTTATTTTCCTCAATTAAGT 6 110 0 TTTATTTTCC 0.868011 -11 CTCCTTGTAATTAATTTTTTACAATATATG 12 23 1 TTAATTTTTT 0.427801 -37 TACTCGGTTTTTTATTTTATAGAGAAAAGA 13 114 1 TTTATTTTAT 0.902818 -35 AAGCCTGATTTTTATTTTTTATACTTTTTG 15 28 0 TTTATTTTTT 0.731098 -78 ATTTATTTATCCTTTTGGAAA 15 95 0 TTTATTTATC 0.420297 -11 TATGGATTTGTTAATTTTCTATATTTTA 17 9 0 TTAATTTTCT 0.804835 -44 ATTAAATGAATTAATTTAACAATATCGCAA 19 68 0 TTAATTTAAC 0.405199 -112 GTTAAATTAATTCATTTAATGACATTTTTA 19 78 1 TTCATTTAAT 0.362253 -102 TTTTTTATCTTTTATTTACTTAATTATTTC 20 41 1 TTTATTTACT 0.90118 -177 TTTATTTGATTTCGGCAACT 21 1 1 TTTATTTGAT 0.540893 -300 TTTTTTTGTGTTTATTTTCTTTATATTTTT 21 173 0 TTTATTTTCT 0.937487 -128 GTTTCGACCATTTATTTAATAATAGATATT 21 210 1 TTTATTTAAT 0.849607 -91 TACAATAAATTTTATTTTCTCTATTATTAA 21 240 1 TTTATTTTCT 0.937487 -61 TGTGGGAAAATTTATTTAATAATAGAGAAA 21 255 0 TTTATTTAAT 0.849607 -46 AGATAGGCGTTTTTTTTTATTCACAAATTG 23 131 1 TTTTTTTTAT 0.501753 -70 CTTCAGTCATTTTATTTTATCAAGAAAGAT 24 77 0 TTTATTTTAT 0.902818 -62 ********** Masking position 5 Map Score: 23.783 Number of sites scoring better than the average of aligned sites = 644 Number in coding regions = 447 Number in noncoding regions = 197 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 8 AAAATTAAAAAAAGCAATTTTTTTGAAAAAAA 2 36 0 AAAGCATTTT 0.96437 -265 AATCAGTGTAAAAGCAATAAATACCCCTCGGA 2 225 1 AAAGCATAAT 0.714145 -76 GCGATATGATAAAGCTATTTTAGATTTTTTC 6 46 0 AAAGCATTT 0.405336 -75 TATTGTTGAAAAAGCTATATTTCTGGTGGGAA 9 17 1 AAAGCATATT 0.951588 -110 ATGAAACAAAAAAGCTATACTTCCCACCAGAA 9 37 0 AAAGCATATT 0.951602 -90 TGCCCTCTGTAAAGTGATTTTTATCGGAAGTT 11 153 1 AAAGTATTTT 0.778315 -148 TATTAAGTTGAAAGGGATTTTTGCGTGCTAAA 11 230 1 AAAGGATTTT 0.957796 -71 AACTAGTGCAAAAGGAATAAGTCAAGCCTGAT 15 49 0 AAAGGATAGT 0.756369 -57 TAAAAGCTAATTTTATACGCCACA 18 3 1 AAAGCAATTT 0.758123 -34 AAGAAAAAAGAAAGGAATAGTTGCCGAAATCA 21 17 0 AAAGGATATT 0.94281 -284 AGGTTTTATTATAGGGATTCTTAGCAATTTGT 23 153 0 ATAGGATTTT 0.724417 -48 TTATGTTTTAAAAGGTTTTATTATAGGGATTC 23 165 0 AAAGGTTTTT 0.724417 -36 ***** *** ** Masking position 3 Map Score: 10.8543 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 122 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 CGCGTTAAATACGCGCTATTTTTAGCCTAT 1 20 0 ACGCGCTATT 0.977347 -265 CGCGTATTTAACGCGCTATTTTTGTTATTA 1 35 1 ACGCGCTATT 0.977347 -250 ATTATCTTTCAGGCGTGATTGTATGTTTGG 2 163 1 AGGCGTGATT 0.926292 -138 CAGTAGAATGAGGCGCTTTTATAAATAAGG 11 274 1 AGGCGCTTTT 0.977896 -27 ACAAAAGTAGAGGCGCAATTATTATAAGTA 21 72 0 AGGCGCAATT 0.961674 -229 CCCCACAGATAGGCGTTTTTTTTTATTCAC 23 125 1 AGGCGTTTTT 0.937315 -76 ********** Masking position 9 Map Score: 4.06947 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 18 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 CCCTATAGAGGTTGAAAAATAGGGTGATTTAT 1 145 1 GTTAAAATAG 0.681511 -140 TGTTTGGAAGATAATAAAATATCTTCCGAGTG 2 186 1 ATATAAATAT 0.574099 -115 TACATATATTGTAAAAAATTAATTACAAGGAG 12 23 0 GTAAAAATAA 0.652852 -37 AAATTTTGTACTATTAAACTAGTGCAAAAGGA 15 65 0 CTATAAATAG 0.933956 -41 TTATTGTGGCGTATAAAATTAGCTTTTA 18 7 0 GTAAAAATAG 0.94394 -30 CTTATTTGTACTATTAAAGTAGTACAAATAAA 19 138 0 CTATAAATAG 0.933956 -42 TACAAATTCCCTATTAAACTATCTTTACAACT 20 92 0 CTATAAATAT 0.82905 -126 TATTTTTGTACTAGTAAACTAGTTCGATATGT 20 141 0 CTATAAATAG 0.933956 -77 TCCCCAATCACTACAAAAGTAGAGGCGCAATT 21 82 0 CTAAAAATAG 0.95391 -219 CTATGTTTAGATAAAAAAATAGAACCCATAAA 22 37 0 ATAAAAATAG 0.850449 -33 AATGACTGAAGTATAAAACTATTCATCACACA 24 96 1 GTAAAAATAT 0.826139 -43 *** **** *** Masking position 6 Map Score: 6.69963 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 53 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 11 TAACGCGCTATTTTTGTTATTAGTCCTAGGT 1 43 1 TTTTGTTATT 0.584057 -242 TGTTCTTTATCTAATTAAATT 1 274 0 TTTCTTTATC 0.907593 -11 ATATACAATATGAATTTTATCTGCACTTACC 2 116 1 TAATTTTATC 0.662686 -185 GCTTTTACACTGATTTTTATTACACTCGGAA 2 209 0 TATTTTTATT 0.690049 -92 TTCGAGGGGTTTTCTTTTATCTCAACTTTAA 2 265 1 TTCTTTTATC 0.667331 -36 GCGTATGCTTTGATCTTTATCTAT 6 4 0 TATCTTTATC 0.889926 -117 AACAGTTCGGTATTCGTTATAATCAGGTCAT 10 21 0 TTTCGTTATA 0.486989 -21 TTGTAATGTGTGATTTTTATCGACAATCTTG 11 85 1 TATTTTTATC 0.939658 -216 CTCTGTAAAGTGATTTTTATCGGAAGTTTGA 11 157 1 TATTTTTATC 0.939658 -144 CTGTAATTTTTATCTTACATATAT 12 46 0 TATTTTTATC 0.939658 -14 TTGTTGTTATCCTTTTAATTC 14 23 0 TGTTGTTATC 0.627709 -11 GCCTGATTTTTATTTTTTATACTTTTTGATT 15 25 0 TTTTTTTATA 0.778843 -81 AAAAGTGCGGTAATTTTTAACCGCACTTTAA 16 18 1 TATTTTTAAC 0.5011 -31 AAAGTGCGGTATTTTTTTATCTTTTATTTAC 20 29 1 ATTTTTTATC 0.693537 -189 TCTTTTTTCTTCTTCGTTATCCACTCTGAAA 21 38 1 TTTCGTTATC 0.836045 -263 TTTGTGTTTATTTTCTTTATATTTTTATTAA 21 168 0 TTTCTTTATA 0.646443 -133 TATGGGTTCTATTTTTTTATCTAAACATAGC 22 39 1 ATTTTTTATC 0.693537 -31 GATTAGATGATAATTGTTATCAATAGCCTTG 23 47 0 TATTGTTATC 0.889926 -154 AGATAGGCGTTTTTTTTTATTCACAAATTGC 23 131 1 TTTTTTTATT 0.730064 -70 AAAGCGTGGTTAATTTTTATAAAATCTTTCT 24 54 1 TATTTTTATA 0.743519 -85 CTTCAGTCATTTTATTTTATCAAGAAAGATT 24 76 0 TTATTTTATC 0.704722 -63 * ********* Masking position 7 Map Score: 19.2149 Number of sites scoring better than the average of aligned sites = 326 Number in coding regions = 226 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 12 ATATTTCGTATTGTTGTATGAAAATTTGAC 4 47 0 TTGTTGTATG 0.781147 -22 TTTTAATCCTTTTTGTGTGGCACATTATA 8 39 0 TTTTTGTGTG 0.945032 -19 GCGGCATCAAGTTGTTTGCGGAGTTTAT 11 9 1 AAGTTGTTTG 0.793902 -292 GACACCTGATAATTTGTTTGAATATTCAAA 11 183 0 AATTTGTTTG 0.706461 -118 TTGAAAGGGATTTTTGCGTGCTAAATTCAA 11 237 1 TTTTTGCGTG 0.764022 -64 GTACAAATAAATTTTGATTGCAAGCAATTT 19 119 0 ATTTTGATTG 0.577139 -61 TTGCTTTCAAATGTTGTGTTTAAATTATGT 20 187 0 ATGTTGTGTT 0.819603 -31 ATCTGTTGGCATTTTGTTTGTTTTACGGTA 21 117 0 ATTTTGTTTG 0.914833 -184 CAGATATATTTTTTTGTGTTTATTTTCTTT 21 181 0 TTTTTGTGTT 0.704905 -120 AATGTTGTGTGCTATGTTTAG 22 59 0 ATGTTGTGTG 0.970326 -11 TTATCTAATATTGTTGTTGGAATGATTAGA 23 71 0 TTGTTGTTGG 0.712948 -130 CCTTATGTATGTGTTGTGTGATGAATAGTT 24 112 0 GTGTTGTGTG 0.909598 -27 ********** Masking position 5 Map Score: 3.2201 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 215 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 13 ********** No masking Map Score: 5.21782e-12 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 Motif number 14 AATGGCGAGTCAAAGCTCGCACTACAT 3 8 0 CAAAGCTCGC 0.839028 -85 AATTATAGATCTAAGCACGACACGTAAGCA 4 17 1 CTAAGCACGA 0.940577 -52 ATCGCCTGTTTTAGGCTCGCCTAACCCGTT 6 73 1 TTAGGCTCGC 0.919873 -48 CATTCGCTATTTAAGCACGAGATGAAACAA 9 60 0 TTAAGCACGA 0.95922 -67 AATCATTGAATTTAGCACGCAAAAATCCCT 11 242 0 TTTAGCACGC 0.909796 -59 GATTAACCTCGATCAATTGAAA 19 3 1 TTAACCTCGA 0.884027 -177 TTTATAAAAATTAACCACGCTTTGATATTT 24 47 0 TTAACCACGC 0.953488 -92 ********** Masking position 6 Map Score: 0.874363 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 42 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 15 ********** No masking Map Score: 5.21782e-12 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