AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00500_hinf_reg_300.orf -o00500_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: HI0812 21 glucosephosphate uridylyltransferase (galU) HI0910 64 mutator mutT protein (mutT) Input sequences: #1 HI0291 74 H. influenzae predicted coding region HI0291 #2 HI0292 76 mercuric ion scavenger protein (merP) #3 HI0316 21 datP pyrophosphohydrolase (ntpA) #4 HI0317 218 aspartyl-tRNA synthetase (aspS) #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 HI0652 62 3-deoxy-d-manno-octulosonic-acid transferase (kdtA) #15 HI0727.1 260 cyaY protein (cyaY) #16 HI0813 77 carbon storage regulator (csrA) #17 HI0814 187 alanyl-tRNA synthetase (alaS) #18 HI0815 101 universal stress protein A (uspA) #19 HI0817 170 conserved hypothetical protein #20 HI0819 37 galactokinase (galK) #21 HI0820 207 galactose-1-phosphate uridylyltransferase (galT) #22 HI0908 79 H. influenzae predicted coding region HI0908 #23 HI0909 124 preprotein translocase SecA subunit (secA) #24 HI1188 300 DNA helicase II (uvrD) #25 HI1354 300 glutaminyl-tRNA synthetase (glnS) #26 HI1355 65 conserved hypothetical protein #27 HI1356 61 4-alpha-glucanotransferase (malQ) #28 HI1358 95 glycogen operon protein (glgX) #29 HI1360 107 glycogen synthase (glgA) #30 HI1361 245 glycogen phosphorylase (glgP) #31 HI1573 300 pyruvate kinase, type II (pykA) #32 HI1574 33 replicative DNA helicase (dnaB) #33 HI1576 54 glucose-6-phosphate isomerase (pgi) #34 HI1711 59 PTS system, glucose-specific IIA component (crr) #35 HI1712 79 phosphoenolpyruvate-protein phosphotransferase (ptsI) #36 HI1713 158 phosphocarrier protein HPr (ptsH) #37 HI1714 70 conserved hypothetical protein #38 HI1741 260 guanosine-3',5'-bis(diphosphate) 3'- pyrophosphohydrolase (spoT) #39 HI1742 62 DNA-directed RNA polymerase, omega chain (rpoZ) #40 HI1743 249 guanylate kinase (gmk) Motif number 1 GGATAAAAATTTACCGCACTT 7 1 0 TACCGCACTT 0.996959 -71 TAAAAGAAAACGACCGCACTTTGCGACCGTT 8 18 0 CACCGCACTT 0.988764 -33 TTTTTAAGTATAACCGAATTTCATTT 14 47 1 TACCGAATTT 0.765028 -16 GCTTTATAATTTGCCGCATTTTATCAGATTT 15 225 1 TGCCGCATTT 0.886561 -36 ACTTAAATTTTAACCGCACTTCTCAAATAGC 17 46 1 TACCGCACTT 0.996959 -142 CTCCAAAATAAAACCGCACTTCACGACGCTA 17 73 0 AACCGCACTT 0.982727 -115 ATTCACGGCGATACCGCTTTTTAATGTGATG 25 29 0 AACCGCTTTT 0.632239 -272 TTCAAAAAACTTACCGCACTTTGTGCATTTA 25 122 1 TACCGCACTT 0.996959 -179 ACGTTTGTTTTGACCGCACTTGGTTGATTAA 26 13 0 TACCGCACTT 0.996959 -53 AACGTGATTTTGACCGCACTTTTTATTTGTA 26 39 1 TACCGCACTT 0.996959 -27 CGGTTAATTTTGACCGCACTTTTCCTAA 29 8 0 TACCGCACTT 0.996959 -100 CGGTCAAAATTAACCGCACTTTCTGAACCTC 29 23 1 TACCGCACTT 0.996959 -85 AATCAAAATTTGACCGCTCTTTGAGTACGTG 30 142 0 TACCGCTCTT 0.980182 -104 TCACTGCATTTTTTGAACAGA 33 1 1 TACTGCATTT 0.765028 -54 AGGGAAAAAACGACCGCACTTTT 37 58 1 CACCGCACTT 0.988764 -13 CCTTTATTTTTTACCGCACTTTTAAAAGA 38 9 0 TACCGCACTT 0.996959 -252 CCGTAAAAAATCACCGCACTTTTGATGATTT 40 174 1 TACCGCACTT 0.996959 -76 * ********* Masking position 10 Map Score: 56.708 Number of sites scoring better than the average of aligned sites = 1411 Number in coding regions = 948 Number in noncoding regions = 463 Number of orfs with sites within 600 bp upstream = 301 Fraction of orfs with sites within 600 bp upstream = 0.0483456 Motif number 2 AAGTGCGGTAAATTTTTATCCAT 7 3 1 GTGCGGTAAT 0.994992 -69 CGGTCGCAAAGTGCGGTCGTTTTCTTTTATA 8 20 1 GTGCGGTGTT 0.972763 -31 TATTTGAGAAGTGCGGTTAAAATTTAAGTTA 17 44 0 GTGCGGTAAA 0.995674 -144 GCGTCGTGAAGTGCGGTTTTATTTTGGAGTT 17 75 1 GTGCGGTTTA 0.938154 -113 AATGCACAAAGTGCGGTAAGTTTTTTGAATG 25 120 0 GTGCGGTAGT 0.978913 -181 AATCAACCAAGTGCGGTCAAAACAAACGTGA 26 15 1 GTGCGGTAAA 0.995674 -51 CAAATAAAAAGTGCGGTCAAAATCACGTTTG 26 37 0 GTGCGGTAAA 0.995674 -29 TTAGGAAAAGTGCGGTCAAAATTAACCGCA 29 10 1 GTGCGGTAAA 0.995674 -98 GGTTCAGAAAGTGCGGTTAATTTTGACCGCA 29 21 0 GTGCGGTAAT 0.994992 -87 CGTACTCAAAGAGCGGTCAAATTTTGATTGA 30 144 1 GAGCGGTAAA 0.960777 -102 AAAAGTGCGGTCGTTTTTTCCCTTG 37 56 0 GTGCGGTGTT 0.972763 -15 TCTTTTAAAAGTGCGGTAAAAAATAAAGGTA 38 11 1 GTGCGGTAAA 0.995674 -250 ATCATCAAAAGTGCGGTGATTTTTTACGGTA 40 172 0 GTGCGGTATT 0.990389 -78 ******* *** Masking position 7 Map Score: 35.4608 Number of sites scoring better than the average of aligned sites = 670 Number in coding regions = 393 Number in noncoding regions = 277 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 3 CAAGCGGCATAATATAACAAAAAATCTGATGAT 4 41 1 AATAAAAAAA 0.80556 -178 GAAAAGTAATAAATATTCAAAATAAAGGCTTTT 4 83 0 AAATTAAAAT 0.797977 -136 TTATGCTGACAAATCAATCAAAAAAGCAAAGAA 4 113 0 AAATACAAAA 0.830437 -106 CTTGCTCCTTAATAATTTAAAAAGAAAGCTGCG 5 48 0 AATATAAAAA 0.746596 -24 TTTTGTAGAGAAATGGATAAAAATTTACCGCAC 7 13 0 AAATAAAAAA 0.886497 -59 ATTATGTTATAAAACCATAAAAAATTTGAGGTT 7 45 1 AAAAAAAAAA 0.926709 -27 AGAGAAAATAAAAAACAACAAAAGGGGCAATTA 11 35 0 AAAAACAAAA 0.888002 -35 CGAACAAGAAAAATGGTGCAAATGCCGTCGCTT 13 50 1 AAATTCAAAT 0.712382 -82 TGAGAAAGAAAAAATGAAAAAATTACTATTAAT 15 155 0 AAAAAAAAAT 0.89992 -106 CATATTTTTGAAATTTATAAAAAGGCTTTTTGC 17 109 0 AAATAAAAAA 0.886497 -79 ATAAATTTCAAAAATATGCAAAAATAGGGCGAC 17 124 1 AAAATCAAAA 0.849364 -64 AGTATGAACTAAATCATAAAAAATTTTGCTTAT 21 93 1 AAATTAAAAA 0.847428 -115 TCTTTGTCACAAAATAAGAAAATAAGCAAAATT 21 114 0 AAAAAAAAAT 0.89992 -94 ATTCTTCACAAAAAACAGAAAAA 23 1 0 AAAAAAAAAA 0.926709 -124 CATGCACAATAATTTTTTAAAATATCGCTATTT 23 44 0 AATTTAAAAT 0.564007 -81 TTTGTTTATAAATAGTATAAAAATAGCTTTCAA 24 117 1 AATAAAAAAA 0.80556 -184 GAATGCAGGCAAAAACAGCAAAATTTCCTATCA 25 56 1 AAAAACAAAA 0.888002 -245 TTCTCTCGTTAAAATAAAAAAATATTCGGCTAT 25 277 0 AAAAAAAAAT 0.89992 -24 TTTGCCTACAAAATCGATAAAAAT 28 82 1 AAATAAAAAA 0.886497 -14 ACGTTTGCAAAAATCAATCAAAATTTGACCGCT 30 155 0 AAATACAAAA 0.830437 -91 AAACGTGCGTAAATTTTGAAAATTCACACACCC 30 182 1 AAATTAAAAT 0.797976 -64 TTACTCCGTCAATAATTACAAAATTTTAAAGGT 31 275 0 AATATCAAAA 0.648813 -26 CAACAATCTAAATATGTTAAAATAAAAGAGCG 32 12 1 AATATAAAAT 0.676922 -22 AGCCTGAATTAAATCATAAAAATAAGCTAAATA 36 39 0 AAATTAAAAT 0.797977 -120 TTAAAAATATAAAACCAGAAAATTGCCCTAGTA 36 112 0 AAAAAAAAAT 0.89992 -47 TCGACTAATCAATAATTAAAAATATAAAACCAG 36 127 0 AATATAAAAT 0.676923 -32 TGTTTTTGGTAAAATGAAAAAAATTTTTGCATA 37 25 0 AAAAAAAAAA 0.926709 -46 TAACTTAAATAAAAGGTGAAAATCT 40 3 0 AAAATAAAAT 0.864767 -247 TTCTCTATAAAAAATCATCAAAAGTGCGGTGAT 40 183 0 AAAAACAAAA 0.888002 -67 **** * ***** Masking position 10 Map Score: 35.4734 Number of sites scoring better than the average of aligned sites = 955 Number in coding regions = 642 Number in noncoding regions = 313 Number of orfs with sites within 600 bp upstream = 235 Fraction of orfs with sites within 600 bp upstream = 0.0377449 Motif number 4 CGACCAGCAGCTTATTGAAAAACAA 5 2 0 CTTTAAAAAA 0.784421 -70 TTTTTATCCATTTCTCTACAAAATTATGTTATAA 7 23 1 TTTCACAAAT 0.702004 -49 TTCTTTATATTTTCCTGAAAAAGATCAAGCTCAA 15 70 0 TTTTAAAAAA 0.890697 -191 GTAATGACATTTTTATTATAAATAATGGC 19 6 0 TTTTATAAAA 0.890107 -165 AGTGTAAACCTTTGTAAATAAAAAAGCCATCGCT 19 119 0 TTTAATAAAA 0.71981 -52 AATCTTATATTTTGATCATAAATAATTTACGATA 21 36 1 TTTTATAAAA 0.890697 -172 TATTTTCTTATTTTGTGACAAAGATCACGGTTTA 21 123 1 TTTTACAAAA 0.836167 -85 TACACGCAATTTTCATAATAAACAACGAGACGA 22 57 1 TTTTATAAAA 0.890697 -23 TAGCAATATTCTTCACAAAAAACAGAAAAA 23 7 0 CTTCAAAAAA 0.892193 -118 AGGTTTCTCATTTTTCCAAAAATACCCATGATGA 24 48 0 TTTCAAAAAA 0.948732 -253 GAATTAAAAGTTTGTTTATAAATAGTATAAAAAT 24 107 1 TTTTATAAAA 0.890107 -194 GCAAATTACATTTGCCCAAAAACATCGGTGGTTT 28 53 0 TTTCAAAAAA 0.948806 -43 GCAAATGTAATTTGCCTACAAAATCGATAAAAAT 28 72 1 TTTCACAAAT 0.702007 -24 AGTTTTTTATTTTCCCTATAAATATAAATAATGC 29 82 0 TTTCATAAAA 0.948806 -26 TTATGCTTATCTTTGCAAAAAACAAGCCCAATCA 30 71 0 CTTCAAAAAA 0.892193 -175 TTATATCGGGTTTTAAGAAAAATACTTGTGTTCA 31 121 0 TTTAAAAAAA 0.720263 -180 TTCTTACTTAGCCATAAAATTGTGAAATTT 35 7 1 CTTCATAAAT 0.626798 -73 ATTTTTTTCATTTTACCAAAAACAAGGGAAAAAA 37 34 1 TTTCAAAAAA 0.948805 -37 ATTATGCAGATTTCTCTATAAAAAATCATCAAAA 40 193 0 TTTCATAAAA 0.947348 -57 *** * ***** * Masking position 3 Map Score: 18.4191 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 136 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 5 GATTTGTCAGCATAAATAACCTTTTTATCT 4 131 1 CATAAATAAC 0.93132 -88 GATTTTTGAGCATAATTAAAAGAGTACAAA 4 189 1 CATAATTAAA 0.717461 -30 GTTATAAAACCATAAAAAATTTGAGGTTAA 7 50 1 CATAAAAAAT 0.710675 -22 AGAAAGAGAAAATAAAAAACAACAAAAGGG 11 42 0 AATAAAAAAC 0.864591 -28 TTCGGTTATACTTAAAAAAATTTCGGCTAG 14 35 0 CTTAAAAAAA 0.501252 -28 CCTTGTTACCCATAATAAAAATAAAAACTA 17 158 0 CATAATAAAA 0.734317 -30 CATTTTGAGCAATAAAAAACTGTGTACTAG 18 32 0 AATAAAAAAC 0.864591 -70 ATATTTTGATCATAAATAATTTACGATAAA 21 42 1 CATAAATAAT 0.692947 -166 TGAACTAAATCATAAAAAATTTTGCTTATT 21 97 1 CATAAAAAAT 0.710675 -111 CGTTTACATTGATAAAAAACAGGAGTCAAA 21 188 1 GATAAAAAAC 0.571108 -20 ACGCAATTTTCATAATAAACAACGAGACGA 22 60 1 CATAATAAAC 0.86868 -20 CAATATTCTTCACAAAAAACAGAAAAA 23 8 0 CACAAAAAAC 0.712212 -117 AAAAACTTGCCATAAAAAACCGCCACGAAA 25 169 0 CATAAAAAAC 0.936546 -132 CTCTCGTTAAAATAAAAAAATATTCGGCTA 25 278 0 AATAAAAAAA 0.727357 -23 TTATAGGGAAAATAAAAAACTCA 29 95 1 AATAAAAAAC 0.864591 -13 AATGCTAAGAAATAATTAACGTAGGGTGTG 30 208 0 AATAATTAAC 0.724318 -38 ACAAAACCAGCTTAAATAACTGAGCCGTTT 31 170 1 CTTAAATAAC 0.68846 -131 TTAACAAAGTAATAAATAAACAATAGCCAT 35 42 0 AATAAATAAA 0.710236 -38 TACCTTCCGAAACAATTAACAAAGTAATAA 35 57 0 AACAATTAAC 0.30597 -23 GATTGTGAATAATAAATAAACTATTTAGCT 36 18 1 AATAAATAAA 0.710236 -141 TCGACTAATCAATAATTAAAAATATAAAAC 36 130 0 AATAATTAAA 0.523465 -29 CAACTATAACCATAATTAACCGTGGGTATA 38 58 0 CATAATTAAC 0.858694 -203 ATTTGTTTAACTTAAATAAAAGGTGAAAAT 40 13 0 CTTAAATAAA 0.48008 -237 ********** Masking position 5 Map Score: 18.0379 Number of sites scoring better than the average of aligned sites = 343 Number in coding regions = 213 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 6 CAATCAAAAAAGCAAAGAAAAGTAATAAATA 4 101 0 AGCAAAGAAA 0.775649 -118 CGGAAAACCAAGAGAGATAAAAAGGTTATTT 4 144 0 AGAGAGAAAA 0.818198 -75 GCACAGTTCTAACAAGGGAAAAGT 9 13 1 AACAAGGAAA 0.950373 -14 AAGCTATAAGAAAGAGAAAATAAAAAACA 11 51 0 AGAAAGAAAA 0.889506 -19 TAGTATAACGAACAAGAAAAATGGTGCAAAT 13 42 1 AACAAGAAAA 0.931345 -90 CCGATAAGTGAGAAAGAAAAAATGAAAAAAT 15 165 0 AGAAAGAAAA 0.889506 -96 TATCAGATTTAAACAGGAAAATTTT 15 246 1 AAACAGGAAA 0.854155 -15 TATAGATTATAACAAGGAAAAAGTT 21 5 0 AACAAGGAAA 0.950373 -203 TCTTCACAAAAAACAGAAAAA 23 1 0 AAACAGAAAA 0.805776 -124 TTATATATTTAAAAAGAGAAATT 23 112 1 AAAAAGAAAA 0.881249 -13 TTTTTATTTTAACGAGAGAAA 25 290 1 AACGAGAAAA 0.883501 -11 TATAACTGGCAAAAAAGTAAACAAAACCAGC 31 150 1 AAAAAAGAAA 0.635498 -151 GCTACATATTAGCCAGATAAAAAATCGGTGC 31 231 0 AGCCAGAAAA 0.891621 -70 GCTAATATGTAGCGAAGTAAAATAACACCTT 31 249 1 AGCGAAGAAA 0.659029 -52 TTTTACCAAAAACAAGGGAAAAAACGACCGC 37 44 1 AACAAGGAAA 0.950373 -27 ******* *** Masking position 5 Map Score: 11.8424 Number of sites scoring better than the average of aligned sites = 326 Number in coding regions = 250 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 7 TTATGCCGCTTGTTGAGATTAAATTACGTT 4 23 0 TGTTGAGATT 0.896851 -196 TTATTGAGTTTGTTGAGCTTGATCTTTTTC 15 58 1 TGTTGAGCTT 0.942978 -203 TAAAAATGTTTAAATTGTGATCTAGT 18 7 1 TGTTTAAATT 0.833711 -95 TCAGTCTCCCTCTTTAGCTTTAGCAAAGAG 20 16 1 TCTTTAGCTT 0.811252 -22 AAATGACATTAGTTTAGATTTCCGTTACAA 22 27 1 AGTTTAGATT 0.642979 -53 AGCATTTAACTATTTAACTTATATATTTAA 23 94 1 TATTTAACTT 0.702615 -31 ATGGTTTTGATGTTGAGTTTAAGGATATAG 24 155 1 TGTTGAGTTT 0.682037 -146 ATCTTTAATCTGTTTAAATTTACAGTTATT 24 276 0 TGTTTAAATT 0.833711 -25 GTTTTTTGAATGTTTAGCTTACCAAACCCA 25 102 0 TGTTTAGCTT 0.9673 -199 TATTTTAACATATTTAGATTGTTGA 32 6 0 TATTTAGATT 0.793848 -28 ATAAATAAACTATTTAGCTTATTTTTATGA 36 29 1 TATTTAGCTT 0.879912 -130 CAAACAGATTTGTTTAACTTAAATAAAAGG 40 20 0 TGTTTAACTT 0.905131 -230 ********** Masking position 6 Map Score: 7.21688 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 93 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 8 GTTTGAAATATTAGGAATGAA 3 5 1 GAATATATAA 0.777324 -17 AGAAAAGTAATAAATATTCAAAATAAAGGCTTTTTTG 4 80 0 TAATATATAA 0.467694 -139 CTTTCTTTTTAAATTATTAAGGAGCAAGA 5 53 1 AAATATAGAA 0.693781 -19 CAAAGTATCAAAAATAAAGGGGCTTAAT 11 2 1 AAATACATAA 0.857705 -68 TTTGTGCATTGAAATACTATTGATAAAGCTGGGAAAA 13 105 1 GAATATATAA 0.777324 -27 AAAATTTTCCTGTTTAAATCTGATAAA 15 244 0 AAATTTTTAA 0.512287 -17 AATTTATCGTAAATTATTTATGATCAAAATATAAGAT 21 37 0 AAATATATAA 0.920697 -171 CATACTTATGAAAGTAACCGCTTTCAATTTATCGTAA 21 62 0 AAATACTTAA 0.820102 -146 AATTTATACTAAATTATTGTAAATAAACCGTGATCTT 21 143 0 AAATATATAA 0.920697 -65 ACGGAAATCTAAACTAATGTCATTTACTGGGGGCAGA 22 15 0 AAATATTTAC 0.78634 -65 ATATTTTAAAAAATTATTGTGCATGAAATAAAGTATT 23 52 1 AAATATATAA 0.920697 -73 CATTTTTCCAAAAATACCCATGATGACAATAATAGCA 24 37 0 AAATACATAC 0.716432 -264 TCTTGCCATAGAAATACTAGATTTAAATAAAAGATTG 25 200 0 GAATATTTAA 0.725282 -101 GTTCAAGTTAAAAATATCTATAATCACGACTACTTCA 31 89 0 AAATACATAC 0.716432 -212 GGTTTTAAGAAAAATACTTGTGTTCAAGTTAAAAATA 31 110 0 AAATATTTAA 0.897756 -191 TATACGCTTAAAACTTTTGGAAATCAAAAACGGCTCA 31 190 0 AAATTTATAA 0.581389 -111 GTAGCGAAGTAAAATAACACCTTTAAAATTTTGTAAT 31 257 1 AAATACTTAA 0.820102 -44 ACAAAATTATTTGATTTTACGTTAAAATAG 34 4 1 AAATATTTAC 0.78634 -56 TTTTCAAAGCAAAATAATCAAGAATAAACACTAAAAA 36 71 0 AAATATAAAA 0.453741 -88 GATTTGTCAAAAATTACTCTATTGAAAGGGCGTTATA 39 26 0 AAATATTGAA 0.631472 -37 AGATCACAAAAAAGTAGTAGGGTTTATAGTTTTATAA 40 107 0 AAATATTTAT 0.413572 -143 *** ** * ** ** Masking position 5 Map Score: 10.8393 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 157 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 9 TGATGATATGGCACAAAAAAGCCTTTATTTTGAATATT 4 67 1 GCAACTTTAT 0.972412 -152 TATAATGGCGGCGTTTTATTAACTTTAATCGGGT 6 63 1 GCTACTTTAA 0.948137 -24 AACAAAAGGGGCAATTAAGCCCCTTTATTTTTGATACT 11 14 0 GCTACTTTAT 0.972412 -56 ACAGGATGTGGCGTAAAAGGTTCTTTATATTTTCCTGA 15 86 0 GCAACTTTAT 0.972412 -175 CCTTTCACAAGCTTGAGAAAGGCTTTATAATTTGCCGC 15 204 1 GCAACTTTAT 0.972412 -57 ATAATTTGCCGCATTTTATCAGATTTAAACAGGAAAAT 15 230 1 GCTAATTTAA 0.717517 -31 ATAGTTAAATGCTTATGAAATACTTTATTTCATGCACA 23 69 0 GCTACTTTAT 0.972412 -56 GCATAGGAATGTTGTTTAATGACTTAATC 24 2 0 GTTACTTAAT 0.523192 -299 AAAAATCGGTGCACATTATACGCTTAAAACTTTTGGAA 31 205 0 GCTACTTAAA 0.803769 -96 ATGTAGCGAAGTAAAATAACACCTTTAAAATTTTGTAA 31 255 1 GTAACTTTAA 0.717517 -46 ATAAAAATAAGCTAAATAGTTTATTTATTATTCACAAT 36 19 0 GCAAATTTAT 0.830433 -140 ATACCTACCCGCGGTAAAATACCTTTATTTTTTACCGC 38 23 0 GCAACTTTAT 0.972412 -238 ** * * ****** Masking position 8 Map Score: 9.42915 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 33 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 AATCGCATTCATCAATAAAACAACTAACAAG 1 46 1 ATCAATAAAC 0.931086 -29 TTGATGGTTAAACTATAAACCTTTACATAAG 2 32 0 AACTATAAAC 0.951878 -45 TAGTTTAACCATCAATAAAACAACTAACAAG 2 48 1 ATCAATAAAC 0.931086 -29 GGCATAATATAACAAAAAATCTGATGATATG 4 46 1 AACAAAAAAC 0.789727 -173 TGACAAATCAATCAAAAAAGCAAAGAAAAGT 4 109 0 ATCAAAAAAC 0.789727 -110 AAATGCGGCAAATTATAAAGCCTTTCTCAAG 15 215 0 AATTATAAAC 0.659767 -46 TCATTACAAGATCTATAAATCAGGTTCATTT 19 33 1 ATCTATAAAC 0.951878 -138 CCTTGTTATAATCTATAAATCTTATATTTTG 21 19 1 ATCTATAAAC 0.951878 -189 CAATAATTAAAAATATAAAACCAGAAAATTG 36 120 0 AAATATAAAC 0.659767 -39 ATTTTTATAAAACTATAAACCCTACTACTTT 40 103 1 AACTATAAAC 0.951878 -147 ********* * Masking position 5 Map Score: 7.25353 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 46 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 11 TTTTACTCCTTGTTAGTTGTTTTA 1 61 0 TTTCTCCTTT 0.9599 -14 TTTTACTCCTTGTTAGTTGTTTTA 2 63 0 TTTCTCCTTT 0.9599 -14 TTCAAAATCCTTTGTACTCTTTTAA 4 204 0 TCAATCCTTT 0.744765 -15 TCTTGCTCCTTAATAATTTAAAAA 5 58 0 TCTCTCCTTT 0.96981 -14 AAAGGGGCAATTAAGCCCCTTTATTTTTGATACT 11 14 0 TTACCCCTTT 0.72662 -56 ATTTTCAATCCTTTTTTTGCTATACT 14 3 1 TTTATCCTTT 0.786682 -60 TTTCATTTTTTCTTTCTCACTTATCGGTAAATCC 15 169 1 TCTCTCACTT 0.6132 -92 CTTTTATCTCCTTAGTTTGCATTTAT 16 62 0 TTTCTCCTTT 0.9599 -16 TATAGTCAGTCTCCCTCTTTAGCTTTAGC 20 6 1 TCACTCCCTT 0.922256 -32 TTTGACTCCTGTTTTTTATCAATG 21 194 0 TTTCTCCTGT 0.818445 -14 ACAGAGGGAGTCATTCTCCCTAATAAAAATTCCA 33 27 1 TCACTCCCTT 0.922256 -28 *** ****** * Masking position 1 Map Score: 4.21887 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 17 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 12 CTTCTTGACCTTAACCTTATGTAAAGGTTTAT 2 17 1 TTAACCTATT 0.938123 -60 GTGGTTATCCTTAACGTAATTTAATCTCAACA 4 11 1 TTAACGTATT 0.855182 -208 ATTTAACCTCAAATTTTTTATGGT 7 58 0 TTAACCTAAT 0.857931 -14 TTATCTATTGTGAACCTTCAATAGAATTGTTA 12 14 1 TGAACCTCAT 0.779599 -57 ACGCTAGAAATGAACCTGATTTATAGATCTTG 19 39 0 TGAACCTATT 0.904723 -132 CACCAGCCTCTTAATCTAATTTAATTGGTCAA 19 88 1 TTAATCTATT 0.789716 -83 ATACCGCTTTTTAATGTGATGTAGTGGAGGGA 25 18 0 TTAATGTATT 0.59395 -283 CCGCACTTTCTGAACCTCCTCTTTAGCAAAGA 29 36 1 TGAACCTCTT 0.898789 -72 GGTTGCTATTTTAACGTAAAATCAAATAATTT 34 14 0 TTAACGTAAT 0.701682 -46 TTTAATCTCCTATCCATTCAAGA 34 47 0 TTAATCTCTT 0.778374 -13 AGAATATTTAACCTTCTCTGACAATTTCA 40 231 0 TTAACCTCTT 0.934118 -19 ******* ** * Masking position 4 Map Score: 4.4328 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 30 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 13 TGATGATATGGCACAAAAAAGCCTTTATTT 4 67 1 GCACAAAAAA 0.342619 -152 TTAATTATGCTCAAAAATCTGTCGCAATTA 4 178 0 TCAAAAATCT 0.90441 -41 TACTCAAAAATATAAAAGAAAAC 8 38 0 TCAAAAATAT 0.782177 -13 CAAAGTATCAAAAATAAAGGGGCTTAA 11 8 1 TCAAAAATAA 0.816686 -62 CTCAACAAACTCAATAATCTATTATCTAAT 15 45 0 TCAATAATCT 0.431794 -216 TTCAGATTATTCAAAAAACAATTTCTTGTT 17 13 0 TCAAAAAACA 0.85749 -175 TTTATAAATTTCAAAAATATGCAAAAATAG 17 121 1 TCAAAAATAT 0.782177 -67 GCAATATTCTTCACAAAAAACAGAAAAA 23 9 0 TCACAAAAAA 0.521753 -116 TTTGATATACTCACAAATCTTATTGTTTCA 24 228 1 TCACAAATCT 0.81884 -73 AGCTAAACATTCAAAAAACTTACCGCACTT 25 113 1 TCAAAAAACT 0.829054 -188 GCTTATCTTTGCAAAAAACAAGCCCAATCA 30 71 0 GCAAAAAACA 0.741903 -175 ACGCACGTTTGCAAAAATCAATCAAAATTT 30 162 0 GCAAAAATCA 0.848664 -84 TCAACAATCTAAATATGTTA 32 1 1 TCAACAATCT 0.5297 -33 GGTATCCTATGCAAAAATTTTTTTCATTTT 37 18 1 GCAAAAATTT 0.385753 -53 CTCCGATTTGTCAAAAATTACTCTATTGAA 39 37 0 TCAAAAATTA 0.619909 -26 TTGATATAGATCACAAAAAAGTAGTAGGGT 40 121 0 TCACAAAAAA 0.521753 -129 AAAAGTACCGTAAAAAATCACCGCACTTTT 40 167 1 TAAAAAATCA 0.506544 -83 GATTTCTCTATAAAAAATCATCAAAAGTGC 40 189 0 TAAAAAATCA 0.506544 -61 ********** Masking position 6 Map Score: 6.9212 Number of sites scoring better than the average of aligned sites = 477 Number in coding regions = 380 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 14 GTCAATAACGTTGGTTAGAGTAACAATTCTATTG 12 32 0 TTGTAGGTAC 0.973242 -39 ATGGAATGTTTTGGATAGTATAACGAACAAGAAA 13 27 1 TTGTAGATAC 0.973759 -105 TAAAAAAATTTCGGCTAGTATAGCAAAAAAAGGA 14 19 0 TCGTAGATAC 0.954572 -44 TCCCTTAGATTTGTATAGAATAGCCGAATATTTT 25 258 1 TTGTAGATAC 0.973759 -43 TATAGCTCAGTTGGTTAGAGCACCACCTTGACAT 31 44 0 TTGTAGGCAC 0.906197 -257 AAAAAAATTTTTGCATAGGATACCTGATATT 37 8 0 TTGTAGATAC 0.973759 -63 TTGAAAAATATCGCCTAGGGTAAGTAGACCCTAG 38 139 0 TCGTAGGTAG 0.773185 -122 GGCGAAATTGAGTATTATAACGCCCTTTCAA 39 8 1 TTGTATATAC 0.805592 -55 *** *** *** * Masking position 7 Map Score: 2.73773 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 7 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 15 TTTTACTCCTTGTTAGTTGTTTTA 1 61 0 ACTCCTTGTT 0.949274 -14 TTTTACTCCTTGTTAGTTGTTTTA 2 63 0 ACTCCTTGTT 0.949274 -14 TTCAAAATCCTTTGTACTCTTTTAA 4 204 0 AATCCTTTGT 0.774631 -15 AACGTTATTGACTCTTTTTTGGATGAG 12 54 1 ACTCTTTTTT 0.696628 -17 ATTTTCAATCCTTTTTTTGCTATACT 14 7 1 AATCCTTTTT 0.942796 -56 TTTTGGCAAAAAGCCTTTTTATAAATTTCA 17 104 1 AAGCCTTTTT 0.774631 -84 TAAAAAGAATCCTTGTTACCCATAATA 17 171 0 AATCCTTGTT 0.921475 -17 TTTGACTCCTGTTTTTTATCAATG 21 194 0 ACTCCTGTTT 0.845709 -14 ATTGCCCTAGTATCCTTTTTCAAAGCAAAA 36 94 0 TATCCTTTTT 0.698713 -65 TATAAACCCTACTACTTTTTTGTGATCTAT 40 116 1 ACTACTTTTT 0.696628 -134 ********** Masking position 6 Map Score: 4.10433 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 44 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172