AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00970_hinf_reg_100.orf -o00970_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: HI0962 28 isoleucyl-tRNA synthetase (isoleucine--tRNA ligase) (ileRS) Input sequences: #1 HI0078 102 cysteinyl-tRNA synthetase (cysS) #2 HI0110 166 seryl-tRNA synthetase (serS) #3 HI0274 300 glutamyl-tRNA synthetase (gltX) #4 HI0317 218 aspartyl-tRNA synthetase (aspS) #5 HI0366 101 fimbrial biogenesis and twitching motility protein, putative #6 HI0367 71 conserved hypothetical protein #7 HI0622 300 polypeptide deformylase (def) #8 HI0623 92 methionyl-tRNA formyltransferase (fmt) #9 HI0637 128 tryptophanyl-tRNA synthetase (trpS) #10 HI0727.1 260 cyaY protein (cyaY) #11 HI0729 84 prolyl-tRNA synthetase (proS) #12 HI0814 187 alanyl-tRNA synthetase (alaS) #13 HI0836 181 lysyl-tRNA synthetase analog (genX) #14 HI0921 248 leucyl-tRNA synthetase (leuS) #15 HI0924 300 glycyl-tRNA synthetase, beta chain (glyS) #16 HI0927 265 glycyl-tRNA synthetase, alpha chain (glyQ) #17 HI0963 34 riboflavin kinase / FMN adenylyltransferase (ribF) #18 HI0964 300 virulence factor (mviN) #19 HI1211 300 lysyl-tRNA synthetase (lysU) #20 HI1276 102 methionyl-tRNA synthetase (metG) #21 HI1302 147 asparaginyl-tRNA synthetase (asnS) #22 HI1311 148 phenylalanyl-tRNA synthetase, alpha subunit (pheS) #23 HI1312 33 phenylalanyl-tRNA synthetase, beta subunit (pheT) #24 HI1354 300 glutaminyl-tRNA synthetase (glnS) #25 HI1367 284 threonyl-tRNA synthetase (thrS) #26 HI1394 221 conserved hypothetical protein #27 HI1583 79 arginyl-tRNA synthetase (argS) #28 HI1610 200 tyrosyl tRNA synthetase (tyrS) Motif number 1 AAGTGCTATAAAAGTGCGGTTTGTTTTTAT 1 63 1 AAAGTGCGGT 0.996068 -40 ATTCTAATACAAAGTGCGGTCAATTTTTCT 2 52 1 AAAGTGCGGT 0.996068 -115 CTTCTAAATAAAAAAGCGGATTTTATGCTT 3 225 0 AAAAAGCGGA 0.819054 -76 CAATCATTTCAAAAAACGGTGGGCTTAAGC 8 34 1 AAAAAACGGT 0.784154 -59 TAATTGATAGGAAGTAGGGTGGGCTTAAGC 8 56 0 GAAGTAGGGT 0.703831 -37 TAAATCTGATAAAATGCGGCAAATTATAAA 10 227 0 AAAATGCGGC 0.823056 -34 GTGTTAAAAGTGCGGTTAAAAATGAC 11 7 1 AAAGTGCGGT 0.996068 -78 AGTATAACAAAAAGTGCGGTCATTTTTAAC 11 25 0 AAAGTGCGGT 0.996068 -60 CGCTATTTGAGAAGTGCGGTTAAAATTTAA 12 48 0 GAAGTGCGGT 0.983361 -140 ATAGCGTCGTGAAGTGCGGTTTTATTTTGG 12 72 1 GAAGTGCGGT 0.983361 -116 AGAGAAATAAAAAGTGCGGTGGTTTTTTAG 14 137 0 AAAGTGCGGT 0.996068 -112 AAATGCTGCAAAAGTGCGGTTAAAATTTAA 14 220 1 AAAGTGCGGT 0.996068 -29 CCTCTTTAGCAAAGAGGGGTAGGGGAGATT 15 60 0 AAAGAGGGGT 0.979011 -241 CCTCTTTGCTAAAGAGGGGAATTCTTGAAT 15 73 1 AAAGAGGGGA 0.878713 -228 CCTCTTTGCTAAAGAGGGGATTGGATCTTT 15 203 0 AAAGAGGGGA 0.878713 -98 CCTCTTTAGCAAAGAGGGGTAGGGGCGATT 15 216 1 AAAGAGGGGT 0.979011 -85 ATAAAGGCGAAAAATGCGGTTGAAAATCAG 16 189 0 AAAATGCGGT 0.980789 -77 GGAAAGTGCGGTATGTTAAGTT 20 3 1 AAAGTGCGGT 0.996068 -100 AGTCCTAAATAAAATAGGGTAAAGCCTTAT 21 34 0 AAAATAGGGT 0.672447 -114 ACATCACATTAAAAAGCGGTATCGCCGTGA 24 28 1 AAAAAGCGGT 0.966824 -273 ATAAATGCACAAAGTGCGGTAAGTTTTTTG 24 124 0 AAAGTGCGGT 0.996068 -177 TGGGTATTTAAAAGTGCGGTTATTCTAGCC 25 25 1 AAAGTGCGGT 0.996068 -260 AAGTAGGGCAAAAGTGCGGTTAATTTTTAT 25 206 1 AAAGTGCGGT 0.996068 -79 TTTGATCCTTAAAGAGCGGTTAGGTTTTAG 26 202 0 AAAGAGCGGT 0.993132 -20 AGAAATATACAAAGAACGGTATCATAACCG 27 23 1 AAAGAACGGT 0.947442 -57 ********** Masking position 3 Map Score: 77.9855 Number of sites scoring better than the average of aligned sites = 1705 Number in coding regions = 1169 Number in noncoding regions = 536 Number of orfs with sites within 600 bp upstream = 333 Fraction of orfs with sites within 600 bp upstream = 0.0534854 Motif number 2 TGCTATAAAAGTGCGGTTTGTTTTTATTTCATTTT 1 66 1 GTGCGGTTTT 0.997845 -37 CTAATACAAAGTGCGGTCAATTTTTCTTTATTTTT 2 55 1 GTGCGGTTTT 0.997845 -112 GTGTTAAAAGTGCGGTTAAAAATGACCGCACTTT 11 10 1 GTGCGGTATG 0.983051 -75 TATTTGAGAAGTGCGGTTAAAATTTAAGTTATTTC 12 40 0 GTGCGGTTTT 0.997845 -148 GCGTCGTGAAGTGCGGTTTTATTTTGGAGTTTTGG 12 75 1 GTGCGGTTTT 0.997845 -113 GAAATAAAAAGTGCGGTGGTTTTTTAGTTGTTTTT 14 129 0 GTGCGGTTTT 0.997845 -120 TGCTGCAAAAGTGCGGTTAAAATTTAAGGTGATTT 14 223 1 GTGCGGTTTT 0.997845 -26 GGAAAGTGCGGTATGTTAAGTTAAAGTTTT 20 6 1 GTGCGGTAAG 0.928549 -97 AATGCACAAAGTGCGGTAAGTTTTTTGAATGTTTA 24 116 0 GTGCGGTTTT 0.997845 -185 GTATTTAAAAGTGCGGTTATTCTAGCCTTTATTTT 25 28 1 GTGCGGTTAG 0.983051 -257 TAGGGCAAAAGTGCGGTTAATTTTTATAGAATTTT 25 209 1 GTGCGGTTTT 0.997845 -76 GATCCTTAAAGAGCGGTTAGGTTTTAGAAAGTTTT 26 194 0 GAGCGGTTTT 0.981697 -28 ******* *** Masking position 7 Map Score: 34.5761 Number of sites scoring better than the average of aligned sites = 511 Number in coding regions = 332 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 3 TTCCCTCTAAAAAATTAAGGGTTGTATTAT 1 17 1 AAAATTAAGG 0.60094 -86 CTCGTAAAATGAAATAAAAACAAACCGCAC 1 76 0 GAAATAAAAA 0.781785 -27 CCAACGTATAAAAATAAAGAAAAATTGACC 2 69 0 AAAATAAAGA 0.930546 -98 TTCAACGAAAAAAGTAAGGAAATTCT 2 151 1 AAAGTAAGGA 0.364887 -16 CAAACTTAGTAAAATTAAGAAAACTTTTTA 3 29 1 AAAATTAAGA 0.671027 -272 TAAACAAAATTTAATAAAAAGGTATTGACT 3 181 0 TTAATAAAAA 0.551597 -120 GTTTGACTTCTAAATAAAAAAGCGGATTTT 3 231 0 TAAATAAAAA 0.863514 -70 ATAAATATTCAAAATAAAGGCTTTTTTGTG 4 78 0 AAAATAAAGG 0.908184 -141 ATTTTTGAGCATAATTAAAAGAGTACAAAG 4 190 1 ATAATTAAAA 0.419116 -29 TTATCTAAGTTAAATAAAAACAGAAGGACC 7 96 1 TAAATAAAAA 0.863514 -205 TTACTTATTGAAAATTAAAATTAGACACTT 7 184 0 AAAATTAAAA 0.787724 -117 CCAAAACTCCAAAATAAAACCGCACTTCAC 12 80 0 AAAATAAAAC 0.861999 -108 ACCCATAATAAAAATAAAAACTAAGTCGCC 12 151 0 AAAATAAAAA 0.96059 -37 CAATCAATAGAAAGTAAAAATAAATCCCCT 13 20 1 AAAGTAAAAA 0.812323 -162 AGGTCTCTCAATAATAAAAATA 14 3 0 ATAATAAAAA 0.825761 -246 AATAGGGAGAGAAATAAAAAGTGCGGTGGT 14 144 0 GAAATAAAAA 0.781785 -105 TGATAACGAGAAAATAAGAATTTAAATCTA 15 255 1 AAAATAAGAA 0.854777 -46 ACAGAATTTTTAAATAAGAGAAACAAA 15 284 1 TAAATAAGAG 0.530056 -17 AAACTATACTAAAATAAAACTTAAAATCTA 16 116 1 AAAATAAAAC 0.861999 -150 GAAAATAAGAGAATTTCGGCA 17 24 0 AAAATAAGAG 0.812924 -11 ATTGATAGACAAAATAAAGGGCATCAATAT 18 28 1 AAAATAAAGG 0.908184 -273 GTAAACAAAGAAAATAAAAATTTCTTATTA 19 259 1 AAAATAAAAA 0.96059 -42 TGGCTTATCAAAAATAAAAATGGAATAACG 22 35 0 AAAATAAAAA 0.96059 -114 AAGTCCTTAAAAAGTAAAAGAATAATGCGA 22 73 0 AAAGTAAAAG 0.761647 -76 TTTTCTCTATAAAATAAAAAACCGAGTAAT 22 112 0 AAAATAAAAA 0.96059 -37 ATACTAGATTTAAATAAAAGATTGTAAAAA 24 194 0 TAAATAAAAG 0.823659 -107 AATCTAAGGGAAAATAAAGGTTCATCTCCT 24 239 0 AAAATAAAGG 0.908184 -62 TTCTCTCGTTAAAATAAAAAAATATTCGGC 24 280 0 AAAATAAAAA 0.96059 -21 TTATCTCTTAAAAATAAAGGCTAGAATAAC 25 43 0 AAAATAAAGG 0.908184 -242 AGAGTTATCATAAATAAAAATTTCATCACA 26 47 0 TAAATAAAAA 0.863514 -175 TTCAAATTGAATAATAAAAATAATCGGTTA 27 47 0 ATAATAAAAA 0.825761 -33 AAGAATCCCTATAATAAAACCTTTTAAAAC 28 163 1 ATAATAAAAC 0.54843 -38 ********** Masking position 5 Map Score: 35.1598 Number of sites scoring better than the average of aligned sites = 564 Number in coding regions = 329 Number in noncoding regions = 235 Number of orfs with sites within 600 bp upstream = 210 Fraction of orfs with sites within 600 bp upstream = 0.0337295 Motif number 4 TTTTATTAAATTTTGTTTAATTGTCGTAAAAATA 3 192 1 TTTTGAATTT 0.875923 -109 TCATCAGATTTTTTGTTATATTATGCCGCTTGTT 4 39 0 TTTTGTATTT 0.865507 -180 AAAGCCTTTATTTTGAATATTTATTACTTTTCTT 4 84 1 TTTTGATTTT 0.908483 -135 TTCTTTGCTTTTTTGATTGATTTGTCAGCATAAA 4 113 1 TTTTGGATTG 0.814324 -106 GGGTTTTAGCTTTTGGGAATTTATTCATTATTTA 7 143 1 TTTTGATTTT 0.908483 -158 AGGGTAGAATTTTAGTGGGATTATAGCACAGCTA 7 260 0 TTTAGGATTT 0.871903 -41 GTGTGCCTGTTTTAGTTATTTTGGGAATGATATT 10 14 1 TTTAGTTTTG 0.79521 -247 TGCGGTTTTATTTTGGAGTTTTGGCAAAAAGCCT 12 86 1 TTTTGTTTTG 0.826336 -102 GTCGCCCTATTTTTGCATATTTTTGAAATTTATA 12 123 0 TTTTGATTTT 0.908483 -65 ATATTACCCTTTTAGGGGATTTATTTTTACTTTC 13 29 0 TTTAGATTTT 0.890122 -153 GCGGTGGTTTTTTAGTTGTTTTTTACAATAAATT 14 118 0 TTTAGTTTTT 0.880736 -131 ATTTTTGCCATTTTACGGTATTCTATGCCACATT 14 175 1 TTTTATATTT 0.645235 -74 GCGGTTAAAATTTAAGGTGATTTT 14 235 1 TTTAAGATTT 0.657966 -14 TATGTTCTACTTTAACGTTTTTTGAAAGCAGATA 15 154 0 TTTAATTTTG 0.523227 -147 TTTTGATTAATTTAATAGATTTCGATTGTTTAAA 16 81 0 TTTAAATTTG 0.546254 -185 ATTTTGAATATTTAGGTAGATTTTAAGTTTTATT 16 128 0 TTTAGGATTT 0.871903 -138 TATGCCGATTTTTTATACTTTTGTCAATGGAAAA 18 55 1 TTTTATTTTT 0.718904 -246 GTGTGGCGGATTTTATCAGTTTTTTTTCACGGAA 18 173 1 TTTTAGTTTT 0.768236 -128 ACCCTAAAATTTTTGCCTAATTGTATAGAAATTT 18 222 0 TTTTGAATTT 0.875923 -79 AGGACTCATTTTTAAGGCGATTTTATTGTTCATA 21 58 1 TTTAAGATTT 0.657966 -90 TGATAGGAAATTTTGCTGTTTTTGCCTGCATTCA 24 55 0 TTTTGTTTTG 0.826336 -246 GCGGTAAGTTTTTTGAATGTTTAGCTTACCAAAC 24 105 0 TTTTGGTTTG 0.860474 -196 TGCGGTTAATTTTTATAGAATTTTAAATGAACAC 25 220 1 TTTTAAATTT 0.66613 -65 ATAAGTTTAGATAATTTATTTCTTGTTTT 26 6 1 TTTAGATTTT 0.890122 -216 TTATTTCTTGTTTTGTCATATTGTGATGAAATTT 26 26 1 TTTTGTATTT 0.865507 -196 CATTACTCAATTTAGTGAATTTTTACCAAGCTGG 26 118 1 TTTAGATTTT 0.890122 -104 TATCAATTGATTTAATACTTTTTTACACCAGCTT 26 145 0 TTTAATTTTT 0.67607 -77 GCGGTTAGGTTTTAGAAAGTTTTTACAAATCCTA 26 183 0 TTTAGGTTTT 0.905404 -39 TATTTTTTTGAGGAATTATTTTCATTTAA 28 6 1 TTTTGAATTT 0.875923 -195 ***** **** * Masking position 11 Map Score: 29.138 Number of sites scoring better than the average of aligned sites = 642 Number in coding regions = 486 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 5 TTTGTTTTCCCTCTAAAAAATTAAGGGTT 1 8 1 TCTCTAAAAA 0.672631 -95 CTAGCGTGCTTTCTTCAAATAAACCAGTTTAA 2 102 0 TCTCAAATAA 0.756873 -65 AAAGTAATAAATATTCAAAATAAAGGCTTTTT 4 82 0 AATCAAAATA 0.45763 -137 TGCTGACAAATCAATCAAAAAAGCAAAGAAAA 4 111 0 TATCAAAAAA 0.958465 -108 AAATTTAATCAAATAATTAGGCGGTA 6 56 0 TATCAAATAA 0.815231 -16 TATTCATTATTTAATCAAATAAGTGTCTAATT 7 164 1 TATCAAATAA 0.815231 -137 TGAGAAAGAAAAAATGAAAAAATTACTATTAA 10 156 0 AATGAAAAAA 0.548971 -105 TTATTTCAGATTATTCAAAAAACAATTTCTTG 12 15 0 TATCAAAAAA 0.958445 -173 TTTTGTGATCTACCTCAAAAAAGCTAAGATTG 13 136 1 TCTCAAAAAA 0.94215 -46 AATTGAAAATTTATTGTAAAAAACAACTAAAA 14 111 1 TATGTAAAAA 0.445343 -138 ATCTATTAAATTAATCAAAAAAAACTATACTA 16 95 1 TATCAAAAAA 0.958464 -171 TACGCTATATTCCGTGAAAAAAAACTGATAAA 18 184 0 TCTGAAAAAA 0.817928 -117 TAAAAGTCGTTTACTCAAAATATTCTTCTCTA 18 255 0 TATCAAAATA 0.815242 -46 GGTAAGCTAAACATTCAAAAAACTTACCGCAC 24 109 1 AATCAAAAAA 0.815244 -192 GATAAAGCCTTTAGTCAGAAAAACATTATTTC 25 68 1 TATCAGAAAA 0.698816 -217 TATTTAACAATACTTCAAGAAAGTGATAGAAT 25 122 1 TCTCAAGAAA 0.620857 -163 ACGAGCGAAATTAGGCAAAAAATGCGTGGCGA 25 154 0 TAGCAAAAAA 0.698816 -131 ATGAAAATAATTCCTCAAAAAAATA 28 4 0 TCTCAAAAAA 0.94215 -197 TGTCAATAGTTAAATGAAAATAATTCCTCAAA 28 17 0 TATGAAAATA 0.548971 -184 TAGCAATTTGTGAATAAAAAAAAACGCCTATC 28 132 0 TATAAAAAAA 0.549494 -69 * * ******** Masking position 12 Map Score: 12.7079 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 186 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 6 CTAGCGTGCTTTCTTCAAATAAACCAGTTTA 2 103 0 TTCTCAAATA 0.647113 -64 AAAGTAATAAATATTCAAAATAAAGGCTTTT 4 83 0 ATATCAAAAT 0.619 -136 TGCTGACAAATCAATCAAAAAAGCAAAGAAA 4 112 0 TCATCAAAAA 0.845348 -107 AAATTTAATCAAATAATTAGGCGGT 6 57 0 TTATCAAATA 0.84361 -15 TATTCATTATTTAATCAAATAAGTGTCTAAT 7 164 1 TTATCAAATA 0.84361 -137 TTATTTCAGATTATTCAAAAAACAATTTCTT 12 16 0 TTATCAAAAA 0.961374 -172 AATTTCAAAAATATGCAAAAATAGGGCGACT 12 127 1 ATAGCAAAAA 0.782138 -61 TTCTAATCTGTTCTGCAAAAATTGAAAATTT 14 92 1 TTCGCAAAAA 0.802057 -157 TACTATCAATTTATTCAAGAATTCCCCTCTT 15 84 0 TTATCAAGAA 0.73558 -217 ATCTATTAAATTAATCAAAAAAAACTATACT 16 95 1 TTATCAAAAA 0.961464 -171 ATCTACCTAAATATTCAAAATTACTTACTTG 16 141 1 ATATCAAAAT 0.619 -125 TTCTATACAATTAGGCAAAAATTTTAGGGTA 18 226 1 TTAGCAAAAA 0.922598 -75 TAAAAGTCGTTTACTCAAAATATTCTTCTCT 18 256 0 TTATCAAAAT 0.843608 -45 GGTAAGCTAAACATTCAAAAAACTTACCGCA 24 109 1 ACATCAAAAA 0.622118 -192 GATAAAGCCTTTAGTCAGAAAAACATTATTT 25 68 1 TTATCAGAAA 0.748114 -217 ACGAGCGAAATTAGGCAAAAAATGCGTGGCG 25 155 0 TTAGCAAAAA 0.922598 -130 ATGAAAATAATTCCTCAAAAAAATA 28 5 0 TTCTCAAAAA 0.894475 -196 GCGTTTTTTTTTATTCACAAATTGCTAAGAA 28 137 1 TTATCACAAA 0.748051 -64 *** ******* Masking position 7 Map Score: 12.7883 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 175 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 7 ATTTGTCAGCATAAATAACCTTTTTATCTCTCTTGG 4 132 1 AAAATCTTTA 0.952338 -87 ATATGAGTTGAAAAATTACTTACTTATTGAAAATTA 7 197 0 AAAATCTTTA 0.952339 -104 AAGCTAGGTTAAAAATGCTATATTTAACGGAAACGT 9 28 0 AAAATTTTTA 0.906903 -101 AAAATTTTCCTGTTTAAATCTGATAA 10 245 0 AAATTCTTTA 0.832473 -16 ATCTTTAGACATAAAAACGTTATTAATTTGTAACG 13 86 0 AAAAACTTTA 0.763345 -96 AATTTATTCAAGAATTCCCCTCTTTAGCAAAGAGGG 15 72 0 AAATTCTTTA 0.832473 -229 TAATGTGATTAAAAATGTTGGTATTATACTTGAATC 16 229 0 AAAATTGTTA 0.879425 -37 CTAATTGTATAGAAATTTTGTTTTTACGCTATATTC 18 204 0 AAAATTTTTA 0.906904 -97 CAAAGAAAATAAAAATTTCTTATTAATTTATAAAAA 19 264 1 AAAATCTTAA 0.630961 -37 TCAAACTAGAAAAAATCCCCTATTTAAAGTAAGATA 20 41 1 AAAATCTTTA 0.952339 -62 TTTTTAGCATACAAAAATTGTGCTTATCTTACTTTA 20 65 0 AAAAATTTTA 0.611279 -38 ATTTTTATGGAAAATTTCCTTCATTAAGGTAAACTA 21 109 1 AAATTCTTTA 0.832473 -39 GAATAATGCGAAAAATCATTGGCTTATCAAAAATAA 22 48 0 AAAATTGTTA 0.879425 -101 TTCTTGCCATAGAAATACTAGATTTAAATAAAAGAT 24 202 0 AAAATTGTTA 0.879425 -99 TTTTCAACTAAAAGATAACTGCATTACTCAATTTAG 26 97 1 AAGATCGTTA 0.654847 -125 GAAAGTTTTTACAAATCCTAGATTTATCAATTGATT 26 167 0 AAAATTGTTA 0.879425 -55 * **** * * *** Masking position 3 Map Score: 11.7052 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 73 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 8 AAGCGGATTTTATGCTTATTTTTACGACAATT 3 210 0 TATGCTTTTT 0.816545 -91 TTTGTTATATTATGCCGCTTGTTGAGATTAAA 4 30 0 TATGCCTTGT 0.847293 -189 GTTGTGTGCCTGTTTTAGTTATTTTG 10 5 1 TGTGCCTTTT 0.946692 -256 TTGTTATACTTGCGCCAATTTTTTCAGTTCTT 11 45 1 TGCGCCTTTT 0.736912 -40 GCCCACACAATATTACCCTTTTAGGGGATTTA 13 40 0 TATTACTTTT 0.724446 -142 GTGTGGGCATTGTGCCATTTTTCGTTACAAAT 13 64 1 TGTGCCTTTT 0.946692 -118 TACGGTATTCTATGCCACATTTTCTATTGTCA 14 188 1 TATGCCATTT 0.78919 -61 AGGGCATCAATATGCCGATTTTTTATACTTTT 18 45 1 TATGCCTTTT 0.972359 -256 ACGGCTTGCGTATTACGGTTTTCTACGCCAGT 19 74 0 TATTACTTTT 0.724446 -227 TTATTATTCTCTTTTTTAGCATACAA 20 87 0 TATTCTTTTT 0.705371 -16 ACGTATTCGCTATTCCATTTTTTCTTG 22 6 0 TATTCCTTTT 0.949804 -143 GCGAATACGTTATTCCATTTTTATTTTTGATA 22 28 1 TATTCCTTTT 0.949804 -121 AGAAAAACATTATTTCCTTTTTGTAAAATATG 25 84 1 TATTTCTTTT 0.598544 -201 ****** **** Masking position 10 Map Score: 7.87392 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 176 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 9 ATTCAAAATAAAGGCTTTTTTGTGCCATAT 4 72 0 AAGGCTTTTT 0.967135 -147 TCAGAAACTCTAGGCTTTTTTAATGTTCGA 9 70 0 TAGGCTTTTT 0.85934 -59 AAGCTTGAGAAAGGCTTTATAATTTGCCGC 10 212 1 AAGGCTTTAT 0.979257 -49 AATTTATAAAAAGGCTTTTTGCCAAAACTC 12 101 0 AAGGCTTTTT 0.967135 -87 GGTTGAAAATCAGGCTTTATAAAGATATAT 16 172 0 CAGGCTTTAT 0.935592 -94 CAATATTAATAAGGCTTTACCCTATTTTAT 21 26 1 AAGGCTTTAC 0.926138 -122 TTTCTGACTAAAGGCTTTATCTCTTAAAAA 25 59 0 AAGGCTTTAT 0.979257 -226 TATGTTTTAAAAGGTTTTATTATAGGGATT 28 166 0 AAGGTTTTAT 0.840555 -35 ********** Masking position 2 Map Score: 8.86226 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 47 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 TTTGTATTAGAATCCACGCCCCATTTAGTTAGT 2 32 0 AACCCGCCCA 0.782022 -135 TCTCCCTATAATGCCAACCCACAACATTAAGGG 3 138 0 ATCCACCCCA 0.616952 -163 CACATGGGGAAACCCCACACTACCATCGGCATT 7 33 0 AACCACACAC 0.924506 -268 TTGCTGGCTAAAGCCCACCCTACGTT 8 4 0 AACCACCCAC 0.964355 -89 CGGTGGGCTTAAGCCCACCCTACTTCCTATCAA 8 50 1 AACCACCCAC 0.964355 -43 CGAAGCGAGTAAATCTCCCCTACCCCTCTTTGC 15 49 1 AATCCCCCAC 0.950686 -252 CATTTCTGCCAAATCGCCCCTACCCCTCTTTGC 15 224 0 AATCCCCCAC 0.950686 -77 TGTCTCACCGAAATCAACACAAATTTTCCATTG 18 79 0 AATCACACAA 0.711634 -222 AAACTGATAAAATCCGCCACACATCGTTTGTGT 18 162 0 AACCCCACCA 0.932911 -139 TATTGTTCATAACCCGCACCAACACTATATTTT 21 81 1 AACCCACCAC 0.824852 -67 TTGCCATAAAAAACCGCCACGAAATTATCGTGG 24 160 0 AACCCCACAA 0.944144 -141 AAAGTGATAGAATTCGCCACGCATTTTTTGCCT 25 141 1 AATCCCACCA 0.817689 -144 ** ** **** ** Masking position 1 Map Score: 6.23032 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 86 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 11 ACCGGTATCGCCCACCACTTCTCTAAAAAGT 3 51 0 CCCCCACTTC 0.954779 -250 CATGGGGAAACCCCACACTACCATCGGCATT 7 33 0 CCCACACTAC 0.976109 -268 GCTGGCTAAAGCCCACCCTACGTT 8 4 0 GCCACCCTAC 0.972682 -89 GTGGGCTTAAGCCCACCCTACTTCCTATCAA 8 52 1 GCCACCCTAC 0.972682 -41 AGTAAATCTCCCCTACCCCTCTTTGCTAAAG 15 56 1 CCCACCCCTC 0.977582 -245 GCCAAATCGCCCCTACCCCTCTTTGCTAAAG 15 219 0 CCCACCCCTC 0.977582 -82 ATACGCCTCCCTCCACTACATCACATTAA 24 9 1 CCCCCACTAC 0.964903 -292 *** ******* Masking position 6 Map Score: 5.51881 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 4 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 12 AGCTAATAAAACATTTATAGGAATGTGACTTC 7 233 0 ACATTATAGA 0.811417 -68 TACGTTATGGTAATTGATAGGAAGTAGGGTGG 8 64 0 TAATTATAGA 0.761031 -29 CTAAGTACTAAAATTAATAGTAATTTTTTCAT 10 143 1 AAATTATAGA 0.961633 -118 CATATTTTTGAAATTTATAAAAAGGCTTTTTG 12 110 0 AAATTATAAA 0.846929 -78 TTTTCGTTACAAATTAATAACGTNTTTTATGT 13 82 1 AAATTATAAG 0.75569 -100 GTTTACCACCAAATTTATAGAGGTCTCTCAAT 14 21 0 AAATTATAGG 0.933386 -228 TAGAACAAAGGAATTCATAGCAAGCCAATATA 14 65 0 GAATTATAGA 0.825176 -184 CAAAAATTGAAAATTTATTGTAAAAAACAACT 14 107 1 AAATTATTGA 0.743792 -142 AAAATGGCAAAAATTAATAGGGAGAGAAATAA 14 157 0 AAATTATAGG 0.933386 -92 ATTCTTGAATAAATTGATAGTAACTGGCTCAT 15 93 1 AAATTATAGA 0.961633 -208 CCTTTTTTATAAATTAATAAGAAATTTTTATT 19 271 0 AAATTATAAA 0.846929 -30 ATACTTCAAGAAAGTGATAGAATTCGCCACGC 25 131 1 AAAGTATAGA 0.811417 -154 ***** **** * Masking position 7 Map Score: 6.00925 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 15 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 13 TGGCACAAAAAAGCCTTTATTTTGAATATTTA 4 75 1 AAGCTTATTT 0.803799 -144 TTTAAAGTCCAATACTTGATTTGGCAATGCT 6 10 0 AATCTGATTT 0.957872 -62 CTAGGTTAAAAATGCTATATTTAACGGAAACG 9 29 0 AATCTTATTT 0.89335 -100 AACATTAAAAAAGCCTAGAGTTTCTGATATGA 9 73 1 AAGCTGAGTT 0.806168 -56 ATATCTTTATAAAGCCTGATTTTCAACCGCAT 16 174 1 AAACCGATTT 0.716166 -92 AACTAACAACAATGCTAGATTTTAAAAGTCGT 18 277 0 AATCTGATTT 0.954458 -24 AACTAGAAAAAATCCCCTATTTAAAGTAAGAT 20 44 1 AATCCTATTT 0.839984 -59 AACCCGCACCAACACTATATTTTTATGGAAAA 21 91 1 AACCTTATTT 0.68953 -57 TTGCCATAGAAATACTAGATTTAAATAAAAGA 24 203 0 AATCTGATTT 0.954458 -98 ATTCAAGCGCAATGCCAGAGTTATCATAAATA 26 61 0 AATCCGAGTT 0.841147 -161 AGTTTTTACAAATCCTAGATTTATCAATTGAT 26 168 0 AATCTGATTT 0.954458 -54 *** ** ***** Masking position 9 Map Score: 5.80853 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 59 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 14 AATTTTTTAGAGGGAAAACAAA 1 2 0 AGGGAAACAA 0.840795 -101 CGTAAAATGAAATAAAAACAAACCGCACTTT 1 73 0 AATAAAACAA 0.488162 -30 TTTTCGTTGAAATGAAAACAACCTTATTCTA 2 131 0 AATGAAACAA 0.860932 -36 TTTTATTTAGAAGTCAAACAAGTCGTAGTAG 3 242 1 AAGTAAACAA 0.812044 -59 AAATTACGTTAAGGATAACCAC 4 2 0 AAGGTAACCA 0.754677 -217 AAATTGGCGCAAGTATAACAAAAAGTGCGGT 11 35 0 AAGTTAACAA 0.734091 -50 TATTTTTATTATGGGTAACAAGGATTCTTTT 12 165 1 ATGGTAACAA 0.800598 -23 ATTTTTAAATAAGAGAAACAAA 15 289 1 AAGAAAACAA 0.812045 -12 GACAGCTCCTAAAGTAAACAAAGAAAATAAA 19 246 1 AAAGAAACAA 0.710154 -55 ATTTATAAAAAAGGTAAACAAT 19 289 1 AAGGAAACAA 0.965568 -12 TTCCTTCATTAAGGTAAACTATCGGCAATTT 21 124 1 AAGGAAACTA 0.764605 -24 TTTGAATTAAAAGGATAACAACAA 23 20 1 AAGGTAACAA 0.947145 -14 TGACAAGGCTATTGATAACAATTATCATCTA 28 44 1 ATTGTAACAA 0.469867 -157 **** ****** Masking position 7 Map Score: 5.22699 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 120 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 15 ATTTCCTTACTTTTTTCGTTGAAATGAAAA 2 144 0 TTTTTTCGTT 0.660446 -23 ATATCATCAGATTTTTTGTTATATTATGCC 4 46 0 ATTTTTTGTT 0.520315 -173 AATTTCTCTTGTTTTTAAGGGTA 7 288 0 TTCTCTTGTT 0.931391 -13 AAAATTTTCCTGTTTAAATCTGAT 10 247 0 TTTTCCTGTT 0.720795 -14 TCAAAAAACAATTTCTTGTTAA 12 3 0 ATTTCTTGTT 0.866981 -185 GCATTGTGCCATTTTTCGTTACAAATTAAT 13 70 1 ATTTTTCGTT 0.568646 -112 AGTTGAGAGTAGCTCTCGTTTACA 13 168 1 AGCTCTCGTT 0.602733 -14 TAAATTCTTATTTTCTCGTTATCATTTCTG 15 249 0 TTTTCTCGTT 0.921181 -52 TTTGTTTCTCTTATTTAAAAATTCT 15 286 0 TTCTCTTATT 0.593027 -15 AATGCCGAAATTCTCTTATTTTC 17 22 1 TTCTCTTATT 0.593027 -13 ATAGGGGATTTTTTCTAGTTTGAAAAACTT 20 34 0 TTTTCTAGTT 0.602536 -69 ATAAAGGTTCATCTCCTGTTCTTGCCATAG 24 226 0 ATCTCCTGTT 0.711819 -75 TTTCTCTCGTTAAAATAAAAA 24 290 0 TTCTCTCGTT 0.942853 -11 TTTGCCTAATTTCGCTCGTTCAATGGTAGG 25 167 1 TTCGCTCGTT 0.691218 -118 TAGATAATTTATTTCTTGTTTTGTCATATT 26 18 1 ATTTCTTGTT 0.866981 -204 ********** Masking position 9 Map Score: 5.50712 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 216 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899