AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00650_hinf_reg_300.orf -o00650_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 HI0180 27 formate acetyltransferase (pfl) #2 HI0181 300 formate transporter #3 HI0195.1 26 conserved hypothetical transmembrane protein (aefA) #4 HI0197 84 penicillin-insensitive murein endopeptidase (mepA) #5 HI0199 46 lipid A biosynthesis (kdo)2-(lauroyl)-lipid IVA acyltransferase (msbB) #6 HI0301 300 hemolysin, putative #7 HI0774 205 acetate CoA-transferase, alpha subunit #8 HI0835 181 fumarate reductase, flavoprotein subunit (frdA) #9 HI0916 107 outer membrane protein, putative #10 HI0920 248 conserved hypothetical protein #11 HI1062 85 (3R)-hydroxymyristol (acyl carrier protein) dehydrase (fabZ) #12 HI1064 56 conserved hypothetical protein #13 HI1233 299 pyruvate dehydrogenase, E1 component (aceE) #14 HI1527 84 lipid A biosynthesis lauroyl acyltransferase (htrB) #15 HI1585 266 acetolactate synthase III large subunit (ilvI) #16 HI1586 300 conserved hypothetical integral membrane protein Motif number 1 ATTCCCCCAGATAATCATCCACTTTTC 2 2 0 AAATATTTTT 0.794719 -299 TGAGCGAATATTAATATGGGAATTTTGTCTTTAATT 2 104 1 TAATTGTTTT 0.835925 -197 AAAGTATTAAATTTTCATCAACTTTTTCAATGTCAA 2 259 1 ATTTATTTTT 0.88593 -42 AGTGCGGTTAAAATTAATTACATTTTATT 5 28 1 AATTATTTTT 0.891381 -19 GGATAACTTGTGAATAATGGATTTTTGATTGTGAAT 6 60 0 TAATATTTTT 0.717289 -241 TCATATAAACAAAATAAGAATATTTTGTTGTCTAGA 6 115 1 AAATAGTTTT 0.489464 -186 ATGTGCGGTTATTTTTTATTGATTTTCCTCTTTTCG 6 208 1 ATTTTATTTT 0.576957 -93 GATTTTTTCTAAAATATGATAATTTTTCGCCGTCAA 6 252 1 AAATTGTTTT 0.514829 -49 GGTATAAGTTATTTTGATAGTGTTTTAAACAATCCT 7 12 0 ATTTATTTTT 0.88593 -194 TTTACGAAATTCTTTTTGCTATTTTTAATATCAATC 7 70 1 TTTTTGTTTT 0.910877 -136 TACTCTCAACTCAATCTTAGCTTTTTTGAGGTAGAT 8 24 1 TAATTTTTTT 0.779322 -158 TTTTCGTTACAAATTAATAACGTTTTTATGTCTAA 8 85 0 AATTATTTT 0.0688472 -97 TATTGTGTGGGCATTGTGCCATTTTTCGTTACAAAT 8 107 0 GATTTGTTTT 0.816795 -75 CAATGCCCACACAATATTACCCTTTTAGGGGATTTA 8 127 1 AAATTTTTTT 0.843471 -55 GTGCGGTTAAAATTTAAGGTGATTTT 10 1 0 ATTTAGTTTT 0.918059 -248 CTCTCCCTATTAATTTTTGCCATTTTACGGTATTCT 10 71 0 TATTTTTTTT 0.887677 -178 AGTGCGGTGGTTTTTTAGTTGTTTTTTACAATAAAT 10 115 1 TTTTAGTTTT 0.880136 -134 TTTTTTACAATAAATTTTCAATTTTTGCAGAACAGA 10 136 1 TAATTTTTTT 0.778881 -113 GCTATATTGAGTGCGTTTTATTTTTAGCT 11 4 1 AATTAGTTTT 0.925921 -82 CGATAGATTTTATTTGTTTATTTTTTGTAAGGTATC 11 57 1 TTTTTTTTTT 0.876305 -29 GTTATTTTATAGAATAAGCCAATTTTTTAAGCCAGA 12 22 0 AAATAGTTTT 0.84733 -35 TTTGTTTTAAAGTTTTTTCAGATTTTTTTCAAAAAG 13 20 0 ATTTTTTTTT 0.915323 -280 AGTGCGGTAATTTTTTTGTGTTTTTTTGTTCGCTAA 13 88 0 TTTTTGTTTT 0.910877 -212 AAATCTTGTAAATTTTAGAAGATTTTTTGAGATAAA 13 185 0 ATTTAGTTTT 0.917703 -115 TGAATAACCAAAATTGTGGCGATTTTACCACAACTC 14 28 1 AATTTGTTTT 0.945634 -57 AAAATATTATTTTTTATTCAAATTTTTGAATGAGAT 15 18 0 TTTTTTTTTT 0.876305 -249 ATAAAAAATAATATTTTTACTATTTTATAAAATGCG 15 37 1 AATTTTTTTT 0.923421 -230 GCATTTTGTCGCATTTTTTTATTTTTATTGATGGAA 15 73 1 GATTTTTTTT 0.755523 -194 GAAAATTTAGTTTTTTATAAATTTTTCCATCAATAA 15 97 0 TTTTATTTTT 0.835789 -170 TTATATTTGGTTTTTTATATTTTTTTAATTGATTTT 15 135 1 TTTTATTTTT 0.835789 -132 TTTTTAATTGATTTTTTTGTTGTTTTAGTGGCTAGA 15 156 1 ATTTTTTTTT 0.915328 -111 AAACATTGACATAATCTGTTCGTTTTTTTAAAAGTG 15 219 1 AAATTGTTTT 0.885998 -48 ATATATTTTTTTGTGTTTATTTTCTTTATATTT 16 8 1 TTTTTGTTTT 0.910877 -293 ATGCCAACAGATTTTATAAAAATTTTATAAACTTTA 16 48 0 ATTTTATTTT 0.576955 -253 AAATCTGTTGGCATTTTGTTTGTTTTACGGTAATCT 16 70 1 GATTTGTTTT 0.816795 -231 AGGCGCAATTATTATAAGTATTTTTTCAGAGTGGAT 16 127 1 ATATAGTTTT 0.833523 -174 * *** ** **** Masking position 5 Map Score: 55.2089 Number of sites scoring better than the average of aligned sites = 1386 Number in coding regions = 998 Number in noncoding regions = 388 Number of orfs with sites within 600 bp upstream = 292 Fraction of orfs with sites within 600 bp upstream = 0.0469001 Motif number 2 ATTAATTTTAACCGCACTTTTGCGCGCTTT 5 16 0 ACCGCACTTT 0.996023 -31 TGTATTTTTAACCGCACTTTAGGTTTAAAC 6 175 1 ACCGCACTTT 0.996023 -126 ATAAAAAATAACCGCACATTGGGTTTAAAC 6 197 0 ACCGCACATT 0.966675 -104 TTAAATTTTAACCGCACTTTTGCAGCATTT 10 20 1 ACCGCACTTT 0.996023 -229 CCGCACTTTTGCAGCATTTTGACAATAGAA 10 31 1 GCAGCATTTT 0.884362 -218 GGTATTCTATGCCACATTTTCTATTGTCAA 10 49 0 GCCACATTTT 0.936745 -200 CTAAAAAACCACCGCACTTTTTATTTCTCT 10 103 0 ACCGCACTTT 0.996023 -146 CAAAAAAATTACCGCACTTTCAAATAATTA 13 106 1 ACCGCACTTT 0.996023 -194 TGGTAAAATCGCCACAATTTTGGTTATTCA 14 28 0 GCCACAATTT 0.818219 -57 GCGACAAAATGCCGCATTTTATAAAATAGT 15 55 0 GCCGCATTTT 0.990705 -212 GCGGCATTTTGTCGCATTTTTTTATTTTTA 15 70 1 GTCGCATTTT 0.884362 -197 CCTTAAATTCACCGCACTTTTAAAAAAACG 15 239 0 ACCGCACTTT 0.996023 -28 ********** Masking position 6 Map Score: 32.1286 Number of sites scoring better than the average of aligned sites = 1299 Number in coding regions = 834 Number in noncoding regions = 465 Number of orfs with sites within 600 bp upstream = 302 Fraction of orfs with sites within 600 bp upstream = 0.0485063 Motif number 3 AATTAAGTACTTTACTTACTCTGAATGTATGAAATT 2 69 1 TTTATTATTT 0.525781 -232 AATATTCTTATTTTGTTTATATGACGAAAAGTATCT 6 103 0 TTTTTTTTTG 0.951984 -198 AATGTGCGGTTATTTTTTATTGATTTTCCTCTTTTC 6 207 1 TATTTTTTGT 0.565086 -94 TTCTTTTTGCTATTTTTAATATCAATCTAGTTCCTT 7 79 1 TATTTTATTT 0.662338 -127 TATTTGTTGATATTCTTTCTTTTAATCTCGTTATTA 7 170 1 TATTTTTTTT 0.83526 -36 ATTAATAACGTTTTTATGTCTAAAGATGGAAAGT 8 73 0 TTTTATTTG 0.20625 -109 GGGATTTATTTTTACTTTCTATTGATTGGAGGATAT 8 155 1 TTTATTTTTT 0.741323 -27 CCACCGCACTTTTTATTTCTCTCCCTATTAATTTTT 10 89 0 TTTTTTTTTT 0.957834 -160 TATTTTTATTATTGAGAGACCTCTAT 10 233 0 TATTTTATTG 0.631274 -16 ATTGAGTGCGTTTTATTTTTAGCTATAAATATCGTA 11 16 1 TTTTTTTTGT 0.853399 -70 ATCCGATAGATTTTATTTGTTTATTTTTTGTAAGGT 11 54 1 TTTTTTTTTT 0.957834 -32 AAGTGCGGTAATTTTTTTGTGTTTTTTTGTTCGCTA 13 89 0 ATTTTTTTTT 0.571519 -211 AGGTTTTCCTTAATCTGTTTTGAGTGAATA 13 280 0 TTTCTTATTT 0.714132 -20 TGTCGCATTTTTTTATTTTTATTGATGGAAAAATTT 15 79 1 TTTTTTTTTT 0.957834 -188 AAAACTAAATTTTCATTTATATTTGGTTTTTTATAT 15 119 1 TTTCTTTTTG 0.849302 -148 GTTTTTTATATTTTTTTAATTGATTTTTTTGTTGTT 15 144 1 TTTTTTATGT 0.692508 -123 TAATTGATTTTTTTGTTGTTTTAGTGGCTAGACAAA 15 160 1 TTTTTTGTTG 0.702397 -107 CTAGACAAATTTTTTTTACTTTGTATTATGTGAAAC 15 187 1 TTTTTTATTT 0.897837 -80 TTTGTGTTTATTTTCTTTATATTTTTATTAAAGTTT 16 20 1 TTTTTTTTTT 0.957834 -281 TCTGTTGGCATTTTGTTTGTTTTACGGTAATCTCCC 16 73 1 TTTTTTTTTG 0.951984 -228 CAACTATTCCTTTCTTTTTTCTTCTTCGTTATCCAC 16 157 0 TTTCTTTTTT 0.8659 -144 ACAAAACGACTTTTATTTGATTTCGGCAACTATTCC 16 183 0 TTTTTTTATG 0.549305 -118 ATAAAAGTCGTTTTGTTTGGTTGGTGGCGTGCTCGA 16 203 1 TTTTTTTGTG 0.643672 -98 **** *** * * * Masking position 6 Map Score: 22.2135 Number of sites scoring better than the average of aligned sites = 534 Number in coding regions = 327 Number in noncoding regions = 207 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 4 ATGTAATTAATTTTAACCGCACTTTTGCGC 5 21 0 TTTTAACCGC 0.96541 -26 AATTGTGTATTTTTAACCGCACTTTAGGTT 6 170 1 TTTTAACCGC 0.96541 -131 AATCAATAAAAAATAACCGCACATTGGGTT 6 202 0 AAATAACCGC 0.9812 -99 TCAAAATAACTTATACCCGCCTAAGAAAGA 7 31 1 TTATACCCGC 0.889306 -175 TCACCTTAAATTTTAACCGCACTTTTGCAG 10 15 1 TTTTAACCGC 0.96541 -234 AACAACTAAAAAACCACCGCACTTTTTATT 10 108 0 AAACCACCGC 0.873503 -141 TTATTCTATAAAATAACCGCTCAAGA 12 41 1 AAATAACCGC 0.9812 -16 AAACACAAAAAAATTACCGCACTTTCAAAT 13 101 1 AAATTACCGC 0.915509 -199 TCACTCCTTAAATTCACCGCACTTTTAAAA 15 244 0 AATTCACCGC 0.959983 -23 ********** Masking position 7 Map Score: 9.64801 Number of sites scoring better than the average of aligned sites = 382 Number in coding regions = 221 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 5 AATGAAAGGGGAGGAGAGTAAAATAGCACCAATT 2 195 1 GAAGGAAAAT 0.988414 -106 TTACCATTTAGATTAGGGAAAAATA 3 12 1 GAAGGAAAAT 0.988414 -15 CAATTTTTACGGAGAGGGGAAAATTCTAGACAAC 6 141 0 GGAGGAAAAT 0.957733 -160 CGCAAAACGCGAAAAGAGGAAAATCAATAAAAAA 6 219 0 GAAGGAAAAT 0.988414 -82 ATAAATCCCCTAAAAGGGTAATATTGTGTGGGCA 8 130 0 TAAGGAATAT 0.777164 -52 ATGTGGCATAGAATACCGTAAAATGGCAAAAATT 10 62 1 GAACGAAAAT 0.981286 -187 GGCTAAACACGAATACGGCAATATTTGCTTTTCA 13 233 0 GAACGAATAT 0.950486 -67 TGATTGGGGAGATTACCGTAAAACAAACAAAATG 16 81 0 GAACGAAAAC 0.933008 -220 ** ** * ***** Masking position 5 Map Score: 6.06176 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 31 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 6 TAAACAAACCTTGCAAAATATCAAAGTTTGTT 2 139 1 TTAAAATATC 0.775859 -162 TTATCATATTTTAGAAAAAATCGCAAAACGCG 6 242 0 TTAAAAAATC 0.960692 -59 TTTGATAGTGTTTTAAACAATCCTT 7 4 0 TTAAACAATC 0.732715 -202 TTGATAAATATCCTTAATTAAA 9 96 0 TTTAAATATC 0.510417 -12 TGAAAATTTATTGTAAAAAACAACTAAAAAAC 10 124 0 TTAAAAAACA 0.67309 -125 GTTGATACCTTACAAAAAATAAACAAATAAA 11 65 0 TTAAAAAATA 0.938176 -21 AATTGGCTTATTCTATAAAATAACCGCTCAAG 12 34 1 TTATAAAATA 0.820482 -23 TGAGTCCTTTTTGAAAAAAATCTGAAAAAACT 13 14 1 TTAAAAAATC 0.960692 -286 ACTATCTTTATCTCAAAAAATCTTCTAAAATT 13 179 1 TCAAAAAATC 0.892572 -121 ATTCAAAAATTTGAATAAAAAATAATATTTTT 15 23 1 TTATAAAAAA 0.513894 -244 AAATGCCGCATTTTATAAAATAGTAAAAATAT 15 47 0 TTATAAAATA 0.820389 -220 AATTTTTCCATCAATAAAAATAAAAAAATGCG 15 82 0 TCTAAAAATA 0.608424 -185 GATGGAAAAATTTATAAAAAACTAAATTTTCA 15 102 1 TTTAAAAAAC 0.629986 -165 AAAAAAATCAATTAAAAAAATATAAAAAACCA 15 142 0 ATAAAAAATA 0.534543 -125 TTCACCGCACTTTTAAAAAAACGAACAGATTA 15 230 0 TTAAAAAAAC 0.849694 -37 TTTATAAACTTTAATAAAAATATAAAGAAAAT 16 29 0 TTTAAAAATA 0.820484 -272 TTTATAAAATTTTTATAAAATCTGTTGGCATT 16 53 1 TTATAAAATC 0.880396 -248 CGTTATCCACTCTGAAAAAATACTTATAATAA 16 135 0 TCAAAAAATA 0.837632 -166 ** ******** Masking position 7 Map Score: 13.3342 Number of sites scoring better than the average of aligned sites = 601 Number in coding regions = 447 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 7 AGACATCAAACACAAATCAAT 6 290 1 CACAAATCAA 0.972647 -11 GAGAGCTACTCTCAACTCAATCTTAGCTTT 8 18 1 CTCAACTCAA 0.949188 -164 GATATCCTCCAATCAATAGAAAGTAA 8 166 0 CTCCAATCAA 0.949189 -16 TTTTCTTCATCAGAACTCAAAAACAACGTT 9 23 1 CAGAACTCAA 0.924989 -85 GCGATTTTACCACAACTCAAATTTACGATA 14 46 1 CACAACTCAA 0.972109 -39 ACGGTAATCTCCCCAATCACTACAAAAGTA 16 96 1 CCCCAATCAC 0.884724 -205 GGAATAGTTGCCGAAATCAAATAAAAGTCG 16 183 1 CCGAAATCAA 0.91251 -118 TCGAGCACGCCACCAACCAAACAAAACGAC 16 209 0 CACCAACCAA 0.902511 -92 ********** Masking position 5 Map Score: 3.44316 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 65 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 ATTCCCATATTAATATTCGCTCAATTTCAT 2 97 0 TAATATTCGC 0.938045 -204 TTTGTTGAAATAATTTTTGCTTTTCTTTGC 2 165 1 TAATTTTTGC 0.961747 -136 TAAAAATACACAATTTTTACGGAGAGGGGA 6 155 0 CAATTTTTAC 0.825884 -146 ATGATGGGTTTAATATTTTCTCTGCCCAAT 9 67 0 TAATATTTTC 0.800706 -41 CTCTCCCTATTAATTTTTGCCATTTTACGG 10 77 0 TAATTTTTGC 0.961747 -172 AATAAATTTTCAATTTTTGCAGAACAGATT 10 144 1 CAATTTTTGC 0.953998 -105 ACGAATACGGCAATATTTGCTTTTCACAAA 13 229 0 CAATATTTGC 0.962335 -71 TTGTCTAAACTAATATTCACTCAAAACAGA 13 267 1 TAATATTCAC 0.77594 -33 AAAATACTTATAATAATTGCGCCTCTACTT 16 121 0 TAATAATTGC 0.830018 -180 ********** Masking position 4 Map Score: 7.04087 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 162 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 TATAATTGGTGCTATTTTACTCTCCTCCCC 2 202 0 GCTATTTTAC 0.96232 -99 TTCGCGTTTTGCGATTTTTTCTAAAATATG 6 240 1 GCGATTTTTT 0.883317 -61 AATTCTTTTTGCTATTTTTAATATCAATCT 7 77 1 GCTATTTTTA 0.830338 -129 TGGGCATTGTGCCATTTTTCGTTACAAATT 8 106 0 GCCATTTTTC 0.975311 -76 ATTAATTTTTGCCATTTTACGGTATTCTAT 10 69 0 GCCATTTTAC 0.975311 -180 CAAAATTGTGGCGATTTTACCACAACTCAA 14 36 1 GCGATTTTAC 0.975311 -49 ********** Masking position 5 Map Score: 2.75756 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 81 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 10 ATTACGCGAATAAAACAAGTTTCAAATTAAGT 2 45 1 TAAACAAGTT 0.799169 -256 TTGTCTTTAATTAAACAAACCTTGCAAAATAT 2 128 1 TTAACAAACT 0.961586 -173 CAAAAATTATTTCAACAAACTTTGATATTTTG 2 152 0 TTAACAAATT 0.875977 -149 ATTTAATACTTTTAACAAGTTTACGACTACAA 2 239 0 TTAACAAGTT 0.853498 -62 TATACTTACCTACAGCAAAACTTTAGA 4 68 1 TAAGCAAACT 0.880266 -17 TGATAGTGTTTTAAACAATCCTT 7 2 0 TTAACAATCT 0.838628 -204 GAAAAAACTTTAAAACAAAGCCCGATGGAATG 13 37 1 TAAACAAACC 0.780978 -263 AATAATTATTTATGGCAAAGCTGATTTGATAT 13 128 1 TAGGCAAACT 0.759683 -172 TTCACAAACATTTAACAAATCTTGTAAATTTT 13 205 0 TTAACAAACT 0.961586 -95 GAATATTAGTTTAGACAAGGCTAAACACGAAT 13 253 0 TTGACAAGCT 0.898766 -47 ** ****** ** Masking position 7 Map Score: 2.22735 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 104 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 11 CGCACTTTTGCGCGCTTTCCGAA 5 2 0 CGCCTTTCGA 0.983999 -45 GATCTTTGCCCTCTTTTTACGAGATCAATTCA 6 33 1 CTCTTTTCGA 0.936228 -268 TTCCTCTTTTCGCGTTTTGCGATTTTTTCTAA 6 232 1 CGCTTTTCGA 0.986765 -69 GGAAAGTATCGGATTTTGTGATCTACCTCAA 8 49 0 CGGTTTTTGA 0.920372 -133 TAAAATCTATCGGATTATACGATATTTATAGC 11 37 0 CGGTTATCGA 0.877692 -49 TTTAAAATCTCTCTATTTGAATAACCAAAA 14 9 1 CTCCTATTGA 0.660751 -76 GACAAAATGCCGCATTTTATAAAATAGTAAAA 15 51 0 CGCTTTTTAA 0.809071 -216 GGCATTTTGTCGCATTTTTTTATTTTTATTGA 15 72 1 CGCTTTTTTA 0.809071 -195 ATGACAGTGTCGCCCCTTTCGAGCACGCCACC 16 225 0 CGCCCTTCGA 0.93493 -76 *** **** *** Masking position 8 Map Score: 2.48364 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 239 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 12 CATTGTGCCATTTTTCGTTACAAATTAATA 8 102 0 TTTTTCGTTA 0.752983 -80 TAAATTGAACTTTTTTCTTCATCAGAACTC 9 11 1 TTTTTTCTTC 0.969224 -97 TGTTTTTTCCTTCTGGCTTAAAA 12 4 1 TTTTTCCTTC 0.968621 -53 TTTTTTGTGTTTTTTTGTTCGCTAAAATAA 13 83 0 TTTTTTGTTC 0.959962 -217 AAAAATATTATTTTTTATTCAAATTTTTGA 15 25 0 TTTTTTATTC 0.857847 -242 TTTTTATAAATTTTTCCATCAATAAAAATA 15 92 0 TTTTTCCATC 0.846902 -175 TTTAATTGATTTTTTTGTTGTTTTAGTGGC 15 158 1 TTTTTTGTTG 0.821726 -109 TATTCCTTTCTTTTTTCTTCTTCGTTATCC 16 159 0 TTTTTTCTTC 0.969224 -142 ********** Masking position 5 Map Score: 5.48254 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 115 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 13 TCCCCTTTCATTGCAAAGAAAAGCAAAAAT 2 177 0 TTGCAAAGAA 0.799583 -124 CGTAAAAAGAGGGCAAAGATCCTTATCACA 6 24 0 GGGCAAAGAT 0.948621 -277 CAATTAAATTAGGCAGAGAACGTTGTTTTT 9 41 0 AGGCAGAGAA 0.958546 -67 TAATTTAATTGGGCAGAGAAAATATTAAAC 9 60 1 GGGCAGAGAA 0.972802 -48 ATAGAAAATGTGGCATAGAATACCGTAAAA 10 55 1 TGGCATAGAA 0.915676 -194 TACCGTAAAATGGCAAAAATTAATAGGGAG 10 75 1 TGGCAAAAAT 0.713215 -174 AAAAATTAATAGGGAGAGAAATAAAAAGTG 10 89 1 AGGGAGAGAA 0.792836 -160 TAATTATTTATGGCAAAGCTGATTTGATAT 13 130 1 TGGCAAAGCT 0.85539 -170 ********** Masking position 5 Map Score: 0.677573 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 146 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 14 AGATTTATTTATTAATTAACAA 1 1 1 AGATTATTTT 0.955493 -27 CACCAATTATAGAAGTATTTGTAGTCGTAAAC 2 221 1 AGAGTATTTT 0.95366 -80 CGCCTAAGAAAGATGTATTTCTTTTACGAAAT 7 48 1 AGAGTATTTT 0.954026 -158 GAAATATAAGATACTTATTTGTTGATATTCTT 7 155 1 ATATTATTTT 0.932747 -51 CCCTTTTAGGGGATTTATTTTTACTTTCTATT 8 146 1 GGATTATTTT 0.854013 -36 GCACTTTCAAATAATTATTTATGGCAAAGCTG 13 119 1 ATATTATTTT 0.906276 -181 ATATATTTTTTTGTGTTTATTTTC 16 3 1 ATATTTTTTT 0.713338 -298 CGCAATTATTATAAGTATTTTTTCAGAGTGGA 16 130 1 ATAGTATTTT 0.92954 -171 *** ****** * Masking position 3 Map Score: 4.12206 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 38 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 15 ********** No masking Map Score: -2.42762e-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