AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00251_hinf_reg_300.orf -o00251_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: HI0221.1 109 H. influenzae predicted coding region HI0221.1 HI1739.2 29 glutamate racemase (murI) Input sequences: #1 HI0161 215 glutathione reductase (gor) #2 HI0162 93 lipoprotein, putative #3 HI0189 300 glutamate dehydrogenase (gdhA) #4 HI0221 129 inosine-5'-monophosphate dehydrogenase (guaB) #5 HI0222 109 GMP synthase (guaA) #6 HI0274 300 glutamyl-tRNA synthetase (gltX) #7 HI0429 111 glucosamine--fructose-6-phosphate aminotransferase (glmS) #8 HI0431 35 conserved hypothetical protein #9 HI0432 66 conserved hypothetical protein #10 HI0433 75 orfG protein #11 HI0439 98 competence protein A (comA) #12 HI0596 300 ornithine carbamoyltransferase (arcB) #13 HI0865 230 glutamine synthetase (glnA) #14 HI1205 214 conserved hypothetical protein #15 HI1206 86 colicin V production protein (cvpA) #16 HI1354 300 glutaminyl-tRNA synthetase (glnS) #17 HI1615 160 phosphoribosylaminoimidazole carboxylase, catalytic subunit (purE) #18 HI1616 69 phosphoribosylaminoimidazole carboxylase, ATPase subunit (purK) #19 HI1617 138 aspartate aminotransferase (aspC) #20 HI1741 260 guanosine-3',5'-bis(diphosphate) 3'- pyrophosphohydrolase (spoT) #21 HI1742 62 DNA-directed RNA polymerase, omega chain (rpoZ) #22 HI1743 249 guanylate kinase (gmk) Motif number 1 TTTGCTGTTTAAAGTGCGGTTGGTTTTTGC 5 37 1 AAAGTGCGGT 0.99794 -73 CCCCTCCTTGTAAGGGAGGTGCTCTCCCAA 6 96 1 TAAGGGAGGT 0.800146 -205 CCCACAACATTAAGGGCGATTAGCTCAGTT 6 124 0 TAAGGGCGAT 0.884246 -177 CGCACTTTCAAAAGTGCGGTCATTATAAAT 9 27 0 AAAGTGCGGT 0.99794 -40 CGCACTTTTGAAAGTGCGGTTATTTTTATG 9 39 1 AAAGTGCGGT 0.99794 -28 ACTGGAAAAAAAAGCGCGATAAGCGTATTA 10 19 1 AAAGCGCGAT 0.951175 -57 TAGCGTATGATAAGTGCGGTCAATTTTTGA 14 186 1 TAAGTGCGGT 0.992383 -29 ATAAATGCACAAAGTGCGGTAAGTTTTTTG 16 124 0 AAAGTGCGGT 0.99794 -177 CCGCACTTTAAAAGTGCGGTCAGATCTAAA 18 18 0 AAAGTGCGGT 0.99794 -52 CCGCACTTTTAAAGTGCGGTTGTTTTTTTC 18 29 1 AAAGTGCGGT 0.99794 -41 TATTCATCAAAAAGTGCGGTCATTTTTTAC 19 12 0 AAAGTGCGGT 0.99794 -127 TAAAAATATCAAAGCGTGGTTAATTTTTAT 19 44 1 AAAGCGTGGT 0.910889 -95 TCTTTTAAAAGTGCGGTAAAAAATAAA 20 8 1 AAAGTGCGGT 0.99794 -253 TACTCTATTGAAAGGGCGTTATAATACTCA 21 19 0 AAAGGGCGTT 0.941526 -44 AAAATCATCAAAAGTGCGGTGATTTTTTAC 22 176 0 AAAGTGCGGT 0.99794 -74 ********** Masking position 3 Map Score: 50.5235 Number of sites scoring better than the average of aligned sites = 1262 Number in coding regions = 816 Number in noncoding regions = 446 Number of orfs with sites within 600 bp upstream = 302 Fraction of orfs with sites within 600 bp upstream = 0.0485063 Motif number 2 TCTATCACGCTATTTCATTCTACATACTAGGC 1 54 1 TATTTCATTA 0.52607 -162 ATTCTGCCTAATTTTTATAAAGAATGCTATAA 1 160 0 ATTTTTATAG 0.912412 -56 CTAATTTTGTTTTTTCATAAAACATATTTTCG 3 12 1 TTTTTCATAA 0.87249 -289 TCTGCTCTATATTTTTATTGAAAATATCATTA 3 73 1 ATTTTTATAA 0.935239 -228 TCGTTTTTTATTTTTTATCTAATAAATACGAT 3 120 1 TTTTTTATAA 0.944744 -181 TCTTGCAACCATTTTTATAAAGGAAATTTAAA 3 186 0 ATTTTTATAG 0.912412 -115 TGTGTATTGTATTTTTATTGTATTCGCCTCGT 3 252 0 ATTTTTATTA 0.868765 -49 TTATGCTATGATTTTCATACTATTTGCCATAA 4 18 0 ATTTTCATTA 0.725994 -112 AAGTTTTCTTAATTTTACTAAGTTTGACCAAG 6 23 0 AATTTTACAG 0.551224 -278 CAGTCAATACCTTTTTATTAAATTTTGTTTAA 6 180 1 CTTTTTATAA 0.632231 -121 TTTTATGCTTATTTTTACGACAATTAAACAAA 6 203 0 ATTTTTACCA 0.705261 -98 TAAAATCCGCTTTTTTATTTAGAAGTCAAACA 6 230 1 TTTTTTATAG 0.925001 -71 TAACGACTAATATTTTATTGAAGATAGGTTAT 6 275 1 TATTTTATAA 0.85816 -26 TGCGCAGGGGTTTTTTATTGTGTAAACGCGTG 7 44 1 TTTTTTATTG 0.849705 -68 AAGTGCGGTTATTTTTATGGAGAAAAA 9 50 1 ATTTTTATAG 0.912414 -17 AGAGTTAGATTATTTTATTAAATTCTAATAAT 12 114 1 TATTTTATAA 0.858155 -187 CAGTATGTAGAATTTTATTGCGAGATTTTTAG 12 147 0 AATTTTATCG 0.647024 -154 AACGACAACAAATTTCATTTTACCTCTCTTAT 12 195 1 AATTTCATTA 0.483888 -106 ATAAGATGCAATTTTTATTGCATTGTTACATA 13 30 1 ATTTTTATCA 0.877769 -201 CATTGCGCCATTTTTTATGTAACAATGCAATA 13 45 0 TTTTTTATAA 0.944744 -186 GCCATGCTATTTTTTCATGAAATTTATTTTTC 13 157 0 TTTTTCATAA 0.872501 -74 AAATTAAACTATTTTTACTAAAAATAGACTTA 14 151 1 ATTTTTACAA 0.827942 -64 TAAACGGCCGTTTTTCATTGAGAGATTTTTTA 15 65 1 TTTTTCATAG 0.831547 -22 TTCGTGGCGGTTTTTTATGGCAAGTTTTTACA 16 170 1 TTTTTTATCA 0.894761 -131 GTTTTTACAATCTTTTATTTAAATCTAGTATT 16 193 1 TCTTTTATAA 0.557865 -108 AGCCGAATATTTTTTTATTTTAACGAGAGAAA 16 279 1 TTTTTTATTA 0.886846 -22 CCTAAGCACAATTTTTATAAGAATAGGTCAAA 17 13 0 ATTTTTATGA 0.579931 -148 TTAAGGATAAAATTTTATCCTAAGCACAATTT 17 31 0 AATTTTATTA 0.700823 -130 AGCGTGGTTAATTTTTATAAAATCTTTCTTGA 19 56 1 ATTTTTATAA 0.935222 -83 TCAGTCATTTTATTTTATCAAGAAAGATTTTA 19 73 0 TATTTTATAG 0.813582 -66 AATACCTTTATTTTTTACCGCACTTTTAAAAG 20 12 0 TTTTTTACCA 0.739105 -249 AAAATAAAGGTATTTTACCGCGGGTAGGTATA 20 30 1 TATTTTACCG 0.419661 -231 TAGCACGAGCATTTTTATAAAACTATAAACCC 22 93 1 ATTTTTATAA 0.935222 -157 TTTACGGTACTTTTTCATTCTAATGATGATTT 22 149 0 TTTTTCATTA 0.758273 -101 AGTGCGGTGATTTTTTACGGTACTTTTTCATT 22 162 0 TTTTTTACTA 0.723108 -88 CTTTTGATGATTTTTTATAGAGAAATCTGCAT 22 192 1 TTTTTTATAG 0.925 -58 ******** ** Masking position 7 Map Score: 37.4396 Number of sites scoring better than the average of aligned sites = 899 Number in coding regions = 531 Number in noncoding regions = 368 Number of orfs with sites within 600 bp upstream = 271 Fraction of orfs with sites within 600 bp upstream = 0.0435271 Motif number 3 GCTGTTTAAAGTGCGGTTGGTTTTTGCAAAGTT 5 40 1 GTGCGGTGTT 0.993679 -70 ACTTTCAAAAGTGCGGTCATTATAAATCTTCTT 9 21 0 GTGCGGTAAT 0.98452 -46 ACTTTTGAAAGTGCGGTTATTTTTATGGAGAAA 9 42 1 GTGCGGTATT 0.996799 -25 ACGTTATAATGTGCGCTTATCTTAATAAGACTA 13 190 1 GTGCGCTATT 0.96815 -41 CGTATGATAAGTGCGGTCAATTTTTGAGGTGTT 14 189 1 GTGCGGTATT 0.996799 -26 TTGTAGAATAGCTCGGTCGTTTTAAACGGCCGT 15 43 1 GCTCGGTGTT 0.765864 -44 AATGCACAAAGTGCGGTAAGTTTTTTGAATGTT 16 118 0 GTGCGGTATT 0.996799 -183 CACTTTAAAAGTGCGGTCAGATCTAAAGATGTT 18 12 0 GTGCGGTATC 0.981636 -58 CACTTTTAAAGTGCGGTTGTTTTTTTCGTAAAT 18 32 1 GTGCGGTGTT 0.993679 -38 TCATCAAAAAGTGCGGTCATTTTTTACA 19 6 0 GTGCGGTATT 0.996799 -133 AAATATCAAAGCGTGGTTAATTTTTATAAAATC 19 47 1 GCGTGGTATT 0.866302 -92 TCTTTTAAAAGTGCGGTAAAAAATAAAGGTATT 20 11 1 GTGCGGTAAA 0.880474 -250 ATCATCAAAAGTGCGGTGATTTTTTACGGTACT 22 170 0 GTGCGGTATT 0.996799 -80 ******* * ** Masking position 7 Map Score: 32.2989 Number of sites scoring better than the average of aligned sites = 911 Number in coding regions = 587 Number in noncoding regions = 324 Number of orfs with sites within 600 bp upstream = 236 Fraction of orfs with sites within 600 bp upstream = 0.0379056 Motif number 4 ATTCTTTATAAAAATTAGGCAGAATACAAAAAAAT 1 167 1 AAAATAGAAT 0.81476 -49 GAATACAAAAAAATTTTAGTTTAAAAAAGGTTCAA 1 188 1 AAATTTGAAA 0.902315 -28 GTTCTCCACAAAAACTAAAATGAAACGCTATACAT 2 16 1 AAAATAAAAA 0.853773 -78 TTTATAAAGGAAATTTAAAGAAAAGGAAAAAGTAA 3 170 0 AAATTAAAAG 0.412768 -131 AATAGTATGAAAATCATAGCATAAATCCTAAAATT 4 26 1 AAATATGAAA 0.786676 -104 TTTCGTTTTCAAAATAAAGTGAAATCTGTATAATC 4 59 1 AAAAAAGAAT 0.637155 -71 CATATTATTTAAAACTTTGCAAAAACCAACCGCAC 5 50 0 AAAATTGAAA 0.934201 -60 ACAATTAAACAAAATTTAATAAAAAGGTATTGACT 6 181 0 AAAATTAAAA 0.807938 -120 TAATTGTCGTAAAAATAAGCATAAAATCCGCTTTT 6 209 1 AAAATAGAAA 0.951705 -92 AACGCGTGGCAAATGTAAAAACAAACTTAGTAATA 7 68 1 AAATTAAAAA 0.791607 -44 CCTCTTCATCAAAAATAAACTAAAACATATTTTCG 12 37 1 AAAATAAAAA 0.853773 -264 ATTGTTACATAAAAAATGGCGCAATGAATTGCACC 13 51 1 AAAAATGAAT 0.558528 -180 TAATTTTTCAAAAAATACGATAAAGTTTGTATTTT 14 122 0 AAAATAGAAG 0.784782 -93 TATTTTTACTAAAAATAGACTTAAAATAGCGTATG 14 160 1 AAAATAAAAA 0.853773 -55 GCCAAAAAGAAAACGTTTGCGTAAA 15 1 0 AAACTTGAAA 0.779984 -86 CTATTCTACAAAAATAAAGCCAAAAAGAAAACGTT 15 19 0 AAAAAAGAAA 0.887227 -68 AGATTTAAATAAAAGATTGTAAAAACTTGCCATAA 16 184 0 AAAAATGAAA 0.850035 -117 TATTCTATACAAATCTAAGGGAAAATAAAGGTTCA 16 245 0 AAATTAGAAA 0.927644 -56 ATACCATTGCAACTTTAAGGATAAAATTTTATCCT 17 42 0 AACTTAGAAA 0.505917 -119 TATATCAGGCAAACGTTTGCTAAATGGCTTTTATA 17 82 0 AAACTTGAAT 0.441738 -79 ATTTCTCGTTAAATTTACGAAAAAAACAACCGCAC 18 42 0 AAATTAGAAA 0.927644 -28 TGATATTTTTAAATATTCATCAAAAAGTGCGGTCA 19 20 0 AAATTTAAAA 0.732392 -119 TCTTTTAAAAGTGCGGTAAAAAATAAAGGTA 20 7 1 AAAATGGAAA 0.727796 -254 TGTTTAACTTAAATAAAAGGTGAAAATCT 22 5 0 AAATAAGAAA 0.83656 -245 ATTTCTCTATAAAAAATCATCAAAAGTGCGGTGAT 22 183 0 AAAAATAAAA 0.626788 -67 **** ** * *** Masking position 13 Map Score: 18.6597 Number of sites scoring better than the average of aligned sites = 1078 Number in coding regions = 759 Number in noncoding regions = 319 Number of orfs with sites within 600 bp upstream = 248 Fraction of orfs with sites within 600 bp upstream = 0.039833 Motif number 5 GTGAGGAAGATTGAACAATCTTCCTCTTTTTCTATCACGCT 1 24 1 TGAATTTTTT 0.532392 -192 AAATATGATTTGTAATCTGCTCTATATTTTTATTGAAAATA 3 58 1 TTAACTTTTT 0.932628 -243 TTATTTTTTATCTAATAAATACGATATTTTTTAGATAATTT 3 127 1 TTAACTTTTT 0.932628 -174 CAATGGCTAATTTAATCTTGCAACCATTTTTATAAAGGAAA 3 192 0 TTAAATTTTT 0.802327 -109 GTGAAATCTGTATAATCTCGTCGCAATATTTTTTAACTTCA 4 77 1 TTAACTATTT 0.927105 -53 CCTTTTGCTGTTTAAAGTGCGGTTGGTTTTTGCAAAGTTTT 5 34 1 TTAAGTTTTT 0.696824 -76 TTATTGATAGTGTAAGCGGTTCATATTATTTAAAACTTTGC 5 65 0 TTAACTATTT 0.927105 -45 CCACCACTTCTCTAAAAAGTTTTCTTAATTTTACTAAGTTT 6 30 0 TTAATAATTT 0.283622 -271 CAAGTCGTAGTAGAATAACGACTAATATTTTATTGAAGATA 6 260 1 TGAACATTTT 0.754666 -41 AATAAAATAATCTAACTCTTTATTGTTATTTGTTTGATTTC 12 92 0 TTAAATATTT 0.788546 -209 GCATTACCAGTTGAAAAACGACAACAAATTTCATTTTACCT 12 179 1 TGAACAATTT 0.738643 -122 CTGCTATGACTAGAATAAGAAAAATAAATTTCATGAAAAAA 13 139 1 TGAAAAATTT 0.453152 -92 AAGCGCACATTATAACGTAGCCATGCTATTTTTTCATGAAA 13 167 0 TTAACTATTT 0.927105 -64 ATCGTATTTTTTGAAAAATTAAACTATTTTTACTAAAAATA 14 136 1 TGAAATTTTT 0.756694 -79 AAAACGGCCGTTTAAAACGACCGAGCTATTCTACAAAAATA 15 38 0 TTAACTATTC 0.525358 -49 TAGATTTGTATAGAATAGCCGAATATTTTTTTATTTTAACG 16 263 1 TGAAATTTTT 0.756693 -38 AGGATAAAATTTTATCCTAAGCACAATTTTTATAAGAATAG 17 19 0 TTATCTTTTT 0.459744 -142 TGACCGCACTTTTAAAGTGCGGTTGTTTTTTTCGTAAATTT 18 26 1 TTAAGTTTTT 0.696824 -44 TGTAAAAAATGACCGCACTTTTTGATGAATATT 19 3 1 TAAACTTTTT 0.542211 -136 TGAATAGTTTTATACTTCAGTCATTTTATTTTATCAAGAAA 19 80 0 TTACCTATTT 0.536778 -59 CGGATTTAGATCGAATTATTCAAGGGTATTTGCCCGCAGAT 20 203 1 TGAAATATTT 0.740758 -58 TTTATAAAACTATAAACCCTACTACTTTTTTGTGATCTATA 22 106 1 TTAACTTTTT 0.932627 -144 AGAATATTTAACCTTCTCTGACAATTTCAGTCTATTA 22 223 0 TTAACAATTT 0.786708 -27 * *** * ***** Masking position 19 Map Score: 16.1045 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 211 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 6 TTCATAAAACATATTTTCGTAGTGATTTAC 3 25 1 ATATTTTCGT 0.833942 -276 AATTATCTAAAAAATATCGTATTTATTAGA 3 137 0 AAAATATCGT 0.814735 -164 TATTTTTTAGATAATTTCTTTACTTTTTCC 3 151 1 ATAATTTCTT 0.625345 -150 CATAAATCCTAAAATTTCGTTTTCAAAATA 4 45 1 AAAATTTCGT 0.923155 -85 TGAAATCTGTATAATCTCGTCGCAATATTT 4 78 1 ATAATCTCGT 0.950563 -52 TGCAATATTCTCGCTAATAAGTTG 4 116 0 ATATTCTCGC 0.879677 -14 CGTAAAATTCTCGCTTCGTTAATG 11 5 1 AAATTCTCGC 0.879677 -94 AAACTAAAACATATTTTCGTTTAAATTCAT 12 53 1 ATATTTTCGT 0.833942 -248 AATAATACTAAAAATCTCGCAATAAAATTC 12 140 1 AAAATCTCGC 0.945912 -161 AATAATCTCCTTGTGTTTTGA 12 290 0 ATAATCTCCT 0.805158 -11 TAAAAAATCTCTCAATGAAAAAC 15 74 0 AAAATCTCTC 0.708444 -13 CAAAAACAGCAAAATTTCCTATCAAATGGG 16 65 1 AAAATTTCCT 0.720814 -236 CATCGCCACGATAATTTCGTGGCGGTTTTT 16 155 1 ATAATTTCGT 0.923155 -146 TTATCGTTGAAAAATATCGCCTAGGGTAAG 20 149 0 AAAATATCGC 0.800003 -112 ********** Masking position 3 Map Score: 12.2567 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 210 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 7 ATTAGTTTGAAATGATTTTATGTGAAGCCTA 1 81 0 AATGATTTTT 0.568997 -135 CTTTTGAACAGATGATTAGTTTGAAATGATT 1 95 0 GATGATTAGT 0.825331 -121 ATCATTACCTGATGGTTTTCTGTCGTTTTTT 3 98 1 GATGGTTTTT 0.910059 -203 TCTAATAGTAGATGAATTTAAACGAAAATAT 12 63 0 GATGAATTTA 0.72344 -238 TAAAGAGTTAGATTATTTTATTAAATTCTAA 12 111 1 GATTATTTTT 0.568997 -190 CATCTTAGATGATGGATTTCTATTAACCTCA 14 29 0 GATGGATTTT 0.866051 -186 CATCATCTAAGATGGTTTGAAAAATCAGACA 14 46 1 GATGGTTTGA 0.602782 -169 TTTCCTTACCGATGAATTTATTTTATTCATC 14 92 0 GATGAATTTT 0.927575 -123 CGCACTTTTTGATGAATATTTAAAAATATCA 19 24 1 GATGAATATT 0.804374 -115 TGTGTTGTGTGATGAATAGTTTTATACTTCA 19 102 0 GATGAATAGT 0.7512 -37 TCATTCTAATGATGATTTGATATAGATCACA 22 136 0 GATGATTTGT 0.936378 -114 TCAAAAGTGCGGTGATTTTTTACGGTACTTT 22 168 0 GGTGATTTTT 0.759691 -82 CCGCACTTTTGATGATTTTTTATAGAGAAAT 22 187 1 GATGATTTTT 0.952479 -63 ********* * Masking position 7 Map Score: 8.1718 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 255 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 8 ATTGGTTTTATGAATATTTTTTACTCTTTTG 1 120 0 TGATATTTTT 0.743922 -96 TTTTGTATTCTGCCTAATTTTTATAAAGAAT 1 167 0 TGCTAATTTT 0.75388 -49 TGTAATCTGCTCTATATTTTTATTGAAAATA 3 68 1 TCTTATTTTT 0.469028 -233 TTTCTGTCGTTTTTTATTTTTTATCTAATAA 3 114 1 TTTTATTTTT 0.768827 -187 TGTTGTGTGTATTGTATTTTTATTGTATTCG 3 258 0 ATTTATTTTT 0.768827 -43 CTAAAAAGTTTTCTTAATTTTACTAAGTTTG 6 29 0 TTCTAATTTT 0.529589 -272 GCGGATTTTATGCTTATTTTTACGACAATTA 6 209 0 TGCTATTTTT 0.881403 -92 TCTATTACTAAGTTTGTTTTTACATTTGCCA 7 74 0 AGTTGTTTTT 0.463815 -38 AAGCGCGATAAGCGTATTATTCCCGATACTT 10 30 1 AGCTATTATT 0.324033 -46 AATATGTTTTAGTTTATTTTTGATGAAGAGG 12 37 0 AGTTATTTTT 0.900484 -264 GAAAAATACATGTATAATTTTTCCTTTTCGA 13 103 0 TGTTAATTTT 0.788557 -128 TTTTTCATGAAATTTATTTTTCTTATTCTAG 13 148 0 AATTATTTTT 0.373432 -83 TAACGTAGCCATGCTATTTTTTCATGAAATT 13 165 0 ATGTATTTTT 0.626715 -66 TACGATAAAGTTTGTATTTTTTCCTTACCGA 14 111 0 TTTTATTTTT 0.768827 -104 TACAAACTTTATCGTATTTTTTGAAAAATTA 14 126 1 ATCTATTTTT 0.732014 -89 TAGTAAAAATAGTTTAATTTTTCAAAAAATA 14 140 0 AGTTAATTTT 0.788557 -75 CGCTATTTTAAGTCTATTTTTAGTAAAAATA 14 160 0 AGTTATTTTT 0.900484 -55 ATAGAATAGCCGAATATTTTTTTATTTTAAC 16 272 1 CGATATTTTT 0.353621 -29 TAACCACGCTTTGATATTTTTAAATATTCAT 19 35 0 TTGTATTTTT 0.626715 -104 TATCAAAGCGTGGTTAATTTTTATAAAATCT 19 50 1 TGGTAATTTT 0.653102 -89 CCCTTTCAATAGAGTAATTTTTGACAAATCG 21 33 1 AGATAATTTT 0.544899 -30 *** ******* Masking position 5 Map Score: 8.94461 Number of sites scoring better than the average of aligned sites = 601 Number in coding regions = 405 Number in noncoding regions = 196 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 9 AATCTTCCTCTTTTTCTATCACGCTATTTC 1 40 1 TTTTTCTATC 0.341917 -176 TTTCTTTACTTTTTCCTTTTCTTTAAATTT 3 165 1 TTTTCCTTTT 0.939041 -136 TTTTCTTTAAATTTCCTTTATAAAAATGGT 3 181 1 ATTTCCTTTA 0.775097 -120 AAATCCTAAAATTTCGTTTTCAAAATAAAG 4 48 1 ATTTCGTTTT 0.585305 -82 AAGTTTTCCTTATTTATTCTATT 7 99 0 TTTTCCTTAT 0.904104 -13 CTTATTTCCTTAATTCGTAAGAG 8 23 0 ATTTCCTTAA 0.67838 -13 CTAAAACATATTTTCGTTTAAATTCATCTA 12 56 1 TTTTCGTTTA 0.720349 -245 CATGTATAATTTTTCCTTTTCGACAAATGT 13 96 0 TTTTCCTTTT 0.939041 -135 TATACATGTATTTTTCTTTTTCTGCTATGA 13 118 1 TTTTTCTTTT 0.703204 -113 ATGAAATTTATTTTTCTTATTCTAGTCATA 13 143 0 TTTTTCTTAT 0.591851 -88 AGTTTGTATTTTTTCCTTACCGATGAATTT 14 104 0 TTTTCCTTAC 0.855176 -111 TACGCAAACGTTTTCTTTTTGGCTTTATTT 15 13 1 TTTTCTTTTT 0.50363 -74 AAACAGCAAAATTTCCTATCAAATGGGAGC 16 68 1 ATTTCCTATC 0.541857 -233 TGCAATGGTATTTTCCTATAAAAGCCATTT 17 66 1 TTTTCCTATA 0.775097 -95 GCGGTTGTTTTTTTCGTAAATTTAACGAGA 18 44 1 TTTTCGTAAA 0.355588 -26 AGCTTTTCCTTATGTATGTGTTG 19 126 0 TTTTCCTTAT 0.904104 -13 ********** Masking position 4 Map Score: 9.19638 Number of sites scoring better than the average of aligned sites = 509 Number in coding regions = 342 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 185 Fraction of orfs with sites within 600 bp upstream = 0.0297141 Motif number 10 CAATTAGAATTGTGCTATTCTTACAAACTTC 2 58 0 TGGCTATTCT 0.973558 -36 TTCTTTACTTTTTCCTTTTCTTTAAATTTCC 3 166 1 TTCCTTTTCT 0.798272 -135 ATTCTTTCCTATTCTTTAAAGGCTG 11 84 0 TTCCTATTCT 0.956675 -15 GAAATTTATTTTTCTTATTCTAGTCATAGCA 13 140 0 TTCTTATTCT 0.68402 -91 TTAAAACGACCGAGCTATTCTACAAAAATAA 15 37 0 CGGCTATTCT 0.895861 -50 TAAAGGTTCATCTCCTGTTCTTGCCATAGAA 16 224 0 TCCCTGTTCT 0.863598 -77 AAAAAAATATTCGGCTATTCTATACAAATCT 16 264 0 TCGCTATTCT 0.950603 -37 AATTTGACCTATTCTTATAAAAATT 17 5 1 TGCCTATTCT 0.978544 -156 ATATGTAAGATGTGCTATTCTACGCCACGTT 17 114 1 TGGCTATTCT 0.973558 -47 ** ******** Masking position 6 Map Score: 5.69605 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 20 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 11 GAAGATTGTTCAATCTTCCTCACTGTAGAT 1 17 0 CAATCTTCCT 0.982664 -199 GAAGATTGAACAATCTTCCTCTTTTTCTAT 1 29 1 CAATCTTCCT 0.982664 -187 GCTATTCTTACAAACTTCCTTATTAATGTA 2 46 0 CAAACTTCCT 0.957326 -48 ACTGAAAATGCATTCTCCCTATAATGCCAA 6 154 0 CATTCTCCCT 0.929374 -147 ********** Masking position 6 Map Score: 0.368257 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 3 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 12 TTGACCAAGCGGGCGATTAGC 6 2 0 GGGCGATTAG 0.978435 -299 GAGAAGTGGTGGGCGATACCGGTCTCGAAC 6 59 1 GGGCGATACC 0.979666 -242 ACAACATTAAGGGCGATTAGCTCAGTTGGG 6 121 0 GGGCGATTAG 0.978435 -180 GGAAAAAAAAGCGCGATAAGCGTATTATTC 10 22 1 GCGCGATAAG 0.948623 -54 CCTGCATTCACGGCGATACCGCTTTTTAAT 16 35 0 CGGCGATACC 0.931897 -266 ********** Masking position 6 Map Score: 0.0865451 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 26 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 13 TTTCATTTTAGTTTTTGTGGAGAACTTATA 2 10 0 GTTTTTGGGA 0.756374 -84 ATTCTAATTGATTTATGGGGAAATT 2 79 1 ATTTATGGGA 0.447639 -15 ATGAATTTCCCTCTTTGTTGATGTTGTGTGT 3 279 0 CTCTTTGTGA 0.921365 -22 CTTTAGCCTGCCTTTTGCTGTTTAAAGTGCG 5 24 1 CCTTTTGTGT 0.862268 -86 AAGTGCGGTTATTTTTATGGAGAAAAA 9 50 1 ATTTTTAGGA 0.608135 -17 GTTTTAGTTTATTTTTGATGAAGAGGAATGT 12 32 0 ATTTTTGTGA 0.888982 -269 AATAATCTAACTCTTTATTGTTATTTGTTTG 12 97 0 CTCTTTATGT 0.437372 -204 ATAGAATACACCTTTTGATGAATAAAATAAA 14 76 1 CCTTTTGTGA 0.93554 -139 AGTGCGGTCAATTTTTGAGGTGTTTTT 14 198 1 ATTTTTGGGT 0.813166 -17 TTTTGGCTTTATTTTTGTAGAATAGCTCGGT 15 29 1 ATTTTTGAGA 0.529796 -58 GGCGATACCGCTTTTTAATGTGATGTAGTGG 16 23 0 CTTTTTATGT 0.583298 -278 AATGACCGCACTTTTTGATGAATATTTAAAA 19 18 1 CTTTTTGTGA 0.954748 -121 ATAGTTGTCCCCCTTTGGGGAACGTAATTTC 20 81 1 CCCTTTGGGA 0.910362 -180 CTAAATGTTACCCTTTGGGGTAGAAATTACG 20 103 0 CCCTTTGGGT 0.814156 -158 TCCTTTGGAACTGTTTGCGGATTTAGATCGA 20 186 1 CTGTTTGGGA 0.807438 -75 AACCCTACTACTTTTTTGTGATCTATATCAA 22 120 1 CTTTTTTTGA 0.562232 -130 AAATCACCGCACTTTTGATGATTTTTTATAG 22 181 1 ACTTTTGTGA 0.84635 -69 ******* *** Masking position 6 Map Score: 8.8371 Number of sites scoring better than the average of aligned sites = 426 Number in coding regions = 364 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 14 GATGGTTTTCTGTCGTTTTTTATTTTTTAT 3 108 1 TGTCGTTTTT 0.900877 -193 TTTAAAGTGCGGTTGGTTTTTGCAAAGTTT 5 44 1 GGTTGGTTTT 0.588872 -66 TAAATAAAAAAGCGGATTTTATGCTTATTT 6 221 0 AGCGGATTTT 0.407633 -80 ATAAAATATTAGTCGTTATTCTACTACGAC 6 263 0 AGTCGTTATT 0.543549 -38 TCGATTGCGCAGGGGTTTTTTATTGTGTAA 7 39 1 AGGGGTTTTT 0.726739 -73 CTTTTGAAAGTGCGGTTATTTTTATGGAGA 9 43 1 TGCGGTTATT 0.599196 -24 TGAAATTTGTTGTCGTTTTTCAACTGGTAA 12 182 0 TGTCGTTTTT 0.900877 -119 AACGTAGCCATGCTATTTTTTCATGAAATT 13 165 0 TGCTATTTTT 0.471799 -66 TCAATTTTTGAGGTGTTTTT 14 205 1 AGGTGTTTTT 0.625146 -10 AGAATAGCTCGGTCGTTTTAAACGGCCGTT 15 47 1 GGTCGTTTTA 0.632085 -40 CGTTTTAAACGGCCGTTTTTCATTGAGAGA 15 60 1 GGCCGTTTTT 0.960633 -27 TAGGAAATTTTGCTGTTTTTGCCTGCATTC 16 56 0 TGCTGTTTTT 0.853102 -245 ATAATTTCGTGGCGGTTTTTTATGGCAAGT 16 165 1 GGCGGTTTTT 0.953402 -136 TTTAAAGTGCGGTTGTTTTTTTCGTAAATT 18 36 1 GGTTGTTTTT 0.91347 -34 CAAAAAGTGCGGTCATTTTTTACA 19 5 0 GGTCATTTTT 0.755394 -134 TCAAAAGTGCGGTGATTTTTTACGGTACTT 22 169 0 GGTGATTTTT 0.721395 -81 ********** Masking position 7 Map Score: 6.92929 Number of sites scoring better than the average of aligned sites = 487 Number in coding regions = 389 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 15 ********** No masking Map Score: -3.94819e-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