AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02020_hinf_reg_300.orf -o02020_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 HI0220 114 arcB; aerobic respiration control sensor protein arcB homolog #2 HI0220.2 300 H. influenzae predicted coding region HI0220.2 #3 HI0266 82 conserved hypothetical protein #4 HI0267 41 nitrate/nitrite sensor protein (narQ) #5 HI0726 205 nitrate/nitrite response regulator protein (narP) #6 HI0727 260 diaminopimelate decarboxylase (lysA) #7 HI0837 53 response regulator (cpxR) #8 HI0839 116 conserved hypothetical protein #9 HI0884 191 aerobic respiration control protein ARCA (arcA) #10 HI1379 94 phosphate regulon transcriptional regulatory protein (phoB) #11 HI1382 90 phosphate ABC transporter, permease protein (pstC) #12 HI1383 300 phosphate ABC transporter, periplasmic-binding protein (pstS) #13 HI1708 62 transcriptional regulatory protein (ygiX) #14 HI1709 114 conserved hypothetical protein #15 HI1710 254 H. influenzae predicted coding region HI1710 #16 HI1711 59 PTS system, glucose-specific IIA component (crr) #17 HI1712 79 phosphoenolpyruvate-protein phosphotransferase (ptsI) #18 HI1713 158 phosphocarrier protein HPr (ptsH) #19 HI1714 70 conserved hypothetical protein Motif number 1 AAATTTTACCGCACTTTTCTAAATTTC 4 8 1 ACCGCACTTT 0.998542 -34 ATAATTTTTTACCGCTCTTTTTTAAGATAA 5 17 0 ACCGCTCTTT 0.987551 -189 CTATTTTTCTACCGCACTTTTTCTATTTTT 5 47 1 ACCGCACTTT 0.998542 -159 TTTATAATTTGCCGCATTTTATCAGATTTA 6 25 0 GCCGCATTTT 0.952029 -236 GCAAATTATAACCGCACTTTTTCAGCAAGA 8 81 0 ACCGCACTTT 0.998542 -36 GTAAAAAATCACCGCACTTTTTTATTGTTA 9 105 1 ACCGCACTTT 0.998542 -87 TTTATTTTATACCGCACTTTATACAAAACC 11 17 1 ACCGCACTTT 0.998542 -74 ATTTAAGATAACCGCACTTTATTAATGTTA 11 54 0 ACCGCACTTT 0.998542 -37 CGAGCTAATGCTCGCATTTTCAGAAATGA 13 10 0 CTCGCATTTT 0.835378 -53 AAAAAATTGACCGCACTTTATAAACAAAA 13 44 0 ACCGCACTTT 0.998542 -19 TAATAAAATACTCGCACTTTGTGCTTTTAA 15 232 0 CTCGCACTTT 0.97335 -23 GGAAAAAACGACCGCACTTTT 19 60 1 ACCGCACTTT 0.998542 -11 ********** Masking position 8 Map Score: 45.2648 Number of sites scoring better than the average of aligned sites = 1162 Number in coding regions = 733 Number in noncoding regions = 429 Number of orfs with sites within 600 bp upstream = 287 Fraction of orfs with sites within 600 bp upstream = 0.046097 Motif number 2 AAATTTTACCGCACTTTTCTAAAT 4 2 1 AATACCGCAC 0.995573 -40 AAATAGATAATTTTTTACCGCTCTTTTTTAAGA 5 20 0 TTTACCGCTC 0.905468 -186 AATTATCTATTTTTCTACCGCACTTTTTCTATT 5 41 1 TTTACCGCAC 0.986908 -165 TCTTTTTATTTTCACCACACTACAATAAGA 7 8 1 ATTACCACAC 0.937155 -46 TTTGCCGCAAATTATAACCGCACTTTTTCAGCA 8 84 0 ATAACCGCAC 0.99376 -33 AATCAGGTAAAAAATCACCGCACTTTTTTATTG 9 99 1 AAAACCGCAC 0.994744 -93 AATCTCTTTATTTTATACCGCACTTTATACAAA 11 11 1 TTTACCGCAC 0.986908 -80 AAAATTATTTAAGATAACCGCACTTTATTAATG 11 57 0 AAAACCGCAC 0.994744 -34 AAAAAATTGACCGCACTTTATAAACA 13 47 0 AATACCGCAC 0.995573 -16 TATAATAAATAAAAAATCCGCACAAAGGCGGAC 15 30 0 AAATCCGCAC 0.960076 -225 AACAAGGGAAAAAACGACCGCACTTTT 19 54 1 AAAACCGCAC 0.994744 -17 ** * ******* Masking position 8 Map Score: 24.3128 Number of sites scoring better than the average of aligned sites = 869 Number in coding regions = 532 Number in noncoding regions = 337 Number of orfs with sites within 600 bp upstream = 235 Fraction of orfs with sites within 600 bp upstream = 0.0377449 Motif number 3 TTATCTAAGTTAAATAAAAACAGAAGGGCC 2 118 1 TAAATAAAAA 0.672259 -183 ATTAAAGTAGAAAATAGAGATTGTATTTCA 2 208 1 AAAATAGAGA 0.895948 -93 AGGCAATACAAAACTAAAAACTTGATATTG 2 236 0 AAACTAAAAA 0.760354 -65 GTGCGGTAGAAAAATAGATAATTTTTTACC 5 34 0 AAAATAGATA 0.7926 -172 TTGATGGATAAAAATAGAAAAAGTGCGGTA 5 56 0 AAAATAGAAA 0.969647 -150 ATGCCAATCTAGAATAGAAAAAAATTTGAT 5 120 0 AGAATAGAAA 0.735462 -86 TATCAGATTTAAACAGGAAAATTTT 6 6 0 AAACAGGAAA 0.590935 -255 TGAGAAAGAAAAAATGAAAAAATTACTATT 6 94 1 AAAATGAAAA 0.941963 -167 CTTTTTCAGGAAAATATAAAGAACCTTTTA 6 171 0 AAAATATAAA 0.892259 -90 TAGTGTGGTGAAAATAAAAAGA 7 3 0 AAAATAAAAA 0.951947 -51 AATGTTAAAAATAAAAAAAATTTGGCT 8 8 1 AAAATAAAAA 0.951947 -109 TTTCAGCAAGAAAAAAGAAATTATTTAGGT 8 62 0 AAAAAAGAAA 0.916731 -55 ATTGAGTATAAAAATATAGATGCTCGAAAT 9 14 1 AAAATATAGA 0.69061 -178 TTTAGATCACAAAAAGGAAAATCAGGTAAA 9 80 1 AAAAAGGAAA 0.900197 -112 CATTATTGTAACAATAAAAAAGTGCGGTGA 9 113 0 ACAATAAAAA 0.632899 -79 TTCTCTTATTAAAAAGTAAAAGTTTGGTGA 10 21 1 AAAAAGTAAA 0.700441 -74 AGTGCGGTATAAAATAAAGAGATT 11 5 0 AAAATAAAGA 0.842261 -86 GTTTATGCATAAAATGAAAAAAAATCTTAT 12 71 1 AAAATGAAAA 0.941963 -230 TAACTAACTTAAAAAGGAAACGTT 14 101 1 AAAAAGGAAA 0.900197 -14 GTAACTATAATAAATAAAAAATCCGCACAA 15 38 0 TAAATAAAAA 0.672259 -217 ATTTTACGTTAAAATAGCAACCATCTTGAA 16 24 1 AAAATAGCAA 0.726843 -36 TTTTGCTTTGAAAAAGGATACTAGGGCAAT 18 94 1 AAAAAGGATA 0.519001 -65 TCAATAATTAAAAATATAAAACCAGAAAAT 18 122 0 AAAATATAAA 0.892259 -37 TGTTTTTGGTAAAATGAAAAAAATTTTTGC 19 28 0 AAAATGAAAA 0.941963 -43 ********** Masking position 3 Map Score: 26.6836 Number of sites scoring better than the average of aligned sites = 663 Number in coding regions = 460 Number in noncoding regions = 203 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 4 TATTATCGTTATAAAAAAAACCTGTGCATA 1 78 0 ATAAAAAAAA 0.914641 -37 TATAGTTTTAATAAATATACCTATTTACAT 2 270 1 ATAAATATAC 0.716091 -31 AGGTTTATTGATGGATAAAAATAGAAAAAG 5 63 0 ATGGATAAAA 0.444677 -143 TTATCCATCAATAAACCTACCTCAAATAGT 5 75 1 ATAAACCTAC 0.437032 -131 AGTTTTTGAGATAAATCAAATTTTTTTCTA 5 106 1 ATAAATCAAA 0.851192 -100 CCAATCTAGAATAGAAAAAAATTTGATTTA 5 117 0 ATAGAAAAAA 0.676485 -89 CATTCCCAAAATAACTAAAACAGGCACACA 6 239 1 ATAACTAAAA 0.618983 -22 CCACACTACAATAAGAATAATTGGTAAAAG 7 25 1 ATAAGAATAA 0.601239 -29 AATGTTAAAAATAAAAAAAATTTGGCTTAT 8 11 1 ATAAAAAAAA 0.914641 -106 ATCGGGTATCATAAGCCAAATTTTTTTTAT 8 21 0 ATAAGCCAAA 0.572713 -96 ATACGCCAAAATAAGTATAAGGATGGAAA 9 173 1 ATAAGTATAA 0.657568 -19 CTTTTATGCCATAAATCAAATGAAGGAGTA 10 73 1 ATAAATCAAA 0.851192 -22 CATTTTATGCATAAACATAACAAATTCTCC 12 57 0 ATAAACATAA 0.815454 -244 TATGCATAAAATGAAAAAAAATCTTATTAC 12 74 1 ATGAAAAAAA 0.763136 -227 ACCGCACTTTATAAACAAAAACAGCGAGCT 13 34 0 ATAAACAAAA 0.909263 -29 GGTAACTATAATAAATAAAAAATCCGCACA 15 39 0 ATAAATAAAA 0.931726 -216 TAACAAAGTAATAAATAAACAATAGCCATA 17 41 0 ATAAATAAAC 0.851192 -39 ATTGTGAATAATAAATAAACTATTTAGCTT 18 19 1 ATAAATAAAC 0.851192 -140 GAATTAAATCATAAAAATAAGCTAAATAGT 18 37 0 ATAAAAATAA 0.825324 -122 TTTTGGTAAAATGAAAAAAATTTTTGCATA 19 25 0 ATGAAAAAAA 0.763136 -46 ********** Masking position 2 Map Score: 14.9035 Number of sites scoring better than the average of aligned sites = 577 Number in coding regions = 381 Number in noncoding regions = 196 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 5 TAAAGCCTATATGCACAGGTTTTTTTTATAACGA 1 69 1 ATGCATTTTT 0.818715 -46 ATTGTATTTCAATATCAAGTTTTTAGTTTTGTAT 2 227 1 AATAATTTTT 0.895975 -74 GCGGTAGAAAAATAGATAATTTTTTACCGCTCTT 5 28 0 AATATTTTTT 0.66637 -178 ACCTACCTCAAATAGTAAGTTTTTGAGATAAATC 5 89 1 AATAATTTTT 0.896029 -117 TTTTGAGATAAATCAAATTTTTTTCTATTCTAGA 5 109 1 AATCATTTTT 0.955253 -97 CCACTTTAAAAAGCATAACATTTTATAAAGAATT 5 157 0 AAGCAATTTT 0.907264 -49 TACTAAAATTAATAGTAATTTTTTCATTTTTTCT 6 100 0 AATAATTTTT 0.896029 -161 CGGGTATCATAAGCCAAATTTTTTTTATTTTTAA 8 15 0 AAGCATTTTT 0.965487 -102 GTAGAACCTAAATAATTTCTTTTTTCTTGCTGAA 8 57 1 AATATTTTTT 0.663666 -60 AATCTCTTTATTTTATACCGCACT 11 1 1 AATCTATTTT 0.636007 -90 GTTAAAACGTAATAAGATTTTTTTTCATTTTATG 12 78 0 AATAATTTTT 0.892387 -223 GAGGCACCAAAATCAACCGTTTTTGCAATAATTT 12 267 0 AATCCTTTTT 0.745458 -34 AAAGATTAAGAGGACTATACTTTTTTGAAAAGAC 14 15 0 AGGAACTTTT 0.448083 -100 ATCCGCACAAAGGCGGACTTTTTTTACCGTAAAC 15 14 0 AGGCATTTTT 0.874777 -241 ATATTTTGCAAAGCGAAATCTTTTGCTGACGTGG 15 170 0 AAGCACTTTT 0.89033 -85 TTTAACGTAAAATCAAATAATTTTGT 16 3 0 AATCAATTTT 0.88271 -57 TCATAAAAATAAGCTAAATAGTTTATTTATTATT 18 25 0 AAGCAAGTTT 0.523461 -134 CAGGTATCCTATGCAAAAATTTTTTTCATTTTAC 19 16 1 ATGCATTTTT 0.818714 -55 **** * ***** Masking position 12 Map Score: 13.0522 Number of sites scoring better than the average of aligned sites = 542 Number in coding regions = 408 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 6 CCTTCTGTTTTTATTTAACTTAGATAAGTAT 2 114 0 TTATTTAATT 0.707458 -187 GAAAAAATTACTATTAATTTTAGTACTTAGT 6 109 1 CTATTAATTT 0.598117 -152 AGATAATAGATTATTGAGTTTGTTGAGCTTG 6 203 0 TTATTGAGTT 0.887873 -58 AAAAAAGAAATTATTTAGGTTCTACCAAATA 8 51 0 TTATTTAGTT 0.955862 -66 TAACCGCACTTTATTAATGTTAAGTGCTAGG 11 45 0 TTATTAATTT 0.775849 -46 TCCTTGAGTGTTATTTAGATTGCGTAGCGAA 12 29 0 TTATTTAGTT 0.955862 -272 AAAAAAAATCTTATTACGTTTTAACCTTAGG 12 87 1 TTATTACGTT 0.804187 -214 TCTTAATCTTTTATTAAGATTTATTTGTTTT 14 38 1 TTATTAAGTT 0.946172 -77 AATAAATAAACTATTTAGCTTATTTTTATGA 18 28 1 CTATTTAGTT 0.903023 -131 TTATTCTTGATTATTTTGCTTTGAAAAAGGA 18 81 1 TTATTTTGTT 0.773442 -78 ******** ** Masking position 5 Map Score: 4.97782 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 68 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 7 TATGGGGTTTTAGCTTTTGGGAATTTATTCAT 2 161 1 TAGCTTGGGA 0.800851 -140 CGTATGCTATCAATTTTGGGTAGAATAACGAA 3 37 1 CAATTTGGTA 0.832781 -46 CAAAAACTTACTATTTGAGGTAGGTTTATTGA 5 82 0 CTATTTGGTA 0.783438 -124 CCTGTTTTAGTTATTTTGGGAATGATATTAGA 6 231 0 TTATTTGGAA 0.594938 -30 AGTGCGGTTATAATTTGCGGCAAATTTTTCAA 8 93 1 TAATTTGGCA 0.7498 -24 ATCTAAATCATAGTTTTAGGTATTCAAATTTC 9 55 0 TAGTTTGGTA 0.943325 -137 TATTACGTTTTAACCTTAGGTACGTTACCTTT 12 98 1 TAACCTGGTA 0.931664 -203 TTTGTTTACGGTAAAAAAAGTCC 15 2 1 TTGTTTGGTA 0.923615 -253 TTTATTATAGTTACCTAGGGTAAGTATACCCT 15 54 1 TTACCTGGTA 0.9075 -201 GCACTTAAATTAGCCTAGGGTATACTTACCCT 15 70 0 TAGCCTGGTA 0.93234 -185 CGACTATAATTAACCGTAGGTATACTTACGCC 15 140 1 TAACCGGGTA 0.701356 -115 GTTTTTTCCCTTGTTTTTGGTAAAATGAAAAA 19 37 0 TTGTTTGGTA 0.923616 -34 ****** **** Masking position 12 Map Score: 3.87856 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 98 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 8 GTTTTTCATTTCTTACGCATA 1 2 1 TTTTTCATTT 0.958659 -113 CAATCTCTATTTTCTACTTTAATCCTTTTC 2 201 0 TTTCTACTTT 0.579207 -100 AATTTCTCCTTTAGTGGTTAGA 5 194 0 TTTCTCCTTT 0.950455 -12 TCATTTTTTCTTTCTCACTTATCGGTAAAT 6 81 0 TTTCTCACTT 0.933268 -180 TAATAGTAATTTTTTCATTTTTTCTTTCTC 6 95 0 TTTTTCATTT 0.958659 -166 AAGCCAAATTTTTTTTATTTTTAACATT 8 9 0 TTTTTTATTT 0.745803 -108 TTTTTACCTGATTTTCCTTTTTGTGATCTA 9 82 0 ATTTTCCTTT 0.674888 -110 GAATGTATTATTTCTCACTTCACTTTTATG 10 51 1 TTTCTCACTT 0.933268 -44 AATAAGATTTTTTTTCATTTTATGCATAAA 12 72 0 TTTTTCATTT 0.958659 -229 TGCTGGAGCGTCTTTCCCTTATCCAATTTA 12 154 1 TCTTTCCCTT 0.671061 -147 TCCCAGTTTCTTTCTCATATAAAGATGCCC 12 192 0 TTTCTCATAT 0.674888 -109 TTTGTGCGGATTTTTTATTTATTATAGTTA 15 37 1 TTTTTTATTT 0.745803 -218 TGCAAAAATTTTTTTCATTTTACCAAAAAC 19 27 1 TTTTTCATTT 0.958659 -44 GTGCGGTCGTTTTTTCCCTTGTTTTTGGTA 19 47 0 TTTTTCCCTT 0.933268 -24 ********** Masking position 5 Map Score: 17.6757 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 190 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 9 ACCCCATATCTTTCGACACGGGGCCCTTCT 2 139 0 TTTCGACACG 0.881698 -162 CAGCTTGTATATTCGCTACAGGATGTGGCG 6 141 1 ATTCGCTACA 0.871377 -120 AAAGAACCTTTTACGCCACATCCTGTAGCG 6 154 0 TTACGCCACA 0.976975 -107 TCTTTTTATTTTCACCACACTACAATAAG 7 10 1 TTTCACCACA 0.883768 -44 CTTTGATAGCATACGCCAAAATAAGTATAA 9 163 1 ATACGCCAAA 0.673405 -29 ATTTTCTACACTTCGCTACGCAATCTAAAT 12 18 1 CTTCGCTACG 0.848005 -283 GTAGGTATACTTACGCCACGTCAGCAAAAG 15 155 1 TTACGCCACG 0.976525 -100 AAATGATGTGTTTCGCCACATTCATATTGA 15 204 0 TTTCGCCACA 0.985328 -51 ********** Masking position 8 Map Score: 4.74207 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 175 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 10 CAAATCTCCTAAAACATTATTATCGT 1 99 0 TCCTAAAACA 0.767819 -16 CCGCCAGGTTACCAAATACTTATCTAAGTT 2 99 1 ACCAAATACT 0.767819 -202 ATCTAAGTTAAATAAAAACAGAAGGGCCCC 2 120 1 AATAAAAACA 0.720739 -181 GCAATACAAAACTAAAAACTTGATATTGAA 2 234 0 ACTAAAAACT 0.805099 -67 TTCCCAAAATAACTAAAACAGGCACACAAC 6 241 1 AACTAAAACA 0.873021 -20 AAATTTGAATACCTAAAACTATGATTTAGA 9 56 1 ACCTAAAACT 0.916696 -136 CGTCAGAGGCACCAAAATCAACCGTTTTTG 12 276 0 ACCAAAATCA 0.863093 -25 GCACTTTATAAACAAAAACAGCGAGCTAAT 13 31 0 AACAAAAACA 0.929112 -32 TTTTCATTTTACCAAAAACAAGGGAAAAAA 19 38 1 ACCAAAAACA 0.975604 -33 ********** Masking position 5 Map Score: 4.3985 Number of sites scoring better than the average of aligned sites = 267 Number in coding regions = 228 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 11 CATACATAGTAATAACAATCTCGTTTACTTTATG 1 28 1 AACAATCTCT 0.923241 -87 CTTGATATTGAAATACAATCTCTATTTTCTACTT 2 212 0 AACAATCTCA 0.977411 -89 GGCAAATTATAAAGCCTTTCTCAAGCTTGTGAAA 6 42 1 AACTTTCTCA 0.844872 -219 TTTCCTGAAAAAGATCAAGCTCAACAAACTCAAT 6 188 1 AACAAGCTCA 0.968479 -73 TCTATTATCTAATATCATTCCCAAAATAACTAAA 6 224 1 AACATTCCCA 0.761602 -37 AATAATTGGTAAAAGGAATCTCCA 7 40 1 AAGAATCTCA 0.84855 -14 TAGATGCTCGAAATTCTATCACAAAGAAATTTGA 9 30 1 AACTATCACA 0.860943 -162 CACTTTATACAAAACCTAGCACTTAACATTAATA 11 31 1 AACTAGCACT 0.549902 -60 TAAGTTAGTTAATTTCAAGCTCCATTGCTTGGAT 14 78 0 AACAAGCTCA 0.968561 -37 TTTATTTATTATTCACAATCTCAATCG 18 4 0 ATCAATCTCA 0.858923 -155 ** ******* * Masking position 1 Map Score: 2.52215 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 135 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 12 ATTCTAGATTGGCATAGAATTGAATTCTTT 5 135 1 GGCATAGAAT 0.942856 -71 TACAGGATGTGGCGTAAAAGGTTCTTTATA 6 157 1 GGCGTAAAAG 0.917375 -104 TTTGATTTATGGCATAAAAGTGAAGTGAGA 10 63 0 GGCATAAAAG 0.973034 -32 TATAAAGTGCGGTATAAAATAAAGAGATT 11 10 0 GGTATAAAAT 0.8743 -81 GTTATGTTTATGCATAAAATGAAAAAAAAT 12 66 1 TGCATAAAAT 0.8743 -235 TTCTTACTTAGCCATAAAATTGTGAAATTT 17 11 1 GCCATAAAAT 0.957676 -69 ATAAACAATAGCCATAAAATTTCACAATTT 17 27 0 GCCATAAAAT 0.957676 -53 ********** Masking position 6 Map Score: 4.25344 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 65 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 13 GAAAGGCTTTATAATTTGCCGCATTTTATCA 6 31 0 ATAATTTGCG 0.98015 -230 AAGGTTCTTTATATTTTCCTGAAAAAGATCA 6 174 1 ATATTTTCCG 0.740776 -87 AAGTGCGGTTATAATTTGCGGCAAATTTTTC 8 92 1 ATAATTTGCG 0.98015 -25 TAGGTTTTGTATAAAGTGCGGTATAAAATAA 11 18 0 ATAAAGTGCG 0.924915 -73 CTTAACATTAATAAAGTGCGGTTATCTTAAA 11 52 1 ATAAAGTGCG 0.924915 -39 CGATGGATTGATAATTAACTTTATTCCCAGT 12 215 0 ATAATTAACT 0.156142 -86 CGTTTTTGCAATAATTTGCTGTTGTCCGCCG 12 253 0 ATAATTTGCG 0.98015 -48 GTTTTTGTTTATAAAGTGCGGTCAATTTTTT 13 42 1 ATAAAGTGCG 0.924915 -21 AGGAACGACTATAATTAACCGTAGGTATACT 15 135 1 ATAATTAACG 0.67927 -120 GCAAAGCGAAATCTTTTGCTGACGTGGCGTA 15 166 0 ATCTTTTGCG 0.787405 -89 TTCATATTGAATATTTTGCAAAGCGAAATCT 15 183 0 ATATTTTGCA 0.632122 -72 ********* * Masking position 1 Map Score: 5.03631 Number of sites scoring better than the average of aligned sites = 337 Number in coding regions = 270 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 14 CATAGTAATAACAATCTCGTTTACTTTATGG 1 32 1 ACAATCTCTT 0.866154 -83 ATATTGAAATACAATCTCTATTTTCTACTTT 2 211 0 ACAATCTCAT 0.963277 -90 TAGCGAATATACAAGCTGAACTAAGTACTAA 6 128 0 ACAAGCTGAC 0.886883 -133 CTGAAAAAGATCAAGCTCAACAAACTCAATA 6 192 1 TCAAGCTCAC 0.948259 -69 TTAGTTAATTTCAAGCTCCATTGCTTGGATG 14 77 0 TCAAGCTCAT 0.956722 -38 TTTATTATTCACAATCTCAATCG 18 3 0 ACAATCTCAT 0.963277 -156 ******** ** Masking position 7 Map Score: 0.196905 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 21 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 15 ********** No masking Map Score: -5.9306e-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