AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -imetR_hinf_opreg_300.orf -g0.38 -x5 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 = 0 Input sequences: #1 HI0885 191 thiol:disulfide interchange protein (dsbD) #2 HI0886 111 H. influenzae predicted coding region HI0886 #3 HI0887 187 phosphoribosylaminoimidazolecarboxamide formyltransferase (purH) #4 HI0888 95 phosphoribosylamine--glycine ligase (purD) #5 HI0889 123 serine hydroxymethyltransferase (serine methylase) (glyA) #6 HI1444 300 5,10 methylenetetrahydrofolate reductase (metF) #7 HI1702 192 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase (metE) #8 HI1704 107 conserved hypothetical protein #9 HI1739 300 transcriptional activator (metR) Motif number 1 TGTGCAACATTATTGTAACAATAAAAAAGTGCGGTG 1 63 1 TTTACTAAAA 0.897131 -129 CTGATTTTCCTTTTTGTGATCTAAATCATAGTTTTA 1 108 1 TTTTATAAAT 0.83578 -84 TCACAAAGAAATTTGAATACCTAAAACTATGATTTA 1 129 0 ATTAATAAAA 0.842933 -63 AAAAATACTTTTTACCAAAAGTAAAAAATAA 2 6 0 TTAAATAAAA 0.870273 -106 AACGGGTAGTTAAACAATAATTAAAATTGAAAAATA 2 35 0 TAAAATAAAA 0.763144 -77 TCCTTTTGTTTAAAGATGAATTAAAACGGCGTCATA 2 80 0 TAATATAAAA 0.899516 -32 ATATAATTTCTTAAAGTGCGGTAAAAATACGATAAA 3 80 0 TAATCTAAAA 0.89577 -108 AGTCCTTGCGTATGCCTAATTTAAAAAAAGTACGGC 4 65 0 TTGTATAAAA 0.761969 -31 CATTCCTAAATTTTCATCACTTAAATGAAATTAATT 5 28 0 TTTTATAAAT 0.881955 -96 GTTTATGGATAAAAATTTAATTAAAATTTCATTCCT 5 57 0 AAATATAAAA 0.842059 -67 AAACAGTTAAACTATCTGCCATAAATTACATAACAG 5 89 1 ATATCTAAAT 0.759539 -35 ATTTTTTGCGCTAAAAAACAAATCTA 6 1 1 ATTTCTAAAA 0.934073 -300 TAACACGCATTTATCTTTCTATAAAAATACACAAAA 6 48 1 TATTCTAAAA 0.919804 -253 AGTTTTGAGTATGTGTTGATCTAAAAATTAGTTATT 6 145 1 AGTTATAAAA 0.756049 -156 TGATTATTATTAATAATTCAATAAATGGATAATTAT 6 189 0 TATTCTAAAT 0.773602 -112 AGTCAATTTCAATTTATTCATTAAAAGTATGATTAT 6 218 0 ATTTCTAAAA 0.934335 -83 TCTAAAATAGTATTTGTACAATAAAATAGGTTTTAA 6 258 0 TTTTCTAAAA 0.960331 -43 AATTCAGCTAACTTATTTCCTTAAAA 7 1 0 ATTTCTAAAA 0.934026 -192 GATTCATCGTTATTTGATAGATAAAAGAATGCTTGA 7 37 1 TTTAATAAAA 0.9008 -156 ATTTTCAGGATTTACATTAAATAAATTCATAATCAA 7 69 0 TTATATAAAT 0.845028 -124 AAATGATTAAAAAAATTACTTTAAATTGGAGTTATT 7 167 1 AAATCTAAAT 0.602604 -26 TTTCGTTTGTTTTTCTAAATCTAAAACGGAGGAAAA 8 78 0 TTTAATAAAA 0.899187 -30 GGGCACCGCCAGGTTATCAAATAAAAAATCTAAATA 9 58 1 AGTTATAAAA 0.756301 -243 TATAAATCTATCTAAGATAGATAAAATTAAATTAAG 9 92 1 TTAAATAAAA 0.87028 -209 ATAAAATTAAATTAAGTTAAGTAAAAACAGAATTAA 9 112 1 ATATATAAAA 0.851288 -189 ACTGGGGTTTTGTATTTTAACTAAAATAATTATCTA 9 189 1 TTATATAAAA 0.949067 -112 TAATAATATTCATATAAAATTAAGAATTA 9 282 0 TATTATAAAA 0.923749 -19 * ** * * ***** Masking position 12 Map Score: 32.6023 Number of sites scoring better than the average of aligned sites = 938 Number in coding regions = 654 Number in noncoding regions = 284 Number of orfs with sites within 600 bp upstream = 245 Fraction of orfs with sites within 600 bp upstream = 0.0393511 Motif number 2 TTTCCATCCTTATACTTATTTTGGCGTATGC 1 6 1 ATTTATATTT 0.963946 -186 AAGTGCGGTGATTTTTTACCTGATTTTCCTTTTTGT 1 89 1 ATTTTAATTT 0.931046 -103 GATCTAAATCATAGTTTTAGGTATTCAAATTTCTTT 1 125 1 ATTTTTATTC 0.794178 -67 GAGCATCTATATTTTTATACTCAATTCT 1 174 1 ATTTATAATT 0.88272 -18 TTTTGGTAAAAAGTATTTTTCAATTTTAATTATTGT 2 22 1 AAATTTATTT 0.731763 -90 GTAGTTTCATAATTTTATCCTTATTTTTGCCCACAT 3 18 1 AATTATATTT 0.908426 -170 AATTATATTTAATCTTTTCTATATTTAAGCAAACGT 3 108 1 AATTTTATTT 0.930863 -80 TTCTCATCGCTTATTTTTAACTATTTAATGAAAGGA 3 155 1 TTTTTTATTT 0.829224 -33 TCCATATCATTATGATGAATTAATTTCATTT 5 6 1 ATTTATAATT 0.88272 -118 TTAGGAATGAAATTTTAATTAAATTTTTATCCATAA 5 55 1 AATTAAATTT 0.543416 -69 AAAGTGCGGTAATTTTTTGTGTATTTTTATAGAAAG 6 62 0 AATTTTATTT 0.930863 -239 TTTGTTAGCAATGATTTACCCCATTTTACAACGAAA 6 101 0 ATTTTAATTT 0.931046 -200 TAAAAGTATGATTATTATTAATAATTCAATAAATGG 6 197 0 ATTTATAATT 0.882655 -104 ATGCAAACTTATTATTTTCAGGATTTACATTAAATA 7 82 0 ATTTTTATTT 0.973253 -111 ATTTAAAGTAATTTTTTTAATCATTTAGACGGCTAA 7 157 0 ATTTTTATTT 0.973235 -36 TCTTAGATAGATTTATATTTAGATTTTTTATTTGAT 9 73 0 ATATATATTT 0.844113 -228 AATTCTGTTTTTACTTAACTTAATTTAATTTTATCT 9 110 0 TTTTAAATTT 0.569696 -191 TTCTATATTTATTCTTTATCTAATTTGTTTAATTCT 9 140 0 ATTTTAATTT 0.931046 -161 TATCTAAATAATTAATTTTATTAATTAGCATATTTC 9 219 1 ATATTTAATT 0.675209 -82 ** **** **** Masking position 6 Map Score: 22.7646 Number of sites scoring better than the average of aligned sites = 588 Number in coding regions = 404 Number in noncoding regions = 184 Number of orfs with sites within 600 bp upstream = 172 Fraction of orfs with sites within 600 bp upstream = 0.0276261 Motif number 3 TAAAAAATCACCGCACTTTTTTATTGTTAC 1 77 0 CCGCACTTTT 0.990456 -115 CGTATTTTTACCGCACTTTAAGAAATTATA 3 85 1 CCGCACTTTA 0.99224 -103 TCTAACTATCCCCCTCTTTACAAAAGAGGG 4 15 1 CCCCTCTTTA 0.974252 -81 CCTGCAATTCCCCCTCTTTTGTAAAGAGGG 4 26 0 CCCCTCTTTT 0.968466 -70 TAAAAAATAGCCGTACTTTTTTTAAATTAG 4 56 1 CCGTACTTTT 0.941137 -40 CAAAAAATTACCGCACTTTCTTTTTCGTTG 6 79 1 CCGCACTTTC 0.988511 -222 CAATGATTTACCCCATTTTACAACGAAAAA 6 99 0 CCCCATTTTA 0.930184 -202 CTCAAAACTACCGCACTTTTGTTAGCAATG 6 124 0 CCGCACTTTT 0.990456 -177 CATGGGGAAACCCCACACTACCATCGGCAT 9 20 0 CCCCACACTA 0.88147 -281 CCTGGCGGTGCCCTACTCTCACATGGGGAA 9 41 0 CCCTACTCTC 0.858508 -260 AAATATAGAACCCCAGTTTAAGGACTGGGG 9 166 1 CCCCAGTTTA 0.9518 -135 ********** Masking position 9 Map Score: 19.6422 Number of sites scoring better than the average of aligned sites = 1328 Number in coding regions = 860 Number in noncoding regions = 468 Number of orfs with sites within 600 bp upstream = 302 Fraction of orfs with sites within 600 bp upstream = 0.0485063 Motif number 4 ATCAGGTAAAAAATCACCGCACTTTTTTATTGTT 1 79 0 AAATACGATT 0.94319 -113 TTATGCCTGAAATTTATCGTATTTTTACCGCACT 3 68 1 AATTACGATT 0.960247 -120 TGCAGGTAAAAAATAGCCGTACTTTTTTTAAATT 4 50 1 AAATGCGATT 0.851197 -46 CATTATGATGAATTAATTTCATTTAAGTGATGAA 5 18 1 AATTATTATT 0.729422 -106 TATGGATAAAAATTTAATTAAAATTTCATTCCTA 5 56 0 AATTATTAAT 0.695985 -68 CCTGTTATGTAATTTATGGCAGATAGTTTAACTG 5 92 0 AATTAGGAAT 0.641545 -32 CTAAAAAACAAATCTATTGTATTTATTTAACACG 6 21 1 AATCATGATT 0.85127 -280 AATACACAAAAAATTACCGCACTTTCTTTTTCGT 6 73 1 AAATACGATT 0.94319 -228 CACATACTCAAAACTACCGCACTTTTGTTAGCAA 6 126 0 AAACACGATT 0.91457 -175 GAATAAATTGAAATTGACTCATATTAAAACCTAT 6 235 1 AAATGCTAAT 0.647728 -66 ACGATGAATCAATTCAGCTAACTTATTTCCTTAA 7 13 0 AATTACTATT 0.738354 -180 ATGATTAAAAAAATTACTTTAAATTGGAGTTATT 7 169 1 AAATATTAAT 0.638228 -24 ATTTCTGTTTAATTCAGCGAAAATAAGTTATCAT 8 24 1 AATTACGAAT 0.939741 -84 AACTGGATAAAATCGGTCGCATATGATAACTTAT 8 46 0 AATCGCGAAT 0.784482 -62 AGATTTAGAAAAACAAACGAAATAAG 8 92 1 AAACACGATA 0.602602 -16 TCTAAATATAAATCTATCTAAGATAGATAAAATT 9 86 1 AATCACTAAT 0.842561 -215 AGATAGATAAAATTAAATTAAGTTAAGTAAAAAC 9 106 1 AATTATTATT 0.738946 -195 TTATCTAAATAATTAATTTTATTAATTAGCATAT 9 218 1 AATTATTATA 0.388221 -83 **** * ** * ** Masking position 11 Map Score: 15.4921 Number of sites scoring better than the average of aligned sites = 1252 Number in coding regions = 925 Number in noncoding regions = 327 Number of orfs with sites within 600 bp upstream = 268 Fraction of orfs with sites within 600 bp upstream = 0.0430453 Motif number 5 AGCATACGCCAAAATAAGTATAAGGATGGAA 1 12 0 AAATAAGTAT 0.937516 -180 TTTTATTGTTACAATAATGTTGCACAGATAG 1 58 0 AAATAATGTT 0.761176 -134 TTAAAATTGAAAAATACTTTTTACCAAAAGT 2 20 0 AAATACTTTT 0.648116 -92 GGGTAGTTAAACAATAATTAAAATTGAAAAA 2 37 0 AAATAATTAA 0.730929 -75 AATGTGGGCAAAAATAAGGATAAAATTATGA 3 24 0 AAATAAGGAT 0.80352 -164 AATATAGAAAAGATTAAATATAATTTCTTAA 3 102 0 AATTAAATAT 0.613801 -86 TTAAATAAATACAATAGATTTGTTTTTTAGC 6 20 0 AAATAGATTT 0.639724 -281 GTTGATCTAAAAATTAGTTATTATTGAACAA 6 159 1 AATTAGTTAT 0.635697 -142 TTATTATTGAACAATAATTATCCATTTATTG 6 176 1 AAATAATTAT 0.938401 -125 TGAATTATTAATAATAATCATACTTTTAATG 6 205 1 AAATAATCAT 0.705627 -96 TTTGTACAATAAAATAGGTTTTAATATGAGT 6 251 0 AAATAGGTTT 0.819519 -50 AATCCTGAAAATAATAAGTTTGCATAATAAA 7 93 1 AAATAAGTTT 0.913937 -100 ACTCCAATTTAAAGTAATTTTTTTAATCATT 7 168 0 AAGTAATTTT 0.645892 -25 TAATTCAGCGAAAATAAGTTATCATATGCGA 8 33 1 AAATAAGTTA 0.636694 -75 AATTAGATAAAGAATAAATATAGAACCCCAG 9 151 1 AAATAAATAT 0.862883 -150 TATTTTAACTAAAATAATTATCTAAATAATT 9 201 1 AAATAATTAT 0.8 -100 CTAATTAATAAAATTAATTATTTAGATAATT 9 216 0 AATTAATTAT 0.761218 -85 * ********* Masking position 6 Map Score: 13.2523 Number of sites scoring better than the average of aligned sites = 280 Number in coding regions = 192 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 6 AAAAAGGAAAATCAGGTAAAAAATCACCGCA 1 92 0 ATCAGTAAAA 0.602776 -100 AAATCATAGTTTTAGGTATTCAAATTTCTTT 1 130 1 TTTAGTATTC 0.622225 -62 TACGATAAATTTCAGGCATAAAAAAGCCCAC 3 58 0 TTCAGCATAA 0.832785 -130 CTTTTCTATATTTAAGCAAACGTTTGCGTTA 3 121 1 TTTAGCAAAC 0.928277 -67 GATGAGAATTATAACGCAAACGTTTGCTTAA 3 132 0 ATAAGCAAAC 0.882343 -56 CTTTTTTTAAATTAGGCATACGCAAGGACTA 4 71 1 ATTAGCATAC 0.96815 -25 TAAATTCATAATCAAGCATTCTTTTATCTAT 7 53 0 ATCAGCATTC 0.961966 -140 ATCTTCATTTATTATGCAAACTTATTATTTT 7 100 0 ATTAGCAAAC 0.961049 -93 ATAAATGAAGATCAAGCATTCTATATTGGTA 7 119 1 ATCAGCATTC 0.961966 -74 **** ****** Masking position 4 Map Score: 3.63951 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 152 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 7 AATGTTGCACAGATAGAATGATAGCTTTGATAGCAT 1 38 0 AAATGAAGCT 0.543147 -154 AGAATTGAGTATAAAAATATAGATGC 1 176 0 AAAGTAAAAA 0.719391 -16 ATTCATCTTTAAACAAAAGGAAAGCAA 2 95 1 AAAGGAAGCA 0.979983 -17 AAATGTGGGCAAAAATAAGGATAAAATTATGAAACT 3 20 0 AAAGGAAAAA 0.967044 -168 AAAATACGATAAATTTCAGGCATAAAAAAGCCCACA 3 57 0 AAAGGCTAAA 0.734816 -131 TAAATTAGGCATACGCAAGGACTACAAC 4 78 1 AAAGGATACA 0.968881 -18 TTAAGTGATGAAAATTTAGGAATGAAATTTTAATTA 5 40 1 AAAGGATGAA 0.904401 -84 GCCATAAATTACATAACAGGAGAACACA 5 106 1 AAAGGAAACA 0.985665 -18 AATTAAACAGAAATTTAAGGACAACAA 8 2 0 AAAGGAAACA 0.985665 -106 TTCTAAATCTAAAACGGAGGAAAACTGGATAAAATC 8 66 0 AAAGGAAACT 0.950283 -42 * * **** **** Masking position 8 Map Score: 6.45692 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 39 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 8 TAGATCACAAAAAGGAAAATCAGGTAAAAA 1 101 0 AAAGGAAAAT 0.825848 -91 ACTACCCGTTAAAGATTAATATGACGCCGT 2 61 1 AAAGATTAAT 0.938205 -51 CCTTTTGTTTAAAGATGAATTAAAACGGCG 2 85 0 AAAGATGAAT 0.942494 -27 GCGGTAAAAATACGATAAATTTCAGGCATA 3 69 0 TACGATAAAT 0.595732 -119 TAAATATAGAAAAGATTAAATATAATTTCT 3 105 0 AAAGATTAAA 0.808444 -83 CTATTTAATGAAAGGAAAATACA 3 175 1 AAAGGAAAAT 0.825848 -13 ATTTTTATAGAAAGATAAATGCGTGTTAAA 6 46 0 AAAGATAAAT 0.960562 -255 TCTATCAAATAACGATGAATCAATTCAGCT 7 28 0 AACGATGAAT 0.875733 -165 TAAAAAATCTAAATATAAATCTATCTAAGA 9 79 1 AAATATAAAT 0.680298 -222 CAAATTAGATAAAGAATAAATATAGAACCC 9 149 1 AAAGAATAAA 0.656477 -152 ********** Masking position 8 Map Score: 4.15023 Number of sites scoring better than the average of aligned sites = 402 Number in coding regions = 317 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 9 GCCCACATAAATGTGGGCAAAAATAAGGAT 3 34 0 ATGTGGGCAA 0.62453 -154 GCCCACATTTATGTGGGCTTTTTTATGCCT 3 46 1 ATGTGGGCTT 0.861509 -142 TAATTTCTTAAAGTGCGGTAAAAATACGAT 3 83 0 AAGTGCGGTA 0.977395 -105 CTCTTTTGTAAAGAGGGGGATAGTTAGATA 4 13 0 AAGAGGGGGA 0.922237 -83 CTCTTTACAAAAGAGGGGGAATTGCAGGTA 4 28 1 AAGAGGGGGA 0.922237 -68 ACGAAAAAGAAAGTGCGGTAATTTTTTGTG 6 77 0 AAGTGCGGTA 0.977395 -224 TTTCGTTGTAAAATGGGGTAAATCATTGCT 6 101 1 AAATGGGGTA 0.91595 -200 TTGCTAACAAAAGTGCGGTAGTTTTGAGTA 6 126 1 AAGTGCGGTA 0.977395 -175 GCCGATGGTAGTGTGGGGTTTCCCCATGTG 9 22 1 GTGTGGGGTT 0.909251 -279 CCAGTCCTTAAACTGGGGTTCTATATTTAT 9 164 0 AACTGGGGTT 0.945959 -137 CCAGTTTAAGGACTGGGGTTTTGTATTTTA 9 178 1 GACTGGGGTT 0.870568 -123 ********** Masking position 5 Map Score: 11.7272 Number of sites scoring better than the average of aligned sites = 943 Number in coding regions = 614 Number in noncoding regions = 329 Number of orfs with sites within 600 bp upstream = 203 Fraction of orfs with sites within 600 bp upstream = 0.0326052 Motif number 10 GTATTTTTCAATTTTAATTATTGTTTAACT 2 34 1 ATTTTAATTA 0.50947 -78 TTTAACGGGTAGTTAAACAATAATTAAAAT 2 44 0 AGTTAAACAA 0.874578 -68 TTTAGTTGTAGTTTCATAATTTTATCCTT 3 10 1 AGTTTCATAA 0.674319 -178 AGAGGGGGATAGTTAGATAAA 4 2 0 AGTTAGATAA 0.89277 -94 GCCGTACTTTTTTTAAATTAGGCATACGCA 4 65 1 TTTTAAATTA 0.402687 -31 TATGGATAAAAATTTAATTAAAATTTCATT 5 60 0 AATTTAATTA 0.509474 -64 ATCCATAAACAGTTAAACTATCTGCCATAA 5 83 1 AGTTAAACTA 0.845562 -41 ATCTGCCATAAATTACATAACAGGAGAACA 5 102 1 AATTACATAA 0.728658 -22 GATAAATGCGTGTTAAATAAATACAATAGA 6 33 0 TGTTAAATAA 0.726945 -268 TATTTTCAGGATTTACATTAAATAAATTCA 7 76 0 ATTTACATTA 0.678302 -117 AATCTATCTAAGATAGATAAAATTAAATTA 9 96 1 AGATAGATAA 0.416021 -205 AGATAGATAAAATTAAATTAAGTTAAGTAA 9 106 1 AATTAAATTA 0.806827 -195 AATTAAATTAAGTTAAGTAAAAACAGAATT 9 116 1 AGTTAAGTAA 0.676535 -185 GTAAAAACAGAATTAAACAAATTAGATAAA 9 132 1 AATTAAACAA 0.692222 -169 TAATTATTTTAGTTAAAATACAAAACCCCA 9 191 0 AGTTAAAATA 0.579486 -110 AAAATTAATTATTTAGATAATTATTTTAGT 9 208 0 ATTTAGATAA 0.728658 -93 ********** Masking position 4 Map Score: 4.05842 Number of sites scoring better than the average of aligned sites = 708 Number in coding regions = 524 Number in noncoding regions = 184 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 11 ATCACCGCACTTTTTTATTGTTACAATAAT 1 71 0 TTTTTTATTG 0.409021 -121 AATTTCGAGCATCTATATTTTTATACTCAA 1 168 1 ATCTATATTT 0.80548 -24 ATTTAATCTTTTCTATATTTAAGCAAACGT 3 114 1 TTCTATATTT 0.947096 -74 AAAATTTCATTCCTAAATTTTCATCACTTA 5 41 0 TCCTAAATTT 0.47897 -83 AATACAATAGATTTGTTTTTTAGCGCAAAA 6 14 0 ATTTGTTTTT 0.237645 -287 CGGTAATTTTTTGTGTATTTTTATAGAAAG 6 62 0 TTGTGTATTT 0.680549 -239 GAATGCTTGATTATGAATTTATTTAATGTA 7 63 1 TTATGAATTT 0.382724 -130 AGATCAAGCATTCTATATTGGTATAGACGT 7 127 1 TTCTATATTG 0.806881 -66 TCGTTTGTTTTTCTAAATCTAAAACGGAGG 8 82 0 TTCTAAATCT 0.643147 -26 TATATTTAGATTTTTTATTTGATAACCTGG 9 66 0 TTTTTTATTT 0.747824 -235 TCTTAGATAGATTTATATTTAGATTTTTTA 9 79 0 ATTTATATTT 0.569435 -222 ATTTGTTTAATTCTGTTTTTACTTAACTTA 9 124 0 TTCTGTTTTT 0.808414 -177 TCTATATTTATTCTTTATCTAATTTGTTTA 9 145 0 TTCTTTATCT 0.684245 -156 TAAACTGGGGTTCTATATTTATTCTTTATC 9 156 0 TTCTATATTT 0.947096 -145 AGGACTGGGGTTTTGTATTTTAACTAAAAT 9 186 1 TTTTGTATTT 0.853508 -115 ATTAGCATATTTCTAATTTTAATGTATTAT 9 242 1 TTCTAATTTT 0.641089 -59 GGTTCCCTAATTCTTAATTTTATATGAATA 9 275 1 TTCTTAATTT 0.800206 -26 ********** Masking position 4 Map Score: 8.94509 Number of sites scoring better than the average of aligned sites = 807 Number in coding regions = 562 Number in noncoding regions = 245 Number of orfs with sites within 600 bp upstream = 205 Fraction of orfs with sites within 600 bp upstream = 0.0329264 Motif number 12 ********** No masking Map Score: 1.45904e-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 Motif number 13 ********** No masking Map Score: 1.45904e-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 Motif number 14 ********** No masking Map Score: 1.45904e-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