AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00310_hinf_reg_100.orf -o00310_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 Input sequences: #1 HI0028 55 conserved hypothetical protein #2 HI0030 51 lipoprotein, putative #3 HI0033 53 conserved hypothetical protein #4 HI0034 124 conserved hypothetical protein #5 HI0121 300 conserved hypothetical protein #6 HI0151 109 hflK protein (hflK) #7 HI0195.1 26 conserved hypothetical transmembrane protein (aefA) #8 HI0197 84 penicillin-insensitive murein endopeptidase (mepA) #9 HI0199 46 lipid A biosynthesis (kdo)2-(lauroyl)-lipid IVA acyltransferase (msbB) #10 HI0301 300 hemolysin, putative #11 HI0419 168 protease, putative #12 HI0587 99 peptidase E (pepE) #13 HI0774 205 acetate CoA-transferase, alpha subunit #14 HI0889 123 serine hydroxymethyltransferase (serine methylase) (glyA) #15 HI0916 107 outer membrane protein, putative #16 HI1024 49 hexulose-6-phosphate synthase, putative #17 HI1027 58 L-xylulose kinase (lyx) #18 HI1028 30 conserved hypothetical protein #19 HI1030 71 conserved hypothetical transmembrane protein #20 HI1031 175 conserved hypothetical protein #21 HI1527 84 lipid A biosynthesis lauroyl acyltransferase (htrB) #22 HI1541 97 protease IV (sppA) #23 HI1661 102 2-oxoglutarate dehydrogenase E2 component, dihydrolipoamide succinyltransferase(sucB) #24 HI1662 157 2-oxoglutarate dehydrogenase E1 component (sucA) #25 HI1682 197 protease, putative (sohB) Motif number 1 AATAAATCAAAAAGTGCGGTCAATTTTCAA 1 18 0 AAAGTGCGGT 0.999025 -38 ATTTTAGTAAAGTGCGGTAAAAAATAAC 3 9 1 AAAGTGCGGT 0.999025 -45 CCTTATCTAAAAAGTGCGGTTATTTTTTAC 3 27 0 AAAGTGCGGT 0.999025 -27 TTAGACATAAAAAGCGCGGTTAATTTCGCG 4 27 1 AAAGCGCGGT 0.99432 -98 CTTAGCAATAAAGGTGCGGAATTCTATCAT 4 95 0 AAGGTGCGGA 0.95721 -30 AAAGCGCGCAAAAGTGCGGTTAAAATTAAT 9 16 1 AAAGTGCGGT 0.999025 -31 GTTTAAACCTAAAGTGCGGTTAAAAATACA 10 175 0 AAAGTGCGGT 0.999025 -126 GTTTAAACCCAATGTGCGGTTATTTTTTAT 10 197 1 AATGTGCGGT 0.992384 -104 CTTGTAAAGGAAAGTGCGGTTAAATTCTTA 11 67 0 AAAGTGCGGT 0.999025 -102 CTTATAAGTAAAAGTGCGGTGGATTATAGC 22 21 1 AAAGTGCGGT 0.999025 -77 TCTCTTAAACAAAGTGCGGTTATTTTTACT 24 22 0 AAAGTGCGGT 0.999025 -136 TTTAAGAGATGAAGTGCGGTTTTTTATTGT 24 43 1 GAAGTGCGGT 0.994352 -115 ********** Masking position 2 Map Score: 52.0525 Number of sites scoring better than the average of aligned sites = 1115 Number in coding regions = 700 Number in noncoding regions = 415 Number of orfs with sites within 600 bp upstream = 285 Fraction of orfs with sites within 600 bp upstream = 0.0457758 Motif number 2 AATTTGAAAATTGACCGCACTTTTTGATTTA 1 15 1 TTACCGCACT 0.998438 -41 GCGGTTATTTTTTACCGCACTTTACTAAAAT 3 11 0 TTACCGCACT 0.998438 -43 GCGGTAAAAAATAACCGCACTTTTTAGATAA 3 24 1 ATACCGCACT 0.996994 -30 AAGCGCGAAATTAACCGCGCTTTTTATGTCT 4 29 0 TTACCGCGCT 0.990972 -96 GTAATTAATTTTAACCGCACTTTTGCGCGCT 9 18 0 TTACCGCACT 0.998438 -29 TTGTGTATTTTTAACCGCACTTTAGGTTTAA 10 172 1 TTACCGCACT 0.998438 -129 TCAATAAAAAATAACCGCACATTGGGTTTAA 10 199 0 ATACCGCACA 0.974626 -102 CACTAAGAATTTAACCGCACTTTCCTTTACA 11 64 1 TTACCGCACT 0.998438 -105 TATGCTATAATCCACCGCACTTTTACTTATA 22 23 0 TCACCGCACT 0.991763 -75 CTTTATTAAATTAACCGCACT 23 1 0 TTACCGCACT 0.998438 -102 ACAAGTAAAAATAACCGCACTTTGTTTAAGA 24 19 1 ATACCGCACT 0.996994 -139 CAAACAATAAAAAACCGCACTTCATCTCTTA 24 45 0 AAACCGCACT 0.976818 -113 ** ******** Masking position 4 Map Score: 45.5922 Number of sites scoring better than the average of aligned sites = 842 Number in coding regions = 496 Number in noncoding regions = 346 Number of orfs with sites within 600 bp upstream = 239 Fraction of orfs with sites within 600 bp upstream = 0.0383874 Motif number 3 CTTTCCTAAAAATAAAATAAATCAAAAAGTGCGGT 1 28 0 AATATAATAA 0.840641 -28 ACAATGGCTCACTATTTACAAAGAAAATAATCAGC 5 97 0 ACTAAAAAAA 0.779574 -204 TAACCACTTCAATAGGAATAAACAATGAAATTTAA 5 154 0 AATAAAAAAA 0.924152 -147 GAAAACGAAAAATATGATAAAACAACTTCTATGAA 5 255 0 AATATAAAAA 0.861264 -46 CGAAAAGAGGAAAATCAATAAAAAATAACCGCACA 10 209 0 AAAAAAAAAA 0.807654 -92 AAAAATTATCATATTTTAGAAAAAATCGCAAAACG 10 244 0 ATATAAAAAA 0.597393 -57 TTGTTTGACGAATATCAAAAAATAAACCGTATCAG 12 20 0 AATAAAAAAA 0.924152 -80 TAGCAAAAAGAATTTCGTAAAAGAAATACATCTTT 13 56 0 AATTTAAAAA 0.72388 -150 TAAAAGAAAGAATATCAACAAATAAGTATCTTATA 13 159 0 AATAAAAAAA 0.924152 -47 TCCATATCATTATGATGAATTAATTTCATTTAA 14 9 1 ATTATAATAA 0.815428 -115 TTGATAAATATCCTTAATTAAATGATGGGTT 15 87 0 AATATAATAA 0.840641 -21 AATAGGCTGGATTTTACATAATAAAAATCCAGCCC 17 13 1 ATTTAAATAA 0.785487 -46 AACGAATCACATTTGTGATAATCAATTGGAGGTGT 19 46 1 ATTTAAATAA 0.785495 -26 TTTATAAATCAATATGTTAAAATAATTTTACTGAT 20 59 0 AATATAAAAA 0.861264 -117 AGCTCAGTCAATAAATGTAAAATAAATAAATTATT 20 92 0 ATAATAAAAA 0.641807 -84 TACGTTTCATAATTTACAAAAATAAGAAAGCTCAG 20 120 0 AATTAAAAAA 0.837277 -56 ACGTAATTTTACTATATAAAATTAAGAGAGGAAAA 20 150 1 ACTAAAATAA 0.750327 -26 ACTTTTACTTATAAGGGATAATAAA 22 1 0 ATAAAAATAA 0.749268 -97 ACAAATTACCTTTAAAAAATTTGTGCTAG 22 79 0 ATTATAAAAA 0.838693 -19 AAAAAAGAAGAAAAGGAAAAATAAA 23 88 1 AAAAAAATAA 0.781087 -15 AACTCTTTAGATTTCAAACAATAAAAAACCGCACT 24 55 0 ATTTAAATAA 0.785495 -103 GCTATGCCAAATTAGCCAAAATGAAAATAAAAAGT 25 47 1 ATTAAAATAA 0.896602 -151 AATGAAAATAAAAAGTAAGAATTAATTTAAAATTT 25 66 1 AAAAAAATAA 0.781087 -132 TGTTTGTGCTATTTATAACAAAAAATTTTAAATTA 25 88 0 ATTTAAAAAA 0.811653 -110 **** * *** ** Masking position 10 Map Score: 25.1882 Number of sites scoring better than the average of aligned sites = 508 Number in coding regions = 358 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 4 GAATAAATGAAAAGCGTTAATATTTT 2 36 1 AAAATATTTT 0.943874 -16 CCTTATCTAAAAAGTGCGGTTATTTTTTACCGCACT 3 21 0 AAAGTATTTT 0.81885 -33 TTTTATGTCTAAATTGAAATTATTTTTA 4 3 0 AAAATATTTT 0.926543 -122 TGCTACATAGAACGGCTGATTATTTTCTTTGTAAAT 5 83 1 AACATATTTT 0.757256 -218 TTAGGCAATAAAAAATCCTTGATTTTATATAAGGAT 6 19 0 AAATGATTTT 0.600327 -91 TTATTGCCTAAAAAGCCTTGTATTTTCATAGACGTG 6 44 1 AAATTATTTT 0.843395 -66 TATTTAGCTAAACTCTTAACAATTTTTTGACAA 6 87 1 AACAAATTTT 0.821231 -23 AATAAAATGTAATTAATTTTAACCGCACTT 9 27 0 AAATAATTTT 0.912104 -20 TCATATAAACAAAATAAGAATATTTTGTTGTCTAGA 10 115 1 AAAATATTTT 0.739057 -186 AAGTGCGGTTAAAAATACACAATTTTTACGGAGAGG 10 158 0 AAAAAATTTT 0.883286 -143 GATTTTTTCTAAAATATGATAATTTTTCGCCGTCAA 10 252 1 AAAAAATTTT 0.751876 -49 TACAACCTATTAAGCGGTTAAATTTTATATAAAATT 11 27 1 TAATAATTTT 0.586149 -142 ACTTTCCTTTACAAGCCAAATATTTTCTCTACAATA 11 82 1 ACAATATTTT 0.616833 -87 GATATTCGTCAAACAATTATAATTTTTCGTTGAAAA 12 39 1 AAAAAATTTT 0.957928 -61 CTAGATCACAAAATCAGTAAAATTATTTTAACATAT 20 47 1 AAAAAATTAT 0.749039 -129 CAATAAATGTAAAATAAATAAATTATTTATAAATCA 20 83 0 AAATAATTAT 0.532392 -93 AGTTGTGGTAAAATCGCCACAATTTTGGTTATTCAA 21 27 0 AAAAAATTTT 0.961348 -58 TCTCTTAAACAAAGTGCGGTTATTTTTACTTGTATT 24 16 0 AAAGTATTTT 0.81885 -142 CTCTTATCGGAAATTGTTACAAATTTGTGATCTAGT 24 93 0 AAAAAAATTT 0.594356 -65 TAAATAGCACAAACAATCACAATGTTTTATTATGTT 25 108 1 AAAAAATGTT 0.70466 -90 CGTTGATATTTAATGGATTAAATTTTCACGACACTG 25 163 0 TAATAATTTT 0.586146 -35 *** * ****** Masking position 16 Map Score: 20.6871 Number of sites scoring better than the average of aligned sites = 606 Number in coding regions = 380 Number in noncoding regions = 226 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 5 TTTCATTTTTTCTTTCTTAAAGAAAGAA 2 7 1 TTTTCTTTTT 0.957365 -45 CGCTTTTCATTTATTCTTTCTTTAAGAAAGAA 2 20 0 TTTTCTTTTT 0.957365 -32 TTTGTTCTCACTTAGCAATAAAG 4 112 0 TTTTCTCATT 0.939633 -13 TGTATTTCTCTGTTGATTAAGGAA 5 287 0 TATTCTCTTT 0.836631 -14 ATAAGGATCTTTGCCCTCTTTTTACGAGATCA 10 28 1 TTCCCTCTTT 0.783591 -273 AGACAACAAAATATTCTTATTTTGTTTATATG 10 116 0 ATTTCTTATT 0.842618 -185 TTTTTATTGATTTTCCTCTTTTCGCGTTTTGC 10 220 1 TTTCCTCTTT 0.961273 -81 AATATTCTCTTTTGTCTGATTTC 11 156 0 ATTTCTCTTT 0.91941 -13 TTATTTGTTGATATTCTTTCTTTTAATCTCGT 13 169 1 ATTTCTTTTT 0.903727 -37 TTGATAAATATCCTTAATTAAATGATGGG 15 89 0 ATTCCTTATT 0.829634 -19 ATATTCTCCTTAGTTTTTTATGGGC 17 44 0 TTTCCTTATT 0.920942 -15 TTTTTCCTCTCTTAATTTTATAT 20 163 0 TTTCCTCTTT 0.961273 -13 ATTTTTCCTTTTCTTCTTTTTTACTATATCTT 23 78 0 TTTTCTTTTT 0.957365 -25 AATTTTAAATTAATTCTTACTTTTTATTTTCA 25 68 0 TATTCTTATT 0.70617 -130 ** ****** ** Masking position 7 Map Score: 14.978 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 163 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 6 GAATAAATGAAAAGCGTTAATATTTT 2 36 1 AATAATATTT 0.870171 -16 TAAAAATAATTTCAATTTAGACATAAAA 4 4 1 AATTCAATTT 0.627317 -121 TGCTACATAGAACGGCTGATTATTTTCTTTGTAAA 5 83 1 AATATTATTT 0.745295 -218 TCAGAAGCACAATGGCTCACTATTTACAAAGAAAA 5 105 0 AATACTATTT 0.929848 -196 TATTTAGCTAAACTCTTAACAATTTTTTGACAA 6 87 1 AATACAATTT 0.962533 -23 GTGCGGTTAAAATTAATTACATTTTATT 9 29 1 AATACATTTT 0.817135 -18 TCATATAAACAAAATAAGAATATTTTGTTGTCTAG 10 115 1 AAAAATATTT 0.441619 -186 AAGTGCGGTTAAAAATACACAATTTTTACGGAGAG 10 159 0 AAAACAATTT 0.699034 -142 GATTTTTTCTAAAATATGATAATTTTTCGCCGTCA 10 252 1 AATATAATTT 0.573324 -49 ACAACCTATTAAGCGGTTAAATTTTATATAAAATT 11 28 1 AATAAATTTT 0.760959 -141 GATATTCGTCAAACAATTATAATTTTTCGTTGAAA 12 39 1 AATATAATTT 0.828113 -61 AATTTCATTTAAGTGATGAAAATTTAGGAATGAAA 14 32 1 AATAAAATTT 0.941315 -92 ATGGATAAAAATTTAATTAAAATTTCATTCCTAAA 14 54 0 ATTAAAATTT 0.760549 -70 TAATTAAATGATGGGTTTAATATTTTCTCTGCCCA 15 69 0 ATTAATATTT 0.584157 -39 TTTAAAATCTCTCTATTTGAATAACCAA 21 4 1 AATTCTATTT 0.61626 -81 AGTTGTGGTAAAATCGCCACAATTTTGGTTATTCA 21 28 0 AACACAATTT 0.762967 -57 CTAGATCACAAATTTGTAACAATTTCCGATAAGAG 24 94 1 AATACAATTT 0.738071 -64 AAAAGTAAGAATTAATTTAAAATTTTTTGTTATAA 25 76 1 ATTAAAATTT 0.760832 -122 TAAATAGCACAAACAATCACAATGTTTTATTATGT 25 108 1 AATACAATGT 0.750699 -90 GTTGATATTTAATGGATTAAATTTTCACGACACTG 25 163 0 AATAAATTTT 0.761064 -35 ** * ******* Masking position 13 Map Score: 15.6659 Number of sites scoring better than the average of aligned sites = 352 Number in coding regions = 254 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 7 GATTTTATATAAGGATTTTTTTGA 6 5 0 AAGGATTTTT 0.971171 -105 ATATAAAATCAAGGATTTTTTATTGCCTAA 6 25 1 AAGGATTTTT 0.971171 -85 ATGAAAATACAAGGCTTTTTAGGCAATAAA 6 43 0 AAGGCTTTTT 0.954839 -67 TTGATGTGATAAGGATCTTTGCCCTCTTTT 10 20 1 AAGGATCTTT 0.883962 -281 CTTGTGAATAATGGATTTTTGATTGTGAAT 10 60 0 ATGGATTTTT 0.952172 -241 AAGGATTGTTTAAAACACTA 13 1 1 AAGGATTGTT 0.864052 -205 TATATTTCAAATGGATATGTTTCTTGCGAT 13 133 0 ATGGATATGT 0.679902 -73 TCATTTAATTAAGGATATTTATCAA 15 93 1 AAGGATATTT 0.903659 -15 TTTTTATGGGCTGGATTTTTATTATGTAAA 17 25 0 CTGGATTTTT 0.789441 -34 GTTTTATATTATGGCGTTTTACTGGAAACA 19 19 0 ATGGCGTTTT 0.701336 -53 AGTTTTTGACAAGGCTTTGTGATACGCTAG 22 53 1 AAGGCTTTGT 0.890313 -45 ********** Masking position 10 Map Score: 10.4426 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 138 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 8 TTTCTTTCCTAAAAATAAAATAAATCAAA 1 37 0 TTTCCATAAA 0.853661 -19 TTTCATTTTTTCTTTCTTAAAGAAAGAATAA 2 7 1 TTTTTTTAAA 0.803572 -45 TTGAATACTTTTTCCAAATTGTAATGCAGGAAGAT 5 47 1 TTTCCATAAT 0.844533 -254 AATCAAGGATTTTTTATTGCCTAAAAAGCCTTGTA 6 31 1 TTTTTTTAAA 0.804953 -79 TATTTTTCCCTAATCTAAATGGTAAA 7 8 0 TTTCCTTAAA 0.896539 -19 ACATAGATACTTTTCGTCATATAAACAAAATAAGA 10 99 1 TTTTCTTAAA 0.922348 -202 AAAAGGTTAATTTTCAACGAAAAATTATAATTGTT 12 50 0 TTTTCAAAAT 0.511277 -50 AAAATTAACCTTTTCTAAGCGTAATATTGGTATTG 12 71 1 TTTTCATAAT 0.928412 -29 CGAAATTCTTTTTGCTATTTTTAATATCAATCTAG 13 74 1 TTTGCATAAT 0.672935 -132 CATTCCTAAATTTTCATCACTTAAATGAAATTAAT 14 29 0 TTTTCTTAAA 0.951327 -95 CGTTTTTCCTTAAATAATATGAGGAAGG 16 32 0 TTTTCTTAAT 0.945782 -18 ATGGGCTGGATTTTTATTATGTAAAATCCAGCCTA 17 15 0 TTTTTTTAAA 0.70334 -44 CTAGATCCTATTTTCTTGTGATAATATTTCATATT 20 16 0 TTTTCTTAAT 0.946557 -160 TTTTTCCTCTCTTAATTTTATATAGT 20 160 0 TTTTCTTAAT 0.948318 -16 CTAGCACAAATTTTTTAAAGGTAATTTGT 22 79 1 TTTTTATAAT 0.713308 -19 TGCGGTTATTTTTACTTGTATTAAAAT 24 3 0 TTTACTTAAA 0.672302 -155 AACTCTTTAGATTTCAAACAATAAAAAACCGCACT 24 55 0 ATTTCATAAA 0.5395 -103 ***** * **** Masking position 3 Map Score: 16.0115 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 275 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 9 AAACAATGAAATTTAAGCGATAAAGCAATTTCA 5 137 0 ATTTAACGTA 0.956037 -164 GTTTATTCCTATTGAAGTGGTTAAATAATAGTT 5 166 1 ATTGAATGTA 0.832723 -135 TTTTTCCCTAATCTAAATGGTAAA 7 2 0 ATCTAATGTA 0.819428 -25 AATAGGTTGTATTTAATTCCTCAAATC 11 5 0 ATTTAATCTA 0.950202 -164 TTTATATAAAATTTAACCGCTTAATAGGTTGTA 11 27 0 ATTTAACGTA 0.956037 -142 ACTTAAATGAAATTAATTCATCATAATGATATG 14 13 0 AATTAATCTA 0.688485 -111 AATTAATTTCATTTAAGTGATGAAAATTTAGGA 14 28 1 ATTTAATGTA 0.963549 -96 TTTAATTAAAATTTCATTCCTAAATTTTCATCA 14 45 0 ATTTCATCTA 0.766118 -79 ATGGCAGATAGTTTAACTGTTTATGGATAAAAA 14 78 0 GTTTAATGTA 0.819428 -46 TCTCTGCCTAATTTAATTGGGCAGAGAAAATAT 15 52 1 ATTTAATGGA 0.819428 -56 CAGAGAAAATATTAAACCCATCATTTAATTAAG 15 73 1 ATTAAACCTA 0.666057 -35 TGTCGTGAAAATTTAATCCATTAAATATCAACG 25 166 1 ATTTAACCTA 0.94011 -32 ****** ** * * Masking position 6 Map Score: 4.01911 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 112 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 10 TTTTTGATTTATTTTATTTTTAGGAAAGAA 1 35 1 ATTTTATTTT 0.814549 -21 ATATTAACGCTTTTCATTTATTCTTTCTTT 2 29 0 TTTTCATTTA 0.809247 -23 TAAAAATAATTTCAATTTAGACATAAAA 4 9 1 ATTTCAATTT 0.377031 -116 TTGGGACTTCAATTCATTTTGCTGAC 5 7 0 AATTCATTTT 0.528852 -294 TATCGCTTAAATTTCATTGTTTATTCCTAT 5 148 1 ATTTCATTGT 0.829689 -153 TTTATCATATTTTTCGTTTTCCTTAATCAA 5 269 1 TTTTCGTTTT 0.618461 -32 AAAATCCTTGATTTTATATAAGGATTTTTT 6 14 0 ATTTTATATA 0.54539 -96 GTTAAAATTAATTACATTTTATT 9 34 1 ATTACATTTT 0.377031 -13 AAATATTCTTATTTTGTTTATATGACGAAA 10 110 0 ATTTTGTTTA 0.668828 -191 AAATAAGAATATTTTGTTGTCTAGAATTTT 10 126 1 ATTTTGTTGT 0.488707 -175 GTGCGGTTATTTTTTATTGATTTTCCTCTT 10 210 1 TTTTTATTGA 0.507637 -91 TCTTAGTGGAATTTTATATAAAATTTAACC 11 42 0 ATTTTATATA 0.54539 -127 CAATTATAATTTTTCGTTGAAAATTAACCT 12 52 1 TTTTCGTTGA 0.480035 -48 AGAAAGATGTATTTCTTTTACGAAATTCTT 13 54 1 ATTTCTTTTA 0.452579 -152 TGATGAATTAATTTCATTTAAGTGATGAAA 14 23 1 ATTTCATTTA 0.911452 -101 TTGTGATAATATTTCATATTGTGAA 20 6 0 ATTTCATATT 0.700265 -170 ATTTATAAATAATTTATTTATTTTACATTT 20 85 1 AATTTATTTA 0.365641 -91 TCCTCTCTTAATTTTATATAGTAAAATTAC 20 152 0 ATTTTATATA 0.54539 -24 GAAGTGCGGTTTTTTATTGTTTGAAATCTA 24 53 1 TTTTTATTGT 0.4845 -105 ATAAGCGAGTATTTCATTTATACCAAAGGA 25 17 0 ATTTCATTTA 0.911452 -181 TTACTTTTTATTTTCATTTTGGCTAATTTG 25 54 0 TTTTCATTTT 0.794546 -144 ********** Masking position 3 Map Score: 10.0529 Number of sites scoring better than the average of aligned sites = 919 Number in coding regions = 740 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 11 TAGAGTATACTACCCTAGGTACAGGA 8 7 0 TACCCTAGGT 0.98603 -78 TAGGGTAGTATACTCTAGGTTAGTTCTTCA 8 20 1 TACTCTAGGT 0.978552 -65 TAGGTAAGTATATCCTAGGTTCAGTCCTAT 8 50 0 TATCCTAGGT 0.94671 -35 GTCAGGGACTTACTCAAGGTAAATCGTTAG 11 124 0 TACTCAAGGT 0.947529 -45 ********** Masking position 7 Map Score: 0.750349 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 5 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 12 TCAAAAAAATCCTTATATAAAATCAA 6 7 1 AAATCCTTAT 0.937221 -103 AGGCAATAAAAAATCCTTGATTTTATATAA 6 23 0 AAATCCTTGA 0.789154 -87 TATTGCCTAAAAAGCCTTGTATTTTCATAG 6 45 1 AAAGCCTTGT 0.956083 -65 AAGAGGGCAAAGATCCTTATCACATCAAAC 10 18 0 AGATCCTTAT 0.947445 -283 TTGAAATATAAGATACTTATTTGTTGATAT 13 153 1 AGATACTTAT 0.736078 -53 AGCGTATCACAAAGCCTTGTCAAAAACTAT 22 51 0 AAAGCCTTGT 0.956083 -47 ATTTCCGATAAGAGGCTTATTTCCGTTGCA 24 115 1 AGAGGCTTAT 0.83306 -43 ********** Masking position 3 Map Score: 0.639493 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 75 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 13 TAAAGTGCGGTAAAAAATAACCGCACTTTT 3 18 1 TAAAAAATAA 0.70268 -36 GGAAAATCAATAAAAAATAACCGCACATTG 10 206 0 TAAAAAATAA 0.70268 -95 CAATAAGACATCAAACACAAATCAAT 10 285 1 TCAAACACAA 0.907723 -16 TTGACGAATATCAAAAAATAAACCGTATCA 12 21 0 TCAAAAAATA 0.790308 -79 AAGGATTGTTTAAAACACTATCAAAATAAC 13 11 1 TAAAACACTA 0.860501 -195 TCATCAGAACTCAAAAACAACGTTCTCTGC 15 29 1 TCAAAAACAA 0.932505 -79 ATCCAGCCCATAAAAAACTAAGGAGAATAT 17 39 1 TAAAAAACTA 0.896519 -20 CAAAGCCTTGTCAAAAACTATGCTATAATC 22 42 0 TCAAAAACTA 0.932505 -56 TAAGATATAGTAAAAAAGAAGAAAAGGAAA 23 77 1 TAAAAAAGAA 0.665154 -26 TCTTTAGATTTCAAACAATAAAAAACCGCA 24 57 0 TCAAACAATA 0.728517 -101 ********** Masking position 5 Map Score: 4.16005 Number of sites scoring better than the average of aligned sites = 171 Number in coding regions = 126 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 14 GGACTTCAATTCATTTTGCTGAC 5 3 0 TCATTTTGTG 0.766434 -298 ATTTAACCGCTTAATAGGTTGTATTTAATTC 11 19 0 TTAATAGGTG 0.894286 -150 TCAAGGTAAATCGTTAGGTGGGGTATTGTAG 11 110 0 TCGTTAGGGG 0.915501 -59 AAATACATCTTTCTTAGGCGGGTATAAGTTA 13 37 0 TTCTTAGGGG 0.846497 -169 TTTAATCTCGTTATTAGGAGGTCTCT 13 190 1 TTATTAGGGG 0.954049 -16 TCCATATCATTATGATGAATTAATTTC 14 7 1 TCATTATGTG 0.912159 -117 TCAATAGGCTGGATTTTACAT 17 1 1 TCAATAGGTG 0.943248 -58 TTTGTGATAATCAATTGGAGGTGTA 19 57 1 TCAATTGGGG 0.871164 -15 TCACAATGTTTTATTATGTTGGCGATCTACA 25 124 1 TTATTATGTG 0.8409 -74 ******** ** Masking position 5 Map Score: 2.10517 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 46 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 15 ********** No masking Map Score: 2.09143e-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