AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00260_hpyl_reg_300.orf -o00260_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -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: HP0106 24 cystathionine gamma-synthase (metB) Input sequences: #1 HP0096 72 phosphoglycerate dehydrogenase #2 HP0098 203 threonine synthase (thrC) #3 HP0107 38 cysteine synthetase (cysK) #4 HP0122 186 H. pylori predicted coding region HP0122 #5 HP0123 39 threonyl-tRNA synthetase (thrS) #6 HP0133 180 serine transporter (sdaC) #7 HP0181 257 H. pylori predicted coding region HP0181 #8 HP0398 28 H. pylori predicted coding region HP0398 #9 HP0399 120 ribosomal protein S1 (rps1) #10 HP0403 80 phenylalanyl-tRNA synthetase, alpha subunit (pheS) #11 HP0653 296 nonheme iron-containing ferritin (pfr) #12 HP0813 132 conserved hypothetical protein #13 HP0818 68 osmoprotection protein (proWX) #14 HP0820 173 H. pylori predicted coding region HP0820 #15 HP0961 131 glycerol-3-phosphate dehydrogenase (NAD(P)+) #16 HP0966 220 conserved hypothetical protein #17 HP0967 285 virulence associated protein D (vapD) #18 HP0971 49 H. pylori predicted coding region HP0971 #19 HP0972 111 glycyl-tRNA synthetase, beta subunit (glyS) #20 HP1050 53 homoserine kinase (thrB) #21 HP1051 72 H. pylori predicted coding region HP1051 #22 HP1054 63 H. pylori predicted coding region HP1054 #23 HP1057 148 H. pylori predicted coding region HP1057 #24 HP1067 290 chemotaxis protein (cheY) #25 HP1190 61 histidyl-tRNA synthetase (hisS) #26 HP1227 73 cytochrome c553 #27 HP1228 150 invasion protein (invA) #28 HP1360 28 4-hydroxybenzoate octaprenyltransferase (ubiA) #29 HP1361 56 competence locus E (comE3) #30 HP1365 83 response regulator #31 HP1368 300 type IIS restriction enzyme M2 protein (mod) #32 HP1483 26 gerC2 protein (gerC2) #33 HP1490 103 hemolysin #34 HP1491 138 phosphate permease Motif number 1 GCTTAGTTTCTTTTAAAAAAGGATTTTGTGGTTTA 1 11 1 TTTTAAAATT 0.915964 -62 CTAGATTTAATTTTAAAGTTATATAATTAAACCAC 1 38 0 TTTTAAAGTA 0.846289 -35 TGCGGCAAAATTTTAAACCGCATTATAGTATTATA 2 46 1 TTTTAAACTA 0.875901 -158 TTAATGATCATTTTAAGGGAGTTTT 4 1 0 TTTTAAGGTT 0.957212 -186 TATATTTTTGTTTTAAGAAACTTAATGATCATTTT 4 22 0 TTTTAAGAAA 0.600944 -165 ATTTTAAGGTTTGAAGAAAGGAAACA 5 2 1 TTTTAAGGAG 0.663832 -38 ATTAATCTTTTTTTAAGCGTTATTATAGCTTGTGC 6 25 1 TTTTAAGCTA 0.919709 -156 AGATTGATTTTTTTAAGGGTAGTTTTTTTTAAGTT 7 76 1 TTTTAAGGTT 0.957212 -182 AGGGTAGTTTTTTTTAAGTTGTGTTATTATTTTCA 7 91 1 TTTTTAAGTT 0.662465 -167 TGGGTGTTTGTTTTAAGACGCTATGACTATCTTTA 7 170 1 TTTTAAGATG 0.87997 -88 ATTCTCATGCTTTTAAAATCACTCT 8 1 0 TTTTAAAACT 0.826491 -28 TTAGCGGTTTTTTTAAAGAAAATTTTCAAAATGTG 9 11 0 TTTTAAAGTT 0.932351 -110 AATTGTTAGTTTTTAAACGATTTTGTAAGCCAAAA 9 44 1 TTTTAAACTG 0.87982 -77 TTTTGCTCCCTTTTAAGGTTTTTCTTTTATTAAAG 10 15 1 TTTTAAGGCT 0.907206 -66 TATATTTTATTTTTAAAAAGCTATAATACAACTTT 10 46 0 TTTTAAAATA 0.81324 -35 TGCCCTTTCGTTTTAAAGATAAACATTGTAGCATT 11 19 1 TTTTAAAGCA 0.70641 -278 AAATATCCCCTTTTAACCCCCTATTGATGCCAACC 11 89 1 TTTTAACCTT 0.838224 -208 GTATGAAAATTTTTAAAAATTTACAAAAATGAGAA 11 201 0 TTTTAAAACA 0.655529 -96 AATAATGACTTTTTAAAACTAGTTTGAAGGGAGTT 12 102 1 TTTTAAAATT 0.915964 -31 GCCTTTAGCATTTTAAAACCCCTTTATCCAAATAA 13 33 1 TTTTAAAATT 0.915964 -36 TTTTAAGGCTGATTTAAAAATTCTG 14 1 1 TTTTAAGGTT 0.957212 -173 GTTTGAAGTTTTTTTAGCGGGTTTTTCATTGAATG 14 79 1 TTTTTAGCTT 0.803295 -95 CTTAACATGCTTTTTAGCGCTTGTAGCAATAACCA 14 141 0 TTTTTAGCTA 0.619986 -33 CGCTTTTTAATTTTAAAATATTATTTAATATGTAT 15 11 1 TTTTAAAATT 0.915964 -121 GTAAGGGCTATTTTAAACTTATTATTGTAAAATGG 15 75 1 TTTTAAACAT 0.790097 -57 GAAAGCGAATTTTTAAGAATAATCATCATTACAAA 16 49 0 TTTTAAGACA 0.755436 -172 TCTTCGCTGCTTTTAAGCCAAAAAGAGCAGGTGAG 17 60 1 TTTTAAGCAG 0.716849 -226 TTCAAGCTTTTTTTAAGCGAGGAAGTCGCTTTACC 17 116 1 TTTTAAGCAG 0.716857 -170 GCGAACTGATTTTTTAAAGCTTTTGCTAGAGGTAA 17 146 0 TTTTTAAATG 0.391427 -140 ACAAAATCACTTTTAAGACTAAATCATGTTAGAAT 19 66 0 TTTTAAGATC 0.81033 -46 GTGATTTTGTTTTTTAGGGAGAATTGAGATT 19 91 1 TTTTTAGGTT 0.761093 -21 ACCCTTTCATTTTTAAAACTAGCATTATACA 20 7 0 TTTTAAAAAT 0.699 -47 ATTTTAAACCCCTATTGTTGATACCC 20 38 0 TTTTAAACTT 0.94643 -16 AACGCTAAAATTTTAAACCTTAACTCCAAGATCAA 22 14 0 TTTTAAACCT 0.885269 -50 TTTTACTCCATTTTAACCGGTCATTTTAATTATTT 23 73 1 TTTTAACCTT 0.838224 -76 TGAAAGAAACTTTTAACAAACAATTCAAGGGATTT 23 117 1 TTTTAACATT 0.761714 -32 ATTTTATTACTTTTAAACGATTATCATAGCAAACA 24 79 1 TTTTAAACTC 0.810112 -212 ATTAGGCTCTTTTTAAACAGCCAAAGCGTCTCTAA 24 237 0 TTTTAAACAA 0.600604 -54 GTGCTTCTCCTTTTAAGATTGCATTTAAATTAGGC 24 265 0 TTTTAAGATT 0.946502 -26 TTTTTAAAGATTTTAAGCTAAAATTTTAGCATACA 25 21 1 TTTTAAGCTT 0.966304 -41 TTCATTTTAAGCAAAACTTAAACTTGTAA 26 5 1 TTTTAAGCTT 0.966304 -69 AATTGTATCATTTTAAGATCATTTTGATAAGTAGA 26 38 1 TTTTAAGATT 0.946502 -36 GCGGTGTCTTTTTTAAGGGAGTGTTTTTTTATAAC 30 20 1 TTTTAAGGTT 0.957212 -64 TTCCTATGTTTTTTAAGGAGCGTTATAATGAAAAC 31 55 0 TTTTAAGGTA 0.899369 -246 GACGATTACCTTTTAAGCGAGAGCGTTAAGGAGTT 31 159 1 TTTTAAGCCG 0.838532 -142 TGACTCATTTTTTTAAAATACCCCCATTTCATTGT 31 224 1 TTTTAAAACC 0.534941 -77 TCTTATTTTTACCTTTTATTAAACTTCAAT 31 281 0 TTTTTACCTT 0.424579 -20 AAGGCTTGATTTTTAAAGTTAGGCTTAATCTTTTA 33 19 1 TTTTAAAGCT 0.857612 -85 TAAAGTAAAATTTTAAAGAGAGTTTTAAAAA 34 7 0 TTTTAAAGTT 0.932351 -132 AAACAACGCTTTTTAAGAGTGGCTCAAGGGCTAAT 34 70 1 TTTTAAGATC 0.81033 -69 ******** ** Masking position 6 Map Score: 65.257 Number of sites scoring better than the average of aligned sites = 1848 Number in coding regions = 1456 Number in noncoding regions = 392 Number of orfs with sites within 600 bp upstream = 289 Fraction of orfs with sites within 600 bp upstream = 0.0464182 Motif number 2 TCCAGTTTAATTTTTGATTTATGCTTATAAT 2 75 0 TTTTTATTTA 0.796133 -129 CCTTAAATGGTTTTTTAATGAGAACGATTGA 2 118 0 TTTTTAATGA 0.544348 -86 TTCCTTTTTATTTTTGGATAATTTCAAGTCG 2 176 0 TTTTTGATAA 0.621026 -28 CATTGTTATATTTTTGTTTTAAGAAACTTAA 4 32 0 TTTTTTTTTA 0.848094 -155 GGGTGTATTCTTTTTGGTTTATGATTTTATT 4 120 1 TTTTTGTTTA 0.780313 -67 TATAGCTATATTTTAATTTAAGAATTTTAGA 7 48 1 TTTTATTTAA 0.878941 -210 AATTTAAGAATTTTAGATTGATTTTTTTAAG 7 62 1 TTTTAATTGA 0.771042 -196 CCCTTAAGGATTTTATATTTATTTTATAGTA 9 91 1 TTTTAATTTA 0.867665 -30 CCTTTTAAGGTTTTTCTTTTATTAAAGTTGT 10 23 1 TTTTTTTTTA 0.848094 -58 GATCCTTATATTTTATTTTTAAAAAGCTATA 10 56 0 TTTTATTTTA 0.903601 -25 ATTGTAGCATTTTTAGATTTAAGAATGCTTT 11 43 1 TTTTAATTTA 0.867665 -254 AAAGGGGATATTTTTATATAATATGTAAAAA 11 71 0 TTTTTTATAA 0.720061 -226 TTAAATAGATTTTTATGATAAAATCTAAGCT 11 145 1 TTTTAGATAA 0.733422 -152 TTTTAGCGGGTTTTTCATTGAATGGAGGGGC 14 90 1 TTTTTATTGA 0.667308 -84 CGCTTTTTAATTTTAAAATATTATT 15 5 1 TTTTATTTTA 0.903601 -127 AAACTCACCATTTTACAATAATAAGTTTAAA 15 86 0 TTTTAAATAA 0.751301 -46 AGATTTTAGTTTTTAATTTTAAAGGATTG 16 202 1 TTTTATTTTA 0.903601 -19 GCGTTAGTCGTTTTAATTTTAGGGGGTTAT 22 44 1 TTTTATTTTA 0.903601 -20 ATTTTAATTATTTTAGTATAATTGAAAGAAA 23 95 1 TTTTATATAA 0.811741 -54 TAAGGGAGTGTTTTTTTATAACCGCTTTTAG 30 33 1 TTTTTTATAA 0.720061 -51 TTATAACCGCTTTTAGTATAAAGGCAATTAG 30 48 1 TTTTATATAA 0.811741 -36 CAAAAAAAGATTTTTTTATTAGAAGACGATT 31 135 1 TTTTTTATTA 0.768798 -166 CATGAAAGAATTTTACAATGAAATGGGGGTA 31 242 0 TTTTAAATGA 0.667305 -59 AGGCTTAATCTTTTATGTTAAAATTCTGAGA 33 39 1 TTTTAGTTAA 0.822045 -65 ATTTTATATATTTTATATTTATCGTTAGGTT 33 69 1 TTTTAATTTA 0.867665 -35 TATCGTTAGGTTTTAGGTTTAAAGTT 33 88 1 TTTTAGTTTA 0.856395 -16 CTCTTTAAAATTTTACTTTAAGATACCATAT 34 22 1 TTTTATTTAA 0.878941 -117 ***** ***** Masking position 4 Map Score: 30.2109 Number of sites scoring better than the average of aligned sites = 426 Number in coding regions = 298 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 3 TTTAAACCGCATTATAGTATTATAAGCATA 2 57 1 ATTATAGTAT 0.832956 -147 AAATATAACAATGATAGCATGATAGAGCTT 4 50 1 ATGATAGCAT 0.759442 -137 TTTAAGCGTTATTATAGCTTGTGCGGGTTA 6 36 1 ATTATAGCTT 0.913127 -145 AAGAGCTTTCATTGTAGCATAAAGCTTTTT 6 133 0 ATTGTAGCAT 0.972374 -48 TTAAAGTTGTATTATAGCTTTTTAAAAATA 10 44 1 ATTATAGCTT 0.913127 -37 AAAGATAAACATTGTAGCATTTTTAGATTT 11 33 1 ATTGTAGCAT 0.972374 -264 TAAAGCTTAGATTTTATCATAAAAATCTAT 11 149 0 ATTTTATCAT 0.61856 -148 TTGTCCCATAATTATAGCATAAATGATAAT 11 252 0 ATTATAGCAT 0.970028 -45 TCTTATTTAGATTTTAGTTTTTAATTTTAA 16 194 1 ATTTTAGTTT 0.522622 -27 AAGCGGCGTATTTATAGCATTCCACATAAA 17 31 0 TTTATAGCAT 0.687707 -255 ATTGGTTTGTGTTATAGCATGTTTTTACTT 17 254 0 GTTATAGCAT 0.765449 -32 AAGGTTTAAAATTTTAGCGTTAGTCGTTTT 22 28 1 ATTTTAGCGT 0.918699 -36 ATATAGTGGCATTGTAGCATGACTTTATTA 23 30 1 ATTGTAGCAT 0.972374 -119 CATTTTAATTATTTTAGTATAATTGAAAGA 23 94 1 ATTTTAGTAT 0.771728 -55 ATCGTTCCAAATAATAGCATGTTTTGATTA 24 191 0 ATAATAGCAT 0.686863 -100 TTAAGCTAAAATTTTAGCATACAAATACAA 25 33 1 ATTTTAGCAT 0.956511 -29 TAAACTTGTAATTGTATCATTTTAAGATCA 26 29 1 ATTGTATCAT 0.721807 -45 TTAAGATGGTATTATAGTGTATACTAGCTT 27 101 0 ATTATAGTGT 0.719264 -50 AGGTCTTTATTTTAGCTCTTTCTTGTTT 27 133 0 ATTTTAGCTC 0.669431 -18 GGGGGTATTGTAGCGCTAATTGCCTT 30 68 0 ATTGTAGCGC 0.837163 -16 GCATGGGGGTATTGTAGCGCTTAATGAGCG 31 106 0 ATTGTAGCGC 0.837163 -195 ********** Masking position 5 Map Score: 21.7946 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 157 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 4 AGTTTCTTTTAAAAAAGGATTTTGTGGTTTA 1 15 1 AAAAAAGGAT 0.929101 -58 AAACTGGATTAAAAAGACGATCAATCGTTCT 2 98 1 AAAAAGACGT 0.713444 -106 TATCCAAAAATAAAAAGGAATCATTTT 2 187 1 TAAAAAGGAT 0.825072 -17 TAAGCTTTTTAATAAGAGGGTGTATTCTTTT 4 103 1 AATAAGAGGT 0.571758 -84 AAAAAAGATTAATAAAGGATTATAGAA 6 7 0 AATAAAGGAT 0.849387 -174 AATAACGCTTAAAAAAAGATTAATAAAGGAT 6 18 0 AAAAAAAGAT 0.781258 -163 ACTACCCTTAAAAAAATCAATCTAAAATTCT 7 68 0 AAAAAATCAT 0.768543 -190 ATATAATATGTAAAAAGCATTCTTAAATCTA 11 56 0 TAAAAAGCAT 0.791018 -241 AATAGGGGGTTAAAAGGGGATATTTTTATAT 11 83 0 TAAAAGGGGT 0.803808 -214 GAATTAGGTAAAAAAAGGGGTTGGCATCAAT 11 111 0 AAAAAAGGGT 0.951709 -186 ATAGCGCAAAAATAAGGCGATTTTGACTAGA 12 61 0 AATAAGGCGT 0.797211 -72 AACTAGTTTTAAAAAGTCATTATTATTGAAA 12 95 0 AAAAAGTCAT 0.657287 -38 AAAAATCCCCAAAAAAGGGTTTATATGGGTT 16 149 0 AAAAAAGGGT 0.951709 -72 CAAAAGCTTTAAAAAATCAGTTCGCTTCTAA 17 156 1 AAAAAATCAT 0.768543 -130 TGCGTTTGAGAATAAAACAATTTCATTTCTT 17 186 0 AATAAAACAT 0.552266 -100 AACACAAACCAATAAAGGAGTTAAA 17 271 1 AATAAAGGAT 0.849387 -15 GATTTAGTCTTAAAAGTGATTTTGTTTTTTA 19 76 1 TAAAAGTGAT 0.462416 -36 GCCTTATAATAATAAATCGTTCCAAATAATA 24 205 0 AATAAATCGT 0.682435 -86 GATTTATTATTATAAGGCGTTAGAGACGCTT 24 218 1 TATAAGGCGT 0.58591 -73 TAAAATCTTTAAAAAAGGGCTATTG 25 5 0 AAAAAAGGGT 0.951709 -57 AAAAATTAAGAAAAAAGGGCTTGAAACTCAT 27 51 0 AAAAAAGGGT 0.951709 -100 TAAAATAAAGCGGTGTCTTTTTTA 30 4 1 AATAAAGCGT 0.871896 -80 AAGCGGTTATAAAAAAACACTCCCTTAAAAA 30 29 0 AAAAAAACAT 0.741349 -55 ACCCCCATGCAAAAAAAGATTTTTTTATTAG 31 126 1 AAAAAAAGAT 0.781258 -175 GGGTATTTTAAAAAAATGAGTCAGTCAAGGC 31 216 0 AAAAAATGAT 0.805358 -85 CGTTGTTTGATAAAAATGGCTCATTATATGG 34 47 0 TAAAAATGGT 0.691321 -92 GAGCCACTCTTAAAAAGCGTTGTTTGATAAA 34 64 0 TAAAAAGCGT 0.850575 -75 ********* * Masking position 5 Map Score: 30.6985 Number of sites scoring better than the average of aligned sites = 1549 Number in coding regions = 1278 Number in noncoding regions = 271 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 5 GATCATTTTAAGGGAGTTTT 4 1 0 AGGGAGTTTT 0.787144 -186 GAGATTAAGGGGTGGTTTTGGGCACGCATT 6 87 0 GGTGGTTTTG 0.835131 -94 TTTTATGATTGGGGTTTTTTGAGATTAAGG 6 107 0 GGGGTTTTTT 0.866419 -74 TTAAGAGTAATGGGTGTTTGTTTTAAGACG 7 160 1 TGGGTGTTTG 0.450108 -98 ACTAACAATTAGCGGTTTTTTTAAAGAAAA 9 24 0 AGCGGTTTTT 0.652585 -97 GGGGTTAAAAGGGGATATTTTTATATAATA 11 79 0 GGGGATATTT 0.863012 -218 GCAAAAATAAGGCGATTTTGACTAGAATAG 12 57 0 GGCGATTTTG 0.881107 -76 ACTAGTTTGAAGGGAGTTTGGAGT 12 119 1 AGGGAGTTTG 0.866721 -14 GTGCTGTTGGTGGGCGTTTGCATAGAAGAA 14 41 1 TGGGCGTTTG 0.676799 -133 AAGTTTTTTTAGCGGGTTTTTCATTGAATG 14 84 1 AGCGGGTTTT 0.574658 -90 ATTGAATGGAGGGGCTTTATAACCGCAAGC 14 106 1 GGGGCTTTAT 0.493498 -68 TTTGAATGTAAGGGCTATTTTAAACTTATT 15 68 1 AGGGCTATTT 0.66963 -64 ATTGTAAAATGGTGAGTTTTACAATCAATG 15 98 1 GGTGAGTTTT 0.594752 -34 ACCCTTTTTTGGGGATTTTTTGGGGATTTT 16 160 1 GGGGATTTTT 0.942143 -61 GGGATTTTTTGGGGATTTTTGCGTCTTATT 16 171 1 GGGGATTTTT 0.942143 -50 CGCAAAGTCTGGCGTTTTTGTTTGGGGGTA 18 21 1 GGCGTTTTTG 0.746957 -29 TAGTCTTAAAAGTGATTTTGTTTTTTAGGG 19 80 1 AGTGATTTTG 0.531164 -32 CTTTAGGCGAGGGGGTCTTGCTCGGG 21 57 1 GGGGGTCTTG 0.827948 -16 TCTTTAAAAAAGGGCTATTG 25 1 0 AGGGCTATTG 0.780912 -61 AACTTTTCAGGGGGCGTTTGAACTTCTTAC 29 18 1 GGGGCGTTTG 0.95452 -39 GGGGGTATTGTAGCGCTAAT 30 74 0 GGGGGTATTG 0.939901 -10 TTTTTTGCATGGGGGTATTGTAGCGCTTAA 31 112 0 GGGGGTATTG 0.939901 -189 ACAATGAAATGGGGGTATTTTAAAAAAATG 31 229 0 GGGGGTATTT 0.898923 -72 ********** Masking position 8 Map Score: 21.7637 Number of sites scoring better than the average of aligned sites = 1853 Number in coding regions = 1649 Number in noncoding regions = 204 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 6 TAATGATCATTTTAAGGGAGTTTT 4 4 0 TTAAGGGAGT 0.726498 -183 AAGCTTTTTATGATTGGGGTTTTTTGAGATT 6 111 0 TATTGGGGTT 0.871433 -70 TGATTTAAGAGTAATGGGTGTTTGTTTTAAG 7 156 1 GAATGGGTGT 0.765139 -102 ATGAGAGAAAGGTTTGGGTTTAGGGTTTGAA 7 215 1 GTTTGGGTTT 0.663358 -43 GGTATGGGTTTATATGGGGGTGAAAAGATAA 16 112 0 TTATGGGGGT 0.984645 -109 AAAAAGGGTTTATATGGGTTTATATGGGTAT 16 138 0 TTATGGGTTT 0.841223 -83 TATAAACCCTTTTTTGGGGATTTTTTGGGGA 16 155 1 TTTTGGGGAT 0.896801 -66 TTTTGGGGATTTTTTGGGGATTTTTGCGTCT 16 166 1 TTTTGGGGAT 0.896801 -55 CTGGCGTTTTTGTTTGGGGGTAACTTTTTTA 18 29 1 TTTTGGGGGT 0.98258 -21 GTCGTTTTAATTTTAGGGGGTTAT 22 50 1 TTTAGGGGGT 0.938146 -14 CAGGTATTCTTTGGGGGTCGTAAGAAGT 29 39 0 TTTTGGGGGT 0.98258 -18 CGGTGTCTTTTTTAAGGGAGTGTTTTTTTAT 30 21 1 TTAAGGGAGT 0.726498 -63 AATCTTTTTTTGCATGGGGGTATTGTAGCGC 31 116 0 TCATGGGGGT 0.923522 -185 ATTTTACAATGAAATGGGGGTATTTTAAAAA 31 233 0 GAATGGGGGT 0.918922 -68 TTATTAAACTTCAATGGGTTTTGCATGAAAG 31 265 0 TAATGGGTTT 0.688942 -36 * ********* Masking position 11 Map Score: 12.9822 Number of sites scoring better than the average of aligned sites = 456 Number in coding regions = 391 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 7 GGTTTTTTGAGATTAAGGGGTGGTTTTGGGC 6 94 0 GATTAAGGGT 0.820847 -87 GAATTATATTGATTTAGCGTTACTT 7 243 1 GATTTAGCGT 0.945258 -15 TAAAAACTAACAATTAGCGGTTTTTTTAAAG 9 28 0 CAATTAGCGT 0.969125 -93 GGGTTGGCATCAATAGGGGGTTAAAAGGGGA 11 94 0 CAATAGGGGT 0.807861 -203 TTGCATAGAAGAATTAGAGCTGTTTGAAGTT 14 58 1 GAATTAGAGT 0.725968 -116 AGGGTATCAACAATAGGGGTTTAAAAT 20 37 1 CAATAGGGGT 0.807861 -17 TCCTGAATTAGGGTTTATTTTTTGG 21 5 1 GAATTAGGGT 0.932547 -68 TTTGGAATTGGATTTAGCGCTTATCTCTTTA 21 31 1 GATTTAGCGT 0.945258 -42 CAATTCAAGGGATTTGGCGATT 23 137 1 GATTTGGCGT 0.897088 -12 ATGGAGCGTTCAATGAGCGTTCTTATTTGTA 24 127 0 CAATGAGCGT 0.880007 -164 AGTATAAAGGCAATTAGCGCTACAATACCCC 30 62 1 CAATTAGCGT 0.969125 -22 AAAGCCCGCTCATTAAGCGCTACAATACCCC 31 100 1 CATTAAGCGT 0.912301 -201 TTATTCTATCCAATTAGCCCTTGAGCCACTC 34 86 0 CAATTAGCCT 0.75395 -53 ********* * Masking position 2 Map Score: 10.8343 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 170 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 TCAAACCCTAAACCCAAACCTTTCTCTCATATA 7 212 0 AACCCACTTT 0.921317 -46 GGTTAAATTGCCCTTTCGTTTTAAAGATAAA 11 9 1 TGCCCTCTTT 0.950888 -288 TATTGATGCCAACCCCTTTTTTTACCTAATTCT 11 110 1 AACCCTTTTT 0.879258 -187 GCGGTTATAAAGCCCCTCCATTCAATGAAAAAC 14 99 0 AGCCCTCTTC 0.967689 -75 AGTTTAAAATAGCCCTTACATTCAAAACGCTGT 15 61 0 AGCCCTCTTC 0.967689 -71 TGCGTTTTACAACCCATGCGTTTGAGAATAAAA 17 200 0 AACCCTCTTT 0.986713 -86 TTCGTTTGATAACCCATGCGTTTTACAACCCAT 17 216 0 AACCCTCTTT 0.986713 -70 AACGCCTACCTTTTGTATTAAGA 19 1 1 AACGCTCTTT 0.915203 -111 CTATTGTTGATACCCTTTCATTTTTAAAACTAG 20 20 0 TACCCTCTTT 0.959139 -34 ***** * * *** Masking position 11 Map Score: 8.44985 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 50 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 9 ATACCTAACTAACCGCCCATTATACAATAAA 4 145 0 AACCGCCCTT 0.986075 -42 AACCACCCTTTCTATTCAAAA 4 176 0 AACCACCCTT 0.986731 -11 GCGTGCCCAAAACCACCCCTTAATCTCAAAA 6 90 1 AACCACCCTT 0.986753 -91 GCTATTAAACCGCCCTTTTATCGTGTTA 6 163 0 AACCGCCCTT 0.98825 -18 ACTTAAAAAAAACTACCCTTAAAAAAATCAA 7 79 0 AACTACCCTA 0.762194 -179 GTCTTAAAACAAACACCCATTACTCTTAAAT 7 158 0 AAACACCCTT 0.920122 -100 GGTTAAATTGCCCTTTCGTTTTAAAG 11 6 1 AATTGCCCTT 0.909646 -291 CAAACCATCCAATGACCCTTTATCGCACTCA 24 41 1 AATGACCCTT 0.868529 -250 CAATAGCCCTTTTTTAAAGATT 25 2 1 AATAGCCCTT 0.851758 -60 ******** ** Masking position 2 Map Score: 8.47541 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 96 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 10 ATCATTAAGTTTCTTAAAACAAAAATATAA 4 28 1 TTCTTAAAAC 0.825201 -159 TATGTTTCCTTTCTTCAAACCTTAAAAT 5 9 0 TTCTTCAAAC 0.871673 -31 TTATTAATCTTTTTTTAAGCGTTATTATAG 6 23 1 TTTTTTAAGC 0.723213 -158 TAGTCATAGCGTCTTAAAACAAACACCCAT 7 169 0 GTCTTAAAAC 0.622985 -89 CTAATTGTTAGTTTTTAAACGATTTTGTAA 9 42 1 GTTTTTAAAC 0.525642 -79 AAATCTAAGCTTTATCAAGCCATTAGCCGG 11 165 1 TTTATCAAGC 0.845421 -132 GATTTTCCTTTCATCAAACTCATCTCAAC 12 10 1 TTCATCAAAC 0.82097 -123 TAATAATGACTTTTTAAAACTAGTTTGAAG 12 101 1 TTTTTAAAAC 0.869868 -32 CAAGCTTGCGGTTATAAAGCCCCTCCATTC 14 109 0 GTTATAAAGC 0.600353 -65 AATTCAAGCTTTTTTTAAGCGAGGAAGTCG 17 114 1 TTTTTTAAGC 0.723213 -172 GCGAACTGATTTTTTAAAGCTTTTGCTAGA 17 151 0 TTTTTAAAGC 0.849129 -135 AAACGCATGGGTTATCAAACGAAATTCTAA 17 226 1 GTTATCAAAC 0.765473 -60 TACCCTTTCATTTTTAAAACTAGCATTATA 20 13 0 TTTTTAAAAC 0.869868 -41 GAAAGAAACTTTTAACAAACAATTCAAGGG 23 118 1 TTTAACAAAC 0.348433 -31 TTGTCTTTCTTTTTTCAAACCATCCAATGA 24 26 1 TTTTTCAAAC 0.924281 -265 TTTAATGGCATTCTTAAAGCTAGTATACAC 27 85 1 TTCTTAAAGC 0.757397 -66 TAATACCATCTTAATCAAACAAGAAAGAGC 27 117 1 TTAATCAAAC 0.415002 -34 ATGAAAAGGTTTTCTAAAACTTCATAAAAT 31 13 1 TTTCTAAAAC 0.574147 -288 ATTTTTACCTTTTATTAAACTTCAATGGGT 31 277 0 TTTATTAAAC 0.727807 -24 TTTTTAAAACTCTCTTTAAA 34 1 1 TTTTTAAAAC 0.869868 -138 ATGAGCCATTTTTATCAAACAACGCTTTTT 34 54 1 TTTATCAAAC 0.892362 -85 ********** Masking position 2 Map Score: 21.6569 Number of sites scoring better than the average of aligned sites = 851 Number in coding regions = 734 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 11 ATATAACTTTAAAATTAAATCTAGGAGTATA 1 49 1 AAATTAAATC 0.452517 -24 TTTGCGGCAAAATTTTAAACCGCATTATAGT 2 44 1 AATTTAAACC 0.89028 -160 ATTTTTGGATAATTTCAAGTCGTAGCATACC 2 167 0 AATTCAAGTC 0.927043 -37 ATTATTTTCAAATTTCAAGTCTAAAGAGTGT 7 116 1 AATTCAAGTC 0.927043 -142 TAAATCAATATAATTCAAACCCTAAACCCAA 7 228 0 TATTCAAACC 0.646635 -30 CCGCTAAAAAAACTTCAAACAGCTCTAATTC 14 68 0 AATTCAAACA 0.729923 -106 AAGATACGCTAAATTCAAGCTTTTTTTAAGC 17 103 1 AATTCAAGCT 0.84727 -183 AACTGAGTGTAAATTCAAGTATAATTCTAAC 19 43 1 AATTCAAGTA 0.617452 -69 CCTTAACTCCAAGATCAAGCC 22 1 0 AAATCAAGCC 0.938872 -63 CTAACGCTAAAATTTTAAACCTTAACTCCAA 22 20 0 AATTTAAACC 0.89028 -44 ATACAATTACAAGTTTAAGTTTTGCTTAAAA 26 15 0 AATTTAAGTT 0.379674 -59 TATTAAAATGAGTTTCAAGCCCTTTTTTCTT 27 44 1 AGTTCAAGCC 0.847526 -107 GGGTCGTAAGAAGTTCAAACGCCCCCTGAAA 29 22 0 AATTCAAACG 0.694595 -35 CCTAACTTTAAAAATCAAGCCTTCAAAAACC 33 11 0 AAATCAAGCC 0.938872 -93 TTTAACATAAAAGATTAAGCCTAACTTTAAA 33 30 0 AAATTAAGCC 0.853571 -74 AACTTTAAACCTAAAACCTAA 33 93 0 AATTTAAACC 0.890244 -11 ** ******** Masking position 5 Map Score: 9.95314 Number of sites scoring better than the average of aligned sites = 528 Number in coding regions = 471 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 12 GCAAAGGGCAAAAAATTTCATCATAGTAAG 2 19 0 AAAAATTTCA 0.897271 -185 CCTTTGCGGCAAAATTTTAAACCGCATTAT 2 42 1 AAAATTTTAA 0.814558 -162 TTTTTTAAAGAAAATTTTCAAAATGTG 9 8 0 AAAATTTTCA 0.948995 -113 AAAATTTTTAAAAATTTACAAAAATGAGAA 11 201 0 AAAATTTACA 0.614217 -96 TAAATTTTTAAAAATTTTCATACTCTCATT 11 213 1 AAAATTTTCA 0.948995 -84 AACCCGCTAAAAAAACTTCAAACAGCTCTA 14 72 0 AAAAACTTCA 0.560315 -102 TTGAGAATAAAACAATTTCATTTCTTTAGA 17 182 0 AACAATTTCA 0.685669 -104 GACTAACGCTAAAATTTTAAACCTTAACTC 22 23 0 AAAATTTTAA 0.814558 -41 AAAATGGAGTAAAATTTTTACCCACCCTAA 23 57 0 AAAATTTTTA 0.571653 -92 TAATTGAAAGAAACTTTTAACAAACAATTC 23 113 1 AAACTTTTAA 0.709253 -36 AACTTTTAACAAACAATTCAAGGGATTTGG 23 124 1 AAACAATTCA 0.457112 -25 CTTATTTGTAAAAAAATTCAGTTTGTTTGC 24 107 0 AAAAAATTCA 0.602546 -184 AAGACAAAACTTTTCAGGGGGCGTTT 29 7 1 AAACTTTTCA 0.911766 -50 AGTTTTAGAAAACCTTTTCATAG 31 4 0 AACCTTTTCA 0.720689 -297 CAAGGCAATCTAAATTTTCAATGAGTCAAA 31 192 0 TAAATTTTCA 0.614108 -109 ATCTTAAAGTAAAATTTTAAAGAGAGTTTT 34 16 0 AAAATTTTAA 0.814558 -123 ********** Masking position 7 Map Score: 10.3231 Number of sites scoring better than the average of aligned sites = 342 Number in coding regions = 300 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 13 CGATTGATCGTCTTTTTAATCCAGTTTAAT 2 95 0 TCTTTTTAAT 0.457098 -109 AACTTAATGATCATTTTAAGGGAGTTTT 4 9 0 TCATTTTAAG 0.779145 -178 TTTTGGTTTATGATTTTATTGTATAATGGG 4 131 1 TGATTTTATT 0.879071 -56 AATTTTAGATTGATTTTTTTAAGGGTAGTT 7 70 1 TGATTTTTTT 0.627067 -188 TTGGTTGAGATGAGTTTGATGAAAGGAAAA 12 13 0 TGAGTTTGAT 0.533901 -120 AAGGCTTTGATGATTTTTTTTATGTGGAAT 17 13 1 TGATTTTTTT 0.627067 -273 TACACTCAGTTTAGTTTATTTCTTAATACA 19 24 0 TTAGTTTATT 0.300894 -88 GTCTTAAAAGTGATTTTGTTTTTTAGGGAG 19 82 1 TGATTTTGTT 0.776425 -30 TTAGCGTTAGTCGTTTTAATTTTAGGGGGT 22 41 1 TCGTTTTAAT 0.555136 -23 CATTGTAGCATGACTTTATTAGGGTGGGTA 23 39 1 TGACTTTATT 0.449147 -110 TTTTAACCGGTCATTTTAATTATTTTAGTA 23 83 1 TCATTTTAAT 0.925433 -66 ACTCAAAGAGTTATTTTATTACTTTTAAAC 24 67 1 TTATTTTATT 0.588719 -224 GTAAAAAAATTCAGTTTGTTTGCTATGATA 24 100 0 TCAGTTTGTT 0.619062 -191 TCGGTCAAGGTAATTTTAATCAAAACATGC 24 175 1 TAATTTTAAT 0.471039 -116 TTCATTTTAAGCAAAACTTAA 26 2 1 TCATTTTAAG 0.779145 -72 TGTAATTGTATCATTTTAAGATCATTTTGA 26 35 1 TCATTTTAAG 0.779145 -39 CATTTTAAGATCATTTTGATAAGTAGAGGA 26 46 1 TCATTTTGAT 0.855679 -28 GGCTTGAAACTCATTTTAATAGCGCCCAAA 27 35 0 TCATTTTAAT 0.925433 -116 TCTTAATTTTTGATTTTAATGGCATTCTTA 27 71 1 TGATTTTAAT 0.888572 -80 AAAAGTCATTTTATTAGGGATCAAA 28 6 1 TCATTTTATT 0.918788 -23 CTTGACTGACTCATTTTTTTAAAATACCCC 31 218 1 TCATTTTTTT 0.723519 -83 ********** Masking position 5 Map Score: 11.0659 Number of sites scoring better than the average of aligned sites = 329 Number in coding regions = 254 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 14 AGCATGATAGAGCTTTAGTTTTAGCTAGTTTG 4 65 1 AGCTTTATTT 0.734813 -122 CGTGTTAAAGAGCTTTCATTGTAGCATAAAGC 6 138 0 AGCTTTCTTT 0.762461 -43 TGTTTTAAGACGCTATGACTATCTTTATGCGA 7 178 1 CGCTATGCTT 0.80154 -80 GGTTAAATTGCCCTTTCGTTTTAAAGATAAAC 11 11 1 CCCTTTCTTT 0.832357 -286 TAGTCAAAATCGCCTTATTTTTGCGCTATGAT 12 63 1 CGCCTTATTT 0.778856 -70 CTTATTTTTGCGCTATGATTTTCAATAATAAT 12 76 1 CGCTATGTTT 0.831007 -57 CTTAAAAATTCGCTTTCTCTCTCTCTCTCTCT 16 67 1 CGCTTTCCTT 0.963534 -154 TCTAGTCAGCCGCTTTATCTTTTCACCCCCAT 16 98 1 CGCTTTACTT 0.958 -123 GCGAGGAAGTCGCTTTACCTCTAGCAAAAGCT 17 132 1 CGCTTTACTT 0.958 -154 ATTGTTGATACCCTTTCATTTTTAAAACTAGC 20 19 0 CCCTTTCTTT 0.832357 -35 AAACGACTAACGCTAAAATTTTAAACCTTAAC 22 25 0 CGCTAAATTT 0.371444 -39 TAGCGTTAGTCGTTTTAATTTTAGGGGGTTAT 22 42 1 CGTTTTATTT 0.734813 -22 GCGTTAGAGACGCTTTGGCTGTTTAAAAAGAG 24 234 1 CGCTTTGCTT 0.941997 -57 AAAAAGACACCGCTTTATTTTA 30 1 0 CGCTTTATTA 0.703817 -83 TTTTTATAACCGCTTTTAGTATAAAGGCAATT 30 45 1 CGCTTTTGTT 0.483803 -39 GCGCTTCGTTCGTTTTCATTATAACGCTCCTT 31 44 1 CGTTTTCTTT 0.762461 -257 ******* ** * Masking position 10 Map Score: 7.41382 Number of sites scoring better than the average of aligned sites = 496 Number in coding regions = 461 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 15 TAGCATACCCTAAAAGAGCGAATGTAACCT 2 146 0 TAAAAGAGCG 0.921232 -58 TTTAACACGATAAAAGGGCGGTTTAATAGC 6 161 1 TAAAAGGGCG 0.967659 -20 AGAAAAACCTTAAAAGGGAGCAAAAAAGC 10 10 0 TAAAAGGGAG 0.96828 -71 AATGAAAAAGTAAATGAGAGTATGAAAATT 11 225 0 TAAATGAGAG 0.652897 -72 CTTATTATTGTAAAATGGTGAGTTTTACAA 15 92 1 TAAAATGGTG 0.74643 -40 AATGACCGGTTAAAATGGAGTAAAATTTTT 23 68 0 TAAAATGGAG 0.922673 -81 ATAACGCTATTAAAACGGAGAGGGT 27 6 0 TAAAACGGAG 0.874986 -145 TAAAACTTCATAAAATTGCGCTTCGTTCGT 31 27 1 TAAAATTGCG 0.644042 -274 AAGTAAAATTTTAAAGAGAGTTTTAAAAA 34 10 0 TTAAAGAGAG 0.652897 -129 ********** Masking position 4 Map Score: 2.86614 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 230 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344