AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -irpoH_hpyl_opreg_300.orf -g0.389 -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 = 0.389 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HP0010 24 chaperone and heat shock protein (groEL) #2 HP0011_HP0012 286 HP0011: co-chaperone (groES), HP0012: DNA primase (dnaG) #3 HP0088 223 RNA polymerase sigma-70 factor (rpoD) #4 HP0090 300 malonyl coenzyme A-acyl carrier protein transacylase (fabD) #5 HP0109 29 chaperone and heat shock protein 70 (dnaK) #6 HP0111 300 H. pylori predicted coding region HP0111 #7 HP0209 300 H. pylori predicted coding region HP0209 #8 HP0210 103 chaperone and heat shock protein C62.5 (htpG) #9 HP0262 157 H. pylori predicted coding region HP0262 #10 HP0263 111 adenine specific DNA methyltransferase (hpaim) #11 HP0264 72 ATP-dependent protease binding subunit (clpB) #12 HP0513 290 H. pylori predicted coding region HP0513 #13 HP0514 60 ribosomal protein L9 (rpl9) #14 HP0562 100 ribosomal protein S21 (rps21) #15 HP0563 247 H. pylori predicted coding region HP0563 #16 HP0795 111 trigger factor (tig) #17 HP0796 28 H. pylori predicted coding region HP0796 #18 HP0797 118 flagellar sheath adhesin hpaA #19 HP0801 72 molybdopterin converting factor, subunit 1 (moaD) #20 HP0802 88 GTP cyclohydrolase II (ribA) #21 HP0803 88 H. pylori predicted coding region HP0803 #22 HP0804 170 GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase (ribA, ribB) #23 HP0805 81 lipooligosaccharide 5G8 epitope biosynthesis-associated protein (lex2B) #24 HP0921 143 glyceraldehyde-3-phosphate dehydrogenase (gap) #25 HP1067 290 chemotaxis protein (cheY) #26 HP1332 124 co-chaperone and heat shock protein (dnaJ) #27 HP1346 88 glyceraldehyde-3-phosphate dehydrogenase (gap) #28 HP1350 209 protease #29 HP1352 300 adenine specific DNA methyltransferase (HINFIM) #30 HP1376 171 (3R)-hydroxymyristoyl-(acyl carrier protein) dehydratase (fabZ) #31 HP1377_HP1378 357 HP1377: H. pylori predicted coding region HP1377, HP1378: competence lipoprotein (comL) #32 HP1379 41 ATP-dependent protease (lon) Motif number 1 AATCCTTGTATTTTTAAACTAATGAAACTTGA 2 117 1 TTTTAACTAA 0.460548 -170 ATCCTTTGTTATTCTACTAAAAAATAGCTTAA 3 133 0 ATTTATAAAA 0.841043 -91 TCGTTAATACATTCTAAACAAAAAGTTTTTAA 4 43 1 ATTTAACAAA 0.817769 -258 ACAAAGTAGAATTATAGTAAAAATAAGTTAAA 4 185 1 ATTTATAAAA 0.841042 -116 ACTTTAATGGTTTCTAAACAAAACTAAGGGCT 4 228 1 TTTTAACAAA 0.615095 -73 ATAATTTAAAATTGTAATATAAAAGCCCTTAG 4 251 0 ATTTATATAA 0.73856 -50 GTTATCCTTTCTTTTAAAATAAATGTT 5 6 0 CTTTAAATAA 0.618592 -24 AATGAGTTTCATTATAAAACAAAAAGGATTAT 6 91 1 ATTTAAACAA 0.844169 -210 TTTTATCACTTTTTTAAAACAAGTGATAGATT 6 237 1 TTTTAAACAA 0.65866 -64 GAACCCTCGCATTATAGCATAAAAAGTTAATA 6 268 0 ATTTACATAA 0.899469 -33 CCGATCGCTCATTGTAGAAAAAAAAAAACGAT 7 217 0 ATTTAAAAAA 0.911841 -84 AATTTTTAAGATTATACAATAAAAGCGCGCTT 8 63 0 ATTTAAATAA 0.846864 -41 TTGAAACAAGCTTATAATAAAAATGAAATTTA 9 100 0 CTTTATAAAA 0.60811 -58 CAAATTATAATACAAAATTTTGATA 9 143 0 ATTTATACAA 0.734557 -15 AAGATAAGCTTTTTTATCAAAAATAATGATGA 15 212 1 TTTTACAAAA 0.830665 -36 TTTTTGTATCATTATAGCTTAATTTGTTTTAA 16 62 0 ATTTACTTAA 0.707773 -50 TCAAAATGTTATTTTACCCTAACATCTTTAGA 18 25 0 ATTTACCTAA 0.794936 -94 ATATTTTAGACTTCTATAACAACAAACCCGAA 18 78 0 CTTTAAACAA 0.613711 -41 AAAAAAAGGTATTCTATCAAAACTCTTTATAA 20 31 0 ATTTACAAAA 0.943682 -58 TAAAACGCATCTTTTAAAAAAAGGTATTCTAT 20 46 0 CTTTAAAAAA 0.752118 -43 AAAAGAGTTTATTATACCTTAAAAACATTACA 21 39 0 ATTTACTTAA 0.707773 -50 GCTTTAGCGATTTGTATCTAAATAAAGCAATA 22 69 1 TTTTACTAAA 0.609538 -102 AATATTGAGTTTTATAGAAAAAAGAAATATAG 22 125 0 TTTTAAAAAA 0.780123 -46 TCTAGCGCAAATTTTAGTAAAATACGCATC 23 9 0 ATTTATAAAA 0.841041 -73 AGCGTTCTTATTTGTAAAAAAATTCAGTTTGT 25 111 0 TTTTAAAAAA 0.776183 -180 GGTCAAGGTAATTTTAATCAAAACATGCTATT 25 177 1 ATTTATCAAA 0.69627 -114 CAAAACGCTTATTTTATCTTAAAAGCGATAAT 26 83 0 ATTTACTTAA 0.707772 -42 AAAAATCACCATTCTATCACAAATGCTCTTAA 27 52 0 ATTTACACAA 0.897588 -37 AGAATGGTGATTTTTAAATAAAGGGAAAAC 27 69 1 TTTTAATAAA 0.48512 -20 TTTTGCGTTTATTCTATCTAAAATTTAGATAA 28 143 0 ATTTACTAAA 0.81937 -67 TACTCTAGCCATTTTAACACAAGCGTTTTAAG 29 255 0 ATTTACACAA 0.897588 -46 AATAACCGCTATTATACCATAAGAAAACCGCT 30 87 0 ATTTACATAA 0.899469 -85 AGCGTTGGTTATTCTAAAAAAATAACCGCTAT 30 107 0 ATTTAAAAAA 0.91195 -65 AGTTATTGGGATTATATCCAAAACTAGCGAAA 31 256 1 ATTTACCAAA 0.878874 -102 GCGAAAATTGATTTTACCAAAATTGTTTGATA 31 282 1 ATTTACAAAA 0.943684 -76 *** ** ***** Masking position 6 Map Score: 34.8932 Number of sites scoring better than the average of aligned sites = 479 Number in coding regions = 275 Number in noncoding regions = 204 Number of orfs with sites within 600 bp upstream = 203 Fraction of orfs with sites within 600 bp upstream = 0.0326052 Motif number 2 AAACATTATTATTAAGGATACAAA 1 2 1 AAATAATAAG 0.88471 -23 ATACTCAATAAATAAAATCTTAAAATAAGGTTTGT 2 63 1 AAAAATTAAA 0.929019 -224 CAAAGCTAATAATATAACTATAAGGATTATTAAGT 2 158 0 AAATAATAGG 0.720903 -129 GAAAAATTCCAATAATATAATTAGAATTTAAGCTA 3 106 1 AAAAAATAGA 0.838306 -118 GAATTATAGTAAAAATAAGTTAAAATAAACCTTAA 4 193 1 AAAAATTAAA 0.929019 -108 CACTTGTTTTAAAAAAGTGATAAAAATTACCCGAT 6 227 0 AAAAGATAAA 0.871042 -74 TTGTAGAAAAAAAAAAACGATAAAATCGCAAAAAA 7 203 0 AAAAAATAAA 0.939034 -98 TATGGCTTAAAAAAAGAACATGAAAGAATGTTTAA 8 15 0 AAAAAATAAA 0.939034 -89 CTTTTCCTTTAATAAAATTTTTAAGATTATACAAT 8 75 0 AAAAATTAAG 0.914698 -29 TATTTTCACTAAAATAATATTGAAAGAATTTAATC 9 23 0 AAATATTAAA 0.88838 -135 GCTTATAATAAAAATGAAATTTAAATTTTAGATAT 9 88 0 AAATATTAAA 0.88838 -70 GGAATTAGGAAATAAAAATATAAAACCCGGTCGCA 15 49 0 AAAAAATAAA 0.939034 -199 AAATCTAAAGAAAAATATTTTTAGATGTGCTAGAA 15 163 1 AAAAATTAGA 0.815003 -85 AGAAGTCTAAAATATTACAATCAAGGATAGAACG 18 95 1 AAATAATAAG 0.88471 -24 CTTAAAATTTAAGAAAATTATAAAGAGTTTTGATA 20 14 1 AAAAAATAAG 0.926575 -75 GGATACTCCTAAAATTAGTTTTAAAACGCATCTTT 20 64 0 AAATATTAAA 0.88838 -25 TTTGTATCTAAATAAAGCAATAAAGTAATAATCGT 22 79 1 AAAAGATAAG 0.846951 -92 TAATGCAAATAAAATCAATATCAAACAGACTTACA 23 42 0 AAATAATAAA 0.903534 -40 TTCTCCTTTTAAGATTGCATTTAAATTAGGCTCTT 25 261 0 AAATGTTAAA 0.777292 -30 ACTTAGATAAAATAACACGATAAAACCATAGTAAT 26 23 0 AAAAAATAAA 0.939034 -102 GATCGCTCCAAAAATGGCATCAAAACGCTTATTT 26 101 0 AAAAGATAAA 0.871042 -24 GCAAAAATTGAATAAAACCTTAAAGGTGATTCTTT 28 169 1 AAAAATTAAG 0.914698 -41 ATTAAACATTAAGATAACCTTAAAACGCTTGTGTT 29 237 1 AAATATTAAA 0.88838 -64 TATAAAATATAATAAGGAGTTGAGGAATGAGCAAA 31 192 0 AAAAGTTAGG 0.612823 -166 ** ** * ** *** Masking position 11 Map Score: 27.7283 Number of sites scoring better than the average of aligned sites = 634 Number in coding regions = 472 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 3 GACATAACTATAGCGCATTTTTAGGGATAAGTC 2 205 0 TAGCGCTTTA 0.79761 -82 TAATAACAATAAGCGCTAAATTTCTATTTTATT 2 241 1 AAGCGCATTT 0.906467 -46 AAAAATACTAAAAAGCTTTTTTACATTCCACCC 3 41 0 AAAAGCTTTA 0.823991 -183 ACCCGCTAAAAAAAGGGGGTTTTTTGCGATTTT 7 184 1 AAAAGGTTTT 0.625074 -117 CCTTTTATCAAACGCCTTTTTTATTGAAGTCT 7 279 0 AAACGCTTTT 0.974642 -22 TACCCCTTTTAAGCGCGCTTTTATTGTATAATC 8 53 1 AAGCGCTTTA 0.940574 -51 AAAAGCCTTTTTAAATCTTCTAA 10 99 0 AAAAGCTTTA 0.823991 -13 AGATGAGCTGAAACGCAATTTTTCA 15 3 0 AAACGCTTTT 0.974695 -245 CACTAACTAAAAAAGGAAATTTTAATGGAATTA 15 77 0 AAAAGGTTTT 0.681655 -171 AACATGAAATAAACGCCGTTTTATATTAAATCT 15 136 1 AAACGCTTTA 0.93316 -112 CCAGTTTATAAAAAGCGGTTTTAATTCTAGTTT 16 27 0 AAAAGCTTTA 0.80435 -85 TTAAATCTTTTAAAGCATGATTTTAAATATTTT 19 39 0 TAAAGCATTT 0.417976 -34 ATTAGTTTTAAAACGCATCTTTTAAAAAAAGGT 20 53 0 AAACGCTTTT 0.966396 -36 ACTTACATTCTAGCGCAAATTTTAGTAAAATAC 23 16 0 TAGCGCTTTT 0.915334 -66 AACGCTCATTGAACGCTCCATTTAGCCAATGAT 25 137 1 GAACGCATTT 0.639729 -154 CGTTCCAAATAATAGCATGTTTTGATTAAAATT 25 186 0 AATAGCTTTT 0.559817 -105 GCTGTTTAAAAAGAGCCTAATTTAAATGCAATC 25 251 1 AAGAGCATTT 0.764678 -40 TTTATCTTAAAAGCGATAATTTTGCGTGTTTTG 26 70 0 AAGCGATTTT 0.644972 -55 AATGGCATCAAAACGCTTATTTTATCTTAAAAG 26 90 0 AAACGCTTTT 0.974642 -35 GATAACCTTAAAACGCTTGTGTTAAAATGGCTA 29 249 1 AAACGCTGTT 0.77034 -52 TATGGTATAATAGCGGTTATTTTTTTAGAATAA 30 98 1 TAGCGGTTTT 0.642494 -74 GATTCAATTAAAGCGCTATTTTTAGCGTTGGTT 30 129 0 AAGCGCTTTT 0.977487 -43 AGAAATCATTGAGCGCTGGTTTTAAGGCGGTCT 31 332 1 GAGCGCTTTT 0.899627 -26 ****** **** Masking position 12 Map Score: 26.0498 Number of sites scoring better than the average of aligned sites = 1186 Number in coding regions = 1084 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 4 AATAGACTTAATAATCCTTATAGTTATATTA 2 153 1 ATAACCTTAT 0.5555 -134 GTGGAATGTAAAAAAGCTTTTTAGTATTTTT 3 43 1 AAAAGCTTTT 0.582583 -181 CATTCTAAACAAAAAGTTTTTAAAGGCAAAA 4 52 1 AAAAGTTTTT 0.472249 -249 TTAAATATGGATAATCCTTTTTGTTTTATAA 6 102 0 ATAACCTTTT 0.696097 -199 GAGAGAGAGTAAAACTCTTTTATCAAATCCA 7 19 0 AAAATCTTTT 0.601345 -282 AATCGCAAAAAACCCCCTTTTTTTAGCGGGT 7 184 0 AACCCCTTTT 0.868061 -117 CCTTTTATCAAACGCCTTTTTTATTGAAGT 7 281 0 AAACCCTTTT 0.572584 -20 AAGCCATAGCATACCCCTTTTAAGCGCGCTT 8 42 1 ATACCCTTTT 0.718986 -62 TGGTGTTTGAAACAAGCTTATAATAAAAATG 9 107 0 AACAGCTTAT 0.780835 -51 AGCTTTGATCAAAATGGTTTTTGGCTAAATA 10 42 0 AAAAGGTTTT 0.529853 -70 AGAAGATTTAAAAAGGCTTTT 10 101 1 AAAAGCTTTT 0.501823 -11 GCGTTTTAAAAACCTTTGAGGGTTAAAA 11 8 1 AAAACCTTTG 0.74019 -65 ATTTAATATAAAACGGCGTTTATTTCATGTT 15 136 0 AAACGCGTTT 0.459487 -112 ATTTTTGATAAAAAAGCTTATCTTGTAACAA 15 205 0 AAAAGCTTAT 0.741252 -43 ACTAGAATTAAAACCGCTTTTTATAAACTGG 16 29 1 AAACGCTTTT 0.883015 -83 CGAAGCAACCAACACGCTTTTGTTGTCAAAA 18 51 0 AACAGCTTTT 0.884791 -68 TATTCTATCAAAACTCTTTATAATTTTCTTA 20 23 0 AAACCTTTAT 0.449012 -66 AAGGTATAATAAACTCTTTTTAAGTCAAGCA 21 51 1 AAACCTTTTT 0.652421 -38 TTACTTGTAAAATCCTTGTCTTTCTTTTT 25 9 1 AAAACCTTGT 0.86983 -282 AAATGGCATCAAAACGCTTATTTTATCTTAA 26 93 0 AAAAGCTTAT 0.793069 -32 TTTTGTAACGAACATGCTTTGCGATTTGCAT 29 89 1 AACAGCTTTG 0.585065 -212 AGATAACCTTAAAACGCTTGTGTTAAAATGG 29 248 1 AAAAGCTTGT 0.883887 -53 CTTTGCATAGAAACCGCTTATGCA 30 4 0 AAACGCTTAT 0.899846 -168 AAAATAAACTCCTTGTTTTGGATTCA 30 156 0 AAACCCTTGT 0.870343 -16 **** ****** Masking position 9 Map Score: 18.7044 Number of sites scoring better than the average of aligned sites = 1257 Number in coding regions = 1056 Number in noncoding regions = 201 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 5 CCTTATTTTAAGATTTTATTTATTGAGTATAATTCATT 2 55 0 ATTTTTTAGT 0.614634 -232 TATATTATTAGCTTTGTTTTTATGGCTTGACTTATCCC 2 177 1 GTTGTTTAGT 0.938489 -110 GGTTTGTTTTTATAGAGGGGTGGAATGG 3 1 1 GTTGTTTAGG 0.718963 -223 TATGGATCTAGCTTTTGATTGAAAGCATGGGTTCTTAC 3 181 1 GTTTTTGAGT 0.808381 -43 GAAAGCATGGGTTCTTACTTTATGGAGTGTCCA 3 201 1 GCTTTTTAGT 0.943067 -23 AAAATTACCCGATTTTTCTTTAAAGTTTAGTCTATATC 6 202 0 GTTTTTTAGT 0.955787 -99 TTTTTTTAGCGGGTTCAATTTAAAGATTTAAGGACTAT 7 160 0 GTTCTTTAGT 0.887168 -141 TCGGCTTTGAGAGTTTGTTTTATGGCATAATATCAGAC 7 245 1 GTTTTTTAGT 0.955787 -56 ATTCTTTCATGTTCTTTTTTTAAGCCATAGCATACCCC 8 21 1 GCTTTTTACT 0.783396 -83 ATTTTCTATGCTCTTGATTTTAGAGCTTTGATCAAAAT 10 58 0 CTTGTTTAGT 0.635193 -54 CATAATAACACTCCTTGATTTAGCGGATTTTACCGCAT 12 113 0 CCTTTTTAGT 0.654023 -178 GCGTTCTTTTTTTATGCGTTATTTGTCT 17 9 0 GCTTTTTACT 0.783396 -20 GAGGCTCGTTAAGTTTTATTGAATGTGTTGTAATGTTT 21 11 1 ATTTTTGAGT 0.237368 -78 TGAATGTGTTGTAATGTTTTTAAGGTATAATAAACTCT 21 30 1 GATGTTTAGT 0.566251 -59 ATTATTTATTGAGTTGAATTCAAGGAGTAAAAC 24 6 0 GTTGTTCAGT 0.618008 -138 CCTTAAGAATGCCTTTATTTAAGAGCATTTGTGATAGA 27 34 1 GTTTTTAAGT 0.731712 -55 ATTAGAAATGGGGCTTACTTTAGAGCCT 28 1 0 GCTTTTTAGT 0.943067 -209 GGAGTTACGCGTTTTTGTTGTATCGTTTAGGCTCAAAA 28 85 1 GTTTTGTAGT 0.783774 -125 GCCTTCCCTTTATTCTGTATTGCCTAAT 29 1 1 GTTCTTTACT 0.631916 -300 ATTAGAAATGGGGCTTACTTTAGAGCCTCTATCGCAAA 29 49 0 GCTTTTTAGT 0.943067 -252 GGAGTTATGCGTTTTTGTTGTATCGTTTAAAATAGGTG 29 133 1 GTTTTGTAGT 0.783774 -168 TCCTTGTTTTGGATTCAATTAAAGCGCTATTTTTAGCG 30 135 0 GTTCTTAACT 0.17803 -37 AAATCATTGAGCGCTGGTTTTAAGGCGGTCTTTT 31 334 1 GCTGTTTAGG 0.662187 -24 * *** **** * * Masking position 9 Map Score: 15.2206 Number of sites scoring better than the average of aligned sites = 564 Number in coding regions = 496 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 6 TAATTAGAATTTAAGCTATTTTTTAGTAGAAT 3 123 1 TTAGCTTTTT 0.936198 -101 CCATTAAAGTTTAAGGTTTATTTTAACTTATT 4 206 0 TTAGGTTATT 0.688859 -95 CTAAACAAAACTAAGGGCTTTTATATTACAAT 4 241 1 CTAGGGTTTT 0.798908 -60 TCTTCTTGGGTTAGGGGGATTTTAAGGGGGGT 6 13 1 TTAGGGATTT 0.834312 -288 TAGCATTAAATTAGGATTTTTTATAGAGTTGA 6 155 0 TTAGATTTTT 0.805457 -146 GTGATAAAAATTACCCGATTTTTCTTTAAAGT 6 214 0 TTACCGTTTT 0.913805 -87 TTTTGCGATTTTATCGTTTTTTTTTTTCTACA 7 205 1 TTACGTTTTT 0.823362 -96 ACTCCTTGATTTAGCGGATTTTACCGCATGCA 12 110 0 TTACGGTTTT 0.913805 -181 AACCACACTATTAGGATTTTTTGAAGAAAATC 12 162 1 TTAGATTTTT 0.805457 -129 CGTTCTTTTTTTATGCGTTATTTGTCT 17 6 0 TTAGCGTATT 0.834312 -23 AATTTCAATTTTAGGGGGTTTTGTTTGGTATT 24 94 0 TTAGGGTTTT 0.970908 -50 CGTAACTATTATCCTATTTTCAGACTTCAA 24 124 0 TTACCTTTTT 0.823362 -20 TGCATTTAAATTAGGCTCTTTTTAAACAGCCA 25 249 0 TTAGCTTTTT 0.936198 -42 AAAGGCATTCTTAAGGGGTTCTGTCTCATTAA 27 18 0 TTAGGGTTCT 0.798908 -71 ATGCCTTTATTTAAGAGCATTTGTGATAGAAT 27 42 1 TTAGAGATTT 0.58691 -47 GATCGGGGAGTTACGCGTTTTTGTTGTATCGT 28 79 1 TTAGCGTTTT 0.970908 -131 GATCGGGGAGTTATGCGTTTTTGTTGTATCGT 29 127 1 TTAGCGTTTT 0.970908 -174 *** *** **** Masking position 3 Map Score: 15.236 Number of sites scoring better than the average of aligned sites = 424 Number in coding regions = 330 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 7 AGGGGCGTTATTAACAAACCTTATTTTAAGAT 2 79 0 TTAACAAATT 0.895677 -208 TCTATTTTATTTATCAAAACTTAGGAGAACTA 2 263 1 TTATCAAATT 0.88111 -24 TTTCCCCGCTTTATTAAATATTCATCACAAAA 3 78 0 TTATTAAATT 0.859115 -146 AAATTATGGATTAATAAAACTTAAAGGATAAC 4 276 1 TTAATAAATT 0.875998 -25 AAGTGATAGATTATTAACTTTTTATGCTATAA 6 257 1 TTATTAACTT 0.638994 -44 ATCTTTTCCTTTAATAAAATTTTTAAGATTAT 8 80 0 TTAATAAATT 0.875998 -24 ACACCAGCCATTATCAAAATTTTGTATTATAA 9 132 1 TTATCAAATT 0.88111 -26 CGCATGCATCTTAATAAAACTTGATACAGATT 12 86 0 TTAATAAATT 0.875998 -205 TATAGCATGTTTAATAACGATTATTACTTTAT 22 98 0 TTAATAACTT 0.67219 -73 GATGCGTATTTTACTAAAATTTGCGCTAGAAT 23 11 1 TTACTAAATT 0.652337 -71 AGCTGTAGGGTTAATTAAAATTATTTATTGAG 24 31 0 TTAATTAATT 0.747041 -113 TCGTGTTATTTTATCTAAGTTTTGGCATGCGC 26 38 1 TTATCTAATT 0.755988 -87 AATGGGCATGTTATCTAAATTTTAGATAGAAT 28 133 1 TTATCTAATT 0.755988 -77 GATTAACTAACCTTTTATATCTGC 29 287 0 TTAACTAATT 0.782095 -14 ******** ** Masking position 7 Map Score: 8.82699 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 64 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 AGCTTTTGATTGAAAGCATGGGTTCTTACTTTATGGA 3 190 1 TGAAAGTGGT 0.886579 -34 TTAAGGACTATGCATGCAAGAGATTATCCCTATTGTC 7 134 0 TGCATGAAGT 0.702414 -167 TCATGGAGCATGAATGAGATGGCCTTTATTTAGCCAA 10 16 1 TGAATGAGGT 0.974323 -96 GAATTGAGTTTGATTGATAGGGGTGATTATAGCATTT 12 31 1 TGATTGAGGT 0.856768 -260 TAAGTTTTATTGAATGTGTTGTAATGTTTTTAAGGTA 21 20 1 TGAATGTGTT 0.829161 -69 GAGCATTTCTTGCATGATAGGGGGAGTTTCATTCAAT 22 22 1 TGCATGAGGT 0.964307 -149 GCGATAATTTTGCGTGTTTTGGCGCATGCCAAAACTT 26 54 0 TGCGTGTGGT 0.902357 -71 GATTTGCATGTGAATGGATCGGGGAGTTACGCGTTTT 28 63 1 TGAATGTGGT 0.982317 -147 TCAAAATGAGTGAATGAATGGGCATGTTATCTAAATT 28 117 1 TGAATGTGGT 0.982317 -93 GATTTGCATGTGAATGGATCGGGGAGTTATGCGTTTT 29 111 1 TGAATGTGGT 0.982317 -190 ****** * ** * Masking position 1 Map Score: 5.27977 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 37 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 AACCTTATTTTAAGATTTTATTTATTGAGT 2 65 0 TAAGATTTTA 0.506841 -222 ATAATATAATTAGAATTTAAGCTATTTTTT 3 117 1 TAGAATTTAA 0.559497 -107 ATTATAGCATAAAAAGTTAATAATCTATCA 6 260 0 AAAAAGTTAA 0.53389 -41 GGTTCAATTTAAAGATTTAAGGACTATGCA 7 157 0 AAAGATTTAA 0.915651 -144 GTATAATCTTAAAAATTTTATTAAAGGAAA 8 78 1 AAAAATTTTA 0.738336 -26 ATAATATTGAAAGAATTTAATCAAAGGGCT 9 15 0 AAGAATTTAA 0.774022 -143 GCAGAATATCTAAAATTTAAATTTCATTTT 9 83 1 TAAAATTTAA 0.79541 -75 AAATTTATTAGAAGATTTAAAAAGGCTTTT 10 92 1 GAAGATTTAA 0.595622 -20 GTAAAATAGTAAAGATTTTAAAACTCAAAA 11 43 1 AAAGATTTTA 0.741317 -30 ATTAGGAAATAAAAATATAAAACCCGGTCG 15 51 0 AAAAATATAA 0.435917 -197 TCTAGTTTTCAAAAATTTAAAAAA 16 5 0 AAAAATTTAA 0.919063 -107 ATAATGATACAAAAATTTAATTTTTTAGCC 16 79 1 AAAAATTTAA 0.919063 -33 GAGGTTTTAAAAATATTTAAAATCATGCTT 19 30 1 AAATATTTAA 0.54797 -43 TCATGCTTTAAAAGATTTAATATAAGGGTA 19 52 1 AAAGATTTAA 0.915651 -21 GAGCTTAAAATTTAAGAAAATTATA 20 6 1 TAAAATTTAA 0.79541 -83 CAAAACCCCCTAAAATTGAAATTGAAGTCT 24 103 1 TAAAATTGAA 0.465834 -41 AAAGAAAGACAAGGATTTTACAAGTAA 25 8 0 AAGGATTTTA 0.463107 -283 GAATAAACGCAAAAATTGAATAAAACCTTA 28 161 1 AAAAATTGAA 0.701625 -49 GAACAAAGCTAAAGATTAAACATTAAGATA 29 223 1 AAAGATTAAA 0.451024 -78 TGAGTTATTCAAAAATTTAACTTTATAAGA 31 19 0 AAAAATTTAA 0.919063 -339 ********** Masking position 5 Map Score: 12.3003 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 140 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 10 TACAAGGATTAGAGAAAGGGGCGTTATTAACAAAC 2 92 0 AGAGGGGGTT 0.989012 -195 GTGAATGAGGACAGGTGGGTGAGTTGGCTGAAACC 4 152 0 AGTGGTGGTT 0.929046 -149 GGTTAGGGGGATTTTAAGGGGGGTTGTAGGGGGAG 6 21 1 ATAGGGGGTT 0.967212 -280 GAACCCGCTAAAAAAAGGGGGTTTTTTGCGATTTT 7 182 1 AAAGGGGTTT 0.836051 -119 ATTGAGTTTGATTGATAGGGGTGATTATAGCATTT 12 33 1 AGTGGGGGAT 0.905873 -258 AAAATCCGCTAAATCAAGGAGTGTTATTATGGAAG 12 120 1 ATAGGAGGTT 0.742897 -171 CATTTCTTGCATGATAGGGGGAGTTTCATTCAATT 22 25 1 AAAGGGGGTT 0.953675 -146 CTTCAATTTCAATTTTAGGGGGTTTTGTTTGGTAT 24 95 0 ATTGGGGTTT 0.86012 -49 AGCATTTGTGATAGAATGGTGATTTTTAAATAAAG 27 57 1 AGAGGTGTTT 0.793991 -32 TTGCATGTGAATGGATCGGGGAGTTACGCGTTTTT 28 66 1 AGTGGGGGTT 0.986969 -144 TTGCATGTGAATGGATCGGGGAGTTATGCGTTTTT 29 114 1 AGTGGGGGTT 0.986969 -187 * * * **** *** Masking position 1 Map Score: 9.59232 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 182 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 11 CTTATCCCTAAAAATGCGCTATAGTTATGTC 2 207 1 AAAAGCGCTA 0.815753 -80 TAAAATAGAAATTTAGCGCTTATTGTTATTA 2 241 0 ATTTGCGCTT 0.80933 -46 CCCGCTAAAAAAAGGGGGTTTTTTGCGATTT 7 185 1 AAAGGGGTTT 0.457949 -116 ACTTCAATAAAAAAGGCGTTTGATAAAAGG 7 281 1 AAAAGCGTTT 0.73298 -20 TTATACAATAAAAGCGCGCTTAAAAGGGGTA 8 53 0 AAAGGCGCTT 0.919569 -51 TGAAAAATTGCGTTTCAGCTCATCT 15 5 1 AAATGCGTTT 0.885353 -243 ATTTTACTAAAATTTGCGCTAGAATGTAAGT 23 18 1 AATTGCGCTA 0.904361 -64 ATTTTACTACATTTTGCGCTATTATATTGGA 24 66 0 ATTTGCGCTA 0.639567 -78 AAACACGCAAAATTATCGCTTTTAAGATAAA 26 72 1 AATTTCGCTT 0.724304 -53 TTTAAGATAAAATAAGCGTTTTGATGCCATT 26 92 1 AATAGCGTTT 0.675829 -33 AAAACATTAGAAATGGGGCTTACTTTAGAGC 28 13 0 AAATGGGCTT 0.894649 -197 AAAACATTAGAAATGGGGCTTACTTTAGAGC 29 61 0 AAATGGGCTT 0.894649 -240 CCAACGCTAAAAATAGCGCTTTAATTGAATC 30 131 1 AAATGCGCTT 0.967521 -41 TGGTAAAATCAATTTTCGCTAGTTTTGGATA 31 270 0 AATTTCGCTA 0.523416 -88 **** ****** Masking position 1 Map Score: 6.46956 Number of sites scoring better than the average of aligned sites = 707 Number in coding regions = 644 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 12 AGGTTTGTTAATAACGCCCCTTTCTCTAATC 2 90 1 AAACGCCCCT 0.895565 -197 CCACCCCTCCATTCCACCCCTCTATAAAAAC 3 16 0 ATCCACCCCT 0.952631 -208 GCTTTTTTACATTCCACCCCTCCATTCCACC 3 29 0 ATCCACCCCT 0.952631 -195 CGAGGGTTCGAATCCCTCCCTGTCCGCCAGC 4 85 0 ATCCCTCCCT 0.848976 -216 GTTGGCTGAAACCACATCCCTGCTAAGGATG 4 134 0 ACACATCCCT 0.626908 -167 AACCCCCCTTAAAATCCCCCTAACCCAAGAA 6 15 0 AAATCCCCCT 0.94354 -286 CTCTCCCCCTACAACCCCCCTTAAAATCCCC 6 27 0 AAACCCCCCT 0.981065 -274 TTTTGAAATAACTCTCCCCCTACAACCCCCC 6 38 0 ATCTCCCCCT 0.93477 -263 GTTATTTCAAAATACCCCACTATCCCCTTAA 6 57 1 ATACCCCACT 0.741724 -244 TAAAATCGCAAAAAACCCCCTTTTTTTAGCG 7 187 0 AAAACCCCCT 0.83551 -114 TTTAAGCCATAGCATACCCCTTTTAAGCGCG 8 39 1 ACATACCCCT 0.810732 -65 TGCTTCCATAATAACACTCCTTGATTTAGCG 12 126 0 AAACACTCCT 0.60703 -165 TAATTGAATGAAACTCCCCCTATCATGCAAG 22 30 0 AACTCCCCCT 0.944534 -141 * ********* Masking position 1 Map Score: 8.80669 Number of sites scoring better than the average of aligned sites = 442 Number in coding regions = 371 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 13 GTTTGTTAATAACGCCCCTTTCTCTAATCC 2 92 1 AACGCCCCTT 0.883785 -195 CCCCCCTTAAAATCCCCCTAACCCAAGAAG 6 14 0 AATCCCCCTA 0.697595 -287 CTCCCCCTACAACCCCCCTTAAAATCCCCC 6 26 0 AACCCCCCTT 0.956368 -275 AATCGCAAAAAACCCCCTTTTTTTAGCGGG 7 185 0 AACCCCCTTT 0.895485 -116 TAAGCCATAGCATACCCCTTTTAAGCGCGC 8 41 1 CATACCCCTT 0.624297 -63 TAACCACCTTTAATTGTTATG 12 2 1 AACCACCTTT 0.752122 -289 GATGTGCTAGAATACCCATTTGTTACAAGA 15 186 1 AATACCCATT 0.729032 -62 CAAACCATCCAATGACCCTTTATCGCACTC 25 41 1 AATGACCCTT 0.741461 -250 TTTATTTAAAAATCACCATTCTATCACAAA 27 61 0 AATCACCATT 0.860804 -28 GCTCTAAAGTAAGCCCCATTTCTAATGTTT 28 13 1 AAGCCCCATT 0.925541 -197 ATTTAGATAACATGCCCATTCATTCACTCA 28 123 0 CATGCCCATT 0.736111 -87 GATTAGAAAGAATCACCTTTAAGGTTTTAT 28 180 0 AATCACCTTT 0.764399 -30 GCTCTAAAGTAAGCCCCATTTCTAATGTTT 29 61 1 AAGCCCCATT 0.925541 -240 CAAATAATGTCAGCACCATTTCTCCAAATC 31 81 1 CAGCACCATT 0.669594 -277 ********** Masking position 2 Map Score: 7.8976 Number of sites scoring better than the average of aligned sites = 516 Number in coding regions = 452 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 14 TCTTCATCTTGCTTTCTTGTTTTAACTCGC 2 22 1 GCTTTCTTGT 0.633723 -265 TGCGATTTTATCGTTTTTTTTTTTCTACAA 7 208 1 TCGTTTTTTT 0.597921 -93 CCTTTTAAGCGCGCTTTTATTGTATAATCT 8 57 1 GCGCTTTTAT 0.711806 -47 ATATAAAACGGCGTTTATTTCATGTTAGAA 15 132 0 GCGTTTATTT 0.821788 -116 TACAAGATAAGCTTTTTTATCAAAAATAAT 15 209 1 GCTTTTTTAT 0.599754 -39 GCGTTCTTTTTTTATGCGTT 17 19 0 GCGTTCTTTT 0.943112 -10 CGTTCAATGAGCGTTCTTATTTGTAAAAAA 25 122 0 GCGTTCTTAT 0.89687 -169 GGGGAGTTACGCGTTTTTGTTGTATCGTTT 28 83 1 GCGTTTTTGT 0.949039 -127 GGGGAGTTATGCGTTTTTGTTGTATCGTTT 29 131 1 GCGTTTTTGT 0.949039 -170 ATACAAGCGAGCGGTTTTCTTATGGTATAA 30 78 1 GCGGTTTTCT 0.795238 -94 TGGTATAATAGCGGTTATTTTTTTAGAATA 30 100 1 GCGGTTATTT 0.720509 -72 GCGGTAGGTGGCGTCTTTTTGGTGCGGCTG 31 116 0 GCGTCTTTTT 0.780749 -242 TGGTTTTAAGGCGGTCTTTT 31 348 1 GCGGTCTTTT 0.902612 -10 ********** Masking position 8 Map Score: 5.75716 Number of sites scoring better than the average of aligned sites = 704 Number in coding regions = 645 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 15 TCTATCACTTGTTTTAAAAAAGTGATAAAA 6 237 0 GTTTTAAAAA 0.904314 -64 TACAATAGTTGTTATCAAAAGCCACGACAA 7 109 1 GTTATCAAAA 0.744745 -192 TTTATTAGAAGATTTAAAAAGGCTTTT 10 95 1 GATTTAAAAA 0.606729 -17 GCGTTTTAAAAACCTTTGAGGG 11 3 1 GTTTTAAAAA 0.904314 -70 TCCTTTTTGAGTTTTAAAATCTTTACTATT 11 47 0 GTTTTAAAAT 0.606635 -26 AGGTTGTATAGTTGGAAAAAGGAATAATGC 12 226 1 GTTGGAAAAA 0.705372 -65 TTTAATTCTAGTTTTCAAAAATTTAAAAAA 16 11 0 GTTTTCAAAA 0.868226 -101 ACACGCTTTTGTTGTCAAAATGTTATTTTA 18 41 0 GTTGTCAAAA 0.759 -78 CTTTAAAGAGGTTTTAAAAATATTTAAAAT 19 23 1 GTTTTAAAAA 0.904314 -50 CCTAAAATTAGTTTTAAAACGCATCTTTTA 20 62 0 GTTTTAAAAC 0.459045 -27 TCATTGGATGGTTTGAAAAAAGAAAGACAA 25 26 0 GTTTGAAAAA 0.833136 -265 AAGCATGCCCGTTACAAAAACATTAGAAAT 28 30 0 GTTACAAAAA 0.689517 -180 AAGCATGTTCGTTACAAAAACATTAGAAAT 29 78 0 GTTACAAAAA 0.689517 -223 ********** Masking position 7 Map Score: 7.89048 Number of sites scoring better than the average of aligned sites = 433 Number in coding regions = 352 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826