AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -irpoH_hpyl_opreg_100.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 HP0109 29 chaperone and heat shock protein 70 (dnaK) #5 HP0111 300 H. pylori predicted coding region HP0111 #6 HP0210 103 chaperone and heat shock protein C62.5 (htpG) #7 HP0263 111 adenine specific DNA methyltransferase (hpaim) #8 HP0264 72 ATP-dependent protease binding subunit (clpB) #9 HP0513 290 H. pylori predicted coding region HP0513 #10 HP0514 60 ribosomal protein L9 (rpl9) #11 HP0562 100 ribosomal protein S21 (rps21) #12 HP0795 111 trigger factor (tig) #13 HP0921 143 glyceraldehyde-3-phosphate dehydrogenase (gap) #14 HP1067 290 chemotaxis protein (cheY) #15 HP1332 124 co-chaperone and heat shock protein (dnaJ) #16 HP1346 88 glyceraldehyde-3-phosphate dehydrogenase (gap) #17 HP1350 209 protease #18 HP1376 171 (3R)-hydroxymyristoyl-(acyl carrier protein) dehydratase (fabZ) #19 HP1378 300 competence lipoprotein (comL) #20 HP1379 41 ATP-dependent protease (lon) Motif number 1 TGTATCAAGTTTCATTAGTTTAAAAATACAAGGATT 2 117 0 TTTTTTAAAA 0.897739 -170 ATTAGTTCTCCTAAGTTTTGATAAATAAAATAGA 2 263 0 TCAATTATAA 0.788312 -24 TAAATATTCATCACAAAATGTAAAAAATACTAAAAA 3 60 0 TCAATTAAAA 0.837453 -164 ATTTAAGCTATTTTTTAGTAGAATAACAAAGGATTA 3 131 1 TTTTTGATAA 0.77719 -93 TAATAATCTATCACTTGTTTTAAAAAAGTGATAAAA 5 237 0 TCTTTTAAAA 0.89581 -64 GAAAGAACCCTCGCATTATAGCATAAAAAGTTAATA 5 268 0 TCATTGATAA 0.800837 -33 CGCGCTTTTATTGTATAATCTTAAAAATTTTATTAA 6 66 1 TTATTTAAAA 0.909992 -38 TGATCTTTTCCTTTAATAAAATTTTTAAG 6 85 0 TCTTTTATAA 0.860995 -19 AAAAGCCTTTTTAAATCTTCTAATAAATTTTCTATG 7 86 0 TTATTTATAA 0.881558 -26 ATTTTAACCCTCAAAGGTTTTTAAAACGC 8 4 0 TCAGTTAAAA 0.786332 -69 TATCAATCCTTTTTGAGTTTTAAAATCTTTACTAT 8 48 0 TTTGTTAAAA 0.760643 -25 CTATCAGAGGTTGTATAGTTGGAAAAAGGAATAATG 9 219 1 TTATTGAAAA 0.850715 -72 GTAATTATACTCTTTATTTTGAATAAGTTGGGTTT 10 10 0 TCTATGATAA 0.635737 -51 AATTCTAGTTTTCAAAAATTTAAAAAA 12 2 0 TTAATTAAAA 0.839665 -110 TTTGTTTTAATTCCAGTTTATAAAAAGCGGTTTTAA 12 36 0 TTAGTTAAAA 0.789813 -76 GAAATTGAAGTCTGAAAATAGGATAATAGTTACG 13 120 1 TCAATGATAA 0.672567 -24 TAAAGGGTCATTGGATGGTTTGAAAAAAGAAAGACA 14 27 0 TTATTTAAAA 0.91175 -264 AAAATTCAGTTTGTTTGCTATGATAATCGTTTAAAA 14 89 0 TTTTTTATAA 0.863481 -202 TCAATGAGCGTTCTTATTTGTAAAAAAATTCAGTTT 14 113 0 TTTATTAAAA 0.81666 -178 ATCAAAACGCTTATTTTATCTTAAAAGCGATAATTT 15 81 0 TTTTTTAAAA 0.846869 -44 GTTTTCCCTTTATTTAAAAATCACCATTCT 16 69 0 TCTTTTAAAA 0.89581 -20 ATTTTTAGCGTTGGTTATTCTAAAAAAATAACCGCT 18 109 0 TTTTTTAAAA 0.897739 -63 AACCGAATCATTATAAAATATAATAAGGAGTTGAGG 19 84 1 TTAATTATAA 0.483987 -217 TCTTATAAAGTTAAATTTTTGAATAACTCATGGTTA 19 267 0 TTATTGATAA 0.80414 -34 ** ** * * **** Masking position 9 Map Score: 25.4373 Number of sites scoring better than the average of aligned sites = 756 Number in coding regions = 576 Number in noncoding regions = 180 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 2 TTTTCATGCTTTCTTCATCTTGCTTTCTTGTTTTAA 2 7 1 TGTTTTTTTT 0.79045 -280 TTTTAAGATTTTATTTATTGAGTATAATTCATTCAAGCGA 2 48 0 TTTTTTTTTC 0.712524 -239 TAACGCCCCTTTCTCTAATCCTTGTATTTTTAAACTAATG 2 101 1 TTTTATTTTT 0.969144 -186 ATCCTTATAGTTATATTATTAGCTTTGTTTTTATGGCTTG 2 166 1 TTTTATTTTT 0.969144 -121 TAAATTCTAATTATATTATTGGAATTTTTCCCCGCTTTAT 3 96 0 TTTTATTTTC 0.953957 -128 TAGGTGTATCTTATCTTATGGATCTAGCTTTTGATTGAAA 3 165 1 TTTTATTCTT 0.759502 -59 ATCCTTTTTGTTTTATAATGAAACTCATTCTCTTAAGGGG 5 80 0 TTTTATTTTC 0.953957 -221 TTAAATTAGGATTTTTTATAGAGTTGATTTAATTTAGATC 5 142 0 ATTTATTTTT 0.789796 -159 AAATTAAACATTCTTTCATGTTCTTTTTTTAAGCCATAGC 6 12 1 TTTTATTTTT 0.969144 -92 CGCGCTTTTATTGTATAATCTTAAAAATTTTATTAAAGGA 6 66 1 TTTTATATTT 0.669513 -38 TTGATTTTAGAGCTTTGATCAAAATGGTTTTTGGCTAAAT 7 43 0 AGTTATTTTT 0.79045 -69 GTAAGTAATTTGTAATTATACTCTTTATTTTGAATAAGTT 10 17 0 TGATATTTTT 0.670386 -44 TTAATTCGTCTTATATAATACTATTTCATTTGTAGCCATT 11 28 1 TTTTATTATT 0.680588 -73 TTACTTGTAAAATCCTTGTCTTTCTTTTTTCAAA 14 5 1 TTTAATTTTC 0.571987 -286 TTTATTACTATGGTTTTATCGTGTTATTTTATCTAAGTTT 15 20 1 TGTTATTTTT 0.969261 -105 TTTCTAATGTTTTTGTAACGGGCATGCTTTGCGATTTGCA 17 31 1 TTTTACTTTT 0.853197 -179 GGTTTTCTTATGGTATAATAGCGGTTATTTTTTTAGAATA 18 90 1 TGTTATTTTT 0.969261 -82 TAGCGAAAATTGATTTTACCAAAATTGTTTG 19 2 0 TGTTACTTTT 0.85369 -299 TCTTGATTTGTGGTTTTATTTTGCTCATTCCTCAACTCCT 19 109 0 TGTTATTTTC 0.95413 -192 CATGGTTATTTTTTCTTATCTTTCTTATTCCCACCAAATA 19 235 0 TTTTATTTTC 0.953957 -66 TTCATCTCTCTGTTATAATGTGTATGGTTTTGAAATATC 20 10 0 TGTTATTTTT 0.969261 -32 ** * * ** * *** Masking position 19 Map Score: 22.8709 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 114 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 3 TCTAATTATATTATTGGAATTTTTCCCCGCTTT 3 98 0 TTAGGATTTT 0.82302 -126 ATAATTAGAATTTAAGCTATTTTTTAGTAGAAT 3 122 1 TTTGCTTTTT 0.859301 -102 TCTTCTTGGGTTAGGGGGATTTTAAGGGGGGTT 5 13 1 TTAGGGTTTT 0.941787 -288 GTGATAAAAATTACCCGATTTTTCTTTAAAGTT 5 213 0 TTACGATTTT 0.702054 -88 ATACCCCTTTTAAGCGCGCTTTTATTGTATAAT 6 52 1 TAAGCGTTTT 0.805457 -52 ATAGGGGTGATTATAGCATTTATGGGGCAAAAA 9 47 1 TTAGCATTAT 0.724686 -244 CACTCCTTGATTTAGCGGATTTTACCGCATGCA 9 110 0 TTTCGGTTTT 0.89992 -181 GCAACCACACTATTAGGATTTTTTGAAGAAAAT 9 160 1 TATGGATTTT 0.677684 -131 GACAACCAGTTAATTCGTCTTATATAATACTAT 11 19 1 TAACGTTTAT 0.630573 -82 ACTGCTATCACCTCTTTTCCATAGCTTA 11 83 0 TATCCTTTTT 0.560521 -18 AAACTAGAATTAAAACCGCTTTTTATAAACTGG 12 27 1 TAACCGTTTT 0.676711 -85 TTTACTACATTTTGCGCTATTATATTGGACCTA 13 62 0 TTTGCTTTAT 0.847732 -82 CAATTTCAATTTTAGGGGGTTTTGTTTGGTATT 13 94 0 TTTGGGTTTT 0.946659 -50 TTACTATGGTTTTATCGTGTTATTTTATCTAAG 15 24 1 TTTCGTTTAT 0.819597 -101 AAAGCGATAATTTTGCGTGTTTTGGCGCATGCC 15 61 0 TTTCGTTTTT 0.832882 -64 TTTTATTCAATTTTTGCGTTTATTCTATCTAAA 17 153 0 TTTGCGTTAT 0.909466 -57 AAGAATCACCTTTAAGGTTTTATTCAATTTTTG 17 170 0 TTTGGTTTAT 0.899661 -40 TCTTATGGTATAATAGCGGTTATTTTTTTAGAA 18 95 1 TAAGCGTTAT 0.79054 -77 CATGGTTAAGTTATTGGGATTATATCCAAAACT 19 41 0 TTAGGGTTAT 0.936499 -260 TTTTTCTTGATTTGTGGTTTTATTTTGCTCATT 19 120 0 TTTGGTTTAT 0.899661 -181 AAAATGAGATTTACTGGGATTATTTTTCTTGAT 19 142 0 TTAGGGTTAT 0.936499 -159 *** *** **** Masking position 10 Map Score: 17.5688 Number of sites scoring better than the average of aligned sites = 1746 Number in coding regions = 1505 Number in noncoding regions = 241 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 4 CGTTATTAACAAACCTTATTTTAAGATTTTATT 2 73 0 AACTATTTTA 0.8373 -214 ATAAGCGCTAAATTTCTATTTTATTTATCAAAA 2 249 1 AATCATTTTA 0.894367 -38 AAAAATACTAAAAAGCTTTTTTACATTCCACCC 3 41 0 AAGCTTTTTA 0.872712 -183 AACATTTATTTTAAAAGAAAGGA 4 1 1 AATTATTTTA 0.840009 -29 TACCCCTTTTAAGCGCGCTTTTATTGTATAATC 6 53 1 AAGCCTTTTA 0.800865 -51 AAAAGCCTTTTTAAATCTTCTAA 7 99 0 AAGCTTTTTA 0.872712 -13 CCAGTTTATAAAAAGCGGTTTTAATTCTAGTTT 12 27 0 AAGCGTTTTA 0.800862 -85 AATGATACAAAAATTTAATTTTTTAGCCATTAA 12 81 1 AATTATTTTT 0.581129 -31 TTCAGACTTCAATTTCAATTTTAGGGGGTTTTG 13 103 0 AATCATTTTA 0.894367 -41 ATCGCACTCAAAGAGTTATTTTATTACTTTTAA 14 62 1 AAGTATTTTA 0.95161 -229 TATTGTCGGTCAAGGTAATTTTAATCAAAACAT 14 170 1 CAGTATTTTA 0.79329 -121 AGCCTAATTTAAATGCAATCTTAAAAGGAGAAG 14 264 1 AAGCATCTTA 0.860892 -27 ATGGCATCAAAACGCTTATTTTATCTTAAAAGC 15 89 0 AACTATTTTA 0.8373 -36 GCTCTTAAATAAAGGCATTCTTAAGGGGTTCTG 16 27 0 AAGCTTCTTA 0.57228 -62 TTTGTGATAGAATGGTGATTTTTAAATAAAGGG 16 61 1 AAGTATTTTT 0.838611 -28 CTAAAAAAATAACCGCTATTATACCATAAGAAA 18 93 0 AAGCATTATA 0.682681 -79 GATTCAATTAAAGCGCTATTTTTAGCGTTGGTT 18 129 0 AAGCATTTTT 0.893393 -43 AAAACTAGCGAAAATTGATTTTACCAAAATTGT 19 14 0 AATTATTTTA 0.839992 -287 TAATCCCAGTAAATCTCATTTTAGCGGTAGGTG 19 153 1 AACTATTTTA 0.8373 -148 TTGAATAACTCATGGTTATTTTTTCTTATCTTT 19 252 0 CAGTATTTTT 0.503508 -49 ** ** ****** Masking position 9 Map Score: 16.8867 Number of sites scoring better than the average of aligned sites = 880 Number in coding regions = 743 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 5 ATAAAATCTTAAAATAAGGTTTGTTAATAACG 2 74 1 AATAAGGTTT 0.74351 -213 TTAGTTTAAAAATACAAGGATTAGAGAAAGGG 2 107 0 AACAAGGATT 0.96652 -180 TAATAATATAACTATAAGGATTATTAAGTCTA 2 155 0 AATAAGGATT 0.961562 -132 ATGGGTTCTTACTTTATGGAGTGTCCA 3 207 1 ATTATGGAGT 0.613746 -17 TCATTATAAAACAAAAAGGATTATCCATATTT 5 99 1 AAAAAGGATT 0.817685 -202 AAAATCCGCTAAATCAAGGAGTGTTATTATGG 9 120 1 ATCAAGGAGT 0.945351 -171 ACGCAACCACACTATTAGGATTTTTTGAAGAA 9 158 1 AATTAGGATT 0.726904 -133 CAACTTATTCAAAATAAAGAGTATAATTACAA 10 16 1 AATAAAGAGT 0.753974 -45 TATTGAGTTGAATTCAAGGAGTAAAAC 13 6 0 ATCAAGGAGT 0.945233 -138 TGAAAAAAGAAAGACAAGGATTTTACAAGTAA 14 11 0 AACAAGGATT 0.966633 -280 ACGATTTATTATTATAAGGCGTTAGAGACGCT 14 216 1 AATAAGGCGT 0.888734 -75 AATTGAATCCAAAACAAGGAGTTTATTTT 18 153 1 AACAAGGAGT 0.981768 -19 ATTATAAAATATAATAAGGAGTTGAGGAATGA 19 93 1 AATAAGGAGT 0.97896 -208 * ********* Masking position 1 Map Score: 13.307 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 69 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 6 CCCTTTCTCTAATCCTTGTATTTTTAAACTA 2 107 1 AATCCTTGAT 0.941059 -180 AGATACACCTAATCCTTTGTTATTCTACTAA 3 145 0 AATCCTTTTT 0.948885 -79 GCGTTATCCTTTCTTTTAAAATAAA 4 15 0 TATCCTTTTT 0.702281 -15 AAATATGGATAATCCTTTTTGTTTTATAATG 5 100 0 AATCCTTTTG 0.876926 -201 TATCAATCCTTTTTGAGTTTTAAAA 8 58 0 AATCCTTTTG 0.876926 -15 CCATAATAACACTCCTTGATTTAGCGGATTT 9 121 0 ACTCCTTGTT 0.96913 -170 CATAGCTTAAAATCATTGCTTAACAATGGCT 11 61 0 AATCATTGTT 0.881047 -40 GTTTTACTCCTTGAATTCAACTCAAT 13 6 1 ACTCCTTGAT 0.909091 -138 TTACTTGTAAAATCCTTGTCTTTCTTTTTTC 14 11 1 AATCCTTGCT 0.961083 -280 GACCGACAATAATCATTGGCTAAATGGAGCG 14 150 0 AATCATTGCT 0.791719 -141 AAAATAAACTCCTTGTTTTGGATTCAAT 18 154 0 ACTCCTTGTT 0.969364 -18 ******** ** Masking position 6 Map Score: 9.26881 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 125 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 7 TCCCCCTACAACCCCCCTTAAAATCCCCCTA 5 24 0 ACCCCCTTAA 0.865675 -277 TTTAGATCTGATCTCATTTAAATATGGATAA 5 119 0 ATCCATTTAA 0.946574 -182 GCCATAGCATACCCCTTTTAAGCGCGCTTTT 6 44 1 ACCCTTTTAA 0.955704 -60 TAACCACCTTTAATTGTTATGAA 9 3 1 ACCCCTTTAA 0.971608 -288 ATCCCCTTTAAGTTGTAAGTA 10 50 0 ATCCCTTTAA 0.973399 -11 TAGAATTAAAACCGCTTTTTATAAACTGGAA 12 31 1 ACCCTTTTTA 0.842601 -81 GAGTTATTTTATTACTTTTAAACGATTATCA 14 74 1 ATTCTTTTAA 0.780422 -217 TCCTTTTAAGATTGCATTTAAATTAGGCTCT 14 262 0 ATTCATTTAA 0.731871 -29 ACGCAAAATTATCGCTTTTAAGATAAAATAA 15 76 1 ATCCTTTTAA 0.958455 -49 ATTAGAAAGAATCACCTTTAAGGTTTTATTC 17 178 0 ATCCCTTTAA 0.973399 -32 ATCCCAGTAAATCTCATTTTAGCGGTAGGTG 19 155 1 ATCCATTTTA 0.81468 -146 *** ******* Masking position 1 Map Score: 12.1805 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 143 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 8 TTAGGGGGATTTTAAGGGGGGTTGTAGGGG 5 23 1 TTTAAGGGGG 0.94883 -278 AACTCATTCTCTTAAGGGGATAGTGGGGTA 5 69 0 CTTAAGGGGA 0.94883 -232 TAAAAGCGCGCTTAAAAGGGGTATGCTATG 6 46 0 CTTAAAAGGG 0.960822 -58 ATTCATAACAATTAAAGGTGGTTA 9 5 0 ATTAAAGGTG 0.656503 -286 TTACTTACAACTTAAAGGGGAT 10 49 1 CTTAAAGGGG 0.988626 -12 TCAATTTCAATTTTAGGGGGTTTTGTTTGG 13 98 0 TTTTAGGGGG 0.722924 -46 TAAATGCAATCTTAAAAGGAGAAGCACT 14 273 1 CTTAAAAGGA 0.828448 -18 CTTATTTTATCTTAAAAGCGATAATTTTGC 15 78 0 CTTAAAAGCG 0.80233 -47 TAAAGGCATTCTTAAGGGGTTCTGTCTCAT 16 21 0 CTTAAGGGGT 0.913161 -68 TGAATAAAACCTTAAAGGTGATTCTTTCTA 17 177 1 CTTAAAGGTG 0.944797 -33 ********** Masking position 5 Map Score: 6.70168 Number of sites scoring better than the average of aligned sites = 601 Number in coding regions = 519 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 9 TTTGTATCCTTAATAATAATGTTT 1 6 0 CTTAATAAAA 0.920089 -19 ATGAATTATACTCAATAAATAAAATCTTAAA 2 56 1 CTCAATAATA 0.701513 -231 TACAAATAGACTTAATAATCCTTATAGTTAT 2 149 1 CTTAATAACC 0.793528 -138 AGTTATGTCGCTTAATAACAATAAGCGCTAA 2 229 1 CTTAATAAAA 0.920089 -58 CATTCCACCCCTCTATAAAAACAAACC 3 7 0 CTCTATAAAA 0.830873 -217 GAATGAGTTTCATTATAAAACAAAAAGGATT 5 90 1 CATTATAAAC 0.681684 -211 ATTAAATCAACTCTATAAAAAATCCTAATTT 5 149 1 CTCTATAAAA 0.830873 -152 CCGCATGCATCTTAATAAAACTTGATACAGA 9 88 0 CTTAATAAAC 0.94853 -203 CGTCTGCTTCCATAATAACACTCCTTGATTT 9 130 0 CATAATAAAC 0.805032 -161 TTGAATTCAACTCAATAAATAATTTTAATTA 13 21 1 CTCAATAATA 0.701513 -123 TTGATGCTTAATGAGACAGAACCCCTT 16 7 1 CTTAATGAAC 0.759826 -82 AAAAATTTAACTTTATAAGACAGGTGGC 19 283 1 CTTTATAAAC 0.905286 -18 ******** ** Masking position 5 Map Score: 7.04504 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 59 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 TAAGCGACATAACTATAGCGCATTTTTAGGGATAAG 2 207 0 AAAAGCTTTT 0.783768 -80 GCTTAATAACAATAAGCGCTAAATTTCTATTTTATT 2 238 1 AAACGCATTT 0.647335 -49 ATATAATTAGAATTTAAGCTATTTTTTAGTAGAATA 3 120 1 AATAGCTTTT 0.54117 -104 AACTTTAAAGAAAAATCGGGTAATTTTTATCACTTT 5 213 1 AAACGGATTT 0.732002 -88 TGAAAACTAGAATTAAAACCGCTTTTTATAAACTGG 12 24 1 AAAAACTTTT 0.540948 -88 ATTTTTGTATCATTATAGCTTAATTTGTTTTAATTC 12 59 0 CAAAGCATTT 0.784354 -53 CTTCAATTTCAATTTTAGGGGGTTTTGTTTGGTATT 13 94 0 AATAGGTTTT 0.639832 -50 AAGAACGCTCATTGAACGCTCCATTTAGCCAATGAT 14 134 1 ATACGCATTT 0.697896 -157 AATCGTTCCAAATAATAGCATGTTTTGATTAAAATT 14 186 0 AAAAGCTTTT 0.952548 -105 TTGGCTGTTTAAAAAGAGCCTAATTTAAATGCAATC 14 248 1 AAAAGCATTT 0.779803 -43 AGGCTCTAAAGTAAGCCCCATTTCTAATGTTTT 17 8 1 AATAGCATTT 0.939704 -202 TTTTAGATAGAATAAACGCAAAAATTGAATAAAACC 17 152 1 AAACGCAATT 0.678709 -58 TTTTGGATTCAATTAAAGCGCTATTTTTAGCGTTGG 18 131 0 AAAAGCATTT 0.575644 -41 TGGTAAAATCAATTTTCGCTAGTTTTGGATATAATC 19 21 1 AATCGCTTTT 0.833624 -280 CCCACCAAATAATGTCAGCACCATTTCTCCAAATCA 19 210 0 AATAGCATTT 0.940493 -91 ** * *** **** Masking position 15 Map Score: 14.858 Number of sites scoring better than the average of aligned sites = 452 Number in coding regions = 392 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 11 ATCCCTAAAAATGCGCTATAGTTATGTCGC 2 210 1 ATGCGCTATA 0.885119 -77 TAATAACAATAAGCGCTAAATTTCTATTTT 2 241 1 AAGCGCTAAA 0.95508 -46 ATTTTGATCAAAGCTCTAAAATCAAGAGCA 7 58 1 AAGCTCTAAA 0.915411 -54 ATTAAGATGCATGCGGTAAAATCCGCTAAA 9 103 1 ATGCGGTAAA 0.876565 -188 ATGCGGTAAAATCCGCTAAATCAAGGAGTG 9 113 1 ATCCGCTAAA 0.876565 -178 AAGTTTTGGCATGCGCCAAAACACGCAAAA 15 54 1 ATGCGCCAAA 0.928476 -71 TCTATCACAAATGCTCTTAAATAAAGGCAT 16 42 0 ATGCTCTTAA 0.796811 -47 AGGCTCTAAAGTAAGCCCCA 17 1 1 AGGCTCTAAA 0.943629 -209 TGTATCGTTTAGGCTCAAAATGAGTGAATG 17 103 1 AGGCTCAAAA 0.74999 -107 ********** Masking position 1 Map Score: 3.9241 Number of sites scoring better than the average of aligned sites = 428 Number in coding regions = 393 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 12 TTATTAAGTCTATTTGTATCAAGTTTCATTA 2 136 0 TATTTGTACA 0.832139 -151 AAAAATTAAATTTTTGTATCATTATAGCTTA 12 73 0 TTTTTGTACA 0.888301 -39 AACATGCTATTATTTGGAACGATTTATTATT 14 198 1 TATTTGGACG 0.955044 -93 TTTGATGCCATTTTTGGAGCGATC 15 111 1 TTTTTGGACG 0.971494 -14 ATTTCTAATGTTTTTGTAACGGGCATGCTTT 17 30 1 TTTTTGTACG 0.972043 -180 TTACGCGTTTTTGTTGTATCGTTTAGGCTCA 17 89 1 TTGTTGTACG 0.902296 -121 ATTAAAGCGCTATTTTTAGCGTTGGTTATTC 18 125 0 TATTTTTACG 0.707627 -47 AGGTGGCGTCTTTTTGGTGCGGCTGGGCTTG 19 181 1 TTTTTGGTCG 0.859302 -120 ******** ** Masking position 5 Map Score: 3.54136 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 126 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 13 TTTTCATGCTTTCTTCATCTTGCT 2 5 1 CATGCTTTCT 0.912343 -282 CTTTCTTCATCTTGCTTTCTTGTTTTAACT 2 19 1 CTTGCTTTCT 0.766845 -268 AGTAAGAACCCATGCTTTCAATCAAAAGCT 3 190 0 CATGCTTTCA 0.970533 -34 GCGTTATCCTTTCTTTTAAAATAAATGT 4 12 0 CTTTCTTTTA 0.725993 -18 TAATGAAACTCATTCTCTTAAGGGGATAGT 5 75 0 CATTCTCTTA 0.720662 -226 AAAATTAAACATTCTTTCATGTTCTTTTT 6 10 1 CATTCTTTCA 0.962382 -94 TTAATCAAAACATGCTATTATTTGGAACGA 14 190 1 CATGCTATTA 0.79805 -101 TAAAAATCACCATTCTATCACAAATGCTCT 16 55 0 CATTCTATCA 0.903526 -34 ATAACATGCCCATTCATTCACTCATTTTGA 17 117 0 CATTCATTCA 0.801307 -93 ********** Masking position 3 Map Score: 4.28707 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 218 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 14 ********** No masking Map Score: -4.11872e-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 15 TTTGTTTTTATGGCTTGACTTATCCCTAAAA 2 189 1 TGCTTGACTT 0.761037 -98 GATTTTTTATAGAGTTGATTTAATTTAGATC 5 142 0 AGGTTGATTT 0.415145 -159 TGAATGAGATGGCCTTTATTTAGCCAAAAAC 7 26 1 GGCTTTATTT 0.937978 -86 AATTTTCTATGCTCTTGATTTTAGAGCTTTG 7 66 0 GCCTTGATTT 0.793198 -46 ACAAATTGATTGTTTTGATTTTCTTCAAAAA 9 179 0 TGTTTGATTT 0.82373 -112 GTAAAATCCTTGTCTTTCTTTTTTCAAACCA 14 17 1 TGCTTTCTTT 0.816975 -274 AATCAAAACATGCTATTATTTGGAACGATTT 14 192 1 TGTATTATTT 0.470928 -99 CCCTTAAGAATGCCTTTATTTAAGAGCATTT 16 33 1 TGCTTTATTT 0.94327 -56 GTTTTCCCTTTATTTAAAAATCACC 16 74 0 TCCTTTATTT 0.749197 -15 TTTTTGTAACGGGCATGCTTTGCGATTTGCA 17 40 1 GGCATGCTTT 0.606469 -170 TCCAAAACAAGGAGTTTATTTT 18 160 1 GGGTTTATTT 0.764721 -12 TCTTGATTTGTGGTTTTATTTTGCTCATTCC 19 118 0 TGTTTTATTT 0.767998 -183 TGGGATTATTTTTCTTGATTTGTGGTTTTAT 19 130 0 TTCTTGATTT 0.607232 -171 TGGTGCGGCTGGGCTTGATTTGGAGAAATGG 19 195 1 GGCTTGATTT 0.955256 -106 GAAATGGTGCTGACATTATTTGGTGGGAATA 19 219 1 TGCATTATTT 0.817214 -82 ** ******** Masking position 6 Map Score: 7.80998 Number of sites scoring better than the average of aligned sites = 565 Number in coding regions = 505 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269