AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00530_hpyl_reg_300.orf -o00530_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 Input sequences: #1 HP0180 257 apolipoprotein N-acyltransferase (cute) #2 HP0194 214 triosephosphate isomerase (tpi) #3 HP0640 62 poly(A) polymerase (papS) #4 HP0643 164 glutamyl-tRNA synthetase (gltX) #5 HP0683 300 UDP-N-acetylglucosamine pyrophosphorylase (glmU) #6 HP0869 58 hydrogenase expression/formation protein (hypA) #7 HP0870 207 flagellar hook (flgE) #8 HP0871 300 CDP-diglyceride hydrolase (cdh) #9 HP0961 131 glycerol-3-phosphate dehydrogenase (NAD(P)+) #10 HP0966 220 conserved hypothetical protein #11 HP0967 285 virulence associated protein D (vapD) #12 HP0971 49 H. pylori predicted coding region HP0971 #13 HP0972 111 glycyl-tRNA synthetase, beta subunit (glyS) #14 HP1054 63 H. pylori predicted coding region HP1054 #15 HP1057 148 H. pylori predicted coding region HP1057 #16 HP1376 171 (3R)-hydroxymyristoyl-(acyl carrier protein) dehydratase (fabZ) #17 HP1377 300 H. pylori predicted coding region HP1377 #18 HP1422 24 isoleucyl-tRNA synthetase (ileS) #19 HP1423 101 conserved hypothetical protein #20 HP1530 152 purine nucleoside phosphorylase (punB) #21 HP1531 42 H. pylori predicted coding region HP1531 Motif number 1 TGAATTGGCATGATTTAAGAGTAATGGGTGTTT 1 100 0 TATTTAAGTA 0.898598 -158 TTAGATTGATTTTTTTAAGGGTAGTTTTTTTTA 1 172 0 TTTTTAAGTA 0.955875 -86 AGCTATATTTTAATTTAAGAATTTTAGATTGAT 1 195 0 TATTTAAGTT 0.892849 -63 AAGGGGCTATTGTTTAAAATTTACATTTTTTAA 2 138 1 TTTTAAAATA 0.637434 -77 TGTTATTATATCTTTTTAGAATTTTTAAGGAAT 3 15 0 TTTTTTAGTT 0.871502 -48 AACACAAAGAAATTTTAAGAGTAAAAAGC 3 44 1 ATTTTAAGTA 0.925139 -19 AAAAACCCTTTATTTAAAAATAGTTTTTGATT 4 143 0 TATTTAAATA 0.579953 -22 GTTTCATCAAAGATTTAAGGCTAGAATTTTGCG 5 219 0 AATTTAAGTA 0.838486 -82 AATAGGGGCTAATTTAAAGATTAAGGTTTAGT 6 37 1 ATTTAAAGTA 0.865567 -22 CCCATAACGCTTTTTAAAGGTTATCGCTCAAGC 7 29 0 TTTTAAAGTA 0.916644 -179 TTGGTTGCGGATTTTAAAGTTTTGTTAATCAAA 7 108 0 ATTTAAAGTT 0.865607 -100 GAATTTCTTTAAATTAAAGGATAACC 7 192 1 AATTAAAGTA 0.724921 -16 CTAAAAGAATTTTTTAAAAAATTAAATAGCTTG 8 84 0 TTTTAAAATT 0.637392 -217 TTTTAAAAAATTCTTTTAGCTTTTTTAATGTTA 8 98 1 TCTTTTAGTT 0.544455 -203 ATAATCATAATGATTAAAGATTTTAACCACTAT 8 219 1 TATTAAAGTT 0.818162 -82 TATTAAATAATATTTTAAAATTAAAAAGCG 9 8 0 TTTTTAAATA 0.605002 -124 ATGTAAGGGCTATTTTAAACTTATTATTGTAAA 9 73 1 TTTTTAAATA 0.772464 -59 GAGAAAGCGAATTTTTAAGAATAATCATCATTA 10 53 0 ATTTTAAGTA 0.926838 -168 CGTCTTATTTAGATTTTAGTTTTTAATTTTAAA 10 192 1 AATTTTAGTT 0.619486 -29 TTAGTTTTTAATTTTAAAGGATTG 10 207 1 ATTTAAAGTT 0.865607 -14 AGAAGCGGCGTATTTATAGCATTCCACATAAAA 11 30 0 TTTTATAGTT 0.775207 -256 GCGAACTGATTTTTTAAAGCTTTTGCTAGAGGT 11 148 0 TTTTAAAGTT 0.916644 -138 AAACAAAATCACTTTTAAGACTAAATCATGTTA 13 70 0 ATTTTAAGTA 0.926942 -42 CTAACGCTAAAATTTTAAACCTTAACTCCAAGA 14 18 0 ATTTTAAATT 0.66974 -46 GTCATTTTAATTATTTTAGTATAATTGAAAGAA 15 92 1 TATTTTAGTA 0.735418 -57 ATAGCGGTTATTTTTTTAGAATAACCAACGCTA 16 107 1 TTTTTTAGTA 0.871371 -65 ATTAAAGCGCTATTTTTAGCGTTGGTTATTCTA 16 123 0 TTTTTTAGTT 0.871654 -49 TTTTACCCTATTCTTTAAGTTTTTATCCATAAC 19 72 0 TCTTTAAGTT 0.79215 -30 GAAACACCTTAATTTTAAGGCTTCATTCACATT 20 66 0 ATTTTAAGTT 0.926943 -87 TTAAGGTGTTTCTTTTAAGGGTTTGTCTATAAT 20 87 1 TTTTTAAGTT 0.955875 -66 * ******* ** Masking position 8 Map Score: 35.2942 Number of sites scoring better than the average of aligned sites = 1362 Number in coding regions = 1096 Number in noncoding regions = 266 Number of orfs with sites within 600 bp upstream = 219 Fraction of orfs with sites within 600 bp upstream = 0.0351751 Motif number 2 AGATTGATTTTTTTAAGGGTAGTTTTTTTTAAGTTG 1 167 0 TTTAGATTTT 0.90358 -91 GTTTTAGTGTATTATAGCTATATTTTAATTTAAGAA 1 207 0 ATTAGTTTTT 0.947742 -51 AATTTTGAGTTTTTAGGAGCAGTTTTT 2 2 0 TTTGGATTTT 0.942791 -213 GCGTCAAGCGATTTTAGGTTAATTTTGAGTTTTTAG 2 22 0 ATTAGATTTT 0.916864 -193 ATGTAGTAGAATTAAGGCAGTGTTTTTGCGTCAAGC 2 49 0 ATTGGTTTTT 0.969598 -166 TTTTTTCTCAATTTAGGTTTTGTTTATAAGAAAAAT 2 93 0 ATTGGTTTTA 0.832039 -122 CAATAGCCCCTTTGAATTGAATTTTTTCTCAATTTA 2 114 0 TTTATATTTT 0.550788 -101 CCTTAAACTCATTTTAGGGAATTTTAACATGCCTTA 5 269 0 ATTAGATTTA 0.631406 -32 ATTATATTGTATTAGAGTAATCTTTTAGC 6 4 0 ATTAGTTTTT 0.947742 -55 TTTCTTATGAATTTGGTCGATCTTTTTGATTAACAA 7 84 1 ATTGTTTTTT 0.80668 -124 CTAAAAAGCTATTTAGGAACAACTTTTGCTTTATTT 7 146 1 ATTGGACTTT 0.756461 -62 TGCTCCTTGTTTTTAATGAGAGTTTTTGCAAACCCT 8 269 0 TTTATATTTT 0.550788 -32 AGCGTTTTGAATGTAAGGGCTATTTTAAACTTATTA 9 63 1 ATGAGTTTTT 0.622982 -69 TATAAACCCTTTTTTGGGGATTTTTTGGGGATTTTT 10 155 1 TTTGGTTTTT 0.964413 -66 TTGCGTCTTATTTAGATTTTAGTTTTTAATTTTAAA 10 189 1 TTTATATTTT 0.550788 -32 AAAAGGCTTTGATGATTTTTTTTATGTGGAATG 11 8 1 TTTTGTTTTT 0.640932 -278 GATACGCTAAATTCAAGCTTTTTTTAAGCGAGGAAG 11 105 1 ATTAGTTTTA 0.738014 -181 GGCGTTTTTGTTTGGGGGTAACTTTTTTA 12 31 1 TTTGGATTTT 0.942791 -19 TTATGGTATAATAGCGGTTATTTTTTTAGAATAACC 16 97 1 ATAGGTTTTT 0.775642 -75 TTTGGATTCAATTAAAGCGCTATTTTTAGCGTTGGT 16 130 0 ATTAGTTTTT 0.947739 -42 AAAATGAGATTTACTGGGATTATTTTTCTTGATTTG 17 90 1 TTAGGTTTTT 0.746043 -211 TTTTTCTTGATTTGTGGTTTTATTTTGCTCATTCCT 17 112 1 TTTGGTTTTT 0.964413 -189 GAGCGCTGGTTTTAAGGCGGTCTTTT 17 285 1 TTTGGTTTTT 0.964413 -16 AAGCCTTAAAATTAAGGTGTTTCTTTTAAGGGTTTG 20 76 1 ATTGGTCTTT 0.836278 -77 *** ** * **** Masking position 14 Map Score: 24.9776 Number of sites scoring better than the average of aligned sites = 1066 Number in coding regions = 895 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 3 TATTTTAATTTAAGAATTTTAGATTGATTT 1 193 0 TAAGAATTTT 0.639003 -65 GTTTTTGCGTCAAGCGATTTTAGGTTAATT 2 34 0 CAAGCGATTT 0.918299 -181 TTAGAATTTTTAAGGAATTTTG 3 3 0 TAAGGAATTT 0.832314 -60 ATAATAACACAAAGAAATTTTAAGAGTAAA 3 39 1 AAAGAAATTT 0.618581 -24 TGGCTAACGCCAAGCTTTTTATGGTTGGTT 4 32 0 CAAGCTTTTT 0.8824 -133 ATTTTTAAATAAAGGGTTTTT 4 154 1 AAAGGGTTTT 0.907727 -11 AGGGTGGTTACAAGCTGTTTAGGATCATTA 5 93 1 CAAGCTGTTT 0.832648 -208 AAAATGAGTTTAAGGATTTTA 5 290 1 TAAGGATTTT 0.860298 -11 ATCATTCTAAAAAGCTATTTAGGAACAACT 7 140 1 AAAGCTATTT 0.810176 -68 TTGTCAAAATAAAGCGTTTTATAA 8 5 0 AAAGCGTTTT 0.905811 -296 CTGCTTAGTGCAAGCTATTTAATTTTTTAA 8 74 1 CAAGCTATTT 0.858114 -227 AAAAAAGCTAAAAGAATTTTTTAAAAAATT 8 94 0 AAAGAATTTT 0.668005 -207 CTATTTTTAAAAAGAGATTTTTGAATACTA 8 152 0 AAAGAGATTT 0.695064 -149 AAAAATCATCAAAGCCTTTT 11 1 0 AAAGCCTTTT 0.619015 -285 ACGCTAAATTCAAGCTTTTTTTAAGCGAGG 11 108 1 CAAGCTTTTT 0.8824 -178 ACAAACAATTCAAGGGATTTGGCGATT 15 132 1 CAAGGGATTT 0.918326 -17 TGCATAAGCGGTTTCTATGCAAAG 16 5 1 TAAGCGGTTT 0.852135 -167 GAATCCAAAACAAGGAGTTTATTTT 16 157 1 CAAGGAGTTT 0.867599 -15 CCACTCTTTTTAAGGAATTTGT 19 3 0 TAAGGAATTT 0.832314 -99 CCATAACTTATAAGGGTTTTAGTTTTAGCA 19 49 0 TAAGGGTTTT 0.89683 -53 GCCTTAAAATTAAGGTGTTTCTTTTAAGGG 20 78 1 TAAGGTGTTT 0.756129 -75 GGATGCGAAAAAAGGATTTTC 20 142 1 AAAGGATTTT 0.875001 -11 ********** Masking position 8 Map Score: 22.6129 Number of sites scoring better than the average of aligned sites = 1784 Number in coding regions = 1511 Number in noncoding regions = 273 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809 Motif number 4 AAGAATTTTAGATTGATTTTTTTAAGGGTA 1 182 0 GATTGATTTT 0.756071 -76 GTGTATTATAGCTATATTTTAATTTAAGAA 1 207 0 GCTATATTTT 0.751493 -51 GGCTAAATTTTGAAACCTTGA 1 247 0 GCTAAATTTT 0.640673 -11 TTAGCCCCGTCATTGATTTTAGTGATGACG 5 32 0 CATTGATTTT 0.625635 -269 AAGATTTAAGGCTAGAATTTTGCGTTTTTT 5 213 0 GCTAGAATTT 0.865123 -88 ACTAAACCTTAATCTTTAAATTAGCC 6 43 0 CCTTAATCTT 0.460579 -16 AACAACTTTTGCTTTATTTTGCATAGATTG 7 163 1 GCTTTATTTT 0.916646 -45 ATTTTGCATAGATTGAATTTCTTTAAATTA 7 178 1 GATTGAATTT 0.690704 -30 GGTTATCCTTTAATTTAAAGAAATTC 7 192 0 CCTTTAATTT 0.810315 -16 TTATAAAACGCTTTATTTTGACAAGTATC 8 10 1 GCTTTATTTT 0.916646 -291 CTTTTTTGCTCCTTGTTTTTAATGAGAGTT 8 281 0 CCTTGTTTTT 0.787428 -20 CTAGTCAGCCGCTTTATCTTTTCACCCCCA 10 99 1 GCTTTATCTT 0.728696 -122 CTTAAAAAAAGCTTGAATTTAGCGTATCTT 11 103 0 GCTTGAATTT 0.958891 -183 TTAGAATTATACTTGAATTTACACTCAGTT 13 43 0 ACTTGAATTT 0.552156 -69 GGCTTGATCTTGGAGTTAAGG 14 2 1 GCTTGATCTT 0.887732 -62 AACGACTAACGCTAAAATTTTAAACCTTAA 14 26 0 GCTAAAATTT 0.562286 -38 TCGCCAAATCCCTTGAATTGTTTGTTAAAA 15 127 0 CCTTGAATTG 0.846509 -22 AAAACCGCTCGCTTGTATTTGCAAAAACAC 16 66 0 GCTTGTATTT 0.83193 -106 TAAAAATAGCGCTTTAATTGAATCCAAAAC 16 138 1 GCTTTAATTG 0.776509 -34 AAAATAAACTCCTTGTTTTGGATTCAATTA 16 152 0 CCTTGTTTTG 0.618963 -20 GTGCGGCTGGGCTTGATTTGGAGAAATGGT 17 38 0 GCTTGATTTG 0.934199 -263 ATCAATTTTCGCTAGTTTTGGATATAATCC 17 207 0 GCTAGTTTTG 0.453098 -94 AAAAGAAACACCTTAATTTTAAGGCTTCAT 20 73 0 CCTTAATTTT 0.777576 -80 GTGATCGCCTTTAATTTAGAATGCTCC 21 26 0 CCTTTAATTT 0.810315 -17 ********** Masking position 3 Map Score: 21.7007 Number of sites scoring better than the average of aligned sites = 1312 Number in coding regions = 1145 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 5 TGCCAATTCACACTCTTTAGACTTGAAATT 1 123 1 CACTCTTTAG 0.655405 -135 TGAATTTTTTCTCAATTTAGGTTTTGTTTA 2 103 0 CTCAATTTAG 0.474418 -112 GTGTTATTATATCTTTTTAGAATTTTTAAG 3 19 0 ATCTTTTTAG 0.71327 -44 TAATCAAAAACTATTTTTAAATAAAGGGTT 4 142 1 CTATTTTTAA 0.596615 -23 TAGCGTCAATCTCTCTTTAAACGCTCCTAA 5 120 0 CTCTCTTTAA 0.92085 -181 GCGCTATCAGCGCTCATTAAAGGGCATATT 5 156 1 CGCTCATTAA 0.425852 -145 AATCCTTAAACTCATTTTAGGGAATTTTAA 5 278 0 CTCATTTTAG 0.894615 -23 CACCCCATAACGCTTTTTAAAGGTTATCGC 7 35 0 CGCTTTTTAA 0.889866 -173 GTTCCTAAATAGCTTTTTAGAATGATTGGT 7 136 0 AGCTTTTTAG 0.543045 -72 ATTCAAAAATCTCTTTTTAAAAATAGGTTA 8 156 1 CTCTTTTTAA 0.944174 -145 TTTGCAAAAACTCTCATTAAAAACAAGGAG 8 273 1 CTCTCATTAA 0.608238 -28 CGCTTTTTAATTTTAAAATA 9 1 1 CGCTTTTTAA 0.889866 -131 CTCTCTCTCTCTCTCTCTAGTCAGCCGCTT 10 83 1 CTCTCTCTAG 0.687803 -138 CGCTCACCTGCTCTTTTTGGCTTAAAAGCA 11 67 0 CTCTTTTTGG 0.762059 -219 TAAATTCAAGCTTTTTTTAAGCGAGGAAGT 11 112 1 CTTTTTTTAA 0.456154 -174 TGAATTTACACTCAGTTTAGTTTATTTCTT 13 30 0 CTCAGTTTAG 0.572832 -82 AATTAAAGCGCTATTTTTAGCGTTGGTTAT 16 127 0 CTATTTTTAG 0.725239 -45 CCCAGTAAATCTCATTTTAGCGGTAGGTGG 17 78 0 CTCATTTTAG 0.894615 -223 TCAGCCACCACTCTTTTTAAGGAATTTGT 19 10 0 CTCTTTTTAA 0.944174 -92 ********** Masking position 8 Map Score: 14.6616 Number of sites scoring better than the average of aligned sites = 817 Number in coding regions = 679 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 6 AAAAATTCAATTCAAAGGGGCTATTGTTTAAA 2 124 1 TTAAGGGGCT 0.876425 -91 CGATCCTTATTTTATAGGTGGTAACTATCCCT 2 189 0 TTATGGTGGT 0.966428 -26 CGCCAAGCTTTTTATGGTTGGTTATCAAAAAG 4 23 0 TTATGTTGGT 0.603422 -142 GGGCGATGACATTAAGGGTGGTTACAAGCTGT 5 79 1 ATAAGGTGGT 0.874383 -222 CTAATACAATATAATAGGGGCTAATTTAAAGA 6 25 1 ATATGGGGCT 0.866045 -34 TTAAAAAGCGTTATGGGGTGGTGTTGCAAAAC 7 45 1 TTTGGGTGGT 0.844262 -163 AATTCATAAGAAAATAGGGGGTTTTGCAACAC 7 65 0 AAATGGGGGT 0.678862 -143 TCACCATGCGATCTTAGGGGGTTGATACTTGT 8 31 0 ATTTGGGGGT 0.961098 -270 ATGAGAGCCATTAAATGGTGCTAGGAGTTTGT 10 22 1 TTAAGGTGCT 0.795074 -199 GGGTATGGGTTTATATGGGGGTGAAAAGATAA 10 112 0 TTTAGGGGGT 0.964415 -109 TTTTTGGGGATTTTTTGGGGATTTTTGCGTCT 10 165 1 TTTTGGGGAT 0.776083 -56 TCTGGCGTTTTTGTTTGGGGGTAACTTTTTTA 12 28 1 TTTTGGGGGT 0.981351 -22 AGTCGTTTTAATTTTAGGGGGTTAT 14 49 1 ATTTGGGGGT 0.961098 -15 GGTGCTGACATTATTTGGTGGGAATAAGAA 17 9 0 TTTTGGTGGG 0.784975 -292 ATTATTTTTCTTGATTTGTGGTTTTATTTTGC 17 108 1 TTATTGTGGT 0.603422 -193 TGAGCGCTGGTTTTAAGGCGGTCTTTT 17 284 1 TTTAGGCGGT 0.797483 -17 ** ** ****** Masking position 10 Map Score: 12.403 Number of sites scoring better than the average of aligned sites = 654 Number in coding regions = 555 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 7 GTAACGCTAAATCAATATAATTCAAACCCTA 1 13 1 ATAATATAAT 0.658632 -245 GACTTGAAATTTGAAAATAATAACACAACTT 1 142 1 TTAAAATAAT 0.729809 -116 TTCTACTACATTTGAAATAATTTTTCTTATA 2 74 1 TTGAAATAAT 0.82975 -141 TTAAACGCTATTAGATATAATAAGGGATAGT 2 167 1 TTGATATAAT 0.937698 -48 AAAATTCTAAAAAGATATAATAACACAAAGA 3 23 1 AAGATATAAT 0.600274 -40 TAAGTATTCTTTAGGTATAATCAAAAACTAT 4 125 1 TTGGTATAAT 0.944829 -40 ATTACTCTAATACAATATAATAGGGGCTAAT 6 19 1 TAAATATAAT 0.78252 -40 GTTAAAATTCATTAAAATAATCATAATGATT 8 203 1 ATAAAATAAT 0.384134 -98 AATTGAGTATAATGAGAGCCATT 10 3 1 TTAGTATAAT 0.904681 -218 AAGCGAATTTTTAAGAATAATCATCATTACA 10 51 0 TTAGAATAAT 0.754504 -170 TTTTAATTATTTTAGTATAATTGAAAGAAAC 15 96 1 TTAGTATAAT 0.904676 -53 GCGGTTTTCTTATGGTATAATAGCGGTTATT 16 88 1 TAGGTATAAT 0.88077 -84 CGAATCATTATAAAATATAATAAGGAGTTGA 17 147 0 TAAATATAAT 0.78252 -154 TTCGCTAGTTTTGGATATAATCCCAATAACT 17 199 0 TTGATATAAT 0.937698 -102 ATCAAACAATTTTGGTAAAATCAATTTTCGC 17 225 0 TTGGTAAAAT 0.720975 -76 ACCAAAATTGTTTGATATAATACAGAGTTTA 17 240 1 TTGATATAAT 0.937698 -61 ACTTAAAGAATAGGGTAAAATAAACGC 19 85 1 TAGGTAAAAT 0.527094 -17 ** ******** Masking position 7 Map Score: 15.3705 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 54 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 8 TAGATTGATTTTTTTAAGGGTAGTTTTTTT 1 174 0 TTTTTAAGGG 0.974195 -84 CTTTTTAGAATTTTTAAGGAATTTTG 3 7 0 TTTTTAAGGA 0.790215 -56 AACGCCAAGCTTTTTATGGTTGGTTATCAA 4 27 0 TTTTTATGGT 0.626484 -138 CCCATAACGCTTTTTAAAGGTTATCGCTCA 7 32 0 TTTTTAAAGG 0.651833 -176 TGGGTATGGGTTTATATGGGGGTGAAAAGA 10 115 0 TTTATATGGG 0.932963 -106 TTTATATGGGTTTATATGGGTATGGGTTTA 10 131 0 TTTATATGGG 0.932963 -90 CAAAAAAGGGTTTATATGGGTTTATATGGG 10 141 0 TTTATATGGG 0.932963 -80 CATATAAACCCTTTTTTGGGGATTTTTTGG 10 153 1 CTTTTTTGGG 0.82303 -68 TTTTTGGGGATTTTTTGGGGATTTTTGCGT 10 165 1 TTTTTTGGGG 0.772531 -56 TTGATGATTTTTTTTATGTGGAATGCTATA 11 19 1 TTTTTATGTG 0.610416 -267 ATTCAAGCTTTTTTTAAGCGAGGAAGTCGC 11 115 1 TTTTTAAGCG 0.747322 -171 GTCTGGCGTTTTTGTTTGGGGGTAACTTTT 12 27 1 TTTGTTTGGG 0.687018 -23 AGTGATTTTGTTTTTTAGGGAGAATTGAGA 13 90 1 TTTTTTAGGG 0.942146 -22 GTAGCATGACTTTATTAGGGTGGGTAAAAA 15 43 1 TTTATTAGGG 0.884336 -106 GCCACCACTCTTTTTAAGGAATTTGT 19 7 0 TTTTTAAGGA 0.790215 -95 TTATCCATAACTTATAAGGGTTTTAGTTTT 19 53 0 CTTATAAGGG 0.865712 -49 TAAGGTGTTTCTTTTAAGGGTTTGTCTATA 20 88 1 CTTTTAAGGG 0.932115 -65 ********** Masking position 5 Map Score: 19.954 Number of sites scoring better than the average of aligned sites = 779 Number in coding regions = 655 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 9 AAATTTACATTTTTTAAACGCTATTAGATATA 2 154 1 TTTAAACGCT 0.92847 -61 TCAATGACGGGGCTAAAACTAAAAGCGTGAGC 5 46 1 GGTAAACTAA 0.406375 -255 CGTCAATCTCTCTTTAAACGCTCCTAATGATC 5 115 0 TCTAAACGCT 0.933611 -186 ATTAAAAAAATGAAAAAACGCAAAATTCTAGC 5 201 1 TGAAAACGCA 0.900932 -100 CTTAAATCTTTGATGAAACGAAGTCAAATTAT 5 233 1 TGTAAACGAA 0.888693 -68 TAAAATCCTTAAACTCATTTTAGGGAA 5 284 0 TCTAAACTCA 0.897126 -17 TTATAAAACGCTTTATTTTGAC 8 1 1 TTTAAACGCT 0.92847 -300 CAAGAGGGTTTGCAAAAACTCTCATTAAAAAC 8 265 1 TGAAAACTCT 0.599345 -36 ATCTCATTGATTGTAAAACTCACCATTTTACA 9 100 0 TTTAAACTCA 0.889493 -32 AATTGTTTTATTCTCAAACGCATGGGTTGTAA 11 195 1 TTTAAACGCA 0.961836 -91 AACGCATGGGTTGTAAAACGCATGGGTTATCA 11 211 1 TTTAAACGCA 0.961836 -75 AACGCATGGGTTATCAAACGAAATTCTAAGTA 11 227 1 TTTAAACGAA 0.856105 -59 TGGCTTCAAACGCAAAGTCTGGCG 12 3 1 GCTAAACGCA 0.879953 -47 GCCATAAGCTTCAAGAAACGCTTTGCATAGAA 16 23 0 TCAAAACGCT 0.790852 -149 AATGCTAACATGCTAAAACTAAAACCCTTATA 19 39 1 TGTAAACTAA 0.71831 -63 ** * ******* Masking position 6 Map Score: 14.1336 Number of sites scoring better than the average of aligned sites = 652 Number in coding regions = 584 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 10 GAATTATATTGATTTAGCGTTACTT 1 6 0 GATTTAGCGT 0.96296 -252 CATAAAGATAGTCATAGCGTCTTAAAACAA 1 72 1 GTCATAGCGT 0.783723 -186 CCTTGAGATTGTTTTAGTGTATTATAGCTA 1 223 0 GTTTTAGTGT 0.787184 -35 TTAAGGCAGTGTTTTTGCGTCAAGCGATTT 2 44 0 GTTTTTGCGT 0.96296 -171 TTAAGGCTAGAATTTTGCGTTTTTTCATTT 5 208 0 AATTTTGCGT 0.882625 -93 TTTTTTGGGGATTTTTGCGTCTTATTTAGA 10 175 1 ATTTTTGCGT 0.942006 -46 AAAAAGCTTGAATTTAGCGTATCTTTACGC 11 98 0 AATTTAGCGT 0.942006 -188 AAAAACGCCAGACTTTGCGTTTGAAGCCA 12 10 0 GACTTTGCGT 0.791771 -40 AAGGTTTAAAATTTTAGCGTTAGTCGTTTT 14 28 1 ATTTTAGCGT 0.972289 -36 TAAAGCGCTATTTTTAGCGTTGGTTATTCT 16 124 0 TTTTTAGCGT 0.879289 -48 AGTAAATCTCATTTTAGCGGTAGGTGGCGT 17 75 0 ATTTTAGCGG 0.846955 -226 AAGGGTTTTAGTTTTAGCATGTTAGCATTC 19 38 0 GTTTTAGCAT 0.787184 -64 GGCGTTATTATAGCGTGAATAAGTGG 20 7 1 ATTATAGCGT 0.877545 -146 ********** Masking position 5 Map Score: 14.3637 Number of sites scoring better than the average of aligned sites = 473 Number in coding regions = 421 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 11 TCAAACCCTAAACCCAAACCTTTCTCTCAT 1 34 1 AACCCAAACC 0.976171 -224 CCCCCATATAAACCCATACCCATATAAACC 10 123 1 AACCCATACC 0.983249 -98 TGCGTTTTACAACCCATGCGTTTGAGAATA 11 203 0 AACCCATGCG 0.977529 -83 TTCGTTTGATAACCCATGCGTTTTACAACC 11 219 0 AACCCATGCG 0.977529 -67 AACATGCTATAACACAAACCAATAAAGGAG 11 261 1 AACACAAACC 0.887004 -25 ********** Masking position 6 Map Score: 1.78898 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 42 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 12 TATGTATATGTTTCAATCAAAGACAGCGTT 9 39 1 TTTCAATCAA 0.903239 -93 AAAATAGCCCTTACATTCAAAACGCTGTCT 9 59 0 TTACATTCAA 0.903212 -73 ATGGTGAGTTTTACAATCAATGAGATTAGG 9 106 1 TTACAATCAA 0.802412 -26 TTGTTAAAAGTTTCTTTCAATTATACTAAA 15 106 0 TTTCTTTCAA 0.816673 -43 GTTATTCCTTTTTCATTCACCACTTATTCA 20 26 0 TTTCATTCAC 0.962843 -127 TTCATTCACATTTCATTCACATGTTATTCC 20 48 0 TTTCATTCAC 0.962843 -105 AATTTTAAGGCTTCATTCACATTTCATTCA 20 59 0 CTTCATTCAC 0.888564 -94 ********** Masking position 9 Map Score: 2.73404 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 88 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 13 ********** No masking Map Score: 9.05475e-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: 9.05475e-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 TAATGGGTGTTTGTTTTAAGACGCTATGACT 1 81 0 TTGTTTAAGA 0.873719 -177 TTTTTTTAAGTTGTGTTATTATTTTCAAATT 1 149 0 TTGTTTATTA 0.735831 -109 TTTAGATTGATTTTTTTAAGGGTAGTTTTTT 1 175 0 TTTTTTAAGG 0.804601 -83 TTGAAATAATTTTTCTTATAAACAAAACCTA 2 85 1 TTTTTTATAA 0.455533 -130 TAAAATTTCTTTGTGTTATTATATCTTTTTA 3 30 0 TTGTTTATTA 0.735831 -33 CGTTTTTTCATTTTTTTAATCCTCATTTGCC 5 190 0 TTTTTTAATC 0.775575 -111 AAACCCCCTATTTTCTTATGAATTTGGTCGA 7 73 1 TTTTTTATGA 0.905451 -135 GATTTTAAAGTTTTGTTAATCAAAAAGATCG 7 101 0 TTTTTTAATC 0.775575 -107 CTTTGATGATTTTTTTTATGTGGAATGCTAT 11 17 1 TTTTTTATGT 0.631836 -269 AAATTCAAGCTTTTTTTAAGCGAGGAAGTCG 11 113 1 TTTTTTAAGC 0.907049 -173 AGCGAACTGATTTTTTAAAGCTTTTGCTAGA 11 151 0 TTTTTAAAGC 0.628752 -135 AGAAATGAAATTGTTTTATTCTCAAACGCAT 11 187 1 TTGTTTATTC 0.763407 -99 CGCCTACCTTTTGTATTAAGAAATAAACTAA 13 13 1 TTGTTTAAGA 0.87371 -99 AAGCGAGCGGTTTTCTTATGGTATAATAGCG 16 82 1 TTTTTTATGG 0.823976 -90 CCTTATTATATTTTATAATGATTCGGTTAAA 17 153 1 TTTTTAATGA 0.624343 -148 **** ****** Masking position 8 Map Score: 5.88998 Number of sites scoring better than the average of aligned sites = 317 Number in coding regions = 249 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577