AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00380_hpyl_reg_300.orf -o00380_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: HP1253 31 tryptophanyl-tRNA synthetase (trpS) Input sequences: #1 HP0243 205 neutrophil activating protein (napA) (bacterioferritin) #2 HP0246 188 flagellar basal-body P-ring protein (flgI) #3 HP0688 143 H. pylori predicted coding region HP0688 #4 HP0690 281 acetyl coenzyme A acetyltransferase (thiolase) (fadA) #5 HP0830 58 amidase #6 HP0832 91 spermidine synthase (speE) #7 HP0833 76 H. pylori predicted coding region HP0833 #8 HP0875 300 catalase #9 HP1067 290 chemotaxis protein (cheY) #10 HP1254 116 biotin synthesis protein (bioC) #11 HP1376 171 (3R)-hydroxymyristoyl-(acyl carrier protein) dehydratase (fabZ) #12 HP1377 300 H. pylori predicted coding region HP1377 #13 HP1483 26 gerC2 protein (gerC2) #14 HP1490 103 hemolysin #15 HP1491 138 phosphate permease Motif number 1 AAATTTTAAAAAGATTAAATAATATTAAATTGA 1 55 1 AATTAATAAT 0.871338 -151 TGACAAAAATAAGATCAAAAAAATTTTTTATTA 1 106 1 AATCAAAAAA 0.930567 -100 TTAGGCTTTTATTTTCATAAAAACCTTGATCGC 1 158 0 ATTCAAAAAA 0.893954 -48 AGCCTAAAACAATTTTAAAAAAAGGACTTTTG 1 184 1 AATTAAAAAA 0.953074 -22 TTTAATTTGAAACTTTATAAAAAGCTAATAAAA 2 29 1 AATTAAAAAA 0.953089 -160 TATACTCAAAAATCTTATAAACTTTAAATCAAA 2 78 0 AATTAAAACT 0.689611 -111 TAAAAGGCTTATGCTAAAATAATTAGAATTTAG 2 147 1 ATTAAATAAT 0.638255 -42 GATATAACTAAAAATTAGAAAAACTTTAATGCG 3 26 0 AATTAAAAAA 0.953089 -118 TATAAGACTAATTGTTATATAATAAAAGCGAGA 3 90 1 ATTTAATAAT 0.810043 -54 GCGAGACAAGAATGTTAAAAAATGAAAGGAGCG 3 117 1 AATTAAAAAT 0.940233 -27 TCCAAAACAAAACCTAAAATAAAATCCAACCTG 4 198 1 AATAAATAAA 0.782777 -84 GTTTTTAGCCTTACAAAAAATTTAATGGT 5 40 0 AGTTAAAAAA 0.707481 -19 AATCTAAATTATTGTAACAAAAGC 6 2 0 ATTAAAAAAG 0.731089 -90 TAGTTATTTAAAGCTTAAATAAGGGTCTAGCG 7 55 1 AATTAATAAG 0.817876 -22 AAATTTAAAAAATAAAAATCAAA 8 1 1 AATTAAAAAT 0.94024 -300 TTAAAAAATAAAAATCAAAAAAAAAAAAAAAAC 8 15 1 AATCAAAAAA 0.930567 -286 GAAAATAAGAAAGATTAAAAACAAAATTTTATT 8 108 0 AATTAAAACA 0.741486 -193 GGGGTTTTTCATTCTTAAAAAAAGGATTTTTTA 8 170 1 ATTTAAAAAA 0.927742 -131 ACTTGTGGTGATTATCACATAATTTGTTATACA 8 227 0 ATTCAATAAT 0.737778 -74 ACGAAGATTTAAGATCATAAAAGGAAAAAAG 8 280 1 AATCAAAAAG 0.873157 -21 TAATCGTTTAAAAGTAATAAAATAACTCTTTGA 9 69 0 AATAAAAAAT 0.866422 -222 TAAATGCCTAAAATTTAGAAAAAATCACGCTTG 10 19 1 AATTAAAAAA 0.953089 -98 ATTCTTAGCAAATTTTAGATAAGATCAAGCGTG 10 44 0 AATTAATAAG 0.817868 -73 AGCGTTGGTTATTCTAAAAAAATAACCGCTATT 11 106 0 ATTAAAAAAT 0.802475 -66 GTTTAACCGAATCATTATAAAATATAATAAGGA 12 152 0 ATTTAAAAAT 0.908454 -149 AAATCTCAGAATTTTAACATAAAAGATTAAGCC 14 40 0 ATTAAATAAA 0.694909 -64 ATCGTCATAAAAACCTTGTTCTA 15 126 0 ATTCAAAAAA 0.894426 -13 ** *** ***** Masking position 7 Map Score: 33.9121 Number of sites scoring better than the average of aligned sites = 798 Number in coding regions = 623 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 2 TATCCCCCTTAAAAATGAGTTTTACTATAAAAC 1 21 1 AAAAATATTT 0.767515 -185 AGTTTTACTATAAAACAAAATTTTAAAAAGATT 1 38 1 TAAAACATTT 0.921786 -168 CAAAAGTCCTTTTTTTAAAATTGT 1 192 0 AAAAGTCTTT 0.650594 -14 ATTGAACGATAAGAATAATATTTTTGTGAAAAA 4 145 1 AAGAATATTT 0.681132 -137 AAACCAGATTAAAAATAAAATTTTGTTTTTAAT 8 95 1 AAAAATATTT 0.918903 -206 AATTTCCTTAAAAAATCCTTTTTTTAAGAATGA 8 178 0 AAAAATCTTT 0.729343 -123 TTAAAAGTAATAAAATAACTCTTTGAGTGCGAT 9 62 0 TAAAATACTT 0.844499 -229 TTATTTGTAAAAAAATTCAGTTTGTTTGCTATG 9 103 0 AAAAATCTTT 0.883867 -188 ATGTTTTGATTAAAATTACCTTGACCGACAATA 9 170 0 TAAAATATTG 0.675051 -121 AAAATTTAGAAAAAATCACGCTTGATCTTATCT 10 28 1 AAAAATACTT 0.78652 -89 CGCTTGAAATTAAAACTAAATTTTAGTGTATTC 10 73 0 TAAAACATTT 0.921786 -44 TGGATTCAATTAAAGCGCTATTTTTAGCGTTGG 11 131 0 TAAAGCCTTT 0.781758 -41 CACCTACCGCTAAAATGAGATTTACTGGGATTA 12 79 1 TAAAATATTT 0.948709 -222 ACAATTTTGGTAAAATCAATTTTCGCTAGTTTT 12 218 0 TAAAATATTT 0.944418 -83 GCTTGATTTTTAAAGTTAGGCTTAATCTTTTAT 14 22 1 TAAAGTACTT 0.750524 -82 TTTTTAAAACTCTCTTTAAAATTTTAC 15 5 1 TAAAACCTTT 0.882326 -134 TATGGTATCTTAAAGTAAAATTTTAAAGAGAGT 15 19 0 TAAAGTATTT 0.898406 -120 AGACCACTATTAGAACAAGGTTTTTATGACGAT 15 116 1 TAGAACATTT 0.720826 -23 ****** * *** Masking position 12 Map Score: 19.1683 Number of sites scoring better than the average of aligned sites = 639 Number in coding regions = 479 Number in noncoding regions = 160 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 3 CTTTTTAAAATTTTGTTTTATAGTAAAACT 1 38 0 TTTTGTTTTA 0.831675 -168 CCCCATTCAATTTAATATTATTTAATCTTT 1 64 0 TTTAATATTA 0.608581 -142 ATCAAAAAAATTTTTTATTAACTCTTTTGG 1 119 1 TTTTTTATTA 0.706367 -87 AATCAAAGATTTTAATTTTAGCCTTTTATT 2 55 0 TTTAATTTTA 0.810074 -134 TACACGCTCCTTTCATTTTTTAACATTCTT 3 124 0 TTTCATTTTT 0.833564 -20 GGGCGATCCGTTTATTTTTTTCACAAAAAT 4 164 0 TTTATTTTTT 0.894952 -118 ACAGGTTGGATTTTATTTTAGGTTTTGTTT 4 202 0 TTTTATTTTA 0.810076 -80 TAAACTACCATTAAATTTTTTGTAAGGCTA 5 34 1 TTAAATTTTT 0.614921 -25 ACTCCTTAGCTTACTTTTTAACAATATCCA 6 68 0 TTACTTTTTA 0.63513 -24 TTTTTTGATTTTTATTTTTTAAATTT 8 7 0 TTTATTTTTT 0.894952 -294 TTTGTTTTTTTTTTTTTTTTGATTTTTATT 8 21 0 TTTTTTTTTT 0.894952 -280 CATTGACGGATTTTGTTTTTTTTTTTTTTT 8 32 0 TTTTGTTTTT 0.864473 -269 AAAACAAAATTTTATTTTTAATCTGGTTTT 8 94 0 TTTATTTTTA 0.868408 -207 AAAAATAAAATTTTGTTTTTAATCTTTCTT 8 105 1 TTTTGTTTTT 0.864473 -196 GTTTTTAATCTTTCTTATTTTCATTAATTG 8 119 1 TTTCTTATTT 0.738541 -182 AAAAACCCCCTTAAGTATTTCTATTCGTAA 8 149 0 TTAAGTATTT 0.402741 -152 AATCCTTGTCTTTCTTTTTTCAAACCATCC 9 21 1 TTTCTTTTTT 0.8857 -270 TTTGGAACGATTTATTATTATAAGGCGTTA 9 210 1 TTTATTATTA 0.706367 -81 TACACTAAAATTTAGTTTTAATTTCAAGCG 10 76 1 TTTAGTTTTA 0.831675 -41 ATAATAGCGGTTATTTTTTTAGAATAACCA 11 104 1 TTATTTTTTT 0.711873 -68 CAACTCCTTATTATATTTTATAATGATTCG 12 148 1 TTATATTTTA 0.55292 -153 GACTTTTCTTTTTTCATGGCTTGT 13 13 0 TTTCTTTTTT 0.8857 -14 ATTTTATATATTTTATATTTATCGTTAGGT 14 69 1 TTTTATATTT 0.667469 -35 ********** Masking position 6 Map Score: 22.783 Number of sites scoring better than the average of aligned sites = 1524 Number in coding regions = 1066 Number in noncoding regions = 458 Number of orfs with sites within 600 bp upstream = 236 Fraction of orfs with sites within 600 bp upstream = 0.0379056 Motif number 4 AGGCTTTTATTTTCATAAAAACCTTGATCGC 1 158 0 TTTCATAAAA 0.761103 -48 AATTAAAATCTTTGATTTAAAGTTTATAAGA 2 68 1 TTTGATTAAA 0.928604 -121 ATACGCTCAATTAGGTTTAAAGTTTTTATAA 2 119 1 TTAGGTTAAA 0.726087 -70 TATATCGTTTTTAGATTAAAAGTCAGCACTA 3 53 1 TTAGATTAAA 0.862365 -91 GTAATCTAATTTTGATTAAATTGAAGCGATA 7 17 0 TTTGATTAAT 0.903622 -60 AATAGCATGTTTTGATTAAAATTACCTTGAC 9 178 0 TTTGATTAAA 0.928604 -113 CCTTTTAAGATTGCATTTAAATTAGGCTCTT 9 261 0 TTGCATTAAA 0.807523 -30 AAGAAACGCTTTGCATAGAAACCGCTTATGC 11 12 0 TTGCATAAAA 0.786853 -160 ACTCCTTGTTTTGGATTCAATTAAAGCGCTA 11 144 0 TTGGATTAAT 0.915655 -28 TTCGCTAGTTTTGGATATAATCCCAATAACT 12 199 0 TTGGATAAAT 0.905328 -102 ATCAAACAATTTTGGTAAAATCAATTTTCGC 12 225 0 TTTGGTAAAT 0.777299 -76 ACCAAAATTGTTTGATATAATACAGAGTTTA 12 240 1 TTTGATAAAT 0.89195 -61 TCGTTAGGTTTTAGGTTTAAAGTT 14 90 1 TTAGGTTAAA 0.726087 -14 AAAAGCGTTGTTTGATAAAAATGGCTCATTA 15 52 0 TTTGATAAAA 0.924026 -87 CAAGGGCTAATTGGATAGAATAAGACCACTA 15 94 1 TTGGATAAAT 0.905327 -45 ******* *** Masking position 9 Map Score: 16.6182 Number of sites scoring better than the average of aligned sites = 411 Number in coding regions = 323 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 5 GGATAACTATCCCCCTTAAAAATGAGTTTT 1 14 1 CCCCCTTAAA 0.972202 -192 TATTGATAAACCCCATTCAATTTAATATTA 1 74 0 CCCCATTCAA 0.965795 -132 TTTGAATGCTCCGCATTAAAGTTTTTCTAA 3 15 1 CCGCATTAAA 0.96794 -129 GATTTTAGATCCCCACTCAAAGCTATATTG 4 105 1 CCCCACTCAA 0.974287 -177 AATAAACGGATCGCCCTCAATCCAAAACAA 4 178 1 TCGCCCTCAA 0.934026 -104 GAATGAAAAACCCCCTTAAGTATTTCTATT 8 154 0 CCCCCTTAAG 0.857224 -147 TGACCCTTTATCGCACTCAAAGAGTTATTT 9 53 1 TCGCACTCAA 0.924366 -238 ACCACCGCCTTTAACGCACCACGC 10 103 0 CCGCCTTTAA 0.862403 -14 TTCTTATTCCCACCAAATAATGTCAGC 12 8 1 TCCCACCAAA 0.81914 -293 TCAAGCCCAGCCGCACCAAAAAGACGCCAC 12 52 1 CCGCACCAAA 0.933519 -249 AGAAAAATAATCCCAGTAAATCTCATTTTA 12 89 0 TCCCAGTAAA 0.749775 -212 AAAAGACCGCCTTAAAACCAGCGCTC 12 285 0 CCGCCTTAAA 0.972202 -16 ********** Masking position 9 Map Score: 11.8553 Number of sites scoring better than the average of aligned sites = 418 Number in coding regions = 365 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 6 TTTATGAAAATAAAAGCCTAAAACAATTTTA 1 170 1 TAAAGCCTAA 0.953682 -36 TGAAACTTTATAAAAAGCTAATAAAAGGCTA 2 36 1 TAAAAGCTAA 0.930125 -153 AAAAAGCTAATAAAAGGCTAAAATTAAAATC 2 47 1 TAAAGGCTAA 0.985422 -142 AAAGTTTTTATAAAAGGCTTATGCTAAAATA 2 137 1 TAAAGGCTTA 0.955269 -52 TCACCACAAGTAATCGGCTTAGTGTCATATT 8 249 1 TAATGGCTTA 0.870545 -52 CCGACAATAATCATTGGCTAAATGGAGCGTT 9 148 0 TCATGGCTAA 0.912601 -143 AGGCTCTTTTTAAACAGCCAAAGCGTCTCTA 9 238 0 TAAAAGCCAA 0.756697 -53 TGATTCCTTAAATGCCTAAAATTTAGAAA 10 9 1 TAAAGCCTAA 0.953682 -108 TAAGAGTGGCTCAAGGGCTAATTGGATAGAA 15 83 1 TCAAGGCTAA 0.970625 -56 **** ****** Masking position 3 Map Score: 8.55021 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 122 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 GTGCATATCTGCTTGATTTTAGATCCCCAC 4 91 1 GCTTGATTTT 0.967657 -191 CCAAATAATAGCATGTTTTGATTAAAATTA 9 185 0 GCATGTTTTG 0.89529 -106 ATAAGATCAAGCGTGATTTTTTCTAAATTT 10 29 0 GCGTGATTTT 0.888225 -88 AAAACCGCTCGCTTGTATTTGCAAAAACAC 11 66 0 GCTTGTATTT 0.792884 -106 AAAATAAACTCCTTGTTTTGGATTCAATTA 11 152 0 CCTTGTTTTG 0.887598 -20 GTGCGGCTGGGCTTGATTTGGAGAAATGGT 12 38 0 GCTTGATTTG 0.983272 -263 GGATTATTTTTCTTGATTTGTGGTTTTATT 12 106 1 TCTTGATTTG 0.867796 -195 ATCAATTTTCGCTAGTTTTGGATATAATCC 12 207 0 GCTAGTTTTG 0.882647 -94 GTTTTTGAAGGCTTGATTTTTAAAGTTAGG 14 12 1 GCTTGATTTT 0.967657 -92 ********** Masking position 8 Map Score: 8.47599 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 271 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 8 TGACTTTTAATCTAAAAACGATATAACTAAAA 3 46 0 TCTAAACGAT 0.874724 -98 TAACAATTAGTCTTATAGCGCTATAGTGCTGA 3 75 0 TCTTAGCGCT 0.957314 -69 TGTGCAATAATCATTGAACGATAAGAATAATA 4 133 1 TCATAACGAT 0.954337 -149 ATAAGAACGCTCATTGAACGCTCCATTTAGCC 9 132 1 TCATAACGCT 0.987115 -159 GCCATAAGCTTCAAGAAACGCTTTGCATAGAA 11 23 0 TCAAAACGCT 0.983288 -149 AGCTTAGAAATCATTGAGCGCTGGTTTTAAGG 12 270 1 TCATAGCGCT 0.980972 -31 GCCATTTTTATCAAACAACGCTTTTTAAGAGT 15 58 1 TCAAAACGCT 0.983288 -81 **** ****** Masking position 7 Map Score: 6.71845 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 88 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 9 TGTTAAAAAATGAAAGGAGCGTGTA 3 129 1 TGAAAGGAGC 0.899245 -15 TGCTTAGAGATAAAACGAGC 5 1 0 TAAAACGAGC 0.973033 -58 TAATTATTATTAAAACCAGATTAAAAATAA 8 83 1 TAAAACCAGA 0.779968 -218 TTTAAGATCATAAAAGGAAAAAAG 8 287 1 TAAAAGGAAA 0.578409 -14 AATCATTGGCTAAATGGAGCGTTCAATGAG 9 141 0 TAAATGGAGC 0.857587 -150 TTTGGCTGTTTAAAAAGAGCCTAATTTAAA 9 247 1 TAAAAAGAGC 0.941225 -44 AATGCAATCTTAAAAGGAGAAGCACT 9 275 1 TAAAAGGAGA 0.945688 -16 TAACCAACGCTAAAAATAGCGCTTTAATTG 11 128 1 TAAAAATAGC 0.610886 -44 CACCTACCGCTAAAATGAGATTTACTGGGA 12 79 1 TAAAATGAGA 0.854728 -222 AAGACCGCCTTAAAACCAGCGCTCAATGAT 12 279 0 TAAAACCAGC 0.906088 -22 TAAGATACCATATAATGAGCCATTTTTATC 15 40 1 TATAATGAGC 0.670487 -99 ********** Masking position 4 Map Score: 6.99604 Number of sites scoring better than the average of aligned sites = 318 Number in coding regions = 262 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 10 GTTTTATAGTAAAACTCATTTTTAAGGGGG 1 24 0 AAAACTCATT 0.550736 -182 CAAATATTGATAAACCCCATTCAATTTAAT 1 78 0 TAAACCCCAT 0.682115 -128 TTTATTTTCATAAAAACCTTGATCGCTATC 1 154 0 TAAAAACCTT 0.809366 -52 CAAAAGTCCTTTTTTTAAAAT 1 195 0 AAAAGTCCTT 0.754919 -11 AGGCTAAAATTAAAATCTTTGATTTAAAGT 2 61 1 TAAAATCTTT 0.665255 -128 TCAAACCCTTTCTTATTCCC 2 179 0 TCAAACCCTT 0.771329 -10 AATTCTATTAAAACCCTGAAACTAGGCA 4 9 1 TAAAACCCTG 0.630286 -273 AAACACTCCTTAGCTTACTTT 6 81 0 AACACTCCTT 0.716329 -11 TTAAGAATGAAAAACCCCCTTAAGTATTTC 8 158 0 AAAACCCCCT 0.798666 -143 AATTTCCTTAAAAAATCCTTTTTTTAAGAA 8 181 0 AAAAATCCTT 0.920612 -120 TTACTTGTAAAATCCTTGTCTTTCTTT 9 8 1 TAAAATCCTT 0.944786 -283 AAAATAAACTCCTTGTTTTGGATT 11 158 0 TAAACTCCTT 0.964863 -14 TGCTCATTCCTCAACTCCTTATTATATTTT 12 137 1 TCAACTCCTT 0.880552 -164 TTTTTAAAACTCTCTTTAAAATTTT 15 6 1 AAAACTCTCT 0.38554 -133 ATCGTCATAAAAACCTTGTTCTAATAG 15 122 0 TAAAAACCTT 0.809366 -17 ********** Masking position 4 Map Score: 7.38553 Number of sites scoring better than the average of aligned sites = 1228 Number in coding regions = 1028 Number in noncoding regions = 200 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 11 AATATTATTTAATCTTTTTAAAATTTTGTTTT 1 49 0 AATCTTTAAA 0.796525 -157 ACTTTATAAAAAGCTAATAAAAGGCTAAAATT 2 40 1 AAGCAAAAAA 0.506797 -149 ATTTTAGCATAAGCCTTTTATAAAAACTTTAA 2 135 0 AAGCTTTATA 0.813858 -54 TGTTTCTCTAACGCTTTAAAAAATTTCTTTCT 4 49 0 ACGCTTAAAA 0.90478 -233 GTTTTTAGCCTTACAAAAAATTTAATG 5 42 0 TAGCTTCAAA 0.695017 -17 GATTAAATTGAAGCGATAAAAAAG 7 3 0 AAGCATAAAA 0.906156 -74 ACCCTTATTTAAGCTTTAAATAACTATAATAT 7 49 0 AAGCTTAATA 0.906156 -28 TTGCTATGATAATCGTTTAAAAGTAATAAAAT 9 79 0 AATCTTAAAA 0.896322 -212 TATAATAATAAATCGTTCCAAATAATAGCATG 9 200 0 AATCTTCAAA 0.860247 -91 GCTTCAAGAAACGCTTTGCATAGAAACCGCTT 11 16 0 ACGCTTCATA 0.684744 -156 AGTTTAACCGAATCATTATAAAATATAATAAG 12 154 0 AATCTTTAAA 0.796525 -147 AGACAAGCCATGAAAAAAGAAAAGTC 13 5 1 AAGCATAAAA 0.906156 -22 TTTAAAAATCAAGCCTTCAAAAACC 14 4 0 AAGCTTAAAA 0.967821 -100 **** ** **** Masking position 10 Map Score: 8.58966 Number of sites scoring better than the average of aligned sites = 1104 Number in coding regions = 975 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 12 ATGAAAATAAAAGCCTAAAACAATTTTAAA 1 173 1 AAGCCTAAAA 0.965893 -33 AACTTTATAAAAAGCTAATAAAAGGCTAAA 2 39 1 AAAGCTAATA 0.638254 -150 AAGCTAATAAAAGGCTAAAATTAAAATCTT 2 50 1 AAGGCTAAAA 0.965893 -139 TAAAAACGATATAACTAAAAATTAGAAAAA 3 36 0 ATAACTAAAA 0.592653 -108 ATCCAAAACAAAACCTAAAATAAAATCCAA 4 197 1 AAACCTAAAA 0.938396 -85 AATTTTTTGTAAGGCTAAAAAC 5 47 1 AAGGCTAAAA 0.965893 -12 ATAGTTATTTAAAGCTTAAATAAGGGTCTA 7 54 1 AAAGCTTAAA 0.59988 -23 GAAAATAAGAAAGATTAAAAACAAAATTTT 8 111 0 AAGATTAAAA 0.467355 -190 TTGTTATACAAAGACTAACAAGATTCAATT 8 207 0 AAGACTAACA 0.819945 -94 GATTCCTTAAATGCCTAAAATTTAGAAAAA 10 12 1 ATGCCTAAAA 0.841628 -105 GCTTGAAATTAAAACTAAATTTTAGTGTAT 10 75 0 AAAACTAAAT 0.592653 -42 TAGAATAACCAACGCTAAAAATAGCGCTTT 11 123 1 AACGCTAAAA 0.824164 -49 ATAAAAGATTAAGCCTAACTTTAAAAATCA 14 25 0 AAGCCTAACT 0.626716 -79 AACTTTAAACCTAAAACCTAACGATA 14 88 0 AAACCTAAAA 0.938396 -16 ********** Masking position 8 Map Score: 11.5164 Number of sites scoring better than the average of aligned sites = 710 Number in coding regions = 598 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 13 CCCTGAAACTAGGCAAAGACTGCTTAGAAA 4 24 1 AGGCAAAGAC 0.976635 -258 ATCAACTTAAAGGCAAAGAC 4 272 1 AGGCAAAGAC 0.976635 -10 TTCTATCTCAATGCATTGACGGATTTTGTT 8 45 0 ATGCATTGAC 0.867686 -256 ATAATTTGTTATACAAAGACTAACAAGATT 8 212 0 ATACAAAGAC 0.86997 -89 TTTTCAAACCATCCAATGACCCTTTATCGC 9 37 1 ATCCAATGAC 0.948045 -254 CGCTCCATTTAGCCAATGATTATTGTCGGT 9 150 1 AGCCAATGAT 0.816147 -141 ********** Masking position 5 Map Score: 0.749272 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 55 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 14 TTTGGATAACTATCCCCCTTAAAAA 1 3 1 TGATAATATC 0.537024 -203 TTTTGAGTATAGCATAAAAATACGCTCAATTAG 2 100 1 AGATAAAATC 0.90921 -89 TAATCATTGAACGATAAGAATAATATTTTTGTG 4 140 1 ACATAAAATA 0.699842 -142 TCGCCCTCAATCCAAAACAAAACCTAAAATAAA 4 188 1 TCAAAAAAAC 0.840026 -94 AGTGATACTATGAATAATAAATCAACTTAAAGG 4 252 1 TGATAAAAAC 0.879147 -30 AAAATAAAAATCAAAAAAAAAAAAAAAACAAAA 8 19 1 TCAAAAAAAA 0.628759 -282 GAGATAGAATAGTATAATAATTATTATTAAAAC 8 66 1 AGATAAAATA 0.763598 -235 CGTTCTTATTTGTAAAAAAATTCAGTTTGTTTG 9 108 0 TGAAAAAATC 0.90921 -183 CCGCTATTATACCATAAGAAAACCGCTCGCTTG 11 81 0 ACATAAAAAC 0.840026 -91 CGTTGGTTATTCTAAAAAAATAACCGCTATTAT 11 104 0 TCAAAAAATA 0.699842 -68 CCACAAATCAAGAAAAATAATCCCAGTAAATCT 12 96 0 AGAAAAAATC 0.90921 -205 TTGAGGAATGAGCAAAATAAAACCACAAATCAA 12 118 0 AGAAAAAAAC 0.879147 -183 ** **** *** * Masking position 7 Map Score: 2.83186 Number of sites scoring better than the average of aligned sites = 409 Number in coding regions = 356 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 15 TTTTAGTTATATCGTTTTTAGATTAAAAGT 3 46 1 ATCGTTTTTA 0.523088 -98 TCAGCACTATAGCGCTATAAGACTAATTGT 3 75 1 AGCGCTATAA 0.579876 -69 ACATTCTTGTCTCGCTTTTATTATATAACA 3 102 0 CTCGCTTTTA 0.946546 -42 ATGTTTCTCTAACGCTTTAAAAAATTTCTT 4 52 0 AACGCTTTAA 0.934955 -230 TATTCATAGTATCACTTTTAGGTGATTGAC 4 238 0 ATCACTTTTA 0.546374 -44 CTTTTTTATCGCTTCAATTTAATCAAA 7 8 1 ATCGCTTCAA 0.830989 -69 TAGAAAAAATCACGCTTGATCTTATCTAAA 10 34 1 CACGCTTGAT 0.700293 -83 TTTAACGCACCACGCTTGAAATTAAAACTA 10 88 0 CACGCTTGAA 0.912501 -29 AAGAAAACCGCTCGCTTGTATTTGCAAAAA 11 69 0 CTCGCTTGTA 0.917292 -103 CGCTAAAAATAGCGCTTTAATTGAATCCAA 11 135 1 AGCGCTTTAA 0.92258 -37 TTTTTAAAACTCTCTTTAAAATTTTACTT 15 10 1 CTCTCTTTAA 0.657624 -129 TTTATCAAACAACGCTTTTTAAGAGTGGCT 15 64 1 AACGCTTTTT 0.700545 -75 ********** Masking position 6 Map Score: 2.76139 Number of sites scoring better than the average of aligned sites = 1653 Number in coding regions = 1542 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856