AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i03010_hpyl_reg_100.orf -o03010_hpyl_100.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: HP1244 22 ribosomal protein S18 (rps18) HP0199 25 H. pylori predicted coding region HP0199 Input sequences: #1 HP0076 89 ribosomal protein S20 (rps20) #2 HP0084 300 ribosomal protein L13 (rpl13) #3 HP0122 186 H. pylori predicted coding region HP0122 #4 HP0123 39 threonyl-tRNA synthetase (thrS) #5 HP0126 93 ribosomal protein L20 (rpl20) #6 HP0194 214 triosephosphate isomerase (tpi) #7 HP0197 64 S-adenosylmethionine synthetase 2 (metX) #8 HP0198 66 nucleoside diphosphate kinase (ndk) #9 HP0296 241 ribosomal protein L21 (rpl21) #10 HP0399 120 ribosomal protein S1 (rps1) #11 HP0491 99 ribosomal protein L28 (rpL28) #12 HP0492 124 H. pylori predicted coding region HP0492 #13 HP0513 290 H. pylori predicted coding region HP0513 #14 HP0514 60 ribosomal protein L9 (rpl9) #15 HP0551 263 ribosomal protein L31 (rpl31) #16 HP0562 100 ribosomal protein S21 (rps21) #17 HP1040 140 ribosomal protein S15 (rps15) #18 HP1147 21 ribosomal protein L19 (rpl19) #19 HP1151 73 ribosomal protein S16 (rpS16) #20 HP1153 130 valyl-tRNA synthetase (valS) #21 HP1197 88 ribosomal protein S12 (rps12) #22 HP1198 223 DNA-directed RNA polymerase, beta subunit (rpoB) #23 HP1199 45 ribosomal protein L7/L12 (rpl7/l12) #24 HP1200 108 ribosomal protein L10 (rpl10) #25 HP1201 44 ribosomal protein L1 (rpl1) #26 HP1203 300 transcription termination factor NusG (nusG) #27 HP1204 35 ribosomal protein L33 (rpL33) #28 HP1205 300 translation elongation factor EF-Tu (tufB) #29 HP1246 153 ribosomal protein S6 (rps6) #30 HP1295 22 ribosomal protein S11 (rps11) #31 HP1297 78 ribosomal protein L36 (rpl36) #32 HP1300 42 preprotein translocase subunit (secY) #33 HP1318 34 ribosomal protein L4 (rpl4) #34 HP1319 36 ribosomal protein L3 (rpl3) #35 HP1320 164 ribosomal protein S10 (rps10) #36 HP1441 120 peptidyl-prolyl cis-trans isomerase B, cyclosporin-type rotamase (ppi) #37 HP1447 71 ribosomal protein L34 (rpl34) #38 HP1554 248 ribosomal protein S2 (rps2) Motif number 1 ATAAAATACCTTTTAAACTATTTTTAATCAATTT 1 15 1 TTTTAAATTT 0.945906 -75 GCGGTAATTTTTTAAGCGGTCTTTTGGGGTTAGG 2 54 1 TTTAAGTTTT 0.920092 -247 AAATAAGGTTTTTTAAAAAATTTGTTTGACTGCT 2 193 0 TTTTAAATTG 0.841315 -108 TATTGCTGAATTTAAGGAAAGTTTAAAGTTTAAA 2 226 0 TTTAAGATTT 0.951894 -75 ATTCAGCAATATTTAAGCTTATTTCCTTATAATG 2 249 1 ATTTAATTTT 0.626306 -52 TTAATGATCATTTTAAGGGAGTTTT 3 2 0 TTTTAAATTT 0.945906 -185 TATATTTTTGTTTTAAGAAACTTAATGATCATTT 3 23 0 TTTTAAATTA 0.735975 -164 AGAGCTTTAGTTTTAGCTAGTTTGTATTACTAAG 3 73 1 TTTTAGGTTG 0.608702 -114 TAGGTGCGTTTTTAAAACGACTTTCCCTTAATAA 5 42 0 TTTAAAATTT 0.93027 -52 TTACCTTTCTTTTTAAAATATTTTTAGGTGCGTT 5 66 0 TTTTAAATTT 0.945906 -28 CGTCAAGCGATTTTAGGTTAATTTTGAGTTTTTA 6 23 0 TTTTAGATTT 0.962874 -192 TCTACTACATTTGAAATAATTTTTCTTATAAACA 6 75 1 TTGAAATTTT 0.671764 -140 ATTTACATTTTTTAAACGCTATTAGATATAATAA 6 156 1 TTTAAATTTA 0.553083 -59 AAGGGTAATATTTTAAAAAATTTTTGTATAATCA 8 22 1 TTTTAAATTT 0.945906 -45 TTTGGAATACTTTTAGCTTGTTTGTTAAAAAACC 9 26 0 TTTTAGGTTG 0.608702 -216 CGCAATTGTTATTAAGCTTATTTTGGAATACTTT 9 47 0 ATTAAGATTT 0.765211 -195 TTAAATCCACATTAAAAGAATTTTTTATTCAAAA 9 133 0 ATTAAAATTT 0.687244 -109 TAGCGGTTTTTTTAAAGAAAATTTTCAAAATGTG 10 11 0 TTTAAAATTT 0.93027 -110 AATTGTTAGTTTTTAAACGATTTTGTAAGCCAAA 10 44 1 TTTTAAATTT 0.945906 -77 AAAGACTGATTTTAAGGCTAATTTTTAAATGGTT 11 21 0 TTTAAGATTT 0.951894 -79 AATCAGTCTTTTTAAAGGCTATTTTAAGTATAAT 11 44 1 TTTAAATTTT 0.885887 -56 TCCTTAATTATTGAAATAAACTTTGCATTATACT 11 70 0 TTGAAAATTT 0.778615 -30 AGCATGGCGATTTTAGGGGATTTT 12 1 0 TTTTAGATTT 0.962874 -124 TTATTTTAATTTTTAGGAATCTTTT 12 110 1 TTTTAGTTTT 0.937858 -15 ACACTCCTTGATTTAGCGGATTTTACCGCATGCA 13 110 0 ATTTAGATTT 0.810312 -181 CCCCTTTAAGTTGTAAGTAATTTGTAATTATACT 14 35 0 TTGTAAATTG 0.582931 -26 ACACTAATTTTTTAAGAATGCTTTAGCTTTTTGT 15 66 0 TTTAAGGTTT 0.796516 -198 TGGTTTGTCTTTTTAGGCTTATTATAATATAAAG 17 41 1 TTTTAGTTTA 0.706388 -100 CTTTTAAGCATGTTTTGGGTGCTTT 19 2 1 TTTTAATTTT 0.910518 -72 AATACGAATATTTTAGGAGATTTTTGTA 19 56 1 TTTTAGATTT 0.962874 -18 CTAATTTTTCTTTTAAAAATCTTAACCGATTTTT 21 15 0 TTTTAATTTA 0.618624 -74 AAAAAAGAAATTTTAAGCTTTTTAGCTCTTACGA 24 41 0 TTTTAATTTA 0.618624 -68 TTTGTTGGAATTGAAAGAAATTTTTAAGGATTAG 25 17 1 TTGAAAATTT 0.778615 -28 TTAATTTTAGTTTAAGCTATTTTGGATAGAATTA 26 17 1 TTTAAGTTTG 0.777338 -284 ACATTTATACATTAAAAGAATTTTTAATTCTATC 26 41 0 ATTAAAATTT 0.687244 -260 ATCACGCTGTTTTTAGCTTTGTTGGATTTTTCTC 26 222 1 TTTTAGTTTG 0.820656 -79 TACCACAAAATTTAAGACATTTTTGTCTTATCGC 28 204 0 TTTAAGTTTT 0.920092 -97 CCTTAATTTTTTGAAATGGATTTTAGAATTATAC 28 267 0 TTGAAAATTT 0.778615 -34 TTGTTTTTGGATTAAATTGAGTTTTATTAGTAAT 29 47 0 ATTAAAATTT 0.687244 -107 ATTTAAGGGTTATTTCAATGAAAAT 31 2 1 TTTAAGTTTT 0.920092 -77 CTTTTGCTATTTTTAGGGCTTTTTAGAGATTTTT 35 39 0 TTTTAGTTTT 0.937858 -126 AAACGAGTTCTTTTAGGAGAGTTT 35 151 1 TTTTAGATTT 0.962874 -14 GCCGATAGTGTTGTAGGATACTTTTGAAATTTAA 36 26 0 TTGTAGATTT 0.872404 -95 TTTTAGTCAATTTTTAGCATTCTT 37 1 1 TTTTAGATTT 0.962874 -71 ****** * *** Masking position 5 Map Score: 58.4647 Number of sites scoring better than the average of aligned sites = 1410 Number in coding regions = 1079 Number in noncoding regions = 331 Number of orfs with sites within 600 bp upstream = 233 Fraction of orfs with sites within 600 bp upstream = 0.0374237 Motif number 2 CCCTATCCCCTTAAGGAAATGAATTTTACTTA 2 134 1 TTAAGGAATA 0.918136 -167 AGCACCCATTATAAGGAAATAAGCTTAAATAT 2 257 0 ATAAGGAATA 0.886068 -44 AATCCCCTTATTAAGGGAAAGTCGTTTTAAAA 5 35 1 TTAAGGGAAT 0.918095 -59 ATTAGATATAATAAGGGATAGTTACCACCTAT 6 176 1 ATAAGGGTAT 0.822369 -39 GATTATTTTAATAAGGACAATCA 7 52 1 ATAAGGAAAC 0.639203 -13 AAAAATATTTTAAGGGTAATATTTTAAAAAA 8 10 1 TTAAGGGAAA 0.928727 -57 TAAAAAACCAATAAGGATTTGATC 9 3 0 ATAAGGATTA 0.822448 -239 CGTTCAATTTTTAAGGAATAGAA 9 229 1 TTAAGGATAA 0.918136 -13 TACAATACCCTTAAGGATTTTATATTTATTTT 10 84 1 TTAAGGATTA 0.869791 -37 GCATGGCGATTTTAGGGGATTTT 12 2 0 TTTAGGGATT 0.741813 -123 CAACCACACTATTAGGATTTTTTGAAGAAAAT 13 161 1 ATTAGGATTT 0.631652 -130 AATTGACATTAAGGAAAACAC 18 9 1 TTAAGGAAAA 0.949571 -13 ATACGAATATTTTAGGAGATTTTTGTA 19 57 1 TTTAGGAATT 0.805898 -17 AACGCTCTATTTTAGGATAATA 20 119 1 TTTAGGAAAA 0.890151 -12 TAAAAGAAAAATTAGGGTAAAATGGGGGAACT 21 34 1 ATTAGGGAAA 0.79544 -55 AATTTTTAGAATAAGGAAAAATA 21 76 1 ATAAGGAAAT 0.918251 -13 AAAGAAATTTTTAAGGATTAGAATC 25 30 1 TTAAGGATAA 0.918136 -15 GTGGCTTTAAATAAGGAGAATA 26 289 1 ATAAGGAAAA 0.928864 -12 CCGCTCCATTTTTAGGATAACATTTTAGTTTT 28 72 1 TTTAGGAAAA 0.890151 -229 TGTGGTAGCATTTAGGAATACTTAGGATTTTG 28 231 1 TTTAGGATAT 0.805898 -70 TTTCAAAAAATTAAGGAGAAATACAA 28 285 1 TTAAGGAAAT 0.941855 -16 CGAATAAGGAGATGATGATTTA 30 4 1 ATAAGGAATA 0.886068 -19 ATTTAAGGGTTATTTCAATGAAAA 31 3 1 TTAAGGGTAT 0.86973 -76 AGATAATAAAATAAGGGTTAGAT 34 24 1 ATAAGGGTAA 0.843305 -13 CTTCCTTTTTATAAGGAAATATAAAAA 35 6 0 ATAAGGAATT 0.869964 -159 TTTTGCTATTTTTAGGGCTTTTTAGAGATTTT 35 40 0 TTTAGGGTTT 0.631164 -125 CAAAATAACTTTAAGGAGAATTCTC 38 234 1 TTAAGGAAAT 0.941855 -15 ******* ** * Masking position 4 Map Score: 31.7687 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 222 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 3 AAAAACCCCCTAACCCCAAAAGACCGCTTAA 2 65 0 TAACCCAAAA 0.891244 -236 AGTTTGACCATAAAATCAAAAGCAGTCAAAC 2 173 1 TAAATCAAAA 0.835709 -128 AGGAAAGTTTAAAGTTTAAAAATAAGGTTTT 2 215 0 AAATTTAAAA 0.602829 -86 TTAAGTTTCTTAAAACAAAAATATAACAATG 3 32 1 TAAACAAAAA 0.860769 -155 AATAAAATCATAAACCAAAAAGAATACACCC 3 120 0 TAACCAAAAA 0.908997 -67 TCCTTTCTTCAAACCTTAAAAT 4 2 0 AAACTTAAAA 0.850412 -38 ACTGCTCCTAAAAACTCAAAATTAACCTAAA 6 15 1 AAACTCAAAA 0.835433 -200 AACGATTTTGTAAGCCAAAAAAGGATACAAT 10 59 1 TAACCAAAAA 0.908997 -62 AAAGATTCCTAAAAATTAAAATAAGCTTCTA 12 103 0 AAAATTAAAA 0.778696 -22 TTGTTGCAATTAAGATAAAAATACAAAAAGC 15 44 1 TAAATAAAAA 0.861114 -220 TTTTTAAATTTAAACTTAAAATTATAGCATA 15 230 0 TAACTTAAAA 0.901996 -34 TATATTATAATAAGCCTAAAAAGACAAACCA 17 41 0 TAACCTAAAA 0.901741 -100 ACAAAGCATTTAAATTAAAAAGGATAGTCCA 20 11 0 TAATTAAAAA 0.727852 -120 TCTAAAAATTTAAAACTAAAAGTTCCCCCAT 21 55 0 TAAACTAAAA 0.850301 -34 TCCATGATAAAAATACCAAAAACCCACCTGC 22 116 0 AAAACCAAAA 0.758047 -108 GTGATGGCTTTAATTTAAAAAAATGTGAAGG 23 17 1 TAATTAAAAA 0.727852 -29 ATCTTCAGCCTAAGATTAAAAACTCCTAACG 24 11 0 TAAATTAAAA 0.850667 -98 TAAGAGCTAAAAAGCTTAAAATTTCTTTTTT 24 44 1 AAACTTAAAA 0.850412 -65 TAGCTTAAACTAAAATTAAAAAATT 26 5 0 TAAATTAAAA 0.850667 -296 AAAATCCAACAAAGCTAAAAACAGCGTGATA 26 221 0 AAACTAAAAA 0.860873 -80 TAGGCGTCTCAAAAACTAAAATGTTATCCTA 28 84 0 AAAACTAAAA 0.7782 -217 TGAATGGCGATAAGACAAAAATGTCTTAAAT 28 198 1 TAAACAAAAA 0.860769 -103 TTGTTTAGTATAATTCTAAAATCCATTTCAA 28 260 1 TAATCTAAAA 0.710157 -41 TAGTAATATTAAAGCTCAAAACGAAAAACGC 29 23 0 AAACTCAAAA 0.835433 -131 AAACTCAATTTAATCCAAAAACAAGCGAAAG 29 57 1 TAACCAAAAA 0.908997 -97 TTTTATAAGGAAATATAAAAA 35 1 0 AAAATAAAAA 0.792952 -164 AATAAAACAATAAAATAAAAACTGAAATACT 35 100 0 TAAATAAAAA 0.861114 -65 CTTACCGCTTAAATTTCAAAAGTATCCTACA 36 18 1 AAATTCAAAA 0.575435 -103 CTTTTTTACTTAAGCTAAAAAACCTTAATCT 38 60 1 TAACTAAAAA 0.909234 -189 *** ******* Masking position 8 Map Score: 38.5532 Number of sites scoring better than the average of aligned sites = 904 Number in coding regions = 696 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 4 TTTTATGGTCAAACTCATTTCTTAAGTAAAATTCATTTCCT 2 147 0 AATCTAAAAA 0.814668 -154 TTAAAGTTTAAAAATAAGGTTTTTTAAAAAATTTGTTTGAC 2 197 0 AATTTTAAAA 0.907456 -104 GATAAAATTAAAGCACCCATTATAAGGAAATAAGCTTAAAT 2 259 0 AATTTAAAAT 0.745731 -42 AACCAAAAAGAATACACCCTCTTATTAAAAAGCTTAGTAAT 3 98 0 AATCTAAAAA 0.814668 -89 ATACCTAACTAACCGCCCATTATACAATAAAATCATAAACC 3 135 0 AATTTATAAA 0.824722 -52 AACCACCCTTTCTATTCAAAAATACCTAACT 3 166 0 AATTTAAAAA 0.958927 -21 TCCCCTTATTAAGGGAAAGTCGTTTTAAAAACGCACCTAAA 5 37 1 AATCTTAAAA 0.648651 -57 ACATTTGAAATAATTTTTCTTATAAACAAAACCTAAATTGA 6 81 1 TATTTAAAAA 0.87059 -134 AGCGTTTAAAAAATGTAAATTTTAAACAATAGCCCCTTTGA 6 135 0 AATTTAAATA 0.806659 -80 AGGTGGTAACTATCCCTTATTATATCTAATAGCGTTTAAAA 6 165 0 TATTTAAATA 0.545675 -50 TCCTTATTAAAATAATCATTCGTATTCAAAATGGGCTTATT 7 28 0 AATCTAAAAA 0.814668 -37 ACTCCTTGTGAATTGTTGATTATACAAAAATTTTTTAAAAT 8 31 0 AATTTAAAAT 0.74573 -36 AATCCACATTAAAAGAATTTTTTATTCAAAATAACCCCATT 9 123 0 AATTTAAAAA 0.958927 -119 ATCTCAATTTAAAGTTACATTTTAGCAAATACTCACTATAA 9 166 1 AATTTAAATA 0.806659 -76 TACTCACTATAATAAGCGTTTATTTTAAAAAGAGCGTTCAA 9 195 1 AATTTTAAAA 0.907456 -47 AACTAACAATTAGCGGTTTTTTTAAAGAAAATTTTCAAAAT 10 14 0 TATTTAAAAA 0.87059 -107 TGTTAGTTTTTAAACGATTTTGTAAGCCAAAAAAGGATACA 10 47 1 TATTTACAAA 0.594957 -74 TATTGAAATAAACTTTGCATTATACTTAAAATAGCCTTTAA 11 55 0 AATTTAAAAA 0.958927 -45 AAATTTAGAAAAAAGAAAATTGTAGCGCAAATTGATTTACT 12 37 1 AATTTACAAA 0.836003 -88 AAACCCAACTTATTCAAAATAAAGAGTATAA 14 1 1 AATTTTAATA 0.636667 -60 TAAATTTCCTTTTAACAAAAAGAGATTTCTA 15 1 1 TATTTAAAAA 0.87059 -263 AAGCATTCTTAAAAAATTAGTGTAACCAAAAGATGCTAATA 15 77 1 AAGTTAAAAA 0.52931 -187 AGTTAAATAAAATTTGACTTTGTTAAAAAAATTATGATAGC 15 162 0 AATTTTAAAA 0.907456 -102 TTTAAATTTAAACTTAAAATTATAGCATAAGTCATAATAAA 15 218 0 AATTTATAAG 0.416491 -46 CAAGTATCCTTTATTTTTAAATTTAAACTTAA 15 242 0 AATTTTAAAT 0.551927 -22 TAATTTAATAAAGTTCGCATTATAGCGTAAAATAAGCTTTT 17 93 0 AATTTATAAA 0.824722 -48 ATTCGTATTAAATTTGAGATTATACAACAAAAGCACCCAAA 19 24 0 AATTTACAAA 0.836003 -50 AAAATTATACAACAAAGCATTTAAATTAAAAAGGATAGTCC 20 12 0 AATTAAAAAA 0.43141 -119 TTTTTTAAGGAACGCTCTATTTTAGGATAATA 20 109 1 AATTTATAAT 0.371491 -22 TATTTTTCCTTATTCTAAAAATTTAAAACTA 21 68 0 TATTTTAAAA 0.738593 -21 TGCATTAAATAACTCAAAATTTTTGATCAAAGGCTTGAAAT 22 193 1 AATTTTCAAA 0.681629 -31 AGACCTCTGCAAGATTATCTTTTTAAAAAAGAAATTTTAAG 24 58 0 AATTTTAAAG 0.597988 -51 ACATTAAAAGAATTTTTAATTCTATCCAAAATAGCTTAAAC 26 26 0 AATTTAAAAA 0.958927 -275 TTTTGGATTAAATTGAGTTTTATTAGTAATATTAAAGCTCA 29 36 0 AATTTTAATA 0.636554 -118 TGTGGTTGTATAGCCCTTTTTTTACTAAAAAAGAGCAAGGT 29 113 0 TATTTAAAAA 0.87059 -41 GCCCTAAAAATAGCAAAAGTTATTGACTAAATGGCGCATTT 35 54 1 TATTTTTAAA 0.362823 -111 AATAAAATAAAAACTGAAATACTACTCAAAATGCGCCATTT 35 82 0 AATATAAAAA 0.457207 -83 TTGTCATTCAAATGCTCTATTATAGCAACAAATTAAAACAA 36 71 0 AATTTAACAA 0.529306 -50 AATTAAACATAAACACAGATTTTAGCTAAAGAATGCTAAAA 37 22 0 AATTTAAAAG 0.779818 -50 TAGCTTAAGTAAAAAAGGCTTTTAGGTTATAATAAAGACAA 38 36 0 AATTTATATA 0.456769 -213 CTAATCCTTGTATTAGGTGTTCTTAAGAAAATTAAGAATCA 38 171 1 TATTTTAAAA 0.738593 -78 ** ** ** **** Masking position 2 Map Score: 44.1319 Number of sites scoring better than the average of aligned sites = 964 Number in coding regions = 705 Number in noncoding regions = 259 Number of orfs with sites within 600 bp upstream = 209 Fraction of orfs with sites within 600 bp upstream = 0.0335689 Motif number 5 AAAATAAGGTTTTTTAAAAAATTTGTTTGAC 2 197 0 TTTTTAAAAA 0.830004 -104 AAGAATCCTTTGATAAAATTAAAGCACC 2 283 0 CTTTGATAAA 0.442282 -18 TTATATTTTTGTTTTAAGAAACTTAATGATC 3 27 0 GTTTTAAAAA 0.646108 -160 ATTACTAAGCTTTTTAATAAGAGGGTGTATT 3 98 1 TTTTTAAAAG 0.775603 -89 AGTTAGGTATTTTTGAATAGAAAGGGTGGTT 3 166 1 TTTTGAAAGA 0.687185 -21 ATTTTAAGGTTTGAAGAAAGGAAACATAA 4 9 1 GTTTGAAAAA 0.658205 -31 TTTACCTTTCTTTTTAAAATATTTTTAGGTG 5 70 0 TTTTTAAATA 0.785154 -24 TTAGGTTTTGTTTATAAGAAAAATTATTTCA 6 86 0 TTTATAAAAA 0.511602 -129 ATACAAAAATTTTTTAAAATATTACCCTTAA 8 20 0 TTTTTAAATA 0.785154 -47 CCTTATTGGTTTTTTAACAAACAAGCTAAAA 9 19 1 TTTTTAAAAA 0.924119 -223 AATGGGGTTATTTTGAATAAAAAATTCTTTT 9 123 1 TTTTGAAAAA 0.92819 -119 TTGAACGCTCTTTTTAAAATAAACGCTTATT 9 205 0 TTTTTAAATA 0.785154 -37 TTAGCGGTTTTTTTAAAGAAAATTTTCAAAA 10 15 0 TTTTAAAAAA 0.484353 -106 ATGCTTGAAATTTAGAAAAAAGAAAATTGTA 12 30 1 TTTAGAAAAA 0.519846 -95 TATTAGGATTTTTTGAAGAAAATCAAAACAA 13 170 1 TTTTGAAAAA 0.928966 -121 TTCCCACCAATTTTTATAATATCATCCCATA 13 263 0 TTTTTATATA 0.509826 -28 ATACTCTTTATTTTGAATAAGTTGGGTTT 14 9 0 TTTTGAAAAG 0.786363 -52 TAAATTTCCTTTTAACAAAAAGAGATTTC 15 9 1 CTTTTAAAAA 0.726436 -255 TTACACTAATTTTTTAAGAATGCTTTAGCTT 15 71 0 TTTTTAAAAT 0.400969 -193 TATCATAATTTTTTTAACAAAGTCAAATTTT 15 164 1 TTTTTAAAAA 0.924119 -100 TGTTGTATAATTTTGAAAAAATACGCAACAA 20 39 1 TTTTGAAAAA 0.91871 -92 TCGGTTAAGATTTTTAAAAGAAAAATTAGGG 21 20 1 TTTTTAAAGA 0.674689 -69 GTTTTTGGTATTTTTATCATGGATGGTTCTA 22 124 1 TTTTTATATG 0.226336 -100 AACTCAAAATTTTTGATCAAAGGCTTGAAAT 22 203 1 TTTTGATAAA 0.78748 -21 CAAGATTATCTTTTTAAAAAAGAAATTTTAA 24 59 0 TTTTTAAAAA 0.830004 -50 TCTAAAAAACTTTTGATTATACCTTGCTTTC 29 83 0 TTTTGATATA 0.523185 -71 TATAGCCCTTTTTTTACTAAAAAAGAGCAAG 29 115 0 TTTTTACAAA 0.513586 -39 GATTTTTCTCCTTTGAAAAAATTAGGCACTA 31 58 0 CTTTGAAAAA 0.734841 -21 TTATGTTTAATTTTTATCAAGGGAGTTTTAA 37 51 1 TTTTTATAAG 0.49697 -21 ******* *** Masking position 6 Map Score: 29.3745 Number of sites scoring better than the average of aligned sites = 1023 Number in coding regions = 788 Number in noncoding regions = 235 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 6 TTTAATCAATTTTTAGATAGAATTATGCCAAAT 1 37 1 TTTGATAAAT 0.835454 -53 TTTTAAACGCTATTAGATATAATAAGGGATAGT 6 165 1 TATGATAAAT 0.686536 -50 AGAATGAAATAAGCTATAATAAGCCCATTT 7 8 1 AATGCTAAAT 0.622547 -57 TTATAGTGAGTATTTGCTAAAATGTAACTTTAA 9 174 0 TATGCTAAAT 0.934382 -68 AGTAAATCAATTTGCGCTACAATTTTCTTTTTT 12 45 0 TTTGCTAAAT 0.970598 -80 TTTTGCCCCATAAATGCTATAATCACCCCTATC 13 46 0 TAAGCTAAAT 0.549229 -245 TTTATTATGACTTATGCTATAATTTTAAGTTTA 15 218 1 CTTGCTAAAT 0.961113 -46 AAAAGCTTATTTTACGCTATAATGCGAACTTTA 17 93 1 TTTGCTAAAT 0.970598 -48 TCCAAAATAGCTTAAACTAAAATTAAAAAATT 26 10 0 CTTACTAAAT 0.550706 -291 GTTTAAGCTATTTTGGATAGAATTAAAAATTCT 26 26 1 TTTGATAAAT 0.835455 -275 CGTTTTTCGTTTTGAGCTTTAATATTACTAATA 29 24 1 TTTGCTTAAT 0.726135 -130 CCTACAACACTATCGGCTAAAATACCATTTGTT 36 43 1 TATGCTAAAT 0.934382 -78 TTGTTTTAATTTGTTGCTATAATAGAGCATTTG 36 71 1 TTGGCTAAAT 0.807189 -50 TTTTAGCATTCTTTAGCTAAAATCTGTGTTTAT 37 22 1 CTTGCTAAAT 0.961114 -50 AAAAAAGGCTTTTAGGTTATAATAAAGACAAAA 38 34 0 TTTGTTAAAT 0.667716 -215 GCCTTTTTTACTTAAGCTAAAAAACCTTAATCT 38 58 1 CTTGCTAAAA 0.665009 -191 AAACCTTAATCTTTTGCTATAATCGTAGGGTTT 38 79 1 CTTGCTAAAT 0.961113 -170 *** **** *** Masking position 8 Map Score: 17.2214 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 91 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 7 AATAGTTTAAAAGGTATTTTATAACG 1 7 0 AAGGTATTTT 0.823858 -83 TTTGGGGTTAGGGGGTTTTTAGTTGGGGGT 2 76 1 GGGGGTTTTT 0.65525 -225 AGGGGATAGGGAGGTATTTTACAATAACCC 2 115 0 GAGGTATTTT 0.635876 -186 GTTTAAAAATAAGGTTTTTTAAAAAATTTG 2 203 0 AAGGTTTTTT 0.844652 -98 GGCGGTTAGTTAGGTATTTTTGAATAGAAA 3 159 1 TAGGTATTTT 0.524031 -28 TTTTTGCGTCAAGCGATTTTAGGTTAATTT 6 33 0 AAGCGATTTT 0.5834 -182 TTTCTCAATTTAGGTTTTGTTTATAAGAAA 6 96 0 TAGGTTTTGT 0.482947 -119 CAATTCAAAGGGGCTATTGTTTAAAATTTA 6 131 1 GGGCTATTGT 0.672688 -84 AAAATCCTTAAGGGTATTGTATCCTTTTTT 10 75 0 AGGGTATTGT 0.884596 -46 GTCTTTTTAAAGGCTATTTTAAGTATAATG 11 49 1 AGGCTATTTT 0.882938 -51 TGGCGATTTTAGGGGATTTT 12 1 0 AGGGGATTTT 0.814096 -124 ATTTCAAGCATGGCGATTTTAGGGGATTTT 12 11 0 TGGCGATTTT 0.425364 -114 TACCCTATTCATGCTATTTTTAAGTAAATC 12 70 0 ATGCTATTTT 0.429403 -55 CCACACTATTAGGATTTTTTGAAGAAAATC 13 164 1 AGGATTTTTT 0.549188 -127 AGCGTAAAATAAGCTTTTTTGTATCATACG 17 81 0 AAGCTTTTTT 0.796105 -60 TTGGGTTTTGTTGGAATTGAA 25 2 1 TGGGTTTTGT 0.677156 -43 ATTTTAGTTTAAGCTATTTTGGATAGAATT 26 20 1 AAGCTATTTT 0.770578 -281 TTTTCTCTAGGGGCTTTTGTCTCTAGTGTT 26 249 1 GGGCTTTTGT 0.704936 -52 AGGAATACTTAGGATTTTGTTTAGTATAAT 28 244 1 AGGATTTTGT 0.470635 -57 AAAATGCCTAAGGCGTTTTTCGTTTTGAGC 29 11 1 AGGCGTTTTT 0.785206 -143 ATTTAAGGGTTATTTCAATGAAAAT 31 6 1 AGGGTTATTT 0.387236 -73 TGCTATTTTTAGGGCTTTTTAGAGATTTTT 35 39 0 AGGGCTTTTT 0.538577 -126 ATTAAAACAAATGGTATTTTAGCCGATAGT 36 51 0 ATGGTATTTT 0.511708 -70 CCTTTGCGATAAGCTTTTGTCATTCAAATG 36 98 0 AAGCTTTTGT 0.740225 -23 GCAAAAGATTAAGGTTTTTTAGCTTAAGTA 38 66 0 AAGGTTTTTT 0.844652 -183 CTATAATCGTAGGGTTTTGTCGTTTTTCTA 38 95 1 AGGGTTTTGT 0.899098 -154 ********** Masking position 8 Map Score: 20.6051 Number of sites scoring better than the average of aligned sites = 1599 Number in coding regions = 1414 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 8 TTCTTTACCTTTCTTTTTAAAATATTTT 5 76 0 CTTTCTTTTT 0.942625 -18 AAAAATTGAACGCTCTTTTTAAAATAAACG 9 211 0 CGCTCTTTTT 0.840995 -31 TGCGCTACAATTTTCTTTTTTCTAAATTTC 12 36 0 TTTTCTTTTT 0.647222 -89 TGTTCGCATTATTCCTTTTTCCAACTATAC 13 231 0 ATTCCTTTTT 0.845218 -60 CAAACTAGAAATCTCTTTTTGTTAAAAGGA 15 17 0 ATCTCTTTTT 0.883421 -247 CAAGTATCCTTTATTTTTAAATTTAAAC 15 246 0 CTTTATTTTT 0.675187 -18 GCGCAAAGGCCTTTCTGTTTTTAAGTC 22 8 0 CTTTCTGTTT 0.838461 -216 AAAGCTTAAAATTTCTTTTTTAAAAAGATA 24 54 1 ATTTCTTTTT 0.881469 -55 CAACGCACTTATTTCTGTTTTGGTGGTGGT 26 185 1 ATTTCTGTTT 0.701443 -116 TTTATGGTAACTCTCTTTTTGCTAATA 27 8 0 CTCTCTTTTT 0.943635 -28 CCGTTTCCCGCTCCATTTTTAGGATAACAT 28 65 1 CTCCATTTTT 0.60867 -236 GTGGTTGTATAGCCCTTTTTTTACTAAAAA 29 123 0 AGCCCTTTTT 0.637414 -31 GAGATTTTTACTTCCTTTTTATAAGGAAAT 35 18 0 CTTCCTTTTT 0.923453 -147 ********** Masking position 6 Map Score: 7.38366 Number of sites scoring better than the average of aligned sites = 570 Number in coding regions = 476 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 9 CTATTTTTAATCAATTTTTAGATAGAATTA 1 32 1 TCAATTTTTA 0.892591 -58 AATCAAGCGGTAATTTTTTAAGCGGTCTTT 2 48 1 TAATTTTTTA 0.670176 -253 AAGGAAAGTTTAAAGTTTAAAAATAAGGTT 2 217 0 TAAAGTTTAA 0.748102 -84 AAAGGAAACATAAGTTTTAAAGA 4 27 1 TAAGTTTTAA 0.502582 -13 TTAAAAAATGTAAATTTTAAACAATAGCCC 6 141 0 TAAATTTTAA 0.842235 -74 CACATTAAAAGAATTTTTTATTCAAAATAA 9 130 0 GAATTTTTTA 0.39471 -112 AAAAGAGCGTTCAATTTTTAAGGAATAGAA 9 222 1 TCAATTTTTA 0.892591 -20 ATTTTAAGGCTAATTTTTAAATGGTTTGTT 11 17 0 TAATTTTTAA 0.600237 -83 GAAGCTTATTTTAATTTTTAGGAATCTTTT 12 105 1 TTAATTTTTA 0.699719 -20 AGAATCTGTATCAAGTTTTATTAAGATGCA 13 84 1 TCAAGTTTTA 0.821031 -207 ATCATTCCCACCAATTTTTATAATATCATC 13 268 0 CCAATTTTTA 0.431404 -23 TTGGTTACACTAATTTTTTAAGAATGCTTT 15 76 0 TAATTTTTTA 0.670176 -188 TTTAACAAAGTCAAATTTTATTTAACTTTA 15 176 1 TCAAATTTTA 0.503172 -88 TGCTATAATTTTAAGTTTAAATTTAAAAAT 15 232 1 TTAAGTTTAA 0.492474 -32 TATTATAATATAAAGTTTAAGCGTATGATA 17 60 1 TAAAGTTTAA 0.748102 -81 TTGTATAATCTCAAATTTAATACGAATATT 19 38 1 TCAAATTTAA 0.434352 -36 CTTTTAGTTTTAAATTTTTAGAATAAGGAA 21 64 1 TAAATTTTTA 0.871383 -25 TGGATGGTTCTAAAGTTTAAAGATCCTTTT 22 143 1 TAAAGTTTAA 0.748102 -81 TTTTAAAAAAGAAATTTTAAGCTTTTTAGC 24 49 0 GAAATTTTAA 0.636579 -60 GGAATTGAAAGAAATTTTTAAGGATTAGAA 25 23 1 GAAATTTTTA 0.703296 -22 TACATTAAAAGAATTTTTAATTCTATCCAA 26 38 0 GAATTTTTAA 0.325113 -263 TATAAATGTATTAAGTTTAAGTGAGGGCGA 26 66 1 TTAAGTTTAA 0.492474 -235 CGTTTCCCGCTCCATTTTTAGGATAACATT 28 66 1 TCCATTTTTA 0.389801 -235 GAGTAGTATTTCAGTTTTTATTTTATTGTT 35 96 1 TCAGTTTTTA 0.606441 -69 TTTTAGTCAATTTTTAGCATTCTTTA 37 7 1 TCAATTTTTA 0.892591 -65 GTGTTTATGTTTAATTTTTATCAAGGGAGT 37 47 1 TTAATTTTTA 0.699719 -25 ********** Masking position 6 Map Score: 14.6754 Number of sites scoring better than the average of aligned sites = 462 Number in coding regions = 337 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 10 CCAAATTTTACATTACAAAGGGATTAAAACAAGGC 1 64 1 CATAAAAGGT 0.816362 -26 AGAAAAAATTCAATTCAAAGGGGCTATTGTTTAAA 6 121 1 CAATAAAGGT 0.941371 -94 CAATTCATAACAATTAAAGGTGGTTA 13 2 0 CAATAAGGGT 0.871609 -289 ATTTATGGGGCAAAAAAAGTAGAATCTGTATCAAG 13 64 1 CAAAAAGTGT 0.76185 -227 TAAAATCCGCTAAATCAAGGAGTGTTATTATGGAA 13 119 1 TAATAAGGGT 0.740723 -172 CCAACTTATTCAAAATAAAGAGTATAATTACAAAT 14 15 1 CAAAAAAGGT 0.959498 -46 AAATTACTTACAACTTAAAGGGGAT 14 46 1 CAATAAAGGT 0.941371 -15 AATTTCCTTTTAACAAAAAGAGATTTCTAGTTTGT 15 13 1 TAAAAAAGGT 0.908838 -251 ACAATGGCTACAAATGAAATAGTATTATATAAGAC 16 35 0 CAATAAATGT 0.836818 -66 AAATACGCAACAATTAAAAGCGTAAAAGCAAAAGG 20 57 1 CAATAAAGGA 0.59512 -74 TATGAAAAATCGGTTAAGATTTTTA 21 1 1 TATAAAATGT 0.374022 -88 ATGGCTCATGCAATATAAATTGGCTAGAGAAGAGC 26 113 1 CAAAAAATGT 0.883262 -188 TATTAGCAAAAAGAGAGTTACCATAAAG 27 4 1 TAGAAAAGGT 0.611261 -32 ACATTGAATATAATATAAAGGGTTTGAT 33 17 1 TAAAAAAGGT 0.908838 -18 AGCAACAAATTAAAACAAATGGTATTTTAGCCGAT 36 54 0 TAAAAAATGT 0.760999 -67 *** * **** * * Masking position 8 Map Score: 9.94434 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 174 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 11 CCCAACTAAAAACCCCCTAACCCCAAAAGAC 2 72 0 AACCCCCAAC 0.937185 -229 CCTCCCCTACAACCCCCAACTAAAAACCCCC 2 86 0 AACCCCCACT 0.974159 -215 ATACCTAACTAACCGCCCATTATACAATAAA 3 145 0 AACCGCCATT 0.843108 -42 AACCCCATTTAACCCGCCATTATTAACCCGC 9 101 0 AACCCGCATT 0.784407 -141 TAAAAAGACAAACCACCTACCAGATTAAGGC 17 25 0 AACCACCACC 0.970227 -116 CCTTATTTAAAGCCACCAACCTATAGAACAC 26 274 0 AGCCACCACC 0.896433 -27 ACGGGACTCGAACCCGCGACCCTCAGCTTGG 28 38 0 AACCCGCACC 0.971526 -263 AGCGGAATTGAACCGCCGACCTCTTCCTTAC 28 143 0 AACCGCCACC 0.980532 -158 ******* *** Masking position 9 Map Score: 3.95201 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 95 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 12 TGAATTGAATTTTTTCTCAATTTAGGTTTTG 6 107 0 TTTTCTCAAT 0.829161 -108 ATTCTACTTTTTTTGCCCCATAAATGCTATA 13 58 0 TTTTCCCCAT 0.960955 -233 ATTTAGCGGATTTTACCGCATGCATCTTAAT 13 103 0 TTTTCCGCAT 0.802894 -188 CGGCAGATGATTTTGCTCCATGATTTTGTTT 22 55 1 TTTTCTCCAT 0.977509 -169 CTTTTCCTCCTTTCTAGACTAG 24 97 0 TTTTCTCCTT 0.964404 -12 TTGTATTTCTCCTTAATTTTTTGA 28 287 0 TATTCTCCTT 0.849048 -14 GATTTTTCTCCTTTGAAAAAATT 31 66 0 TTTTCTCCTT 0.964404 -13 ATTTTGGTTCTCTTCCTCCATGCTCATTTGA 38 209 0 TCTTCTCCAT 0.930427 -40 **** ****** Masking position 4 Map Score: 2.63609 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 90 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 13 AAGCCCATTTTGAATACGAATGATTATTTT 7 31 1 TGAATACGAA 0.645668 -34 GGAAAAAGGAATAATGCGAACAATTATGGG 13 239 1 ATAATGCGAA 0.782817 -52 TCTCTTTTTGTTAAAAGGAAATTTA 15 6 0 TTAAAAGGAA 0.618579 -258 ATAGTATTATATAAGACGAATTAACTGGTT 16 22 0 ATAAGACGAA 0.806787 -79 ATTTTACGCTATAATGCGAACTTTATTAAA 17 101 1 ATAATGCGAA 0.782817 -40 AATCTCAAATTTAATACGAATATTTTAGGA 19 44 1 TTAATACGAA 0.906329 -30 TATCTGCTCTTTAATAGGAAATATCACTTT 26 153 0 TTAATAGGAA 0.886511 -148 TTTCAAAAAATTAAGGAGAAATACAA 28 285 1 TTAAGGAGAA 0.727851 -16 TCAGCTTGATTTAAGAGGAATAAGTTATT 32 24 1 TTAAGAGGAA 0.894329 -19 TTCTATCATTTTAATAGGAACAAGGCAAAG 38 120 1 TTAATAGGAA 0.886511 -129 CAAAATAACTTTAAGGAGAATTCTC 38 234 1 TTAAGGAGAA 0.727851 -15 ********** Masking position 4 Map Score: 3.13824 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 28 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 14 GGTATTTTTACGATCAAATAGTAAAGAGCT 2 10 1 ACATCAAATA 0.804391 -291 AATGAGTTTGACCATAAAATCAAAAGCAGTC 2 169 1 ACATAAAATC 0.938178 -132 CGCCCATTATACAATAAAATCATAAACCAAA 3 132 0 ACATAAAATC 0.938178 -55 ATAGTTACCACCTATAAAATAAGGATCGTTC 6 193 1 CCATAAAATA 0.804391 -22 CTATAAAATAAATATAAAATCCTTAAGGGTA 10 89 0 AAATAAAATC 0.66312 -32 TGACTGCCTTACTATAAAATAAATATAAAAT 10 100 0 ACATAAAATA 0.939329 -21 ACGCATTGAGATAATAAAATAAGGGTTAGAT 34 16 1 ATATAAAATA 0.667578 -21 ACAGAATAAAACAATAAAATAAAAACTGAAA 35 104 0 ACATAAAATA 0.939329 -61 ** ******** Masking position 7 Map Score: 1.50019 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 36 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 15 AGGTTTTTTAAAAAATTTGTTTGACTGCTT 2 192 0 AAAAATTTGT 0.749824 -109 TTTAAAGTTTAAAAATAAGGTTTTTTAAAA 2 209 0 AAAAATAAGG 0.395109 -92 AAACGCACCTAAAAATATTTTAAAAAGAAA 5 65 1 AAAAATATTT 0.539785 -29 TGTTTATAAGAAAAATTATTTCAAATGTAG 6 79 0 AAAAATTATT 0.769837 -136 AAAAATATTTTAAGGGTAAT 8 1 1 AAAAATATTT 0.539785 -66 TAATATTTTAAAAAATTTTTGTATAATCAA 8 27 1 AAAAATTTTT 0.490443 -40 ATTTTGAATAAAAAATTCTTTTAATGTGGA 9 132 1 AAAAATTCTT 0.664001 -110 AGCATTCTTAAAAAATTAGTGTAACCAAAA 15 78 1 AAAAATTAGT 0.802521 -186 ACTTTGTTAAAAAAATTATGATAGCATAGC 15 157 0 AAAAATTATG 0.788859 -107 TTTTTAAAAGAAAAATTAGGGTAAAATGGG 21 30 1 AAAAATTAGG 0.738462 -59 GCCTTTGATCAAAAATTTTGAGTTATTTAA 22 197 0 AAAAATTTTG 0.738427 -27 TCTAATCCTTAAAAATTTCTTTCAATTCCA 25 22 0 AAAAATTTCT 0.473452 -23 GGATAGAATTAAAAATTCTTTTAATGTATA 26 40 1 AAAAATTCTT 0.664001 -261 AGGTATAATCAAAAGTTTTTTAGACCTTGC 29 90 1 AAAAGTTTTT 0.633043 -64 ATGTTAATATAAAAGTTTTTAGTAGTGCCT 31 36 1 AAAAGTTTTT 0.633043 -43 TCTCCTTTGAAAAAATTAGGCACTACTAAA 31 53 0 AAAAATTAGG 0.738462 -26 TAAAAATAGCAAAAGTTATTGACTAAATGG 35 58 1 AAAAGTTATT 0.664703 -107 ********** Masking position 6 Map Score: 10.4115 Number of sites scoring better than the average of aligned sites = 393 Number in coding regions = 327 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454