AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i03010_hpyl_reg_300.orf -o03010_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: 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 HP0403 80 phenylalanyl-tRNA synthetase, alpha subunit (pheS) #12 HP0491 99 ribosomal protein L28 (rpL28) #13 HP0492 124 H. pylori predicted coding region HP0492 #14 HP0513 290 H. pylori predicted coding region HP0513 #15 HP0514 60 ribosomal protein L9 (rpl9) #16 HP0551 263 ribosomal protein L31 (rpl31) #17 HP0562 100 ribosomal protein S21 (rps21) #18 HP0563 247 H. pylori predicted coding region HP0563 #19 HP1040 140 ribosomal protein S15 (rps15) #20 HP1147 21 ribosomal protein L19 (rpl19) #21 HP1151 73 ribosomal protein S16 (rpS16) #22 HP1153 130 valyl-tRNA synthetase (valS) #23 HP1197 88 ribosomal protein S12 (rps12) #24 HP1198 223 DNA-directed RNA polymerase, beta subunit (rpoB) #25 HP1199 45 ribosomal protein L7/L12 (rpl7/l12) #26 HP1200 108 ribosomal protein L10 (rpl10) #27 HP1201 44 ribosomal protein L1 (rpl1) #28 HP1203 300 transcription termination factor NusG (nusG) #29 HP1204 35 ribosomal protein L33 (rpL33) #30 HP1205 300 translation elongation factor EF-Tu (tufB) #31 HP1246 153 ribosomal protein S6 (rps6) #32 HP1253 31 tryptophanyl-tRNA synthetase (trpS) #33 HP1254 116 biotin synthesis protein (bioC) #34 HP1295 22 ribosomal protein S11 (rps11) #35 HP1297 78 ribosomal protein L36 (rpl36) #36 HP1300 42 preprotein translocase subunit (secY) #37 HP1318 34 ribosomal protein L4 (rpl4) #38 HP1319 36 ribosomal protein L3 (rpl3) #39 HP1320 164 ribosomal protein S10 (rps10) #40 HP1441 120 peptidyl-prolyl cis-trans isomerase B, cyclosporin-type rotamase (ppi) #41 HP1447 71 ribosomal protein L34 (rpl34) #42 HP1554 248 ribosomal protein S2 (rps2) Motif number 1 AAAATTGATTAAAAATAGTTTAAAAGGTATTTTAT 1 15 0 AAAATTAAAA 0.965411 -75 TTTGTAATGTAAAATTTGGCATAATTCTATCTAAA 1 48 0 AAAACATAAT 0.39181 -42 ATTTTACATTACAAAGGGATTAAAACAAGGCT 1 68 1 ACAATTAAAA 0.902656 -22 CCTAACCCCAAAAGACCGCTTAAAAAATTACCGCT 2 53 0 AAAGTTAAAA 0.885888 -248 AAGCAGTCAAACAAATTTTTTAAAAAACCTTATTT 2 192 1 ACAATTAAAA 0.902656 -109 AAAACTCCCTTAAAATGATCATTAA 3 1 1 AAAATTAAAA 0.965411 -186 GCTTAGTAATACAAACTAGCTAAAACTAAAGCTCT 3 73 0 ACAACTAAAA 0.806729 -114 TTATTAAGGGAAAGTCGTTTTAAAAACGCACCTAA 5 42 1 AAAGTTAAAA 0.885888 -52 AAACGCACCTAAAAATATTTTAAAAAGAAAGGTAA 5 65 1 AAAATTAAAA 0.965411 -29 CTAAAAACTCAAAATTAACCTAAAATCGCTTGACG 6 22 1 AAAACTAAAA 0.926275 -193 TGTTTATAAGAAAAATTATTTCAAATGTAGTAGAA 6 74 0 AAAATTCAAA 0.925622 -141 AAATTGAGAAAAAATTCAATTCAAAGGGGCTATTG 6 115 1 AAAATTCAAA 0.925622 -100 TTGATTATACAAAAATTTTTTAAAATATTACCCTT 8 22 0 AAAATTAAAA 0.965411 -45 TGGTTTTTTAACAAACAAGCTAAAAGTATTCCAAA 9 25 1 ACAACTAAAA 0.806729 -217 ATTTTGAATAAAAAATTCTTTTAATGTGGATTTAA 9 132 1 AAAATTTAAT 0.817685 -110 GTTTATTTTAAAAAGAGCGTTCAATTTTTAAGGAA 9 212 1 AAAATTCAAT 0.849655 -30 CACATTTTGAAAATTTTCTTTAAAAAAACCGCTA 10 10 1 AAAATTTAAA 0.908059 -111 TTTGGCTTACAAAATCGTTTAAAAACTAACAATTA 10 43 0 AAAATAAAAA 0.899054 -78 TTTGTAAGCCAAAAAAGGATACAATACCCTTAAGG 10 65 1 AAAATACAAT 0.643281 -56 GAAAAACCTTAAAAGGGAGCAAAAAAGC 11 4 0 AAAACAAAAA 0.800362 -77 TTCTTAAACAAACCATTTAAAAATTAGCCTTA 12 8 1 ACAATTAAAA 0.902656 -92 CATTATACTTAAAATAGCCTTTAAAAAGACTGATT 12 44 0 AAAATTTAAA 0.908059 -56 AGTATAATGCAAAGTTTATTTCAATAATTAAGGAT 12 70 1 AAAGTTCAAT 0.611182 -30 AAAATCCCCTAAAATCGCCATGCTT 13 1 1 AAAATAAAAT 0.801762 -124 AAAAGATTCCTAAAAATTAAAATAA 13 110 0 AAAACTAAAA 0.926275 -15 ACAAAAAGCTAAAGCATTCTTAAAAAATTAGTGTA 16 66 1 AAAGTTAAAA 0.885888 -198 AAACCACTCTAAAGTTAAATAAAATTTGACTTTGT 16 180 0 AAAGTAAAAT 0.529399 -84 ACTAACTAAAAAAGGAAATTTTAATGGAATTAGGA 18 74 0 AAAGTTTAAT 0.555059 -174 AAAAGCACCCAAAACATGCTTAAAAG 21 2 0 AAAATTAAAA 0.965411 -72 TACAAAAATCTCCTAAAATATTCGTATT 21 56 0 AAAACTAAAA 0.926275 -18 AAATTATACAACAAAGCATTTAAATTAAAAAGGAT 22 17 0 ACAATTAAAT 0.808095 -114 TAAGCATTGCAAAAGGATCTTTAAACTTTAGAACC 24 148 0 AAAATTTAAA 0.908059 -76 CTAATCCTTAAAAATTTCTTTCAATTCCAACAAAA 27 16 0 AAAATTCAAT 0.849655 -29 TTTATACATTAAAAGAATTTTTAATTCTATCCAAA 28 37 0 AAAATTTAAT 0.817685 -264 GCGATAAGACAAAAATGTCTTAAATTTTGTGGTAG 30 204 1 AAAATTAAAT 0.926872 -97 GTATAATTCTAAAATCCATTTCAAAAAATTAAGGA 30 267 1 AAAATTCAAA 0.925622 -34 TATTACTAATAAAACTCAATTTAATCCAAAAACAA 31 46 1 AAAATTTAAT 0.817685 -108 TTTCCTTATAAAAAGGAAGTAAAAATCTCTAAAAA 39 19 1 AAAATAAAAA 0.899054 -146 AAAAATCTCTAAAAAGCCCTAAAAATAGCAAAAGT 39 39 1 AAAATAAAAA 0.899054 -126 ACAGAATAAAACAATAAAATAAAAACTGAAATACT 39 100 0 ACAATAAAAA 0.747406 -65 AAAGAATGCTAAAAATTGACTAAAA 41 1 0 AAAACTAAAA 0.926275 -71 TCCCTTGATAAAAATTAAACATAAACACAGATTTT 41 40 0 AAAACATAAA 0.586545 -32 **** ****** Masking position 3 Map Score: 58.8327 Number of sites scoring better than the average of aligned sites = 1941 Number in coding regions = 1488 Number in noncoding regions = 453 Number of orfs with sites within 600 bp upstream = 243 Fraction of orfs with sites within 600 bp upstream = 0.0390299 Motif number 2 TGATTAAAGATAAGCTCTTTACTATTTGAT 2 23 0 TAAGCTCTTT 0.839209 -278 AGTTTAAAAATAAGGTTTTTTAAAAAATTT 2 204 0 TAAGGTTTTT 0.981338 -97 CAGCAATATTTAAGCTTATTTCCTTATAAT 2 252 1 TAAGCTTATT 0.898968 -49 TTTGTATTACTAAGCTTTTTAATAAGAGGG 3 93 1 TAAGCTTTTT 0.982843 -94 GGGCGGTTAGTTAGGTATTTTTGAATAGAA 3 158 1 TTAGGTATTT 0.662666 -29 TTTTCTCAATTTAGGTTTTGTTTATAAGAA 6 97 0 TTAGGTTTTG 0.88823 -118 AAAAAACCAATAAGGATTTGATC 9 4 0 TAAGGATTTG 0.863782 -238 CAATTGTTATTAAGCTTATTTTGGAATACT 9 49 0 TAAGCTTATT 0.898968 -193 ACAATACCCTTAAGGATTTTATATTTATTT 10 85 1 TAAGGATTTT 0.935318 -36 TGCTCCCTTTTAAGGTTTTTCTTTTATTAA 11 18 1 TAAGGTTTTT 0.981338 -63 AACCACACTATTAGGATTTTTTGAAGAAAA 14 162 1 TTAGGATTTT 0.832869 -129 TAAGAATGCTTTAGCTTTTTGTATTTTTAT 16 58 0 TTAGCTTTTT 0.951787 -206 TGTTACAAGATAAGCTTTTTTATCAAAAAT 18 206 1 TAAGCTTTTT 0.982843 -42 TTTGTCTTTTTAGGCTTATTATAATATAAA 19 44 1 TAGGCTTATT 0.749687 -97 TAGCGTAAAATAAGCTTTTTTGTATCATAC 19 82 0 TAAGCTTTTT 0.982843 -59 AAAAATCGGTTAAGATTTTTAAAAGAAAAA 23 15 1 TAAGATTTTT 0.790492 -74 AAAGAAATTTTAAGCTTTTTAGCTCTTACG 26 42 0 TAAGCTTTTT 0.982843 -67 TTGGGTTTTGTTGGAATTGA 27 1 1 TTGGGTTTTG 0.727886 -44 AATTTTAGTTTAAGCTATTTTGGATAGAAT 28 19 1 TAAGCTATTT 0.861297 -282 TTAGGAATACTTAGGATTTTGTTTAGTATA 30 242 1 TTAGGATTTT 0.832869 -59 AAAAACGCCTTAGGCATTTT 31 1 0 TAGGCATTTT 0.841327 -153 ACCTTTGCGATAAGCTTTTGTCATTCAAAT 40 99 0 TAAGCTTTTG 0.961716 -22 AGCAAAAGATTAAGGTTTTTTAGCTTAAGT 42 67 0 TAAGGTTTTT 0.981338 -182 GCTATAATCGTAGGGTTTTGTCGTTTTTCT 42 94 1 TAGGGTTTTG 0.88587 -155 ********** Masking position 9 Map Score: 31.8193 Number of sites scoring better than the average of aligned sites = 497 Number in coding regions = 422 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 3 CTATCTAAAAATTGATTAAAAATAGTTTAAAA 1 25 0 ATTTTAAAAA 0.754196 -65 AGTCAAACAAATTTTTTAAAAAACCTTATTTT 2 196 1 ATTTTAAAAA 0.754111 -105 AGGAAAGTTTAAAGTTTAAAAATAAGGTTTTT 2 214 0 AAATTAAAAA 0.729306 -87 AAAACTCCCTTAAAATGATCATTAAG 3 5 1 CTCTTAAAAT 0.650849 -182 TCCTTTCTTCAAACCTTAAAAT 4 1 0 AAATTAAAAT 0.706633 -39 GCACCTAAAAATATTTTAAAAAGAAAGGTAAA 5 69 1 ATATTAAAAA 0.815767 -25 AAACTCAAAATTAACCTAAAATCGCTTGACGC 6 26 1 TTACTAAAAT 0.81572 -189 CAAAGGGGCTATTGTTTAAAATTTACATTTTT 6 136 1 ATTTTAAAAT 0.732844 -79 TTTAAAATATTACCCTTAAAATATTTTT 8 7 0 TACTTAAAAT 0.60163 -60 TTTAAGGGTAATATTTTAAAAAATTTTTGTAT 8 19 1 ATATTAAAAA 0.815767 -48 TATAGTGAGTATTTGCTAAAATGTAACTTTAA 9 174 0 ATTCTAAAAT 0.7685 -68 TAATAAGCGTTTATTTTAAAAAGAGCGTTCAA 9 204 1 TTATTAAAAA 0.803587 -38 TTCTATTCCTTAAAAATTGAACGCTC 9 226 0 ATTTTAAAAA 0.754196 -16 TTTTGAAAATTTTCTTTAAAAAAACCGCTAAT 10 15 1 TTTTTAAAAA 0.739246 -106 GGCTTACAAAATCGTTTAAAAACTAACAATTA 10 43 0 ATCTTAAAAA 0.750292 -78 AATAAAAGAAAAACCTTAAAAGGGAGCAAAAA 11 14 0 AAATTAAAAG 0.5598 -67 CCTTATATTTTATTTTTAAAAAGCTATAATAC 11 52 0 TATTTAAAAA 0.633027 -29 AACTTTGCATTATACTTAAAATAGCCTTTAAA 12 54 0 TATTTAAAAT 0.606641 -46 AAAATCCCCTAAAATCGCCATGCTT 13 4 1 ATCCTAAAAT 0.764752 -121 CGCAAATTGATTTACTTAAAAATAGCATGAAT 13 62 1 TTTTTAAAAA 0.739247 -63 AAAGATTCCTAAAAATTAAAATAAGCTTCTAT 13 102 0 AAATTAAAAT 0.706633 -23 AGAAATCTCTTTTTGTTAAAAGGAAATTTA 16 9 0 TTTTTAAAAG 0.572315 -255 AAAGCTAAAGCATTCTTAAAAAATTAGTGTAA 16 70 1 CATTTAAAAA 0.564368 -194 TAAAATTTGACTTTGTTAAAAAAATTATGATA 16 164 0 CTTTTAAAAA 0.680427 -100 TTTTTAAATTTAAACTTAAAATTATAGCATAA 16 229 0 TAATTAAAAT 0.68998 -35 CCTCTTTTCCATAGCTTAAAATCATTGCTTAA 17 69 0 ATATTAAAAT 0.798335 -32 TATTTCCTAATTCCATTAAAATTTCCTTTTTT 18 70 1 TTCTTAAAAT 0.712814 -178 GGTATTCTAGCACATCTAAAAATATTTTTCTT 18 170 0 CACCTAAAAA 0.605568 -78 TATATTATAATAAGCCTAAAAAGACAAACCAC 19 40 0 TAACTAAAAA 0.750785 -101 GCACCCAAAACATGCTTAAAAG 21 1 0 CATTTAAAAG 0.379459 -73 TACAAAAATCTCCTAAAATATTCGTATTA 21 55 0 ATCCTAAAAT 0.764752 -19 AACAAAGCATTTAAATTAAAAAGGATAGTCCA 22 11 0 TTATTAAAAA 0.803588 -120 AAAAATACGCAACAATTAAAAGCGTAAAAGCA 22 55 1 AACTTAAAAG 0.463213 -76 TATTATCCTAAAATAGAGCGTTCC 22 117 0 TTACTAAAAT 0.81572 -14 ACCCTAATTTTTCTTTTAAAAATCTTAACCGA 23 20 0 TTCTTAAAAA 0.735188 -69 TCTAAAAATTTAAAACTAAAAGTTCCCCCATT 23 54 0 TAACTAAAAG 0.587115 -35 TATTTTTCCTTATTCTAAAAATTTAAAACTA 23 68 0 TTACTAAAAA 0.831966 -21 TGTGATGGCTTTAATTTAAAAAAATGTGAAGG 25 16 1 TTATTAAAAA 0.803588 -30 ATCTTCAGCCTAAGATTAAAAACTCCTAACG 26 10 0 TAATTAAAAA 0.713418 -99 TAAGAGCTAAAAAGCTTAAAATTTCTTTTTTA 26 44 1 AAATTAAAAT 0.706633 -65 CTTAAAATTTCTTTTTTAAAAAGATAATCTTG 26 58 1 CTTTTAAAAA 0.680387 -51 GATTCTAATCCTTAAAAATTTCTTTCAA 27 27 0 AATTTAAAAA 0.651193 -18 CCAAAATAGCTTAAACTAAAATTAAAAAATT 28 10 0 TTACTAAAAT 0.81572 -291 TAATACATTTATACATTAAAAGAATTTTTAAT 28 47 0 ATATTAAAAG 0.676379 -254 AAAAATCCAACAAAGCTAAAAACAGCGTGATA 28 221 0 CAACTAAAAA 0.693489 -80 AACTAAAATGTTATCCTAAAAATGGAGCGGGA 30 70 0 TTACTAAAAA 0.831967 -231 TAGGCGTCTCAAAAACTAAAATGTTATCCTAA 30 83 0 AAACTAAAAT 0.744568 -218 TTGTTTAGTATAATTCTAAAATCCATTTCAAA 30 260 1 TAACTAAAAT 0.729243 -41 ATAGCCCTTTTTTTACTAAAAAAGAGCAAGGT 31 113 0 TTTCTAAAAA 0.774311 -41 AAACTAAGATAAATTAAAATATTAAAATTA 32 9 1 ATATTAAAAT 0.798335 -23 TGATTCCTTAAATGCCTAAAATTTAGAAAAAA 33 11 1 AATCTAAAAT 0.66886 -106 CACGCTTGATCTTATCTAAAATTTGCTAAGAA 33 44 1 CTTCTAAAAT 0.697301 -73 TTTGCTAAGAATACACTAAAATTTAGTTTTAA 33 65 1 ATACTAAAAT 0.827309 -52 AAAAATTAGGCACTACTAAAAACTTTTATATT 35 41 0 CACCTAAAAA 0.605568 -38 AGGAAGTAAAAATCTCTAAAAAGCCCTAAAAA 39 32 1 AATCTAAAAA 0.693184 -133 AAACTCTCCTAAAAGAACTCGTTTT 39 150 0 CTCCTAAAAG 0.543588 -15 CTACAACACTATCGGCTAAAATACCATTTGTT 40 44 1 ATCCTAAAAT 0.764752 -77 TTTAGCATTCTTTAGCTAAAATCTGTGTTTAT 41 23 1 TTTCTAAAAT 0.754137 -49 TGAGATCTATCCTAAAATTCTAATTTTG 42 7 1 CTACTAAAAT 0.768755 -242 TGTCTTTATTATAACCTAAAAGCCTTTTTTAC 42 37 1 ATACTAAAAG 0.716657 -212 CCTTTTTTACTTAAGCTAAAAAACCTTAATCT 42 59 1 TTACTAAAAA 0.831967 -190 *** ******* Masking position 7 Map Score: 63.8497 Number of sites scoring better than the average of aligned sites = 2044 Number in coding regions = 1565 Number in noncoding regions = 479 Number of orfs with sites within 600 bp upstream = 334 Fraction of orfs with sites within 600 bp upstream = 0.053646 Motif number 4 TTACCGCTTGATTAAAGATAAGCTCTTTACT 2 30 0 ATTAAAGAAA 0.7461 -271 ATATTGCTGAATTTAAGGAAAGTTTAAAGTT 2 230 0 ATTTAAGGAA 0.467124 -71 TAATCCCCTTATTAAGGGAAAGTCGTTTTAA 5 34 1 ATTAAGGGAA 0.852315 -60 TATTAGATATAATAAGGGATAGTTACCACCT 6 175 1 AATAAGGGTA 0.916614 -40 TGATTATTTTAATAAGGACAATCA 7 51 1 AATAAGGAAA 0.941007 -14 TTAAAAAACCAATAAGGATTTGATC 9 5 0 AATAAGGATT 0.703629 -237 TTTGTAAGCCAAAAAAGGATACAATACCCTT 10 65 1 AAAAAAGGTA 0.707213 -56 TACAACTTTAATAAAAGAAAAACCTTAAAAG 11 24 0 ATAAAAGAAA 0.545937 -57 TTATTTCAATAATTAAGGATACACA 12 85 1 AATTAAGGTA 0.625426 -15 TGAAATTTAGAAAAAAGAAAATTGTAGCGCA 13 35 1 AAAAAAGAAA 0.778026 -90 GTATAGTTGGAAAAAGGAATAATGCGAACAA 14 231 1 AAAAAGGATA 0.810041 -60 ACTTATTCAAAATAAAGAGTATAATTACAAA 15 18 1 AATAAAGATA 0.848419 -43 AGTTTGTTGCAATTAAGATAAAAATACAAAA 16 41 1 AATTAAGAAA 0.707848 -223 TAAATTTAAAAATAAAGGATACTTG 16 249 1 AATAAAGGTA 0.855146 -15 ATTTTAATGGAATTAGGAAATAAAAATATAA 18 61 0 AATTAGGAAT 0.506833 -187 CACACTAACTAAAAAAGGAAATTTTAATGGA 18 81 0 AAAAAAGGAA 0.787092 -167 AATTGACATTAAGGAAAACAC 20 8 1 ATTAAGGAAA 0.845481 -14 TTAAAAGAAAAATTAGGGTAAAATGGGGGAA 23 33 1 AATTAGGGAA 0.82634 -56 AAATTTTTAGAATAAGGAAAAATA 23 75 1 AATAAGGAAA 0.941007 -14 TTATCTTTTTAAAAAAGAAATTTTAAGCTTT 26 54 0 AAAAAAGAAT 0.443964 -55 GGTGGCTTTAAATAAGGAGAATA 28 288 1 AATAAGGAAA 0.941007 -13 TTGTGGTAGCATTTAGGAATACTTAGGATTT 30 230 1 ATTTAGGATA 0.502774 -71 ATTTCAAAAAATTAAGGAGAAATACAA 30 284 1 ATTAAGGAAA 0.845481 -17 TTTTTAGTAAAAAAAGGGCTATACAACCACA 31 123 1 AAAAAGGGTA 0.818105 -31 CGAATAAGGAGATGATGATTTA 34 3 1 AATAAGGAAT 0.784187 -20 GAGATAATAAAATAAGGGTTAGAT 38 23 1 AATAAGGGTA 0.916614 -14 TTTAGGTTATAATAAAGACAAAATTAGAATT 42 26 0 AATAAAGAAA 0.895468 -223 TAGCTTAAGTAAAAAAGGCTTTTAGGTTATA 42 46 0 AAAAAAGGTT 0.354938 -203 ******** ** Masking position 5 Map Score: 23.9254 Number of sites scoring better than the average of aligned sites = 566 Number in coding regions = 441 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 5 AAGCTCTATCATGCTATCATTGTTATATTT 3 50 0 ATGCTATCAT 0.912131 -137 AGAATGAAATAAGCTATAATAAGCCCATTT 7 11 1 AAGCTATAAT 0.949647 -54 TAGTGAGTATTTGCTAAAATGTAACTTTAA 9 174 0 TTGCTAAAAT 0.788012 -68 TATTTTTAAAAAGCTATAATACAACTTTAA 11 44 0 AAGCTATAAT 0.949647 -37 TGCCCCATAAATGCTATAATCACCCCTATC 14 46 0 ATGCTATAAT 0.969601 -245 ATTCTTTGCTATGCTATCATAATTTTTTTA 16 150 1 ATGCTATCAT 0.912131 -114 ATTATGACTTATGCTATAATTTTAAGTTTA 16 221 1 ATGCTATAAT 0.969601 -43 AGCTTATTTTACGCTATAATGCGAACTTTA 19 96 1 ACGCTATAAT 0.894695 -45 AAGCGAAAGCAAGGTATAATCAAAAGTTTT 31 79 1 AAGGTATAAT 0.667301 -75 TTTTAATTTGTTGCTATAATAGAGCATTTG 40 74 1 TTGCTATAAT 0.943151 -47 TAGCATTCTTTAGCTAAAATCTGTGTTTAT 41 25 1 TAGCTAAAAT 0.686689 -47 CCTTAATCTTTTGCTATAATCGTAGGGTTT 42 82 1 TTGCTATAAT 0.943151 -167 ********** Masking position 6 Map Score: 13.1824 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 13 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 6 CTAACCCCAAAAGACCGCTTAAAAAATTACCG 2 55 0 AAGACCTTAA 0.760829 -246 CCCCCAACTAAAAACCCCCTAACCCCAAAAGA 2 73 0 AAAACCCTAA 0.97983 -228 GTTATTGTAAAATACCTCCCTATCCCCTTAAG 2 117 1 AATACCCCTA 0.246559 -184 CCATAAAATCAAAAGCAGTCAAACAAATTTTT 2 180 1 AAAACGTCAA 0.581577 -121 AAAACTCCCTTAAAATGATCATT 3 2 1 AAACCCTTAA 0.878975 -185 CTTTCTATTCAAAAATACCTAACTAACCGCCC 3 158 0 AAAATCCTAA 0.739804 -29 GTCGTTTTAAAAACGCACCTAAAAATATTTTA 5 55 1 AAACCCCTAA 0.937744 -39 AAATTAACCTAAAATCGCTTGACGCAAAAACA 6 33 1 AAAACCTTGA 0.828082 -182 TTTTCTTTAAAAAAACCGCTAATTGTTAGTTT 10 24 1 AAAACGCTAA 0.922705 -97 TTTGGCTTACAAAATCGTTTAAAAACTAACAA 10 46 0 AAAACTTTAA 0.427456 -75 AAAATCCCCTAAAATCGCCATG 13 1 1 AAAACCCTAA 0.97983 -124 TGCATGCGGTAAAATCCGCTAAATCAAGGAGT 14 110 1 AAAACGCTAA 0.922705 -181 GATTTTCTTCAAAAAATCCTAATAGTGTGGTT 14 162 0 AAAAACCTAA 0.841394 -129 TAGTGTAACCAAAAGATGCTAATAAGTGGCCC 16 94 1 AAAAAGCTAA 0.565896 -170 ATAATAAATTAAAACCACTCTAAAGTTAAATA 16 194 0 AAAACCTCTA 0.490626 -70 ATTATACAACAAAAGCACCCAAAACATGCTTA 21 15 0 AAAACCCCAA 0.921451 -59 TACAAAAATCTCCTAAAATATTCGTA 21 58 0 AAAACCCTAA 0.97983 -16 TATGAAAAATCGGTTAAGATTTTTAAA 23 6 1 AAAACGTTAA 0.85198 -83 GCCTAAGATTAAAAACTCCTAACG 26 3 0 AAAACCCTAA 0.97983 -106 AATTCTATCCAAAATAGCTTAAACTAAAATTA 28 18 0 AAAAACTTAA 0.718934 -283 TTTAATAGGAAATATCACTTTAGAAAGCTCTT 28 142 0 AATACCTTTA 0.395191 -159 CACTAGAGACAAAAGCCCCTAGAGAAAAATCC 28 245 0 AAAACCCTAG 0.750776 -56 CGATAAGACAAAAATGTCTTAAATTTTGTGGT 30 205 1 AAAAGCTTAA 0.679547 -96 GCTCAAAACGAAAAACGCCTTAGGCATTTT 31 9 0 AAAACCCTTA 0.892153 -145 ATTTAGAAAAAATCACGCTTGATCTTATCTAA 33 31 1 AATCCCTTGA 0.196568 -86 GATCTTATCTAAAATTTGCTAAGAATACACTA 33 51 1 AAAATGCTAA 0.411308 -66 TTTTCATTGAAATAACCCTTAAAT 35 3 0 AATACCTTAA 0.793265 -76 AAAAATCTCTAAAAAGCCCTAAAAATAGCAAA 39 39 1 AAAAGCCTAA 0.814747 -126 AAACTCTCCTAAAAGAACTCGT 39 153 0 AAACCCCTAA 0.937744 -12 TTAAAACTCCCTTGATAAAAATTAA 41 57 0 AAACCCTTGA 0.598958 -15 TACTTAAGCTAAAAAACCTTAATCTTTTGCTA 42 66 1 AAAAACTTAA 0.718934 -183 TAATTTTCTTAAGAACACCTAATACAAGGATT 42 173 0 AAGACCCTAA 0.868378 -76 **** * ***** Masking position 2 Map Score: 34.9782 Number of sites scoring better than the average of aligned sites = 1420 Number in coding regions = 1201 Number in noncoding regions = 219 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 7 GTTTGACTGCTTTTGATTTTATGGTCAAAC 2 174 0 TTTTGATTTT 0.761008 -127 GCTTAAATATTGCTGAATTTAAGGAAAGTT 2 237 0 TGCTGAATTT 0.645482 -64 ATGCTATCATTGTTATATTTTTGTTTTAAG 3 40 0 TGTTATATTT 0.668506 -147 CCCTTAAGGATTTTATATTTATTTTATAGT 10 91 1 TTTTATATTT 0.795261 -30 GATCCTTATATTTTATTTTTAAAAAGCTAT 11 57 0 TTTTATTTTT 0.779776 -24 ATTTTCTTTTTTCTAAATTTCAAGCATGGC 13 27 0 TTCTAAATTT 0.810529 -98 ACCCTATTCATGCTATTTTTAAGTAAATCA 13 69 0 TGCTATTTTT 0.648581 -56 TAGAAGCTTATTTTAATTTTTAGGAATCTT 13 103 1 TTTTAATTTT 0.795261 -22 AAATTGATTGTTTTGATTTTCTTCAAAAAA 14 178 0 TTTTGATTTT 0.761008 -113 TGCTTTAGCTTTTTGTATTTTTATCTTAAT 16 52 0 TTTTGTATTT 0.761008 -212 ATGCCACAAGTGTTGAATTTCGTAATTCTT 16 126 1 TGTTGAATTT 0.644578 -138 TATCCTTTATTTTTAAATTTAAACTTAAAA 16 240 0 TTTTAAATTT 0.809922 -24 TGCGACCGGGTTTTATATTTTTATTTCCTA 18 49 1 TTTTATATTT 0.795261 -199 GAACTTTTAGTTTTAAATTTTTAGAATAAG 23 61 1 TTTTAAATTT 0.809922 -28 GCAAAGGCCTTTCTGTTTTTAAGTC 24 6 0 TTCTGTTTTT 0.744518 -218 AATTTTTTAATTTTAGTTTAAGCT 28 5 1 TTTTAATTTT 0.795261 -296 GCGTGATTTTTTCTAAATTTTAGGCATTTA 33 19 0 TTCTAAATTT 0.810529 -98 TTTTTATATTTCCTTATAAAA 39 2 1 TTTTATATTT 0.795261 -163 CAATAACTTTTGCTATTTTTAGGGCTTTTT 39 49 0 TGCTATTTTT 0.648581 -116 TATTGTTTTATTCTGTTTTTTAGTAACGGA 39 119 1 TTCTGTTTTT 0.744518 -46 TATCCTAAAATTCTAATTTTGTCTTTATTA 42 18 1 TTCTAATTTT 0.795903 -231 ********** Masking position 4 Map Score: 21.4528 Number of sites scoring better than the average of aligned sites = 861 Number in coding regions = 676 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 8 GACCGCTTAAAAAATTACCGCTTGATTAAAGATAA 2 40 0 AAATTACCTA 0.600243 -261 TTCTTAAGTAAAATTCATTTCCTTAAGGGGATAGG 2 135 0 AAATCATCTA 0.968174 -166 TTTTATGGTCAAACTCATTTCTTAAGTAAAATTCA 2 153 0 AAATCATCTA 0.968179 -148 CGCTTGACGCAAAAACACTGCCTTAATTCTACTAC 6 48 1 AAAACATCTA 0.882786 -167 CCTATCAATCAAACTCAATTCATAACAATTAAAGG 14 17 0 AAATCATCTA 0.968179 -274 CTGCTTCCATAATAACACTCCTTGATTTAGCGGAT 14 123 0 AATACATCTA 0.750437 -168 CAATTTTTATAATATCATCCCATAATTGTTCGCAT 14 252 0 AATTCACCTA 0.883592 -39 AAGAATTACGAAATTCAACACTTGTGGCATGGGCC 16 121 0 AAATCACCTT 0.707716 -143 TCCATAGCTTAAAATCATTGCTTAACAATGGCTAC 17 59 0 AAATCATCTA 0.968172 -42 AATCTAAAATCAATGCCTTAATCTGGTAGG 19 6 1 AAATCATCTA 0.96791 -135 CTTATTTTATTATCTCAATGCGTTAGGA 38 4 0 TATTCATCTA 0.606243 -33 *** *** * * * * Masking position 7 Map Score: 5.59582 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 53 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 CGTTATAAAATACCTTTTAAACTATTTTTAA 1 11 1 TACCTTTAAA 0.86824 -79 AACCCCAAAAGACCGCTTAAAAAATTACCGC 2 54 0 GACCGTTAAA 0.501898 -247 TTAAGGGAAAGTCGTTTTAAAAACGCACCTA 5 45 1 GTCGTTTAAA 0.809906 -49 TTCTTTACCTTTCTTTTTAAAATATTTTTAG 5 73 0 TTCTTTTAAA 0.786397 -21 AAAATAATCATTCGTATTCAAAATGGGCTTA 7 30 0 TTCGTTTCAA 0.580138 -35 CTTAAAATCAGTCTTTTTAAAGGCTATTTTA 12 39 1 GTCTTTTAAA 0.590105 -61 TAAATTTCCTTTTAACAAAAAGAGAT 16 6 1 TTCCTTTAAC 0.770661 -258 AACCAGTTAATTCGTCTTATATAATACTATT 17 22 1 TTCGTTTATA 0.637524 -79 TCCTAAAATATTCGTATTAAATTTGAGATTA 21 43 0 TTCGTTTAAA 0.915934 -31 TACCCTAATTTTTCTTTTAAAAATCTTAACC 23 22 0 TTTCTTTAAA 0.583435 -67 AAAGTGATATTTCCTATTAAAGAGCAGATAC 28 153 1 TTCCTTTAAA 0.963633 -148 GGCGGTTCAATTCCGCTTATAGGCTCCAGTT 30 157 1 TTCCGTTATA 0.625836 -144 AATAACTTATTCCTCTTAAATCAAGCTGAT 36 23 0 TTCCTTTAAA 0.963633 -20 TTTTTATATTTCCTTATAAAAAGGAAGTAA 39 10 1 TTCCTATAAA 0.693933 -155 TATCCAACTTACCGCTTAAATTTCAAAAGT 40 10 1 TACCGTTAAA 0.720419 -111 CTTTGCCTTGTTCCTATTAAAATGATAGAAA 42 119 0 TTCCTTTAAA 0.963633 -130 ***** ***** Masking position 8 Map Score: 8.00016 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 158 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 10 TTTGACTGCTTTTGATTTTATGGTCAAACT 2 173 0 TTTGATTTTA 0.475668 -128 TAATGGGTGCTTTAATTTTATCAAAGGATT 2 278 1 TTTAATTTTA 0.795199 -23 ATTGTTATATTTTTGTTTTAAGAAACTTAA 3 32 0 TTTTGTTTTA 0.888704 -155 ATGATAGAGCTTTAGTTTTAGCTAGTTTGT 3 68 1 TTTAGTTTTA 0.8027 -119 GGTGTATTCTTTTTGGTTTATGATTTTATT 3 121 1 TTTTGGTTTA 0.748829 -66 AGGATTTTATATTTATTTTATAGTAAGGCA 10 97 1 ATTTATTTTA 0.530657 -24 CTTTTAAGGTTTTTCTTTTATTAAAGTTGT 11 24 1 TTTTCTTTTA 0.655513 -57 CTTTTTGTATTTTTATCTTAATTGCAACAA 16 44 0 TTTTATCTTA 0.585088 -220 TTTAGAGTGGTTTTAATTTATTATGACTTA 16 202 1 TTTTAATTTA 0.579415 -62 ATGCTATAATTTTAAGTTTAAATTTAAAAA 16 231 1 TTTAAGTTTA 0.591786 -33 ATAAACGCCGTTTTATATTAAATCTAAAGA 18 144 1 TTTTATATTA 0.629759 -104 TTTTGGGTGCTTTTGTTGTATAATCTCAAA 21 23 1 TTTTGTTGTA 0.389406 -51 GGACTATCCTTTTTAATTTAAATGCTTTGT 22 12 1 TTTTAATTTA 0.579415 -119 TTACCCTAATTTTTCTTTTAAAAATCTTAA 23 24 0 TTTTCTTTTA 0.655513 -65 TGGGGGAACTTTTAGTTTTAAATTTTTAGA 23 56 1 TTTAGTTTTA 0.8027 -33 AATTTTTTAATTTTAGTTTAAGCTA 28 6 1 TTTAATTTTA 0.795199 -295 GTATAAATGTATTAAGTTTAAGTGAGGGCG 28 65 1 ATTAAGTTTA 0.177011 -236 TTTAAGACATTTTTGTCTTATCGCCATTCA 30 198 0 TTTTGTCTTA 0.59638 -103 CGTTTTGAGCTTTAATATTACTAATAAAAC 31 31 1 TTTAATATTA 0.464277 -123 TTTCGCTTGTTTTTGGATTAAATTGAGTTT 31 57 0 TTTTGGATTA 0.399558 -97 AATTTTAATATTTTAATTTATCTTAGTTT 32 10 0 TTTTAATTTA 0.579415 -22 TACACTAAAATTTAGTTTTAATTTCAAGCG 33 76 1 TTTAGTTTTA 0.8027 -41 TACTAAAAACTTTTATATTAACATATTTTC 35 30 0 TTTTATATTA 0.629759 -49 GTATTTCAGTTTTTATTTTATTGTTTTATT 39 101 1 TTTTATTTTA 0.884 -64 CTAAAATACCATTTGTTTTAATTTGTTGCT 40 59 1 ATTTGTTTTA 0.542271 -62 ********** Masking position 3 Map Score: 15.8241 Number of sites scoring better than the average of aligned sites = 463 Number in coding regions = 354 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 11 CAAAACCTAAATTGAGAAAAAATTCAATTCA 6 107 1 ATGAGAAAAA 0.694116 -108 AAACCTTAAAAGGGAGCAAAAAAGC 11 5 0 AGGAGCAAAA 0.976302 -76 TATAGCATTTATGGGGCAAAAAAAGTAGAAT 14 58 1 AGGGGCAAAA 0.916264 -233 AGATCAGAGAAAGGCGCAAAGGCCTTTCTGT 24 20 0 AGGCGCAAAG 0.896467 -204 AAACAAAATCATGGAGCAAAATCATCTGCCG 24 55 0 AGGAGCAAAA 0.976302 -169 CTAGTCTAGAAAGGAGGAAAAG 26 97 1 AGGAGGAAAA 0.95562 -12 AGTTTAAGTGAGGGCGAAAAGGAACTATGGA 28 79 1 AGGCGAAAAG 0.845177 -222 TCAAAAAATTAAGGAGAAATACAA 30 287 1 AGGAGAAATA 0.803709 -14 AATTTTTTCAAAGGAGAAAAATC 35 66 1 AGGAGAAAAA 0.962926 -13 TCAAATGAGCATGGAGGAAGAGAACCAAAAT 42 209 1 AGGAGGAAGA 0.834191 -40 * ********* Masking position 8 Map Score: 4.71756 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 116 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 12 CGCTTGATTAAAGATAAGCTCTTTACTATTT 2 26 0 AAATAAGCTC 0.666789 -275 TTAAAGTTTAAAAATAAGGTTTTTTAAAAAA 2 207 0 AAATAAGGTT 0.910743 -94 CCATTATAAGGAAATAAGCTTAAATATTGCT 2 253 0 GAATAAGCTT 0.666894 -48 CCCATTATACAATAAAATCATAAACCAAAAA 3 130 0 AAAAAATCAT 0.362706 -57 GAAGAAAGGAAACATAAGTTTTAAAGA 4 23 1 AAATAAGTTT 0.569432 -17 TACCACCTATAAAATAAGGATCGTTCA 6 198 1 AAATAAGGAT 0.889156 -17 TGTCCTTATTAAAATAATCATTCGTATTCAA 7 40 0 AAATAATCAT 0.77895 -25 AAAGTATTCCAAAATAAGCTTAATAACAATT 9 47 1 AAATAAGCTT 0.943772 -195 TTAAAAATAAAATATAAGGATCGTTA 11 65 1 AAATAAGGAT 0.889158 -16 CCTAAAAATTAAAATAAGCTTCTATCCTACC 13 96 0 AAATAAGCTT 0.943772 -29 CATTTGTTACAAGATAAGCTTTTTTATCAAA 18 202 1 AAATAAGCTT 0.942524 -46 TTTTTTATCAAAAATAATGATGACATAGGGG 18 221 1 AAATAATGAT 0.681624 -27 ATTATAGCGTAAAATAAGCTTTTTTGTATCA 19 85 0 AAATAAGCTT 0.943772 -56 CACGCTCACAAACAAAATCATGGAGCAAAAT 24 64 0 AAAAAATCAT 0.3627 -160 CTTTTTTAAAAAGATAATCTTGCAGAGGTCT 26 68 1 AAATAATCTT 0.762065 -41 TTGAGATAATAAAATAAGGGTTAGAT 38 21 1 AAATAAGGGT 0.680577 -16 AAGAACACCTAATACAAGGATTAGCATGTGT 42 164 0 AAACAAGGAT 0.521166 -85 ** ******** Masking position 6 Map Score: 12.9334 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 174 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 13 GTCTTTTGGGGTTAGGGGGTTTTTAGTTGGG 2 72 1 GTTGGGGGTT 0.933989 -229 GGGGGTTTTTAGTTGGGGGTTGTAGGGGAGG 2 86 1 AGTGGGGGTT 0.972789 -215 TTTATTGTATAATGGGCGGTTAGTTAGGTAT 3 145 1 AATGGCGGTT 0.835965 -42 GCGGGTTAATAATGGCGGGTTAAATGGGGTT 9 101 1 AATGCGGGTT 0.775299 -141 GCCTTAATCTGGTAGGTGGTTTGTCTTTTTA 19 25 1 GGTGGTGGTT 0.968656 -116 GTGTTCTATAGGTTGGTGGCTTTAAATAAGG 28 274 1 GGTGGTGGCT 0.891403 -27 CCAAGCTGAGGGTCGCGGGTTCGAGTCCCGT 30 38 1 GGTGCGGGTT 0.970021 -263 GTAAGGAAGAGGTCGGCGGTTCAATTCCGCT 30 143 1 GGTGGCGGTT 0.979494 -158 *** ******* Masking position 3 Map Score: 3.20498 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 14 GATCCTTATTTTATAGGTGGTAACTATCCCT 6 189 0 TTATAGGGGT 0.953479 -26 TAATGGCGGGTTAAATGGGGTTATTTTGAAT 9 110 1 TTAAATGGGT 0.785943 -132 ATCAGTCTTTTTAAAGGCTATTTTAAGTATA 12 45 1 TTAAAGGTAT 0.698325 -55 AGCATGGCGATTTTAGGGGATTTT 13 4 0 TTTTAGGGAT 0.825493 -121 TTCATAACAATTAAAGGTGGTTA 14 3 0 TTAAAGGGGT 0.970484 -288 TACTTACAACTTAAAGGGGAT 15 50 1 TTAAAGGGAT 0.953979 -11 AATACGAATATTTTAGGAGATTTTTGTA 21 56 1 TTTTAGGGAT 0.825493 -18 GCGTGGTGCGTTAAAGGCGGTGGT 33 103 1 TTAAAGGGGT 0.970484 -14 ******* *** Masking position 5 Map Score: 3.12276 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 84 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 15 CAAACAAATTTTTTAAAAAACCTTATTTTT 2 199 1 TTTTAAAAAA 0.639211 -102 AAGAATCCTTTGATAAAATTAAAGCACC 2 283 0 TTTGATAAAA 0.771778 -18 TATATTTTTGTTTTAAGAAACTTAATGATC 3 27 0 TTTTAAGAAA 0.449937 -160 ATTTTAAGGTTTGAAGAAAGGAAACATAA 4 10 1 TTTGAAGAAA 0.826494 -30 TTCTACTACATTTGAAATAATTTTTCTTAT 6 74 1 TTTGAAATAA 0.506228 -141 AAGGGTAATATTTTAAAAAATTTTTGTATA 8 22 1 TTTTAAAAAA 0.639211 -45 TTTTAGCTTGTTTGTTAAAAAACCAATAAG 9 20 0 TTTGTTAAAA 0.447689 -222 ATGGGGTTATTTTGAATAAAAAATTCTTTT 9 124 1 TTTGAATAAA 0.554667 -118 GAAAATTTTCTTTAAAAAAACCGCTAATTG 10 19 1 TTTAAAAAAA 0.604331 -102 TGCTTGAAATTTAGAAAAAAGAAAATTGTA 13 31 1 TTAGAAAAAA 0.655667 -94 ATTAGGATTTTTTGAAGAAAATCAAAACAA 14 171 1 TTTGAAGAAA 0.826494 -120 GAAATCTCTTTTTGTTAAAAGGAAATTTA 16 10 0 TTTGTTAAAA 0.447689 -254 AAAATTTGACTTTGTTAAAAAAATTATGAT 16 165 0 TTTGTTAAAA 0.447689 -99 CATCATTATTTTTGATAAAAAAGCTTATCT 18 213 0 TTTGATAAAA 0.771778 -35 GTTGTATAATTTTGAAAAAATACGCAACAA 22 40 1 TTTGAAAAAA 0.91759 -91 ACTCAAAATTTTTGATCAAAGGCTTGAAAT 24 204 1 TTTGATCAAA 0.343044 -20 ATGGCTTTAATTTAAAAAAATGTGAAGGAT 25 20 1 TTTAAAAAAA 0.604331 -26 AAGATTATCTTTTTAAAAAAGAAATTTTAA 26 59 0 TTTTAAAAAA 0.639211 -50 CTAAAATCCATTTCAAAAAATTAAGGAGAA 30 275 1 TTTCAAAAAA 0.538958 -26 TGCCTAAAATTTAGAAAAAATCACGCTTGA 33 23 1 TTAGAAAAAA 0.655667 -94 ATTTTTCTCCTTTGAAAAAATTAGGCACTA 35 58 0 TTTGAAAAAA 0.91759 -21 ********** Masking position 2 Map Score: 20.087 Number of sites scoring better than the average of aligned sites = 505 Number in coding regions = 433 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038