AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -irpoH_mpneu_opreg_100.orf -g0.400 -x5 Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.4 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 grpE 22 heat shock protein GrpE; similar to GenBank Accession Number I64046, from H. influenzae #2 1673683 300 DnaJ homolog protein, from M. capricolum #3 dnaJ 45 heat shock protein DnaJ; similar to Swiss-Prot Accession Number P17631, from B. subtilis #4 pmd1 300 transport ATP-binding protein; similar to Swiss-Prot Accession Number P36619, from S. pombe #5 ftsH 180 cell division protein FtsH; similar to Swiss-Prot Accession Number P37476, from B. subtilis #6 groES 187 heat shock protein GroES; similar to Swiss-Prot Accession Number P28599, from B. subtilis #7 clpB 175 ATP-dependent protease binding subunit ClpB; similar to GenBank Accession Number F64098, from H. influenzae #8 lip3 117 triacylglycerol lipase (lip) 3; similar to GenBank Accession Number JC4111, from M. mycoides #9 1674088 300 putative lipoprotein, MG307 homolog, from M. genitalium #10 dnaK 55 heat shock protein DnaK; similar to GenBank Accession Number A49230, from E. rhusiopathiae #11 cbiO 157 abc transport ATP-binding protein; similar to Swiss-Prot Accession Number Q05596, from S. typhimurium #12 gap 30 glycerladehyde-3-phosphate dehydrogenase; similar to GenBank Accession Number S34254, from C. pasteurianum #13 lig 167 DNA ligase; similar to Swiss-Prot Accession Number P15042, from E. coli #14 grs1 21 glycyl-tRNA synthetase; similar to Swiss-Prot Accession Number P38088, from S. cerevisiae #15 sigA 52 RNA polymerase sigma-A factor; similar to Swiss-Prot Accession Number P06224, from B. subtilis #16 lon 70 ATP-dependent protease Lon; similar to Swiss-Prot Accession Number P37945, from B. subtilis #17 tig 24 trigger factor; similar to GenBank Accession Number C64088, from H. influenzae #18 rpl21 146 ribosomal protein L21; similar to Swiss-Prot Accession Number P26908, from B. subtilis Motif number 1 AGTTTTATAATTAACACTCGAATGATTAAAGT 3 19 1 TTACACTCAA 0.925076 -27 TTATCACTTTAATCATTCGAGT 3 34 0 TTTCACTTAA 0.885271 -12 GAGCACCTGATTTGCACTCAGGAGGTTGAGGG 4 83 0 TTGCACTCGG 0.910952 -218 ATTATTTTTATTTGCACTTTAAGCATTTAACT 6 132 1 TTGCACTTAA 0.989889 -56 TTATTAACAATTAGCAGTTAAATGCTTAAAGT 6 147 0 TTGCAGTTAA 0.912388 -41 AGCCCACTCGTTAGCACTCAAGCCATTCGAGT 7 106 1 TTGCACTCAG 0.981923 -70 TTATATAAAATTAGCACTCGAATGGCTTGAGT 7 121 0 TTGCACTCAA 0.99363 -55 TTGCTTTATTTTGGCACTTTAAAAGCTAGTTT 9 246 0 TTGCACTTAA 0.989889 -55 TAACGCGGTTTTTGCTCTCTAAAGGTTAAATT 9 279 0 TTGCTCTCAA 0.947764 -22 AAACAAATCGTTAGCACTTTTAGCGTTTGAGT 10 12 0 TTGCACTTTA 0.925612 -44 TTTATAATATTTAGCACATAAACAT 10 41 1 TTGCACATAA 0.918979 -15 AACACATTTTTTAGCACTCTAATACTTTGAGT 16 12 0 TTGCACTCAA 0.99363 -59 ** ****** ** Masking position 2 Map Score: 20.35 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 38 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 2 TGATTTTGTCCTTATGAATTAAAACAGCACTTACAGCAAT 2 141 1 CTAAAAAGAC 0.791087 -160 AGATTCATCACTGCCAATTAGGTAAAGTGCGGTTGTGTTT 2 205 1 CTATTAAGGC 0.841459 -96 TTATAATTAACACTCGAATGATTAAAGTGATAA 3 23 1 CAAATAAGGA 0.910822 -23 AATGGGGATGTAGCTCAACTGATAGAGCACCTGATTTGCA 4 99 0 TAAATAAGAC 0.6443 -202 TAAACCATCGCATAAAATTCTAAATAGCGCGAC 5 4 0 CAATAAAGGC 0.934226 -177 AATAATTTAGCAACACTACCGAAATAGTGCTGCTAAATTA 6 98 0 CATAAAAGGC 0.876911 -90 TAACAATTAGCAGTTAAATGCTTAAAGTGCAAATAAAAAT 6 135 0 CAAATAAGGC 0.991511 -53 TCAAAACCGTCTTTATAAATGAAAGAGAGCAGCACTTGGG 7 20 1 CTAAAAAGGC 0.965932 -156 TTTTTTGGTGGTTATAAAGTAAAAGAGAGCCAACCCCCAA 7 55 0 GTAAAAAGGC 0.734595 -121 ATAAAATTAGCACTCGAATGGCTTGAGTGCTAACGAGTGG 7 109 0 CAAATTAGGC 0.961906 -67 ATTGATAAGTAAGAAAAACTGCTTTAGTGCCCACTGGTGC 9 190 0 AAAATTAGGC 0.807777 -111 TTTTTAGGTAAAAACTAGCTTTTAAAGTGCCAAAATAAAG 9 235 1 AAAGTAAGGC 0.711398 -66 AATAAAGCAAAAATTTAACCTTTAGAGAGCAAAAACCGCG 9 268 1 AAAATAAGGC 0.95107 -33 CACTCAAACGCTAAAAGTGCTAACGATTTG 10 1 1 CAAAAAAGGC 0.989489 -55 ACTGTTGCAGTAGATCAATAAAAAGAGGGCAGTTAAACTG 11 13 1 TAAAAAAGGC 0.916202 -145 ACCTGGTTGGCATTGTAAGCTAATCAGGGCTTTTTATTAA 13 135 1 CAAAATAGGC 0.953167 -33 CACTCAAAGTATTAGAGTGCTAAAAAATGT 16 1 1 CAAATAAGGC 0.991511 -70 TAATACATATAAATACATATAGTAAGTCTAGCCTT 18 6 1 CAAATAAGAA 0.577001 -141 ** ** ** ** ** Masking position 16 Map Score: 21.1786 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 96 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 CTTTAGTGCCTAAAATCAAGGCAGCGGTTC 2 51 0 TAAAATCAAG 0.780902 -250 TGCAATGGCTTATAAATTAATAAAATTATA 2 251 1 TATAAATTAA 0.688163 -50 TAAGACCGCTTAAAAACTAGCTTTGGCTAA 4 260 0 TAAAAACTAG 0.907843 -41 TAAGCGGTCTTATAATTAAAGCAAGTAGTT 4 278 1 TATAATTAAA 0.443804 -23 GTTGTTAGAATAAAAACCAGTCAAATCACC 5 145 1 TAAAAACCAG 0.890912 -36 AAAGTGCAAATAAAAATAATTTAGCAACAC 6 122 0 TAAAAATAAT 0.672284 -66 AGTTTTTACCTAAAAATAAGTATTGATAAG 9 221 0 TAAAAATAAG 0.899689 -80 TATTTTTAGGTAAAAACTAGCTTTTAAAGT 9 233 1 TAAAAACTAG 0.907843 -68 TGCTAAATATTATAAACAAATCGTTAGCAC 10 27 0 TATAAACAAA 0.900108 -29 TAAAGACGTCTATAAACCATTATTACAGGT 11 75 0 TATAAACCAT 0.586503 -83 TTTTAAATTTTAAAAATAAGACTAATTGAA 11 125 0 TAAAAATAAG 0.899689 -33 TTTTAAAATTTAAAAATAAAAACTTAAA 11 140 1 TAAAAATAAA 0.848566 -18 AGTAGTAAAATATAAACTAATTAGAGGATT 12 11 1 TATAAACTAA 0.823741 -20 TGGTATTTTGTATAAACAAAATTTAGGAAC 18 106 0 TATAAACAAA 0.900108 -41 ********** Masking position 5 Map Score: 9.85856 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 143 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 4 ACGCTTAATGTAACTTGGTCATGAACCGCT 2 29 1 TAACTTGGTC 0.899876 -272 GCAAGGGTGATAGCTTTGGCGGAATTGCTG 2 174 0 TAGCTTTGGC 0.983775 -127 CATATAAGATTAAGTTAGGCGTTT 4 5 0 TAAGTTAGGC 0.90366 -296 GCTTAAAAACTAGCTTTGGCTAAATTAATA 4 253 0 TAGCTTTGGC 0.983775 -48 ATTACCTTTCTAACTTTGGCTGGTTTTGCA 5 88 1 TAACTTTGGC 0.989024 -93 TTTGAAATTGTAAGTTTGTCATGCCATCGT 9 118 1 TAAGTTTGTC 0.912064 -183 ACCCGCATCTTAACCTTGGCAAGGTTATGT 13 63 0 TAACCTTGGC 0.965187 -105 ********** Masking position 2 Map Score: 6.57183 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 30 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 5 GTTAATTATAAAACTGCTTTGAT 3 4 0 AAACTGCTTT 0.975022 -42 TCATTTATAAAGACGGTTTTGAGTTACTTA 7 12 0 AGACGGTTTT 0.932163 -164 TGCTTTAACTAACCTGCTTTTATCTAACTA 9 57 0 AACCTGCTTT 0.912266 -244 TTACAATTTCAAACGTTTTTTTTTTTTTTT 9 101 0 AAACGTTTTT 0.84731 -200 TAAGTAAGAAAAACTGCTTTAGTGCCCACT 9 195 0 AAACTGCTTT 0.975022 -106 GAGGGCAGTTAAACTGCTCTTTTTTTATGT 11 37 1 AAACTGCTCT 0.912231 -121 AATGGTTTATAGACGTCTTTAAGCACTTTT 11 84 1 AGACGTCTTT 0.889398 -74 ATACCAAAAGAAACGGTTTTATTGAAA 18 130 1 AAACGGTTTT 0.960362 -17 ********** Masking position 1 Map Score: 6.01121 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 110 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 CCAAGTTACATTAAGCGTTGATGCTAAAAC 2 17 0 TTAAGCGTTG 0.891382 -284 TAAGATTAAGTTAGGCGTTT 4 1 0 TTAGGCGTTT 0.950865 -300 ATATGACTAGTTAGACGTTTGGATCTTTAA 4 30 1 TTAGACGTTT 0.603929 -271 AAGCTAGTTTTTAAGCGGTCTTATAATTAA 4 267 1 TTAAGCGGTC 0.853868 -34 TACTAGTAGATTAAGCGTTTATTGCCAATA 6 52 0 TTAAGCGTTT 0.96865 -136 TATTTGCACTTTAAGCATTTAACTGCTAAT 6 140 1 TTAAGCATTT 0.942012 -48 TTTGCTTTATTTTGGCACTTTAAAAGCTAG 9 249 0 TTTGGCACTT 0.810294 -52 CGTTAGCACTTTTAGCGTTTGAGTG 10 6 0 TTTAGCGTTT 0.947964 -50 ATAGACGTCTTTAAGCACTTTTTAAACCAT 11 92 1 TTAAGCACTT 0.920424 -66 TAACACATTTTTTAGCACTCTAATACTTTG 16 15 0 TTTAGCACTC 0.829224 -56 TGTGTTACAATTTAGCATTCTTCAACCTCT 16 38 1 TTTAGCATTC 0.872117 -33 ********** Masking position 2 Map Score: 9.04245 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 109 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 GCAGTGATGAATCTGGCAAGGGTGATAGCTTTGGC 2 184 0 ACGGAAGGGA 0.929014 -117 CATTTACTTCCACCAATAATGGGGATGTAGCTCAA 4 121 0 CCAAAAGGGA 0.992284 -180 TAGAGCACACCCCTGATAAGGGTGAGGTCGATGGT 4 163 0 CCGAAAGGGA 0.992129 -138 ACTTTATAACCACCAAAAAAGGTAAATCTTTAGCC 7 75 1 CCAAAAGGAA 0.972286 -101 TTGGCCTATTAACAAAGAAAGGGGATAAAATAG 7 153 1 ACAAAAGGGA 0.980495 -23 CCCAAATTTACCCTAAAAAAGGACACCAATTGTGT 8 61 1 CCAAAAGGCA 0.9672 -57 TTTAATATGGAGCAGATAACGGGAATCGAACCCGC 13 87 0 ACGAAAGGAA 0.930756 -81 CCGCAGAAGACGCAAATAAGCGTGAAATTATAACA 18 72 0 CCAAAACGGA 0.955127 -75 * * ** ** ** ** Masking position 8 Map Score: 5.86614 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 21 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 8 AGGCACTAAAGCTTTAATTTGGTAATCGTT 2 70 1 GCTTTAATTT 0.905107 -231 TGTAAGTGCTGTTTTAATTCATAAGGACAA 2 146 0 GTTTTAATTC 0.72907 -155 AAGTAGAGTTGGTATAATTTTATTAATTTA 2 263 0 GGTATAATTT 0.736326 -38 AATCATTCGAGTGTTAATTATAAAACTGCT 3 16 0 GTGTTAATTA 0.858048 -30 AACTAGCTTTGGCTAAATTAATATAATTAT 4 246 0 GGCTAAATTA 0.465627 -55 AAAACTACTTGCTTTAATTATAAGACCGCT 4 280 0 GCTTTAATTA 0.804472 -21 TTAGTTTTAATTACTAACCACAT 6 4 1 GTTTTAATTA 0.880377 -184 AGCCATTCGAGTGCTAATTTTATATAATTG 7 126 1 GTGCTAATTT 0.639913 -50 TCCTTTTTTAGGGTAAATTTGGGTTTGGAA 8 54 0 GGGTAAATTT 0.76671 -64 TGTGCAAGGTGTTTTACTTTTCTTAAAAGG 8 93 1 GTTTTACTTT 0.683914 -25 TTAATCTCTTGGCTTAATTTTGTACATTTT 9 153 0 GGCTTAATTT 0.90332 -148 TTAAATTTTTGCTTTATTTTGGCACTTTAA 9 256 0 GCTTTATTTT 0.590019 -45 GCTCTCTAAAGGTTAAATTTTTGCTTTATT 9 268 0 GGTTAAATTT 0.800058 -33 TTTTCAATTAGTCTTATTTTTAAAATTTAA 11 123 1 GTCTTATTTT 0.565132 -35 TTTAAGTTTTTATTTTTAAATTTTA 11 143 0 GTTTTTATTT 0.563546 -15 AGTGTTAATTAATCTTAAAAA 14 11 0 GTGTTAATTA 0.858048 -11 ACTTTAGCAGGGGTTAATTTGTTATAATTT 18 53 1 GGGTTAATTT 0.938277 -94 GGGTTAATTTGTTATAATTTCACGCTTATT 18 63 1 GTTATAATTT 0.720222 -84 ********** Masking position 8 Map Score: 10.8817 Number of sites scoring better than the average of aligned sites = 290 Number in coding regions = 229 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 9 TACACTCCACCAAATTGGTGTGGGGGATTC 2 110 0 CAAATTGGTG 0.924614 -191 AACTAATACACCCACTGCTGCAAAACCAGC 5 106 0 CCCACTGCTG 0.973744 -75 GAGCCAACCCCCAAGTGCTGCTCTCTTTCA 7 39 0 CCAAGTGCTG 0.960487 -137 CACCTTGCACACAATTGGTGTCCTTTTTTA 8 74 0 ACAATTGGTG 0.924617 -44 ACCAATTGGTGATAAGCGGAT 9 2 1 CCAATTGGTG 0.987544 -299 TGCTTTAGTGCCCACTGGTGCAACTAGCTT 9 181 0 CCCACTGGTG 0.986099 -120 ********** Masking position 6 Map Score: 4.06046 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 33 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 10 TGATTTTAGGCACTAAAGCTTTAATTTGGT 2 63 1 CACTAAAGCT 0.909115 -238 AAAATCAATACACTCCACCAAATTGGTGTG 2 118 0 CACTCCACCA 0.942933 -183 GCCATTGCAACACGCAAACACAACCGCACT 2 230 0 CACGCAAACA 0.912413 -71 GGGTCTCAAACCCTCAACCTCCTGAGTGCA 4 73 1 CCCTCAACCT 0.908998 -228 GAAACCAACACACTAAACCATCGCATAAAA 5 27 0 CACTAAACCA 0.914268 -154 GCCAATAAGGCACTCAACCTTGTATATGTG 6 29 0 CACTCAACCT 0.981496 -159 CACTCGTTAGCACTCAAGCCATTCGAGTGC 7 110 1 CACTCAAGCC 0.936571 -66 CACCAGTGGGCACTAAAGCAGTTTTTCTTA 9 191 1 CACTAAAGCA 0.89034 -110 CACTCAAACGCTAAAAGTGC 10 1 1 CACTCAAACG 0.924398 -55 CGTATACACGCACGCCAAGTGGAATTGTAC 15 16 0 CACGCCAAGT 0.539981 -37 CACTCAAAGTATTAGAGTGC 16 1 1 CACTCAAAGT 0.888503 -70 ********** Masking position 7 Map Score: 7.80209 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 82 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 11 TGTGGGGGATTCGAAGCAATTTAACGATTAC 2 91 0 TGAAGCAATT 0.855798 -210 AAAACAGCACTTACAGCAATTCCGCCAAAGC 2 161 1 TACAGCAATT 0.855798 -140 ATCAAAGCAGTTTTATAATTAA 3 2 1 TAAAGCAGTT 0.952967 -44 ATTAATTTAGCCAAAGCTAGTTTTTAAGCGG 4 254 1 CAAAGCTAGT 0.786558 -47 GGTCTTATAATTAAAGCAAGTAGTTTTT 4 283 1 TAAAGCAAGT 0.968584 -18 AATAGTTAGATAAAAGCAGGTTAGTTAAAGC 9 55 1 TAAAGCAGGT 0.95643 -246 AGCAGGTTAGTTAAAGCAATCAATTTCTTTC 9 69 1 TAAAGCAATC 0.855798 -232 TTTTTTTTTTTGAAAGAAATTGATTGCTTTA 9 80 0 TAAAGAAATT 0.713158 -221 CCAGTGGGCACTAAAGCAGTTTTTCTTACTT 9 193 1 CAAAGCAGTT 0.897037 -108 TTTGGCACTTTAAAAGCTAGTTTTTACCTAA 9 238 0 TAAAGCTAGT 0.895511 -63 * ********* Masking position 5 Map Score: 6.06021 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 97 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 12 GATTCATCACTGCCAATTAGGTAAAGTGCGG 2 206 1 TGCCAATAGG 0.990196 -95 ACCTCCTGAGTGCAAATCAGGTGCTCTATCA 4 89 1 TGCAAATAGG 0.950868 -212 AAGCGTTTATTGCCAATAAGGCACTCAACCT 6 39 0 TGCCAATAGG 0.990196 -149 ATGGCTTGAGTGCTAACGAGTGGGCTAAAGA 7 101 0 TGCTAACAGT 0.842409 -75 AAGTTTGTCATGCCATCGTGGTTTAAAATGT 9 129 1 TGCCATCTGG 0.840171 -172 TAGCTTACAATGCCAACCAGGTGCTTTTAGG 13 126 0 TGCCAACAGG 0.991867 -42 TGGCATTGTAAGCTAATCAGGGCTTTTTATT 13 142 1 AGCTAATAGG 0.876314 -26 ******* *** Masking position 5 Map Score: 5.13268 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 36 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 13 AATAATGGGGATGTAGCTCAACTGATAGAG 4 112 0 ATGTAGCTCA 0.967608 -189 TTGCCTGGAAGTATAGCTCAGTTGGTTAGA 4 194 0 GTATAGCTCA 0.958231 -107 TGTTTATAATATTTAGCACATAAACAT 10 39 1 ATTTAGCACA 0.859669 -17 AGCTGCGCAGATATAGTTCAATGGCAGAAC 13 35 1 ATATAGTTCA 0.907051 -133 AATATAGCTCAGATCTAGTTT 17 2 1 ATATAGCTCA 0.980742 -23 ********** Masking position 5 Map Score: 0.705797 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 9 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 14 AATGTAACTTGGTCATGAACCGCTGCCTTGA 2 35 1 GGTCTGAACC 0.964701 -266 TTGGTGTGGGGGATTCGAAGCAATTTAACGA 2 95 0 GGATCGAAGC 0.901376 -206 GGAGATGAAGGGTCTCAAACCCTCAACCTCC 4 64 1 GGTCCAAACC 0.92263 -237 GGAAGTAAATGGACTTGAACCATCGACCTCA 4 145 1 GGACTGAACC 0.981341 -156 AATATAATTATGAAGCGAACCTGTACGAAGA 4 226 0 TGAACGAACC 0.915955 -75 GCAGATAACGGGAATCGAACCCGCATCTTAA 13 80 0 GGAACGAACC 0.985647 -88 **** ****** Masking position 8 Map Score: 0.465133 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 21 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 15 CATTAAGCGTTGATGCTAAAACTTACAA 2 9 0 TGATGCTAAA 0.954672 -292 GTGTTGGTTTCCCTGGTAAAAAAGCACAAA 5 46 1 CCCTGGTAAA 0.860034 -135 ATACACCCACTGCTGCAAAACCAGCCAAAG 5 101 0 TGCTGCAAAA 0.928109 -80 ACCGAAATAGTGCTGCTAAATTAGCGTGCC 6 91 0 TGCTGCTAAA 0.984214 -97 ATTTCGGTAGTGTTGCTAAATTATTTTTAT 6 113 1 TGTTGCTAAA 0.922624 -75 CCTGCTAAAGTCATGCTTAAGGCTAGACTT 18 34 0 TCATGCTTAA 0.769106 -113 ACAAATTAACCCCTGCTAAAGTCATGCTTA 18 45 0 CCCTGCTAAA 0.969662 -102 ********** Masking position 9 Map Score: 2.18671 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 49 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493