AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -iphoB_mpneu_opreg_300.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 ugpC 23 sn-glycerol-3-phosphate transport system permease protein; similar to Swiss-Prot Accession Number P10907, from E. coli #2 1673668 300 putative lipoprotein, MG186 homolog, from M. genitalium #3 potA 300 spermidine/putrescine transport ATP-binding prot; similar to Swiss-Prot Accession Number P23858, from E. coli #4 hsdS 300 restriction-modification enzyme subunit S1B; similar to GenBank Accession Number L25415_6, from M. pulmonis #5 1673895 85 MG413 homolog, from M. genitalium #6 1673897 114 MG414 homolog, from M. genitalium #7 1673898 241 MG412 homolog, from M. genitalium #8 1674099 184 P115 protein homolog; similar to GenBank Accession Number JQ0894, from M. hyorhinis #9 1674105 130 MG294 homolog, from M. genitalium #10 1674151 300 A19_orf229V Protein #11 rpsJ 93 ribosomal protein S10; similar to Swiss-Prot Accession Number P38518, from T. maritima #12 1674374 246 VXpSPT7_orf112 Protein #13 1674375 121 putative lipoprotein, MG149 homolog, from M. genitalium #14 1674376 153 MG148 homolog, from M. genitalium #15 hlyC 25 hemolysin (hlyC) homolog protein; similar to GenBank Accession Number G64060, from H. influenzae #16 infB 280 protein synthesis initiation factor 2; similar to Swiss-Prot Accession Number P04766, from B. stearothermophilus Motif number 1 TACATCAATTAAATGCTTGATCAAAACCAAGGTGTC 2 36 1 AAATGCAAAA 0.960212 -265 TTTTGACCCTAAAACTAATTCAAAAACGGTTAATTT 2 136 0 AAAATAAAAA 0.917413 -165 ATTTTGGTTCAAAATTTAGTCCAAAAACAGTCAAAT 3 120 1 AAAAGCAAAA 0.929846 -181 TTTTGCAGTTAAATTTGTGCTAAAAATTTGACTGTT 3 145 0 AAATGAAAAA 0.960993 -156 TTTAACTGCAAAAACTGTTCAAAAAATCTCACAAAA 3 168 1 AAATTAAAAA 0.952888 -133 AACTGGGATAAATTTTCTTGCAAAAAAATGATTGCA 3 205 0 AATTTAAAAA 0.785241 -96 ATCAGCAAACTATATATCAAAAACAATCCAGG 4 7 1 AAAATCAAAA 0.915836 -294 AAAATAACAAAAAGCAGTTGTCAAAACGGATAAATA 6 21 1 AAATTCAAAA 0.951953 -94 ACGGATAAATAAAAACTTTTAAAAAATTGGCGTCAA 6 46 1 AAATTAAAAA 0.952888 -69 GCCTCTCGTAAAAAGAAATTAGCAAAGGAAACAATT 7 116 1 AAAATGCAAA 0.628011 -126 TTGCTTAATTAAAAGTTGGTTAAAAAGTACCGAAA 7 217 1 AAAGGAAAAA 0.782315 -25 ATTTATTGCAAAAAGTGAGAGGAAAACCGTAT 9 7 0 AAAAGGAAAA 0.917444 -124 TTTTTGCAATAAATGTATGCCAAAAACGTTTTTCTA 9 29 1 AAATGAAAAA 0.960993 -102 GCTTGCCAAAAAATAAATTAGAAAAACGTTTTTGGC 9 47 0 AAATTAAAAA 0.952888 -84 TTAAGGGTGAAATTTGATGGTCAAAATGACTACGCT 11 58 0 AATTGCAAAA 0.813527 -36 CATTGAAATTAAACAACTTCAAAAAAGTAGTAACCC 12 133 0 AAATTAAAAA 0.952888 -114 GTTTAATTTCAATGATTATGGGAAAATAATAAGGCC 12 155 1 AATATGAAAA 0.622546 -92 TGCAAGCGGCAAACTAGTTTGGAAAAAGATAAGGAA 12 191 1 AAATTGAAAA 0.943221 -56 TTTAGGGTAGAAATTAGTTTCCAAAAACGGTTTTAA 13 30 1 AAATTCAAAA 0.951953 -92 AGCTGCTTTAAAACTGGAGCGGAAAAACTTTAAAGC 16 172 1 AAAAGGAAAA 0.917444 -109 GAAAAACTTTAAAGCACTGTTACAAAAACGCTTAAA 16 193 1 AAATGACAAA 0.820104 -88 *** ** ***** Masking position 14 Map Score: 25.8641 Number of sites scoring better than the average of aligned sites = 297 Number in coding regions = 209 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 2 GTAAAACTACTTAAATTGCTAAAAATTAACCGTTT 2 114 1 TTTCTAAAAA 0.909607 -187 ATTTCCCGCTTTCTTTTTTTAAAAAATCTCTACTT 2 180 1 TTTTTAAAAA 0.956577 -121 AAAAAGAGAAGTTGTAGGCTAAAAGAAGGGGAATT 3 17 0 GTACTAAAAG 0.688832 -284 AACTTCTCTTTTTTCTTGTTAAAAGATTCCCTTTC 3 39 1 TTTTTAAAAG 0.970374 -262 AAAAAGAGATTTTCTTGATAAAAAGAAAGGGAATC 3 63 0 TTTTAAAAAG 0.901437 -238 AAGACCACTTTTAAGACATAAAAAAAGAGATTTTC 3 84 0 TTATAAAAAA 0.750475 -217 CTGGGATAAATTTTCTTGCAAAAAAATGATTGCAA 3 204 0 TTTCAAAAAA 0.73758 -97 ATAAATACCGTTTTTTCTTTAAAAATTAAGTAGTT 3 273 1 TTTTTAAAAA 0.905656 -28 TTTCTAAAAATTGGCAAGTTAAAAACTTTAGTTCA 5 38 1 TTATTAAAAA 0.914371 -48 ACTGCTTTTTGTTATTTTTTAAAAGTTT 6 4 0 GTTTTAAAAG 0.91273 -111 CGGCCATTGGTTGAATGATTAAAAGAAAAGCAGCC 7 84 1 TTTTTAAAAG 0.970392 -158 TAGTTGTGCTTTAAGTAGTTAAAAACAACGATTTT 7 171 0 TTTTTAAAAA 0.9575 -71 GAAATGCAACTTGCTTAATTAAAAGTTGGTTAAAA 7 207 1 TTTTTAAAAG 0.970378 -35 AAAAGACCCATTTAATTGTTAAAAGAAACTTACTA 12 68 0 TTTTTAAAAG 0.970392 -179 CGATCTTATTGTGTCACTTTAAAAGACCCATTTAA 12 88 0 GTATTAAAAG 0.832167 -159 TGGAAACTAATTTCTACCCTAAAAAGACTACTTAA 13 18 0 TTACTAAAAA 0.823858 -104 TTTGCTTATTTTGAATTTTTAAAAATAAGCCTCTA 13 68 0 TTTTTAAAAA 0.957511 -54 AGCAATTTCCTTTATATATAAAAAAGGTAATACAA 14 41 1 TTATAAAAAA 0.745071 -113 GATCACATTATTGCTTGTTTAAAGGAAAGGGAAAG 16 254 1 TTTTTAAAGG 0.776556 -27 ** * ******* Masking position 2 Map Score: 24.6858 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 90 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 3 TTTTTGGACTAAATTTTGAACCAAAATAAAGACCA 3 112 0 AATTGAAAAA 0.914365 -189 TTAACTACTTAATTTTTAAAGAAAAAACGGTATTT 3 275 0 AATTAAAAAA 0.958681 -26 ATGTTTGTGGAATTCTTAAGGTAAAAAGTGATGAA 4 195 1 AATTAAGAAA 0.870715 -106 TTAAGGTAAAAAGTGATGAAATTAATCCTAAGTTT 4 210 1 AAATGAATAA 0.667073 -91 AAACTTTTAAAAAATAACAAAAAGCA 6 2 1 AATTAAAATA 0.695459 -113 CAGTTGTCAAAACGGATAAATAAAAACTTTTAAAA 6 35 1 AAATAAAAAA 0.813223 -80 CCATTGGTTGAATGATTAAAAGAAAAGCAGCCTCT 7 87 1 AATTAAAAAA 0.958681 -155 GTTCAGTTAAAAAAATTAAGCTTAATTAAGT 8 7 0 AATTAAGTAA 0.870715 -178 AGACCCATTTAATTGTTAAAAGAAACTTACTAACA 12 65 0 AATTAAAAAA 0.958681 -182 ATTTTCCCATAATCATTGAAATTAAACAACTTCAA 12 147 0 AATTGAATAA 0.914365 -100 GCTTATTTTGAATTTTTAAAAATAAGCCTCTAATT 13 65 0 AATTAAATAA 0.958681 -57 CACCTGGCAAACAATTTAAAGTTAATGCCAT 14 133 1 ACTTAAATAA 0.77193 -21 ATAAAATTTAAACCTAATTTAACTT 15 3 1 AATTAAATAA 0.958681 -23 CTGTTACAAAAACGCTTAAAGGTAAGCTGTTCTGA 16 209 1 AATTAAATAA 0.958682 -72 ** ***** *** Masking position 9 Map Score: 12.6851 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 61 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 4 TTTTTGATATATAGTTTGCTGAT 4 4 0 ATAGTTTGCT 0.903282 -297 TTCCACAAACATTGGTTGCGTTAAATTGAC 4 177 0 ATTGGTTGCG 0.81363 -124 TCTGGCGTTTATTCTTTGCCAATTGTTTCC 7 142 0 ATTCTTTGCC 0.763728 -100 ATTACAAGTACTAGTTTGCCAAAGACAAGT 8 71 1 CTAGTTTGCC 0.970597 -114 CTAGATTATTCTAGTTGGCTTTAAGGAAAG 8 132 0 CTAGTTGGCT 0.904533 -53 CTGCACTTTGATAGTTGGCCTGTGTACTCT 10 216 0 ATAGTTGGCC 0.946075 -85 AGCATTGGGACTTGTTTGCGCTAGTTAAGC 12 14 0 CTTGTTTGCG 0.974517 -233 TAGCTTGGAGCTTTTTTGCTGTTAGTAAGT 12 46 1 CTTTTTTGCT 0.674999 -201 AGTAACCCCGCTTTTTGGCGATCTTATTGT 12 111 0 CTTTTTGGCG 0.795983 -136 TTTTTCCAAACTAGTTTGCCGCTTGCAGGC 12 188 0 CTAGTTTGCC 0.970597 -59 TTAACTTTAAATTGTTTGCCAGGTGAAACA 14 128 0 ATTGTTTGCC 0.965132 -26 CACACTATGCAAAGTTGGCGCCAATGTTTA 16 29 1 AAAGTTGGCG 0.670197 -252 CCGACCTGGTAGTGTTTGCGCTAAATCCAC 16 125 0 AGTGTTTGCG 0.826137 -156 ********** Masking position 6 Map Score: 9.97779 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 81 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 TTAGTGCACAATTGCTAAGAGCGCCTGTAT 2 77 1 ATTGCTAAGA 0.723014 -224 AACTACTTAAATTGCTAAAAATTAACCGTT 2 118 1 ATTGCTAAAA 0.956384 -183 CAGTTAAATTTGTGCTAAAAATTTGACTGT 3 146 0 TGTGCTAAAA 0.593592 -155 CACAAATTTAACTGCAAAAACTGTTCAAAA 3 162 1 ACTGCAAAAA 0.944025 -139 GATAAATTTTCTTGCAAAAAAATGATTGCA 3 205 0 CTTGCAAAAA 0.806714 -96 GGGGTCAAAAATTGCTACAATAAATACCGT 3 254 1 ATTGCTACAA 0.91845 -47 CATCTATTAAATTGCTCAAAAAGGGAATTG 6 79 0 ATTGCTCAAA 0.723005 -36 ACTAGTGCTAAAACTAACCAGAT 7 4 1 AGTGCTAAAA 0.893795 -238 GTAATGCACTATTGCAAAATCTAACCTGAT 8 161 1 ATTGCAAAAT 0.555287 -24 GCATACATTTATTGCAAAAAGTGAGAGGAA 9 19 0 ATTGCAAAAA 0.939562 -112 ATTAGATTACCCTGCAACAATTCATTATTC 10 49 1 CCTGCAACAA 0.699293 -252 TTATTTGCTACAATCTTAAGGCT 11 4 1 TTTGCTACAA 0.661549 -90 AAACTTACTAACAGCAAAAAAGCTCCAAGC 12 48 0 ACAGCAAAAA 0.575301 -199 GACCCATTTAATTGTTAAAAGAAACTTACT 12 69 0 ATTGTTAAAA 0.671451 -178 AAATTAAACAACTTCAAAAAAGTAGTAACC 12 134 0 ACTTCAAAAA 0.455454 -113 TTCAATTGTGACTGCTAAAAGC 12 235 1 ACTGCTAAAA 0.959656 -12 ACTTTAAAGCACTGTTACAAAAACGCTTAA 16 198 1 ACTGTTACAA 0.532437 -83 ********** Masking position 3 Map Score: 13.143 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 174 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 6 ATTGCTGGTTTAAACTGCTTTCA 1 7 0 TGGTTAAATG 0.758525 -17 TTAGCAATTGTGCACTAAATTTTGACACCTTG 2 63 0 TGCCTAAATT 0.975094 -238 AGCGGGAAATTGGCCTAATTTTGACCCTAAAA 2 158 0 TGGCTAATTT 0.803574 -143 TGACTGTTTTTGGACTAAATTTTGAACCAAAA 3 121 0 TGGCTAAATT 0.952448 -180 CCCCTAAAACTGGGATAAATTTTCTTGCAAAA 3 216 0 TGGATAAATT 0.691045 -85 AAACATTGGTTGCGTTAAATTGACCGTTACGA 4 169 0 TGCTTAAATG 0.85998 -132 AGAAAATTAGTGCTTTAAAGCTTTTTAAATTA 5 11 0 TGCTTAAACT 0.919671 -75 TTCAATAAATTGAACTAAAGTTTTTAACTTGC 5 51 0 TGACTAAATT 0.793311 -35 CTAGTTGAGGGGCGCTAAACCTTTCCTTAAAG 8 112 1 GGCCTAAACT 0.819294 -73 CCGTAGTTGATGCTCTAATTTTACAAGACGCA 16 93 0 TGCCTAATTT 0.888845 -188 TGGTAGTGTTTGCGCTAAATCCACCCGTAGTT 16 117 0 TGCCTAAACC 0.844087 -164 TAAGTGTAGCTGCTTTAAAACTGGAGCGGAAA 16 165 1 TGCTTAAACT 0.928426 -116 TTTGTAACAGTGCTTTAAAGTTTTTCCGCTCC 16 187 0 TGCTTAAATT 0.946452 -94 *** ***** ** Masking position 7 Map Score: 9.36602 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 45 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 TTTAGGGGGTAAAAAGTAGAGATTTTTTAAA 2 197 0 AAAAAGAGAG 0.717679 -104 GTAGGCTAAAAGAAGGGGAATTAACAAA 3 8 0 AGAAGGGAAT 0.676227 -293 TTTAACAAGAAAAAAGAGAAGTTGTAGGCTA 3 31 0 AAAAAGGAAG 0.954373 -270 CTTGATAAAAAGAAAGGGAATCTTTTAACAA 3 54 0 AGAAAGGAAT 0.939 -247 TAAGACATAAAAAAAGAGATTTTCTTGATAA 3 77 0 AAAAAGGATT 0.945237 -224 GCTGATGAATAAACAGGGAATTCTCCTGGAT 4 36 0 AAACAGGAAT 0.775551 -265 TTCTTAAGGTAAAAAGTGATGAAATTAATCC 4 207 1 AAAAAGGATG 0.934109 -94 AAAAAATAACAAAAAGCAGTTGTCAAAACGG 6 19 1 AAAAAGAGTT 0.677183 -96 TAAATTGCTCAAAAAGGGAATTGACGCCAAT 6 71 0 AAAAAGGAAT 0.962217 -44 TTAATAGATGAAAAAGTGAATTAATT 6 99 1 AAAAAGGAAT 0.962217 -16 AGCCTCTCGTAAAAAGAAATTAGCAAAGGAA 7 115 1 AAAAAGAATT 0.832256 -127 TTAGCACCTAAGAAAGTGGTTTCAAAGTT 10 9 0 AGAAAGGGTT 0.815198 -292 AACTTAACAAAGAAAGTAATGCCGTGATTAG 10 102 0 AGAAAGAATG 0.711243 -199 ACTAGTTTGGAAAAAGATAAGGAATTAGTCA 12 203 1 AAAAAGTAAG 0.763169 -44 TTTATATATAAAAAAGGTAATACAACGATAG 14 51 1 AAAAAGTAAT 0.796889 -103 ****** **** Masking position 3 Map Score: 13.5187 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 90 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 TGCCATACATCAATTAAATGCTTGATCAAAACC 2 31 1 CAATAAACTT 0.703576 -270 TGAAATCGGTAAGATAAAGGATTGTGATTTTAA 4 82 1 AAGTAAAATT 0.932576 -219 CTAAGTGCATAAGCTAAAAACTTAGGATTAATT 4 229 0 AAGTAAACTT 0.965482 -72 AAAAATTGGCAAGTTAAAAACTTTAGTTCAATT 5 43 1 AAGTAAACTT 0.965482 -43 ATGAGCGGTTCAGTTAAAAAAATTAAGCTTAAT 8 16 0 CAGTAAAAAT 0.733275 -169 TTTCTTTGTTAAGTTAGATCCTTGAACCAAGCT 10 118 1 AAGTAGACTT 0.913654 -183 AAAAAGCTCCAAGCTAAAAGCATTGGGACTTGT 12 29 0 AAGTAAACAT 0.915645 -218 AGTTTGGAAAAAGATAAGGAATTAGTCAGTTCA 12 206 1 AAGTAAGATT 0.72259 -41 AAACGGTTTTAAATTAGAGGCTTATTTTTAAAA 13 54 1 AAATAGACTT 0.595376 -68 AAGGTAAATAATTTAGCTTTTTG 14 1 1 AAGTAAAATT 0.932576 -153 TTGCAGAAAACAGCTAAACCATTGTTTCACCTG 14 106 1 CAGTAAAATT 0.885486 -48 AAACAATTTAAAGTTAATGCCAT 14 141 1 AAGTAATCAT 0.579862 -13 *** **** *** Masking position 6 Map Score: 6.2451 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 106 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 9 ATTCAAAAACGGTTAATTTTTAGCAATTTA 2 125 0 GGTTAATTTT 0.80563 -176 TGAACAATTTAGATAAATTTACATTAATTG 2 255 0 AGATAAATTT 0.666194 -46 CACCGTAGTTAGTTCAATTTAGGTAAAG 2 283 1 AGTTCAATTT 0.827911 -18 GTCCAAAAACAGTCAAATTTTTAGCACAAA 3 138 1 AGTCAAATTT 0.626511 -163 CAGTTTTTGCAGTTAAATTTGTGCTAAAAA 3 155 0 AGTTAAATTT 0.929712 -146 CCTAAAACTGGGATAAATTTTCTTGCAAAA 3 216 0 GGATAAATTT 0.715485 -85 ACATTGGTTGCGTTAAATTGACCGTTACGA 4 169 0 CGTTAAATTG 0.693782 -132 TAAAAACTTTAGTTCAATTTATTGAATGTA 5 57 1 AGTTCAATTT 0.827911 -29 GTCAACATCTGGTTAGTTTTAGCACTAGT 7 10 0 GGTTAGTTTT 0.740339 -232 CGCTCATGATAGTTAGATTGTAAGTAAGTA 8 42 1 AGTTAGATTG 0.88198 -143 TTAAATCAGGTTAGATTTTGCAATAGTG 8 167 0 GGTTAGATTT 0.919776 -18 GGGTTAATCCGGTTAGCTTGCCAAAAAATA 9 68 0 GGTTAGCTTG 0.578704 -63 AGTTCTTAAGGGTGAAATTTGATGGTCAAA 11 69 0 GGTGAAATTT 0.678836 -25 GGAATTAGTCAGTTCAATTGTGACTGCTAA 12 223 1 AGTTCAATTG 0.798035 -24 GTTCTAGGGGAGTTAATTTGCAGAAAACAG 14 89 1 AGTTAATTTG 0.729854 -65 AAGTTAAATTAGGTTTAAATT 15 15 0 AGTTAAATTA 0.747706 -11 AGTGTGAAATGGTTAGATTAACGA 16 5 0 GGTTAGATTA 0.719793 -276 ********** Masking position 8 Map Score: 10.2238 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 88 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 10 CCTAAATTTGTTAATTATGCTTGCCCTATT 4 272 1 TTAATTATGC 0.923844 -29 GTTGCATTTCTTAGTTGTGCTTTAAGTAGT 7 187 0 TTAGTTGTGC 0.88518 -55 TAACCAACTTTTAATTAAGCAAGTTGCATT 7 209 0 TTAATTAAGC 0.940461 -33 ACTTAATTAAGCTTAATTTTTT 8 3 1 TTAATTAAGC 0.940461 -182 CTAGAATAATCTAGTAATGCACTATTGCAA 8 148 1 CTAGTAATGC 0.880015 -37 AATGCCGTGATTAGTAAAGCTCTTTAAAGG 10 86 0 TTAGTAAAGC 0.934177 -215 CTTGTTTGCGCTAGTTAAGCCGT 12 4 0 CTAGTTAAGC 0.956433 -243 ********** Masking position 3 Map Score: 2.55222 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 25 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 11 TGGCCTAATTTTGACCCTAAAACTAATTCAA 2 149 0 TGACCCTAAA 0.967629 -152 CTCTACTTTTTACCCCCTAAATAACCTAACA 2 207 1 TCCCCCTAAA 0.974691 -94 GGACTAAATTTTGAACCAAAATAAAGACCAC 3 111 0 TGAACCAAAA 0.705897 -190 TGACCCCGCTTGCCCCCTAAAACTGGGATAA 3 230 0 TCCCCCTAAA 0.974691 -71 CCAATGGCCGTGGCACCTAAAGCTAACACTC 7 63 0 TGCACCTAAA 0.951461 -179 GGATCACTGTTAGCACCTAAGAAAGTGGTTT 10 18 0 TGCACCTAAG 0.820785 -283 ACCATCAAATTTCACCCTTAAGAACTGAGAT 11 73 1 TCACCCTTAA 0.825038 -21 GCAAAAAAGCTCCAAGCTAAAAGCATTGGGA 12 34 0 TCAAGCTAAA 0.68869 -213 GAAACTAATTTCTACCCTAAAAAGACTACTT 13 20 0 TTACCCTAAA 0.851442 -102 * ********* Masking position 10 Map Score: 2.80688 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 31 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 12 CAACTACACAATTAATTCCCAATTAATGTA 2 236 1 ATTAATTCCC 0.963871 -65 TTTGTTAATTCCCCTTCTTTTAG 3 4 1 GTTAATTCCC 0.96181 -297 AACAATCCAGGAGAATTCCCTGTTTATTCA 4 32 1 GAGAATTCCC 0.844189 -269 AAAAATTGGCGTCAATTCCCTTTTTGAGCA 6 67 1 GTCAATTCCC 0.944909 -48 AATTAATTCACTTTTTCATCT 6 104 0 ATTAATTCAC 0.748439 -11 AACTAGCGCAAACAAGTCCCAATGCTTTTA 12 18 1 AACAAGTCCC 0.775108 -229 TTTTCTGCAAATTAACTCCCCTAGAACCCC 14 86 0 ATTAACTCCC 0.8915 -68 GCTACACTTAAATAATACCCCCGACCTGGT 16 145 0 AATAATACCC 0.748935 -136 ********** Masking position 5 Map Score: 1.57514 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 45 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 13 GTTGTAGGCTAAAAGAAGGGGAATTAACAAA 3 10 0 AAAGAGGGGA 0.811822 -291 CACCGTTATTAACTGTTGCTGATGAATAAACA 4 52 0 AATGTGCTGA 0.939824 -249 TGTTTTTATCGATTGCTGCTGACCATTGCTGT 10 162 0 GATGTGCTGA 0.805757 -139 AGCAATCGATAAAAACAGCTGACTTTATTGCT 10 177 1 AAAAAGCTGA 0.748089 -124 CCAACTATCAAAGTGCAGCTGAAAGTCAACTT 10 228 1 AATGAGCTGA 0.977097 -73 TACAAGACGCAAAAGTAGCGGCTTAGCAAAAG 16 72 0 AAAGAGCGGC 0.93655 -209 GGTATTATTTAAGTGTAGCTGCTTTAAAACTG 16 156 1 AATGAGCTGC 0.960251 -125 GCTGCTTTAAAACTGGAGCGGAAAAACTTTAA 16 173 1 AATGAGCGGA 0.976644 -108 ** ** ****** Masking position 2 Map Score: 1.66459 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 45 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 14 TCAAAACCAAGGTGTCAAAATTTAGTGCAC 2 56 1 GGTGTCAAAA 0.954621 -245 AATTAGTTTTAGGGTCAAAATTAGGCCAAT 2 152 1 AGGGTCAAAA 0.9703 -149 GGTTATTTAGGGGGTAAAAAGTAGAGATTT 2 203 0 GGGGTAAAAA 0.9703 -98 GGGGGCAAGCGGGGTCAAAAATTGCTACAA 3 244 1 GGGGTCAAAA 0.98466 -57 TGGAATTCTTAAGGTAAAAAGTGATGAAAT 4 202 1 AAGGTAAAAA 0.683232 -99 ACAAAAAGCAGTTGTCAAAACGGATAAATA 6 27 1 GTTGTCAAAA 0.827931 -88 CATTGCTGTCGGTGTAAAAAAGCTTGGTTC 10 141 0 GGTGTAAAAA 0.914583 -160 GTGAAATTTGATGGTCAAAATGACTACGCT 11 58 0 ATGGTCAAAA 0.881971 -36 TAGTCTTTTTAGGGTAGAAATTAGTTTCCA 13 23 1 AGGGTAGAAA 0.795298 -99 ********** Masking position 5 Map Score: 9.06462 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 62 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 15 ********** No masking Map Score: 5.92183e-13 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