AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i316_synecho_ctra_100.orf -o316_synecho_ctra_100.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RCY43260 300 Synechocystis #2 RCT00329 300 Chlamydia_trachomatis #3 RCT00330 61 Chlamydia_trachomatis #4 RCT00331 53 Chlamydia_trachomatis #5 RCT00332 35 Chlamydia_trachomatis #6 RCT00677 300 Chlamydia_trachomatis #7 RCT00695 91 Chlamydia_trachomatis #8 RCT00696 23 Chlamydia_trachomatis #9 RCT00697 36 Chlamydia_trachomatis #10 RCT00698 41 Chlamydia_trachomatis Motif number 1 TTAAGGTCTGTAAAAGCTTGCATTACAAGG 1 94 0 TAAAAGCTTG 0.838752 -207 GTTTCTAGTTAAAAAGTTTTATAAATAAGA 2 23 0 AAAAAGTTTT 0.927443 -278 TATGAGTGAAAAGAAGCTCGTCGGTGATAA 2 62 0 AAGAAGCTCG 0.971758 -239 TAAACACAAGAAAAAGCTCGTTATGAGTGA 2 83 0 AAAAAGCTCG 0.962463 -218 CTTGCAAGGTAAGAGGTTTTGGAATGTAGG 2 210 0 AAGAGGTTTT 0.783644 -91 CTTATGAGCTAAGAAGCTTTCGGGTTGTTT 3 26 0 AAGAAGCTTT 0.983256 -36 CTTAGAGTACAAGAAGTTTGCCGGTGTAG 4 10 0 AAGAAGTTTG 0.947377 -44 CTTGTACTCTAAGAAGGTCTTTGTTATCCT 4 27 1 AAGAAGGTCT 0.928658 -27 AGGTTTTACAAAAAAACTTTGGAAAAAGGT 6 115 1 AAAAAACTTT 0.77505 -186 AAAACTTTGGAAAAAGGTTTTTTGAGAAGG 6 127 1 AAAAAGGTTT 0.937929 -174 ATTGGACTGCAAACAGCTTTAAAAAGGGGA 6 181 1 AAACAGCTTT 0.891585 -120 ********** Masking position 2 Map Score: 11.1478 Number of sites scoring better than the average of aligned sites = 411 Number in coding regions = 339 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 2 ACAAAAGATTTGATCTGCTGTTGATCACCCAC 1 10 1 TTGATCCTTT 0.983177 -291 ACTATCCAAATTGTCCCACTGCTTTTTGGAAAC 1 44 1 TTGTCCCTCT 0.955866 -257 AGCGAAAATCTTGTCCGCCTTTTTGTACTATGC 1 200 1 TTGTCCCTTT 0.989327 -101 CTTCTTATCCTCTCTTATTTATAAAA 2 4 1 CTTATCCTTT 0.874212 -297 CATAACGAGCTTTTTCTTGTGTTTAGGCTTAGT 2 88 1 TTTTTCGTTT 0.841893 -213 AAGAAGGTCTTTGTTATCCTTTTGTCC 4 37 1 TTGTTACTTT 0.875909 -17 TTTTTCTTTTTTTACCACCTCTTCACCTTCTCA 6 149 0 TTTACCCTTT 0.974552 -152 TCTTCCTCTATTTTTCCCCTTTTTAAAGCTGTT 6 192 0 TTTTTCCTTT 0.973438 -109 AATGAAAATTTTGACCCTCTCTTCTTCCTCTAT 6 214 0 TTGACCCTTT 0.986883 -87 ****** ** ** Masking position 10 Map Score: 7.56886 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 244 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 3 AGTGGGACAATTTGGATAGTGGTGGGTGATCAACA 1 29 0 TGTAGGGTGG 0.932832 -272 CAATTTACGTGGTAGTTTGTGGAAGCCCATAGCGA 1 170 1 GATTGGGAAG 0.914869 -131 GAAGCTCGTCGGTGATAACAGGTAGGAGTTTCTAG 2 45 0 GGAACGGTAG 0.907061 -256 TTCTTGTGTTTAGGCTTAGTGGAAGTTATAATTTT 2 101 1 TGTAGGGAAG 0.979549 -200 AAGAGGTTTTGGAATGTAGGGATGGAATTGTTGCA 2 195 0 GATAGGATGG 0.658737 -106 CTCTTACCTTGCAAGCAAGAGGAAGTCGCTTGTTA 2 225 1 GAAAGGGAAG 0.982048 -76 AGAGCGCCACGTTGCCAACGTGAAGGTCGTG 6 7 0 GGAACTGAAG 0.723339 -294 TCTCGCGGGTGTAGCTCAGTGGTAGAGCGCCACGT 6 30 0 GGCAGGGTAG 0.953393 -271 AAAAAGGTTTTTTGAGAAGGTGAAGAGGTGGTAAA 6 137 1 TGAAGTGAAG 0.796905 -164 TTAAAAAGGGGAAAAATAGAGGAAGAAGAGAGGGT 6 199 1 GATAGGGAAG 0.989337 -102 AAAATTTTCATTGATTTAGCGGAAGTAAAAAGGTA 6 235 1 TATAGGGAAG 0.967665 -66 TAGTGAGATAGAAAGCTAGAGGAGCGGCACG 9 16 1 GATAGGGAGC 0.846533 -21 * * *** ***** Masking position 8 Map Score: 7.10322 Number of sites scoring better than the average of aligned sites = 1104 Number in coding regions = 989 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 4 GTGAAAAGAAGCTCGTCGGTGATAACAGGTA 2 56 0 GCTCGTGGTG 0.953063 -245 ACTTCCTCTTGCTTGCAAGGTAAGAGGTTTT 2 220 0 GCTTGCAGGT 0.965924 -81 AGAGGAAGTCGCTTGTTAGGGCATAAATGAT 2 242 1 GCTTGTAGGG 0.896537 -59 AAGGAAGAGATCTCTCAAGGTGAAATCATTT 2 266 0 TCTCTCAGGT 0.651128 -35 GAGCTAAGAAGCTTTCGGGTTGTTTCCAACA 3 20 0 GCTTTCGGTT 0.96833 -42 AGTACAAGAAGTTTGCCGGTGTAG 4 4 0 GTTTGCGGTG 0.945865 -50 ATGCTCTTCTTCTCGCGGGTGTAGCTCAGTG 6 44 0 TCTCGCGGTG 0.953063 -257 GCAATCCTTTGCTTGTAGGTTTTACAAAAAA 6 99 1 GCTTGTGGTT 0.9634 -202 CTGCTTACGAGTTGTATAATGAA 7 3 1 GCTTACAGTT 0.837769 -89 CGCTATCTGATTTTTCAGGTTGAGTAT 10 7 0 TTTTTCGGTT 0.598612 -35 ****** **** Masking position 3 Map Score: 5.46094 Number of sites scoring better than the average of aligned sites = 985 Number in coding regions = 896 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 5 CCACCACTATCCAAATTGTCCCACTGCTTT 1 39 1 CCAAATTGTC 0.949699 -262 ATCTCTCTAATAAGATTTTCTGGGGCCTAA 1 136 1 TAAGATTTTC 0.763445 -165 AAAAGGCGGACAAGATTTTCGCTATGGGCT 1 193 0 CAAGATTTTC 0.966038 -108 TTATGTCTCTCCACAGTTTCAGAGAAAAAT 2 131 0 CCACAGTTTC 0.939974 -170 GAAAAACTCCCCAGATTATCTAGAATGCTC 6 69 0 CCAGATTATC 0.938988 -232 AAACCTTTTTCCAAAGTTTTTTTGTAAAAC 6 117 0 CCAAAGTTTT 0.79514 -184 TGTTTGCAGTCCAATTTTTCTTTTTTTACC 6 166 0 CCAATTTTTC 0.916647 -135 AAGAGAGGGTCAAAATTTTCATTGATTTAG 6 224 1 CAAAATTTTC 0.944439 -77 ********** Masking position 3 Map Score: 3.75419 Number of sites scoring better than the average of aligned sites = 720 Number in coding regions = 627 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 6 TTGGAATGTAGGGATGGAATTGTTGCAAAG 2 192 0 GGGATGGAAT 0.95244 -109 CGTTGCCAACGTGAAGGTCGTG 6 3 0 GTGAAGGTCG 0.955788 -298 GAGTTGTATAATGAAGGAATATCTGTAGGC 7 19 1 ATGAAGGAAT 0.848568 -73 CTTCCCGCAAGGGAAGGAAGTCTTGCTGTT 7 51 0 GGGAAGGAAG 0.993309 -41 CTTCCCTTGCGGGAAGGACGCGAATAACAT 7 65 1 GGGAAGGACG 0.993799 -27 ********** Masking position 4 Map Score: 2.05474 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 132 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 7 ACAAAAGATTTGATCTGCTGTT 1 1 1 AAAAGATTTG 0.934481 -300 ATTACAAGGTGTAAAGAATTTGTTCCGTTTCC 1 71 0 GAAAAATTTG 0.956074 -230 ATTAAGGTCTGTAAAAGCTTGCATTACAAGGT 1 93 0 GAAAGCTTGC 0.934293 -208 AGACGAGAATGAAAACAATTTCTTATGTCTCT 2 151 0 GAAAAATTTC 0.917795 -150 TTGTTAGGGCATAAATGATTTCACCTTGAGAG 2 254 1 AAAAGATTTC 0.920037 -47 ATTGTAAGCAGGAAATAATTGGAGTCAC 5 18 1 GAAAAATTGG 0.965494 -18 AAACCTACAAGCAAAGGATTGCGAAAAACTCC 6 89 0 GAAAGATTGC 0.965011 -212 TAGGTTTTACAAAAAAACTTTGGAAAAAGGTT 6 114 1 AAAAACTTTG 0.844124 -187 GTGGTAAAAAAAGAAAAATTGGACTGCAAACA 6 164 1 AGAAAATTGG 0.76919 -137 * *** ****** Masking position 5 Map Score: 5.55457 Number of sites scoring better than the average of aligned sites = 467 Number in coding regions = 410 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 8 GCTTGCATTACAAGGTGTAAAGAATTTGTTC 1 78 0 CAAGTGTAAA 0.726597 -223 TGTGGAAGCCCATAGCGAAAATCTTGTCCGC 1 187 1 CATGCGAAAA 0.918612 -114 ATCAGAGGTCGGTGGTGAAAACTCAGGCAAA 1 269 0 GGTGTGAAAA 0.971578 -32 AGAGATCTCTCAAGGTGAAATCATTTATGCC 2 261 0 CAAGTGAAAT 0.726597 -40 ACAAGCAAAGGATTGCGAAAAACTCCCCAGA 6 84 0 GATGCGAAAA 0.956335 -217 GGTTTTTTGAGAAGGTGAAGAGGTGGTAAAA 6 142 1 GAAGTGAAGA 0.896788 -159 AAGGTGAAGAGGTGGTAAAAAAAGAAAAATT 6 153 1 GGTGTAAAAA 0.870657 -148 TTGATTTAGCGGAAGTAAAAAGGTACAAGTA 6 245 1 GGAGTAAAAA 0.892395 -56 CTTGCGGGAAGGACGCGAATAACATCCCTGT 7 70 1 GGAGCGAATA 0.8616 -22 *** ******* Masking position 9 Map Score: 2.02531 Number of sites scoring better than the average of aligned sites = 751 Number in coding regions = 658 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 9 AAACTTTGTTTATCTCTCTAATAAGATTTT 1 125 1 TATCTCTCTA 0.982338 -176 AACAATTTCTTATGTCTCTCCACAGTTTCA 2 140 0 TATGTCTCTC 0.944608 -161 TTAAGGAAGAGATCTCTCAAGGTGAAATCA 2 269 0 GATCTCTCAA 0.908398 -32 TCTAGCTTTCTATCTCACTATAAGG 9 6 0 TATCTCACTA 0.944153 -31 CCTTGCATCTCTCTCGCTATCTGAT 10 27 0 CATCTCTCTC 0.972392 -15 ********** Masking position 5 Map Score: 0.769609 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 7 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 TTTGGATAGTGGTGGGTGATCAACAGCAGA 1 24 0 GGTGGGTGAT 0.971906 -277 CCCCAATTTACGTGGTAGTTTGTGGAAGCC 1 167 1 CGTGGTAGTT 0.814204 -134 TTGAATCAGAGGTCGGTGGTGAAAACTCAG 1 274 0 GGTCGGTGGT 0.987333 -27 GGTGATAACAGGTAGGAGTTTCTAGTTAAA 2 40 0 GGTAGGAGTT 0.960955 -261 AAAAGAAGCTCGTCGGTGATAACAGGTAGG 2 54 0 CGTCGGTGAT 0.955084 -247 TTGCTTGCAAGGTAAGAGGTTTTGGAATGT 2 213 0 GGTAAGAGGT 0.804313 -88 ACTCTAAGAAGGTCTTTGTTATCCTTTTGT 4 32 1 GGTCTTTGTT 0.75292 -22 ********** Masking position 3 Map Score: 0.506082 Number of sites scoring better than the average of aligned sites = 721 Number in coding regions = 667 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 11 ********** No masking Map Score: -2.49157e-12 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 Motif number 12 ********** No masking Map Score: -2.49157e-12 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 Motif number 13 ********** No masking Map Score: -2.49157e-12 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