AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i316_synecho_ctra_300.orf -o316_synecho_ctra_300.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 CCTTGTAATGCAAGCTTTTACAGACCTTAA 1 94 1 CAAGCTTTTA 0.842335 -207 TCTTATTTATAAAACTTTTTAACTAGAAAC 2 23 1 AAAACTTTTT 0.928843 -278 TTATCACCGACGAGCTTCTTTTCACTCATA 2 62 1 CGAGCTTCTT 0.972483 -239 TCACTCATAACGAGCTTTTTCTTGTGTTTA 2 83 1 CGAGCTTTTT 0.963417 -218 CCTACATTCCAAAACCTCTTACCTTGCAAG 2 210 1 AAAACCTCTT 0.788135 -91 AAACAACCCGAAAGCTTCTTAGCTCATAAG 3 26 1 AAAGCTTCTT 0.98369 -36 CTACACCGGCAAACTTCTTGTACTCTAAG 4 10 1 CAAACTTCTT 0.948694 -44 AGGATAACAAAGACCTTCTTAGAGTACAAG 4 27 0 AGACCTTCTT 0.930409 -27 ACCTTTTTCCAAAGTTTTTTTGTAAAACCT 6 115 0 AAAGTTTTTT 0.779668 -186 CCTTCTCAAAAAACCTTTTTCCAAAGTTTT 6 127 0 AAACCTTTTT 0.939394 -174 TCCCCTTTTTAAAGCTGTTTGCAGTCCAAT 6 181 0 AAAGCTGTTT 0.89413 -120 ********** Masking position 3 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 TCTTATTAGAGAGATAAACAAAGTTTATTAAGG 1 118 0 GGTAACAAAG 0.811389 -183 TCATCCACGCATAGTACAAAAAGGCGGACAAGA 1 208 0 AATAAAAAAG 0.899109 -93 TATAAATAAGAGAGGATAAGAAG 2 1 0 AAGAAAGAAG 0.969133 -300 AGCTCGTTATGAGTGAAAAGAAGCTCGTCGGTG 2 66 0 GGGAAAGAAG 0.984818 -235 CTAAGCCTAAACACAAGAAAAAGCTCGTTATGA 2 87 0 AAAAAAAAAG 0.794949 -214 CTTACCTTGCAAGCAAGAGGAAGTCGCTTGTTA 2 227 1 AGAAAGGAAG 0.922186 -74 TGCTGTACTTATGAGCTAAGAAGCTTTCGGGTT 3 30 0 AGGCAAGAAG 0.922525 -32 AGACCTTCTTAGAGTACAAGAAGTTTGCCGGTG 4 14 0 AATAAAGAAG 0.951663 -40 TGAGCTACACCCGCGAGAAGAAGAGCATTCTAG 6 47 1 CGGAAAGAAG 0.948515 -254 AGGTGAAGAGGTGGTAAAAAAAGAAAAATTGGA 6 154 1 GGTAAAAAAG 0.948486 -147 AAAAAGGGGAAAAATAGAGGAAGAAGAGAGGGT 6 201 1 AATAAGGAAG 0.924987 -100 CCTTATAGTGAGATAGAAAGCTAGAGGAGC 9 8 1 GGGAAGAAAG 0.948428 -29 * * ** ****** Masking position 8 Map Score: 9.18253 Number of sites scoring better than the average of aligned sites = 306 Number in coding regions = 251 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 3 TATCCAAATTGTCCCACTGCTTTTTGGAAACGGA 1 46 1 GTCCCTCTTT 0.924047 -255 GTCCCAGGCAGTCCCACTCATCCACGCATAGTAC 1 224 0 GTCCCTACCA 0.983341 -77 TTTTCACCACCGACCTCTGATTCAATCGGGGT 1 279 1 CGCCCTATCA 0.939337 -22 AAAATTATAACTTCCACTAAGCCTAAACACAAGA 2 102 0 CTCCCTACCT 0.989358 -199 ACGTGGCGCTCTACCACTGAGCTACACCCGCGAG 6 30 1 CTCCCTACTA 0.983136 -271 TCTTTTTTTACCACCTCTTCACCTTCTCAAAAAA 6 144 0 CCCCCTCCCT 0.960323 -157 ACCCTCTCTTCTTCCTCTATTTTTCCCCTTTTTA 6 200 0 CTCCCTTTTT 0.855946 -101 TACCTTTTTACTTCCGCTAAATCAATGAAAATTT 6 236 0 CTCCCTATCA 0.983136 -65 CGTGCCGCTCCTCTAGCTTTCTATC 9 22 0 GTCCCTCCTA 0.967158 -15 ** ** ** * *** Masking position 8 Map Score: 7.30047 Number of sites scoring better than the average of aligned sites = 414 Number in coding regions = 368 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 4 GGAAACGGAACAAATTCTTTACACCTTGTAATGCAAG 1 71 1 CAAATTCCTT 0.929362 -230 CCTTGTAATGCAAGCTTTTACAGACCTTAATAAACTT 1 94 1 CAAGTTACCT 0.75946 -207 AGCCCATAGCGAAAATCTTGTCCGCCTTTTTGTACTA 1 193 1 GAAATTCCCT 0.980677 -108 AGAGACATAAGAAATTGTTTTCATTCTCGTCTTATTT 2 151 1 GAAATTCTCT 0.947294 -150 TTATATCTTTGCAACAATTCCATCCCTACATTCCAAA 2 186 1 GCAATTACCT 0.92393 -115 TCCCTACATTCCAAAACCTCTTACCTTGCAAGCAAGA 2 208 1 CCAACTTCTT 0.677509 -93 CTCTCAAGGTGAAATCATTTATGCCCTAACAAGCGAC 2 249 0 GAAATTTCCT 0.958286 -52 CTACACCGGCAAACTTCTTGTACTCTAAGAAGGTCT 4 10 1 CAAACTTTCT 0.702508 -44 GTGACTCCAATTATTTCCTGCTTACAATGAGCG 5 13 0 CCAATTCCTT 0.941141 -23 TCTTTTTTTACCACCTCTTCACCTTCTCAAAAAACCT 6 141 0 CCACTTCTCT 0.789467 -160 TGTTTGCAGTCCAATTTTTCTTTTTTTACCACCTCTT 6 159 0 CCAATTTTTT 0.719349 -142 CTAAATCAATGAAAATTTTGACCCTCTCTTCTTCCTC 6 217 0 GAAATTCTCT 0.947294 -84 AGGCAGAACAGCAAGACTTCCTTCCCTTGCGGGAAGG 7 45 1 GCAATTTCCT 0.965421 -47 AACAGGGATGTTATTCGCGTCCTTCCCGCAAGG 7 69 0 GATGTTCCCT 0.612118 -23 **** ** * *** Masking position 9 Map Score: 6.46263 Number of sites scoring better than the average of aligned sites = 1368 Number in coding regions = 1187 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 187 Fraction of orfs with sites within 600 bp upstream = 0.0300353 Motif number 5 TTTGTTCCGTTTCCAAAAAGCAGTGGGACA 1 55 0 TTCCAAAAAG 0.810673 -246 GATTGGTGAGTCCCAGGCAGTCCCACTCAT 1 237 0 TCCCAGGCAG 0.836204 -64 ACCTCTTACCTTGCAAGCAAGAGGAAGTCG 2 223 1 TTGCAAGCAA 0.91679 -78 GCATATACTGTTGGAAACAACCCGAAAGCT 3 12 1 TTGGAAACAA 0.606552 -50 ACTTCTTGTACTCTAAGAAGGTCTTTGTTA 4 23 1 CTCTAAGAAG 0.744044 -31 ATCGCTCATTGTAAGCAGGAAATAATTG 5 9 1 TTGTAAGCAG 0.956 -27 TGAGCTACACCCGCGAGAAGAAGAGCATTC 6 47 1 CCGCGAGAAG 0.865598 -254 AAGCAAAGGATTGCGAAAAACTCCCCAGAT 6 83 0 TTGCGAAAAA 0.578848 -218 CAAAAAAACTTTGGAAAAAGGTTTTTTGAG 6 123 1 TTGGAAAAAG 0.806431 -178 AAAAATTGGACTGCAAACAGCTTTAAAAAG 6 177 1 CTGCAAACAG 0.934813 -124 ATTATACAACTCGTAAGCAG 7 1 0 TCGTAAGCAG 0.92222 -91 GAAGGAATATCTGTAGGCAGAACAGCAAGA 7 31 1 CTGTAGGCAG 0.882447 -61 CTTCCTTCCCTTGCGGGAAGGACGCGAATA 7 61 1 TTGCGGGAAG 0.897525 -31 ********** Masking position 9 Map Score: 6.09926 Number of sites scoring better than the average of aligned sites = 1663 Number in coding regions = 1498 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 6 TTTGATCTGCTGTTGATCACCCACCACTAT 1 19 1 TGTTGATCAC 0.723659 -282 TCCCACTGCTTTTTGGAAACGGAACAAATT 1 57 1 TTTTGGAAAC 0.957621 -244 ACGTGGTAGTTTGTGGAAGCCCATAGCGAA 1 176 1 TTGTGGAAGC 0.855076 -125 CAGAGGTCGGTGGTGAAAACTCAGGCAAAT 1 268 0 TGGTGAAAAC 0.956922 -33 AGAAGCTCGTCGGTGATAACAGGTAGGAGT 2 51 0 CGGTGATAAC 0.904511 -250 CGCATATACTGTTGGAAACAACCCGAAAG 3 10 1 TGTTGGAAAC 0.98304 -52 ACGACCTTCACGTTGGCAACGTGGCGCTCT 6 12 1 CGTTGGCAAC 0.954086 -289 TACAAAAAAACTTTGGAAAAAGGTTTTTTG 6 121 1 CTTTGGAAAA 0.712338 -180 ********** Masking position 4 Map Score: 1.24233 Number of sites scoring better than the average of aligned sites = 903 Number in coding regions = 862 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 7 ACTAGAAACTCCTACCTGTTATCACCGACG 2 44 1 CCTACCTGTT 0.97805 -257 TCCCAAACCTGCTGTACTTATGA 3 49 0 CAAACCTGCT 0.961933 -13 AGGGGGTTGACAGACCTGTTACTTGTACCT 6 265 0 CAGACCTGTT 0.984576 -36 ACGCGAATAACATCCCTGTT 7 82 1 CATCCCTGTT 0.97805 -10 ********** Masking position 7 Map Score: 0.348591 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 14 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 8 GACAATTTGGATAGTGGTGGGTGATCAACAGC 1 27 0 AATGGTGGGT 0.98657 -274 ACTACCACGTAAATTGGGGGTTAGGCCCCAGA 1 154 0 AATGGGGGTT 0.98657 -147 TCAGGCAAATAGATTGGTGAGTCCCAGGCAGT 1 246 0 AATGGTGAGT 0.970242 -55 CATTCTAGATAATCTGGGGAGTTTTTCGCAAT 6 72 1 ATTGGGGAGT 0.95708 -229 CTCCTCTAAAACATAGGGGGTTGACAGACCTG 6 277 0 AAAGGGGGTT 0.957133 -24 * * ******** Masking position 1 Map Score: 0.122491 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 81 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 9 ********** 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 10 ********** 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 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