AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i149_synecho_ctra_100.orf -o149_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 RCY51535 95 Synechocystis #2 RCY29531 40 Synechocystis #3 RCY03241 110 Synechocystis #4 RCT00097 300 Chlamydia_trachomatis #5 RCT00513 300 Chlamydia_trachomatis Motif number 1 CATCCGTTACACTGAAAATAAGCAGAGTATTAAGA 1 21 1 ACTAATAACG 0.980616 -75 CTTTGGATGAGCTAAAACCTAGCTCCGTATTTATT 3 33 1 GCTAACTACC 0.856617 -78 TCATTAGTTAACCAATATTAAGCCGAGGAGAGGCC 3 84 1 ACCTATAACG 0.857376 -27 TTTCCCTTGCACTACAAGTAATAAGATGCATCTCT 4 21 1 ACTAATAAAG 0.926097 -280 AAAATCTAAAACTAAAATTACACAGAAACTAGTGA 4 71 0 ACTAATACCG 0.979301 -230 AAAAAAAGGAACTATAACCAACCCGACTTTTTCCG 4 208 0 ACTAACAACG 0.985484 -93 AGATAAAAGAGCTTTAAATACGCAGGAAAAAGGTT 4 255 0 GCTAATACCG 0.967349 -46 GCTCACTAGAACCTGAATCTAGCGCGTCTACCGGT 5 68 0 ACCAACTACC 0.899192 -233 AGCTAAGAAGACTTGAACTTCCATGAGCAAAAGCT 5 100 0 ACTAATTCAG 0.873494 -201 AGGCCAGTTAGCCATAACCTCTACGAAAAAGTCAA 5 178 0 GCCAACTCAG 0.84451 -123 TTCCCTAAGAACCGCAAGCAAACGGGGCTAGCCGT 5 221 0 ACCAACAACG 0.984494 -80 *** ** *** * * Masking position 7 Map Score: 9.4084 Number of sites scoring better than the average of aligned sites = 573 Number in coding regions = 505 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 2 ACCATGGGTTGGGAATTTTTTTCGCTAGAGA 1 73 1 GGGAATTTTT 0.944215 -23 TGTAGTGCAAGGGAAATCTTGCCTTT 4 6 0 GGGAATCTTG 0.98565 -295 ACAGAAACTAGTGAAACTTTTTTTAATAAAG 4 54 0 GTGAACTTTT 0.964664 -247 GGAAAGGACTGTCAATCCTTGAGATTTTCAA 4 148 1 GTCAACCTTG 0.955151 -153 TGTAAAAGCCGGGAACCTTTTTCCTGCGTAT 4 242 1 GGGAACTTTT 0.977427 -59 TCAGGTTCTAGTGAGCTTTTGCTCATGGAAG 5 87 1 GTGAGTTTTG 0.8788 -214 GCGGTTCTTAGGGAAGCCCTGAAACCTCCTA 5 241 1 GGGAACCCTG 0.979023 -60 TAAAATCTATGTAAATCCTTGCTAGGAGGTT 5 263 0 GTAAACCTTG 0.934935 -38 ***** ***** Masking position 4 Map Score: 6.49332 Number of sites scoring better than the average of aligned sites = 607 Number in coding regions = 547 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 3 TTAAGCCGAGGAGAGGCCCC 3 101 1 GAGAGGCCCC 0.996104 -10 TTTTAATAAAGAGATGCATCTTATTACTTG 4 35 0 GAGATGCATC 0.834254 -266 CATCCCCATGGAAAGGACTGTCAATCCTTG 4 139 1 GAAAGGACTG 0.904531 -162 ATAGCTGCATGAGAGGCCAGTATAGAGAGA 5 32 0 GAGAGGCCAG 0.993396 -269 TTCTTTTCAACAAACGCCCGGGACAGGGGC 5 141 1 CAAACGCCCG 0.951724 -160 AAAGTCAAGACAGATGCCCCTGTCCCGGGC 5 156 0 CAGATGCCCC 0.973557 -145 GCCGTGTTCTGAAAGGCCAGTTAGCCATAA 5 196 0 GAAAGGCCAG 0.986496 -105 ********** Masking position 4 Map Score: 5.34312 Number of sites scoring better than the average of aligned sites = 281 Number in coding regions = 258 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 4 TGAGCTAAAACCTAGCTCCGTATTTATTTG 3 40 1 CCTAGCTCCG 0.900671 -71 AAAAAGTTTCACTAGTTTCTGTGTAATTTT 4 63 1 ACTAGTTTCT 0.668316 -238 AACCAACCCGACTTTTTCCGCAAACGACAT 4 198 0 ACTTTTTCCG 0.973604 -103 GGTTATAGTTCCTTTTTTTGTAAAAGCCGG 4 224 1 CCTTTTTTTG 0.666917 -77 AAGCCGGGAACCTTTTTCCTGCGTATTTAA 4 247 1 CCTTTTTCCT 0.961688 -54 TAGCGCGTCTACCGGTTCCGCCATAGCTGC 5 54 0 ACCGGTTCCG 0.918174 -247 AGACAGATGCCCCTGTCCCGGGCGTTTGTT 5 149 0 CCCTGTCCCG 0.933556 -152 ATCTGTCTTGACTTTTTCGTAGAGGTTATG 5 171 1 ACTTTTTCGT 0.722622 -130 ACGGGGCTAGCCGTGTTCTGAAAGGCCAGT 5 205 0 CCGTGTTCTG 0.878172 -96 AAAACTTGTTCCTAATTTAAAAT 5 288 0 ACTTGTTCCT 0.973604 -13 ********** Masking position 2 Map Score: 3.48027 Number of sites scoring better than the average of aligned sites = 1575 Number in coding regions = 1443 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 5 GTATTTTCCCTCGCAAAGATATTAATCCAG 2 20 0 TCGCAAAGAT 0.97763 -21 TCCTTGAAAATCTCAAGGATTGACAGTCCT 4 152 0 TCTCAAGGAT 0.99117 -149 TCCTTGAGATTTTCAAGGATATCGGAGGGG 4 163 1 TTTCAAGGAT 0.976271 -138 TGAAACCTCCTAGCAAGGATTTACATAGAT 5 260 1 TAGCAAGGAT 0.984534 -41 ********** Masking position 5 Map Score: 2.66621 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 28 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 AGCTCATCCAAAGTTTCTATTCTTAGTATA 3 16 0 AAGTTTCTAT 0.84085 -95 AAACTAGTGAAACTTTTTTTAATAAAGAGA 4 51 0 AACTTTTTTT 0.903639 -250 GGGTTGGTTATAGTTCCTTTTTTTGTAAAA 4 219 1 TAGTTCCTTT 0.681364 -82 AAAAGCCGGGAACCTTTTTCCTGCGTATTT 4 245 1 AACCTTTTTC 0.777484 -56 TGCGTATTTAAAGCTCTTTTATCTAAGTTC 4 266 1 AAGCTCTTTT 0.967085 -35 TCTTTTATCTAAGTTCATATTGGGGGTTCC 4 280 1 AAGTTCATAT 0.723195 -21 AACCTTTTATTAAAACAGCT 5 1 1 AACCTTTTAT 0.910831 -300 TATAGAGAGAAAGCTGTTTTAATAAAAGGT 5 12 0 AAGCTGTTTT 0.870747 -289 CTTAGCTGCAAACTTCTTTTCAACAAACGC 5 128 1 AACTTCTTTT 0.948518 -173 GAAGCCCTGAAACCTCCTAGCAAGGATTTA 5 253 1 AACCTCCTAG 0.794561 -48 ********** Masking position 5 Map Score: 2.46731 Number of sites scoring better than the average of aligned sites = 491 Number in coding regions = 405 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 7 ********** No masking Map Score: -5.44113e-14 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 8 ********** No masking Map Score: -5.44113e-14 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 9 ********** No masking Map Score: -5.44113e-14 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