AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i217_synecho_ctra_100.orf -o217_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 RCY11650 125 Synechocystis #2 RCY51581 32 Synechocystis #3 RCY24462 49 Synechocystis #4 RCY49641 136 Synechocystis #5 RCT00240 300 Chlamydia_trachomatis #6 RCT00753 300 Chlamydia_trachomatis Motif number 1 TGTATTTGTTCCCTTTCCTTCCCC 1 4 0 CCCTTCCTTC 0.941747 -122 GGGGAAAAATCCCCGCCCCCCAACCATCTGG 1 43 1 CCCCCCCCCC 0.991378 -83 TGCCTCCATACCATCTTCCCCTATTTCTACA 1 77 0 CCATTTCCCC 0.841791 -49 CCATTGAGCCCCCCAGTCTTCCCGGCAACCT 4 49 1 CCCCGTCTTC 0.960676 -88 AAATAACCATCCCCCCTCTCTACATCAAAAA 5 56 0 CCCCCTCTCT 0.978049 -245 AGAGATTCAACTCTGCTCTTCCGAACGGAGC 5 144 0 CTCTCTCTTC 0.976925 -157 AAGACAAAACCTCTCCACTTCTTGTCGAGAA 5 191 0 CTCTCACTTC 0.856264 -110 AGGAACGAGGCTTCCCTCCCCATAGGGAGAA 5 264 1 CTTCCTCCCC 0.888115 -37 TCTCTGCTCTCTACGCATTCCT 6 2 1 CTCTCTCTCT 0.959216 -299 GTTGTTAATCCTCCTTTATCCGGGAAGGCTC 6 73 0 CTCCTTATCC 0.724304 -228 ACAAAATTTACCCTTTTCCTCACTTTTTGAC 6 111 1 CCCTTTCCTC 0.967178 -190 TTAAACTCGTCCCTAGTCTCTTGGGGGCAGA 6 245 1 CCCTGTCTCT 0.930159 -56 TCTCTAGGGACTCTGCCCCCAAGAGACTAGG 6 256 0 CTCTCCCCCA 0.841335 -45 **** ****** Masking position 1 Map Score: 12.2591 Number of sites scoring better than the average of aligned sites = 3352 Number in coding regions = 2904 Number in noncoding regions = 448 Number of orfs with sites within 600 bp upstream = 370 Fraction of orfs with sites within 600 bp upstream = 0.0594282 Motif number 2 GCCCCCCAGTCTTCCCGGCAACCTTGGCAAT 4 56 1 CTTCCCGCAA 0.921864 -81 ATCTAGAGAGCTTGTTAGCAATGGATTTTGG 4 91 1 CTTGTTGCAA 0.992676 -46 AGTTGAATCTCTTGTAAGCAAAAGACGATTC 5 163 1 CTTGTAGCAA 0.970961 -138 CTCTCCACTTCTTGTCGAGAATCGTCTTTTG 5 181 0 CTTGTCAGAA 0.956355 -120 TTAAAGCAACCTTGATAGGAACGAGGCTTCC 5 248 1 CTTGATGGAA 0.9536 -53 CGGGAAGGCTCTTGTTTGCAATTCTGTGTAT 6 53 0 CTTGTTGCAA 0.992676 -248 CTTTTCCTCACTTTTTGACAATAAGAGACTT 6 123 1 CTTTTTACAA 0.872965 -178 CAATAAGAGACTTGCTCAGAATTCTATCTAC 6 141 1 CTTGCTAGAA 0.956355 -160 ****** **** Masking position 10 Map Score: 7.53759 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 = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 3 AGGGAACAAATACAATTTTAGTGGGGAAAAATCCCC 1 21 1 TCTTTAGGGG 0.928642 -105 TACAATCCCAGATGGTTGGGGGGCGGGGATTTTTCC 1 45 0 GTTTGGGGGG 0.982495 -81 TATGCTTGTGCCATTGCAGGGGGTGAAATGCCTC 1 102 0 TCTTGAGGGT 0.980938 -24 TGAGCAATGATACAATTGGAGACTGTGTCTTTTTTT 3 15 1 TCTTGAGCGT 0.959789 -35 AGACTGTGTCTTTTTTTGTGGAGTAA 3 34 1 TTTTGGGGAA 0.772677 -16 TAGAGTCGCTTTCAGATGTGGACGCTAGCAATATAT 5 12 0 TCATGGGCCT 0.879727 -289 ACATCAAAAAGTTTAATGTAGAGTCGCTTTCAGATG 5 30 0 GTATGAGGCG 0.900108 -271 ACATTAAACTTTTTGATGTAGAGAGGGGGGATGGTT 5 47 1 TTATGAGGGG 0.972491 -254 AGGTGGGTTCTCCCTATGGGGAGGGAAGCCTCGTTC 5 266 0 TCATGGGGGA 0.978811 -35 TTTGCAATTCTGTGTATGGAGCGTGGGCTAGTGCCT 6 34 0 TTATGAGGGG 0.972491 -267 GCCCTGTATTGATCTTTTAGGTGAGATCCTTTAAAC 6 215 1 GTTTTGGGGA 0.783293 -86 CTCGTCCCTAGTCTCTTGGGGGCAGAGTCCCTAGAG 6 250 1 GCTTGGGCGA 0.960341 -51 ACTCTCCTAATACTCTTGAAGTCTCTAGGGACTCTG 6 272 0 TCTTGAGCCT 0.892302 -29 * * *** ** * ** Masking position 7 Map Score: 8.62426 Number of sites scoring better than the average of aligned sites = 1566 Number in coding regions = 1447 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 4 TATGCTTGTGCCATTGCAGGGGGT 1 112 0 CTTGTGCCAT 0.829155 -14 TCCATGAGCAATGATACAATTG 3 3 1 CATGAGCAAT 0.805759 -47 TAATCAAGCACTGGAGCCATTGAGCCCCCC 4 33 1 CTGGAGCCAT 0.919795 -104 AACAAGCTCTCTAGATAAATATTGCCAAGG 4 77 0 CTAGATAAAT 0.584996 -60 AAACCGATACCAAAATCCATTGCTAACAAG 4 101 0 CAAAATCCAT 0.545382 -36 AAAATGACGCCAAGTTACATAGTATGAAGC 5 116 1 CAAGTTACAT 0.757596 -185 GGAGCGTGGGCTAGTGCCTTAGGAATGCGT 6 23 0 CTAGTGCCTT 0.951362 -278 GAATTGCAAACAAGAGCCTTCCCGGATAAA 6 60 1 CAAGAGCCTT 0.986968 -241 TTTTTGACAATAAGAGACTTGCTCAGAATT 6 134 1 TAAGAGACTT 0.740748 -167 ACTCTGCCCCCAAGAGACTAGGGACGAGTT 6 248 0 CAAGAGACTA 0.821822 -53 GGCAGAGTCCCTAGAGACTTCAAGAGTATT 6 270 1 CTAGAGACTT 0.966585 -31 CTAGAGACTTCAAGAGTATTAGGAGAGTAT 6 280 1 CAAGAGTATT 0.684411 -21 ********** Masking position 10 Map Score: 6.74182 Number of sites scoring better than the average of aligned sites = 871 Number in coding regions = 778 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 5 ATTTGTTCCCTTTCCTTCCCC 1 2 0 TTTCCTTCCC 0.985826 -124 GGCGGGGATTTTTCCCCACTAAAATTGTAT 1 30 0 TTTCCCCACT 0.957735 -96 TATGGAGGCATTTCACCCCCTGCAATGGCA 1 98 1 TTTCACCCCC 0.970293 -28 TCAAGGTTGCTTTAATTCCCTAATCAAAAA 5 233 0 TTTAATTCCC 0.752984 -68 GGAACGAGGCTTCCCTCCCCATAGGGAGAA 5 265 1 TTCCCTCCCC 0.977876 -36 AATTTACCCTTTTCCTCACTTTTTGACAAT 6 115 1 TTTCCTCACT 0.971161 -186 ATGGAAGTACTTTCTTTACTCAAGAAATCA 6 174 1 TTTCTTTACT 0.757537 -127 ********** Masking position 2 Map Score: 3.20927 Number of sites scoring better than the average of aligned sites = 1535 Number in coding regions = 1309 Number in noncoding regions = 226 Number of orfs with sites within 600 bp upstream = 244 Fraction of orfs with sites within 600 bp upstream = 0.0391905 Motif number 6 CCCCCTGCAATGGCACAAGCATA 1 113 1 TGGCACAAGC 0.896042 -13 AATTGTATCATTGCTCATGGA 3 2 0 TTGCTCATGG 0.858174 -48 GGGGGCTCAATGGCTCCAGTGCTTGATTAA 4 32 0 TGGCTCCAGT 0.882539 -105 TATCTTTTCCATGCACTTGGAAAATAACCA 5 78 0 ATGCACTTGG 0.932927 -223 CGCATTCCTAAGGCACTAGCCCACGCTCCA 6 24 1 AGGCACTAGC 0.969498 -277 TTATCCGGGAAGGCTCTTGTTTGCAATTCT 6 59 0 AGGCTCTTGT 0.970557 -242 ACTCGTCCCTAGTCTCTTGGGGGCAGAGTC 6 249 1 AGTCTCTTGG 0.957107 -52 ATACTCTTGAAGTCTCTAGGGACTCTGCCC 6 269 0 AGTCTCTAGG 0.957107 -32 ********** Masking position 6 Map Score: 4.45844 Number of sites scoring better than the average of aligned sites = 634 Number in coding regions = 572 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 7 CCAGATGGTTGGGGGGCGGGGATTTTTCCC 1 44 0 GGGGGGCGGG 0.95639 -82 TTGTGCCATTGCAGGGGGTGAAATGCCTCC 1 101 0 GCAGGGGGTG 0.891355 -25 TGATACAATTGGAGACTGTGTCTTTTTTTG 3 22 1 GGAGACTGTG 0.975391 -28 AGGTTGCCGGGAAGACTGGGGGGCTCAATG 4 50 0 GAAGACTGGG 0.957406 -87 TTTTTGATGTAGAGAGGGGGGATGGTTATT 5 56 1 AGAGAGGGGG 0.977355 -245 TTCTGTGTATGGAGCGTGGGCTAGTGCCTT 6 33 0 GGAGCGTGGG 0.988502 -268 TCTGCCCCCAAGAGACTAGGGACGAGTTTA 6 246 0 AGAGACTAGG 0.837164 -55 ********** Masking position 4 Map Score: 1.25817 Number of sites scoring better than the average of aligned sites = 1413 Number in coding regions = 1288 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 8 ********** No masking Map Score: -9.92328e-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 Motif number 9 ********** No masking Map Score: -9.92328e-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 Motif number 10 ********** No masking Map Score: -9.92328e-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