AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i277_synecho_ctra_100.orf -o277_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 RCY15315 62 Synechocystis #2 RCY46789 93 Synechocystis #3 RCY19481 25 Synechocystis #4 RCY39291 74 Synechocystis #5 RCY09718 300 Synechocystis #6 RCY10327 39 Synechocystis #7 RCY51049 79 Synechocystis #8 RCT00329 300 Chlamydia_trachomatis Motif number 1 AGGGAAGTTAGAGGCGATGGGCCGGCAAACTCAAGCAGAAA 1 29 1 GGGATGGAAT 0.991605 -34 CTAATATTTGGGGGACAGCTTTTGGGGCACTGGAGGGTTTA 2 60 1 GGGAGCGGAT 0.987145 -34 AGCGTTATATTTGTTGAGGGGCTGGGGGATTATTACCTTTT 5 49 1 TGTAGGGGAT 0.978948 -252 GACCGTGAGGGCGGCCATGCCAAGGAAGATTCCCCCAGGTA 5 90 0 GGGATGGAAT 0.991605 -211 TAGGTCAATGTTGGTAATGCTGGGGTAAAATTCAGACCGCA 5 170 1 TGGATGGAAT 0.983638 -131 TAATGGTGTAGGGGACAGGCTGGGCGGTAATTTAAGTTTTT 7 19 0 GGGAGGGGAT 0.997849 -61 AAGAAGCTCGTCGGTGATAACAGGTAGGAGTTTCTAGTTAA 8 41 0 TGGATAGGAT 0.953453 -260 GCTTTTTCTTGTGTTTAGGCTTAGTGGAAGTTATAATTTTT 8 96 1 GGTAGGGGAT 0.989173 -205 GGTAAGAGGTTTTGGAATGTAGGGATGGAATTGTTGCAAAG 8 192 0 TTGATGGGAT 0.94732 -109 * ** *** * * * * Masking position 7 Map Score: 11.292 Number of sites scoring better than the average of aligned sites = 416 Number in coding regions = 379 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 2 ATAAACCTGTCTTAGGGTCACCAG 2 5 0 CTTAGGGTCA 0.813568 -89 TAAGCTAATATTTGGGGGACAGCTTTTGGG 2 56 1 TTTGGGGGAC 0.966136 -38 GGGGACAGCTTTTGGGGCACTGGAGGGTTT 2 70 1 TTTGGGGCAC 0.950767 -24 ACAAAAAAAATTTGGGGCTAAGAACCATTC 4 42 0 TTTGGGGCTA 0.743959 -33 CAAATATAACGCTAGGGTCAATCCTACCAA 5 32 0 GCTAGGGTCA 0.803192 -269 TTGTTGAGGGGCTGGGGGATTATTACCTTT 5 59 1 GCTGGGGGAT 0.946561 -242 TACCTTTTTACCTGGGGGAATCTTCCTTGG 5 82 1 CCTGGGGGAA 0.985802 -219 CCCTCACGGTCTTGGTGGCCCTGTTGTACG 5 120 1 CTTGGTGGCC 0.798581 -181 TGTTGGTAATGCTGGGGTAAAATTCAGACC 5 178 1 GCTGGGGTAA 0.948376 -123 AACGAACAAACCTGCGGCAATGATCACAAC 5 215 0 CCTGCGGCAA 0.821043 -86 CCATTAATGGTGTAGGGGACAGGCTGGGCG 7 34 0 TGTAGGGGAC 0.750698 -46 TGTGTTTAGGCTTAGTGGAAGTTATAATTT 8 105 1 CTTAGTGGAA 0.75084 -196 GAAGTCGCTTGTTAGGGCATAAATGATTTC 8 246 1 GTTAGGGCAT 0.80442 -55 ********** Masking position 3 Map Score: 9.01541 Number of sites scoring better than the average of aligned sites = 6242 Number in coding regions = 5475 Number in noncoding regions = 767 Number of orfs with sites within 600 bp upstream = 620 Fraction of orfs with sites within 600 bp upstream = 0.0995824 Motif number 3 CGGCCCATCGCCTCTAACTTCCCTATTTTA 1 23 0 CCTCTAACTT 0.973133 -40 CTTCTTATCCTCTCTTATTTATAAAACTTT 8 11 1 TCTCTTATTT 0.943704 -290 TTTTCATTCTCGTCTTATTTATATCTTTGC 8 168 1 CGTCTTATTT 0.919192 -133 CATTCCAAAACCTCTTACCTTGCAAGCAAG 8 214 1 CCTCTTACCT 0.981713 -87 CAAGCGACTTCCTCTTGCTTGCAAGGTAAG 8 227 0 CCTCTTGCTT 0.985106 -74 CCTTGAGAGATCTCTTCCTTAAAGAGGATA 8 277 1 TCTCTTCCTT 0.957171 -24 ********** Masking position 5 Map Score: 3.65353 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 65 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 4 CCCAGCCCCTCAACAAATATAACGCTAGGGTCA 5 42 0 CAACAATAAC 0.980235 -259 CCCAGCCGTACAACAGGGCCACCAAGACCGTGA 5 123 0 CAACAGGACC 0.963429 -178 GGCAACTCAGCAATTGAACCAGATTTAGAT 5 281 0 CAGCAATACC 0.98631 -20 AGAAAGCCAACAACTTGATGCTAAATGATT 6 20 0 CAACAATATG 0.903496 -20 AAAAAAGAAACAACAAATTCACCATTAATGGTG 7 52 0 CAACAATACC 0.994948 -28 TATATCTTTGCAACAATTCCATCCCTACATTCC 8 187 1 CAACAATATC 0.988692 -114 ****** * *** Masking position 5 Map Score: 3.48242 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 129 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 5 TGATTAGTTTTTAACTCAATTTTTA 3 8 1 TTTTTAACTC 0.973212 -18 TTTTGCTTAACATTTAACTCTGTTTCCGAT 5 244 1 CATTTAACTC 0.970179 -57 CGATTCGATTCATCTAAATCTGGTTCAATT 5 270 1 CATCTAAATC 0.833832 -31 GTAATTTAAGTTTTTAAATCAGC 7 4 0 TTTTTAAATC 0.941597 -76 TTTATAAAACTTTTTAACTAGAAACTCCTA 8 28 1 TTTTTAACTA 0.82357 -273 CGACGAGCTTCTTTTCACTCATAACGAGCT 8 69 1 CTTTTCACTC 0.931579 -232 ATTCTCGTCTTATTTATATCTTTGCAACAA 8 173 1 TATTTATATC 0.734271 -128 ********** Masking position 5 Map Score: 2.45429 Number of sites scoring better than the average of aligned sites = 281 Number in coding regions = 225 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 6 TTAAAACGCGAGAAGCCCCGCGCCATAAAC 2 29 0 AGAAGCCCCG 0.976258 -65 TTTGGAAAACCCCTATTGGGTTTG 5 5 1 GAAAACCCCT 0.893346 -296 CTTTTTAACTAGAAACTCCTACCTGTTATC 8 37 1 AGAAACTCCT 0.968301 -264 ATGAGTGAAAAGAAGCTCGTCGGTGATAAC 8 61 0 AGAAGCTCGT 0.972907 -240 AAACACAAGAAAAAGCTCGTTATGAGTGAA 8 82 0 AAAAGCTCGT 0.963187 -219 ********** Masking position 4 Map Score: 0.561151 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 102 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 AAGAACCATTCTAGGCGGTGCTATACCACT 4 23 0 CTAGGCGGTG 0.994643 -52 TGGGAATTGACTAGCCGTTAGGTCAATGTT 5 152 1 CTAGCCGTTA 0.947219 -149 AGGGGACAGGCTGGGCGGTAATTTAAGTTT 7 21 0 CTGGGCGGTA 0.99101 -59 TGAAAAGAAGCTCGTCGGTGATAACAGGTA 8 56 0 CTCGTCGGTG 0.984183 -245 ********** Masking position 2 Map Score: 0.378337 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 118 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 8 TAGCCCCAAATTTTTTTTGTAAGCACTTTT 4 52 1 TTTTTTTTGT 0.882682 -23 GAATTTGTTGTTTCTTTTTTTCATT 7 65 1 TTTCTTTTTT 0.94573 -15 CTTCTTATCCTCTCTTATTTATAAAACTTT 8 11 1 TCTCTTATTT 0.887008 -290 TAACGAGCTTTTTCTTGTGTTTAGGCTTAG 8 90 1 TTTCTTGTGT 0.97059 -211 ATGAAAACAATTTCTTATGTCTCTCCACAG 8 145 0 TTTCTTATGT 0.975164 -156 ********** Masking position 5 Map Score: 1.01958 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 29 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 ********** No masking Map Score: -3.23764e-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: -3.23764e-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: -3.23764e-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