AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i026_synecho_ctra_300.orf -o026_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 RCY27056 300 Synechocystis #2 RCY16813 175 Synechocystis #3 RCY36770 293 Synechocystis #4 RCY48012 163 Synechocystis #5 RCT00850 300 Chlamydia_trachomatis Motif number 1 TTCCAACCAGCCTTGGCCATGAAGGTTAAC 1 20 1 CCTTGGCCAT 0.92266 -281 GACGGGAATACCTTTGGAAAGTTTTATTGA 1 222 0 CCTTTGGAAA 0.959452 -79 ACTATTTTCAACTATGGATTAGCTAGGTGA 2 41 0 ACTATGGATT 0.592173 -135 AAGGCAGGCCCCTAGGGATTGTCATTGTTG 2 137 1 CCTAGGGATT 0.962481 -39 TTCACCCAGTCCTAGAGCATA 3 2 0 CCTAGAGCAT 0.82596 -292 ATTCGCTGCCCCCTGGGCATTAACCCATGG 3 59 1 CCCTGGGCAT 0.989641 -235 TGGGCATTAACCCATGGAAAGTATGGAAAA 3 72 1 CCCATGGAAA 0.928812 -222 GGGGCGATCGCCTTGGGAATTTTAGTGGCA 3 127 1 CCTTGGGAAT 0.990928 -167 GGTGTCAAAGACTTGGGAAAATAGGCACAA 3 178 1 ACTTGGGAAA 0.908443 -116 AGGAAATACCCTGGGAAAAGCAATATGG 3 276 0 CCCTGGGAAA 0.983668 -18 AGGTAATGAACCCTTGGCTTTTAGCTAAGA 5 149 0 CCCTTGGCTT 0.933248 -152 ********** Masking position 2 Map Score: 12.6978 Number of sites scoring better than the average of aligned sites = 3085 Number in coding regions = 2784 Number in noncoding regions = 301 Number of orfs with sites within 600 bp upstream = 293 Fraction of orfs with sites within 600 bp upstream = 0.0470607 Motif number 2 AAAGATACTTAGCCAGATGGGCAAGGTGAAAG 1 159 1 AGCAATGGGC 0.989061 -142 AGTTTTATTGAGCCCCATAGGTTAACCAATGA 1 201 0 AGCCATAGGT 0.885915 -100 TTCAGCATTAGGGAAGGCAGGCCCCTAGGGAT 2 124 1 GGGAGCAGGC 0.8985 -52 TCAAAGACTTGGGAAAATAGGCACAATTCTAG 3 182 1 GGGAATAGGC 0.983291 -112 CCCTGGGAAAAGCAATATGGGCGGAGGCTACC 3 264 0 AGCAATGGGC 0.989023 -30 GGATTAGGGCAGGAAAATGGTCCGGCCTTGGT 4 58 0 AGGAATGGTC 0.914058 -106 AGCCAAATGTGGGTCGATGGGCAATGGACTTT 4 101 0 GGGCATGGGC 0.981433 -63 CAAGCGGAAGAGCTAAACAGGTAATCTCAATT 5 216 0 AGCAACAGGT 0.886054 -85 *** * ****** Masking position 10 Map Score: 4.50935 Number of sites scoring better than the average of aligned sites = 638 Number in coding regions = 573 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 3 ATTGATCAATCACCAAAAATGATTCAGCAT 2 102 1 CACCAAAAAT 0.93778 -74 AAGGCGATCGCCCCTAAAATCCAATCTAAA 3 111 0 CCCCTAAAAT 0.988127 -183 ACTAAGCCTGCCACTAAAATTCCCAAGGCG 3 135 0 CCACTAAAAT 0.965661 -159 TGTCGAGAACCCCCTAGAATTGTGCCTATT 3 197 0 CCCCTAGAAT 0.985708 -97 TTGGCTCGGTAACCTAGAATTGGAGAGCCT 4 127 1 AACCTAGAAT 0.887256 -37 GGAGATGTTCACACAAAAATAAAGTAAACA 5 95 0 ACACAAAAAT 0.835873 -206 ********** Masking position 6 Map Score: 3.81607 Number of sites scoring better than the average of aligned sites = 308 Number in coding regions = 248 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 4 TTAGAGATAAATCTGGAGCACTGTGCCGCAAA 1 130 1 ATTGGAGCAT 0.929644 -171 CACCTTGCCCATCTGGCTAAGTATCTTTGCGG 1 155 0 ATTGGCTAAT 0.968207 -146 GTGAAAGTCAATGGTGATCATTGGTTAACCTA 1 184 1 ATGTGATCAT 0.904021 -117 TGGTTAACCTATGGGGCTCAATAAAACTTTCC 1 205 1 ATGGGCTCAT 0.970827 -96 ACCTGTGTATATTTTTCTAACTATTTTCAACT 2 58 0 ATTTTCTAAT 0.627028 -118 GGGGCAAAAAAAATTGATCAATCACCAAAAAT 2 90 1 AATTGATCAT 0.730555 -86 AGTATGGAAAATACGGCTAATTTAGATTGGAT 3 91 1 ATCGGCTAAT 0.890859 -203 AGGCTTAGTGATGTTGCTCAATGGTGTCAAAG 3 156 1 ATTTGCTCAT 0.97767 -138 GGCAATAATTTTGAGAAATGAAATCTCTT 4 8 1 ATTTGAGAAT 0.776736 -156 ATCGACCCACATTTGGCTCGGTAACCTAGAAT 4 115 1 ATTGGCTCGT 0.936938 -49 ** ******* * Masking position 1 Map Score: 3.28486 Number of sites scoring better than the average of aligned sites = 531 Number in coding regions = 465 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 5 CGGACAGCGCCCGGTTGAGGGTATTTCGCGG 1 59 1 CGGTTGAGGG 0.977456 -242 AAAAATGATTCAGCATTAGGGAAGGCAGGCC 2 116 1 CGCATTAGGG 0.985651 -60 ATTTTAGTGGCAGGCTTAGTGATGTTGCTCA 3 145 1 CGGCTTAGTG 0.989088 -149 GAAAATGGTCCGGCCTTGGTGGGTTTAGGTA 4 47 0 CGCCTTGGTG 0.955214 -117 TGCCTTTGCTCTGGATTAGGGCAGGAAAATG 4 71 0 CGGATTAGGG 0.992489 -93 CATTCCGTATCGGGATGTGTGTTTACTTTAT 5 76 1 CGGATGTGTG 0.954909 -225 * ********* Masking position 6 Map Score: 3.15827 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 217 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 6 GAAAGTCAATGGTGATCATTGGTTAACCTA 1 186 1 GGTGATCATT 0.952653 -115 GTTAACCTATGGGGCTCAATAAAACTTTCC 1 207 1 GGGGCTCAAT 0.972864 -94 CAGTTAATTCGTTGATCAATTAATCACCTA 2 18 1 GTTGATCAAT 0.688273 -158 GGCAAAAAAAATTGATCAATCACCAAAAAT 2 92 1 ATTGATCAAT 0.497513 -84 GCTTAGTGATGTTGCTCAATGGTGTCAAAG 3 158 1 GTTGCTCAAT 0.946067 -136 ********** Masking position 6 Map Score: 2.44903 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 102 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 AGCCAGATGGGCAAGGTGAAAGTCAATGGT 1 169 1 GCAAGGTGAA 0.912148 -132 CTATGGATTAGCTAGGTGATTAATTGATCA 2 30 0 GCTAGGTGAT 0.835596 -146 TAGGTACACTGCAAAGAGATTTCATTTCTC 4 23 0 GCAAAGAGAT 0.946581 -141 CTGGATTAGGGCAGGAAAATGGTCCGGCCT 4 62 0 GCAGGAAAAT 0.758374 -102 GTTCATATGAGGAGGGAGATAGTACAAAAA 5 13 1 GGAGGGAGAT 0.984669 -288 TGAAACGAATGTAGGAAGATTTTTGTACTA 5 32 0 GTAGGAAGAT 0.904736 -269 TAAGATATTTGTAAGGAGATGTTCACACAA 5 109 0 GTAAGGAGAT 0.963206 -192 CTTCTTTGAGGGAGAGAGAATTTTTTCTCT 5 277 1 GGAGAGAGAA 0.84321 -24 ********** Masking position 9 Map Score: 2.69596 Number of sites scoring better than the average of aligned sites = 783 Number in coding regions = 696 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 8 CCAAGGCTGGTTGGAAGTAATTTGA 1 5 0 TTGGAATAAT 0.85823 -296 GGGAATACCTTTGGAAAGTTTTATTGAGCCC 1 218 0 TTGGAAGTTT 0.838033 -83 GCATTAACCCATGGAAAGTATGGAAAATACG 3 75 1 ATGGAAGTAT 0.975081 -219 ACATCATATAATGAAACGAATGTAGGAAGAT 5 42 0 ATGAAAGAAT 0.918664 -259 ACATCCCGATACGGAATGAATACATCATATA 5 63 0 ACGGAAGAAT 0.963893 -238 AAATCCGATGATGGAATGAATACCAAGCGGA 5 240 0 ATGGAAGAAT 0.986478 -61 ****** **** Masking position 6 Map Score: 1.62319 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 96 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 9 GGAGCACTGTGCCGCAAAGATACTTAGCCA 1 144 1 GCCGCAAAGA 0.985207 -157 GGAAAAACCTTCAAAGAAGCAACAATG 2 159 0 CCTTCAAAGA 0.979839 -17 GTTTAGGTACACTGCAAAGAGATTTCATTT 4 26 0 ACTGCAAAGA 0.966662 -138 AATTCTCTCTCCCTCAAAGAAGATAGCTAA 5 269 0 CCCTCAAAGA 0.987468 -32 ********** Masking position 6 Map Score: 1.35621 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 47 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 10 CCGCAAAGATACTTAGCCAGATGGGCAAGGT 1 155 1 ACTAGCCAGA 0.836916 -146 TCAATTAATCACCTAGCTAATCCATAGTTGA 2 33 1 ACCAGCTAAT 0.905903 -143 AGTCATGGTTACCCATCCAAATCATTCGCTG 3 36 1 ACCATCCAAA 0.970605 -258 CTGGGCATTAACCCATGGAAAGTATGGAAAA 3 71 1 ACCATGGAAA 0.789555 -223 GCCCCTAAAATCCAATCTAAATTAGCCGTAT 3 101 0 TCCATCTAAA 0.884892 -193 ATTCTAGGTTACCGAGCCAAATGTGGGTCGA 4 116 0 ACCAGCCAAA 0.9883 -48 GCCTCTTCTTTCTTAGCTAAAAGCCAAGGGT 5 139 1 TCTAGCTAAA 0.818125 -162 TGGAATGAATACCAAGCGGAAGAGCTAAACA 5 229 0 ACCAGCGGAA 0.939036 -72 *** ******* Masking position 5 Map Score: 1.37968 Number of sites scoring better than the average of aligned sites = 641 Number in coding regions = 561 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 11 ********** No masking Map Score: 1.21746e-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: 1.21746e-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: 1.21746e-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