AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i307_synecho_ctra_100.orf -o307_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 RCY40674 143 Synechocystis #2 RCY52862 204 Synechocystis #3 RCT00577 197 Chlamydia_trachomatis Motif number 1 CATATAAGTCAAGTTTCTCTGAATTTGAATT 1 28 0 AAGTTCTCTG 0.958761 -116 GATTACAAATCAGTTGCTCTACCACTGAGCT 2 79 1 CAGTTCTCTA 0.958761 -126 TGAGCTACACCAGCATCTCTGATACAGAATA 2 104 1 CAGCACTCTG 0.94362 -101 GGTTAATCTTCTGCTATTCTGTATCAGAGAT 2 118 0 CTGCTTTCTG 0.92917 -87 AAAAATTAGCCAGACCCTCTGGGTTAATCTT 2 139 0 CAGACCTCTG 0.801582 -66 TTTTGATCTACAGCAACCCTGTTGGAAACCT 3 67 1 CAGCACCCTG 0.979959 -131 AAAAAAGAAACAGCACCTCTGTATAGAGAGT 3 156 0 CAGCACTCTG 0.94362 -42 ***** ***** Masking position 10 Map Score: 10.8293 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 171 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 2 ATAGATGAAGTAAATAGGTTTTGGTCACCAT 1 65 0 TAAAAGGTTT 0.98972 -79 CTTTCCTTAATTAACAGGTATAGTTCCATAC 1 120 1 TTAAAGGTAT 0.959731 -24 TACGGATCGTTAAAAAAGTTTTTCGGGGACA 2 169 0 TAAAAAGTTT 0.970293 -36 GGTTTTACTAGGTTTTACGGATCGT 2 190 0 TTACAGGTTT 0.972151 -15 CTTTTTTATTTTAAGAGGTTTCCAACAGGGT 3 82 0 TTAAAGGTTT 0.989761 -116 CCTCTTAAAATAAAAAAGCTTAGTGAAAGAA 3 95 1 TAAAAAGCTT 0.92275 -103 **** ****** Masking position 6 Map Score: 6.94877 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 36 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 3 TCATATAAGTCAAGTTTCTCTGAATTTGAA 1 30 0 CAAGTTTCTC 0.865432 -114 GTTTTGGTCACCATATCCTTCATATAAGTC 1 49 0 CCATATCCTT 0.86161 -95 GTTTCAATGACAAGCATCTTTCCTTAATTA 1 103 1 CAAGCATCTT 0.929173 -41 AATCCCGTCACCAGCTTATTTTGAATTCAT 2 32 0 CCAGCTTATT 0.864956 -173 CTGAGCTACACCAGCATCTCTGATACAGAA 2 103 1 CCAGCATCTC 0.993231 -102 CAAAAATTAGCCAGACCCTCTGGGTTAATC 2 141 0 CCAGACCCTC 0.986872 -64 ATCATCCTGCCCATACTCTCTATACAGAGG 3 142 1 CCATACTCTC 0.946068 -56 AAAAAAAGAAACAGCACCTCTGTATAGAGA 3 158 0 ACAGCACCTC 0.941386 -40 ********** Masking position 3 Map Score: 5.84248 Number of sites scoring better than the average of aligned sites = 1159 Number in coding regions = 1046 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 4 TGAAGGATATGGTGACCAAAACCTATTTACT 1 57 1 GGGACCAAAA 0.995147 -87 AAAGTTTTTCGGGGACAAAAATTAGCCAGAC 2 155 0 GGGACAAAAA 0.994764 -50 CAGGGTTGCTGTAGATCAAAAAAACAAAAAT 3 57 0 GTGATCAAAA 0.958174 -141 GGATGATAGCGGCGATAAGAATTTTCTTTCA 3 118 0 GGGATAAGAA 0.974347 -80 AATCCCTTTGGATGACAAAAAAAAGAAACAG 3 174 0 GAGACAAAAA 0.979514 -24 ** ******** Masking position 5 Map Score: 4.72794 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 129 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 TCAAGTTTCTCTGAATTTGAATTCTATGGA 1 21 0 CTGAATTTGA 0.914127 -123 CCGTCACCAGCTTATTTTGAATTCATTAAC 2 28 0 CTTATTTTGA 0.95039 -177 GGTAGAGCAACTGATTTGTAATCAGTCGGT 2 72 0 CTGATTTGTA 0.950095 -133 GAGGGTCTGGCTAATTTTTGTCCCCGAAAA 2 151 1 CTAATTTTTG 0.952877 -54 CCTTATCTTCCTGATTTTTGTTTTTTTGAT 3 44 1 CTGATTTTTG 0.987882 -154 GGTGCTGTTTCTTTTTTTTGTCATCCAAAG 3 170 1 CTTTTTTTTG 0.899641 -28 ********** Masking position 6 Map Score: 3.48119 Number of sites scoring better than the average of aligned sites = 358 Number in coding regions = 298 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 6 CTTGACTTATATGAAGGATATGGTGACCAA 1 46 1 ATGAAGGATA 0.925149 -98 CGAATAATAGATGAAGTAAATAGGTTTTGG 1 72 0 ATGAAGTAAA 0.790357 -72 AAAGATGCTTGTCATTGAAACACGAATAAT 1 94 0 GTCATTGAAA 0.851272 -50 ATACCTGTTAATTAAGGAAAGATGCTTGTC 1 111 0 ATTAAGGAAA 0.937429 -33 ACGATGATCAATGATAGGTTAATGAA 2 7 1 ATCAATGATA 0.911696 -198 TCAATGATAGGTTAATGAATTCAAAATAAG 2 18 1 GTTAATGAAT 0.658309 -187 GGTTTCCCTTGTCAAAGAGAGATCCAAAGG 3 16 0 GTCAAAGAGA 0.917846 -182 GTTGCTGTAGATCAAAAAAACAAAAATCAG 3 54 0 ATCAAAAAAA 0.758997 -144 AAAAAGCTTAGTGAAAGAAAATTCTTATCG 3 107 1 GTGAAAGAAA 0.965088 -91 ********** Masking position 4 Map Score: 1.91828 Number of sites scoring better than the average of aligned sites = 975 Number in coding regions = 816 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 182 Fraction of orfs with sites within 600 bp upstream = 0.0292323 Motif number 7 ********** No masking Map Score: -8.21797e-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 8 ********** No masking Map Score: -8.21797e-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: -8.21797e-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