AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i337_synecho_ctra_300.orf -o337_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 RCY25137 127 Synechocystis #2 RCY52910 84 Synechocystis #3 RCY38727 285 Synechocystis #4 RCT00675 166 Chlamydia_trachomatis #5 RCT00676 300 Chlamydia_trachomatis Motif number 1 GTAGCTCCTTGACAAACCGGTCACCAAAGTTGC 2 12 1 GAAAAGGTCA 0.970851 -73 AATCATGGTGGAAGACCAGGGGTAAACCCAGTT 3 188 1 GAGACGGGGT 0.807839 -98 CCATTTTATCGAAAAACTGGGTTTACCCCTGGT 3 202 0 GAAAAGGGTT 0.859129 -84 CCAGTTTTTCGATAAAATGGGCCCCAGACCAAG 3 215 1 GAAAAGGGCC 0.96501 -71 AATTTACCAGGAAAAATTGAGCAGACTGGCAAA 3 256 0 GAAAAGAGCA 0.974407 -30 AATAGAGGAAGAAGAGAGGGTCAAAATTTTCAT 5 20 0 GAGAGGGTCA 0.925958 -281 TTAAAAAGGGGAAAAATAGAGGAAGAAGAGAGG 5 34 0 GAAAAGAGGA 0.969626 -267 GGTAAAAAAAGAAAAATTGGACTGCAAACAGCT 5 67 0 GAAAAGGACT 0.90252 -234 AAGGTTTTTTGAGAAGGTGAAGAGGTGGTAAAA 5 93 0 GAAAGGAAGA 0.871964 -208 GAGCATTCTAGATAATCTGGGGAGTTTTTCGCA 5 164 0 GAAATGGGGA 0.953591 -137 CTACACCCGCGAGAAGAAGAGCATTCTAGATAA 5 182 0 GAAAGGAGCA 0.976331 -119 ATCCGGGAAAGAGAAGCGGGTGATGAGGCTTGA 5 258 0 GAAAGGGTGA 0.968005 -43 ** *** ***** Masking position 5 Map Score: 12.4059 Number of sites scoring better than the average of aligned sites = 777 Number in coding regions = 657 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 2 CCAGTTTCAAGGCTTGCCGGGATGATA 1 7 1 TCAAGGTTGC 0.978421 -121 CTAACTTTAATCAAGGTTTGTTAGAAAACCT 1 107 1 TCAAGGTTGT 0.956178 -21 AAAGTTGCCACAATGATTTGTTAGCTAATGC 2 37 1 CAATGATTGT 0.778819 -48 CTCGATGTTACCAAGAGAAGCT 2 73 1 CCAAGAAAGC 0.911959 -12 AAACACGACCCATAGGGATGCCTAAACAGGT 3 116 1 CATAGGATGC 0.768924 -170 TGGTCTTCCACCATGATTTGCCCTAGCCAAA 3 175 0 CCATGATTGC 0.970354 -111 GGGCCCCAGACCAAGGCTTGTAATTTGCCAG 3 233 1 CCAAGGTTGT 0.978421 -53 TTTTCTAGGGTCAAGAGTAGCCATAACGTAA 4 107 1 TCAAGATAGC 0.914828 -60 AACCTACAAGCAAAGGATTGCGAAAAACTCC 5 146 1 CAAAGGTTGC 0.985247 -155 ****** **** Masking position 5 Map Score: 8.41672 Number of sites scoring better than the average of aligned sites = 855 Number in coding regions = 773 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 3 GGGATGATATCTTTTGCCAGTGGAATGTCG 1 29 1 CTTTTGCCAG 0.94403 -99 CCGGTCACCAAAGTTGCCACAATGATTTGT 2 28 1 AAGTTGCCAC 0.902081 -57 CCGTTGCTCGATGTTACCAAGAGAAGCT 2 67 1 ATGTTACCAA 0.9384 -18 CCATGATTTGCCCTAGCCAAAATCGAAAAT 3 166 0 CCCTAGCCAA 0.796216 -120 CAAGGCTTGTAATTTGCCAGTCTGCTCAAT 3 244 1 AATTTGCCAG 0.939648 -42 ACGGGGAAATTTACCAGGAAAAATTGA 3 269 0 AATTTACCAG 0.88795 -17 GTAAGCACACCTGTAACCAAATGATTTGAG 4 134 1 CTGTAACCAA 0.821004 -33 CTCAAAAAACCTTTTTCCAAAGTTTTTTTG 5 113 1 CTTTTTCCAA 0.759828 -188 GTAGAGCGCCACGTTGCCAACGTGAAGGTC 5 222 1 ACGTTGCCAA 0.961273 -79 TTTCCCGGATAACTTACCAATGGGTATTCT 5 281 1 AACTTACCAA 0.888455 -20 ********** Masking position 4 Map Score: 4.61626 Number of sites scoring better than the average of aligned sites = 1192 Number in coding regions = 1064 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 4 GCCTTCCTAACGTGAGACCAAGGGCGATGT 3 9 1 AACGTGACCA 0.936323 -277 TAGGGCGGCAAAAACACGACCCATAGGGATGC 3 105 1 AAAACGACCC 0.984965 -181 GTTTTTCGATAAAATGGGCCCCAGACCAAGGC 3 218 1 AAAATGCCCC 0.8939 -68 ATCGCAGGAAAACGCTTGACCCAAGAGACACT 4 16 1 AACGCGACCC 0.995747 -151 TGACCCTAGAAAAGAAAGACCCCATCTAATTC 4 88 0 AAAGAGACCC 0.965854 -79 ACGTTATGGCTACTCTTGACCCTAGAAAAGAA 4 104 0 TACTCGACCC 0.963877 -63 AAATCAATGAAAATTTTGACCCTCTCTTCTTC 5 14 1 AAATTGACCC 0.978472 -287 ATGAGGCTTGAACTCACGACCTTCACGTTGGC 5 237 0 AACTCGACCT 0.950755 -64 ***** ***** Masking position 2 Map Score: 7.10575 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 165 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 5 AATCAAGGTTTGTTAGAAAACCT 1 115 1 TTTAAAACCT 0.986956 -13 GGCGCTCCATTGTTTAACCACCTGTTTAGGCAT 3 133 0 TTTACCACCT 0.988786 -153 CAATTTTTCTTTTTTTACCACCTCTTCACCTTC 5 81 1 TTTACCACCT 0.988788 -220 CTCTTCACCTTCTCAAAAAACCTTTTTCCAAAG 5 102 1 TTCAAAACCT 0.971506 -199 TCCAAAGTTTTTTTGTAAAACCTACAAGCAAAG 5 128 1 TTTAAAACCT 0.986958 -173 * ** ******* Masking position 7 Map Score: 2.70517 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 42 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 TAGGGTAGCTTACGGCGACATCGCCCTTGG 3 28 0 TACGGCGACA 0.975027 -258 ACATCCCTTTTAGGGCGGCAAAAACACGAC 3 95 1 TAGGGCGGCA 0.982574 -191 GGTTAAACAATGGAGCGCCATTTTCGATTT 3 147 1 TGGAGCGCCA 0.705205 -139 AGCTCAGTGGTAGAGCGCCACGTTGCCAAC 5 213 1 TAGAGCGCCA 0.96568 -88 ********** Masking position 1 Map Score: 2.31121 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 40 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 GGGATTAATTCGACATTCCACTGGCAAAAGAT 1 37 0 CGACATCACT 0.94681 -91 AGTTAGATATCAACATTATCCTTTGCCTCGAA 1 81 0 CAACATACCT 0.849407 -47 TAGCTTACGGCGACATCGCCCTTGGTCTCACG 3 21 0 CGACATGCCT 0.985351 -265 CAAAAATGAACGAAAATCCCCTAAAGTAGGGT 3 52 0 CGAAAACCCT 0.984288 -234 TAGCCAAAATCGAAAATGGCGCTCCATTGTTT 3 151 0 CGAAAAGCGC 0.841167 -135 CCATCTAATTCAAAATACACCTACGCATCAAA 4 67 0 CAAAATCCCT 0.95831 -100 CAAAGGATTGCGAAAAACTCCCCAGATTATCT 5 156 1 CGAAAACCCC 0.972583 -145 CTTGAACTCACGACCTTCACGTTGGCAACGTG 5 231 0 CGACCTCCGT 0.937419 -70 ****** * *** Masking position 3 Map Score: 2.66034 Number of sites scoring better than the average of aligned sites = 376 Number in coding regions = 328 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 8 TCGATTTTGGCTAGGGCAAATCATGGTGGA 3 170 1 CTAGGGCAAA 0.962644 -116 GGTGGAAGACCAGGGGTAAACCCAGTTTTT 3 194 1 CAGGGGTAAA 0.945294 -92 AAGCCTTGGTCTGGGGCCCATTTTATCGAA 3 222 0 CTGGGGCCCA 0.984318 -64 AAGCGTTTTCCTGCGATCAAAA 4 3 0 CTGCGATCAA 0.880276 -164 TTAAGTGTCTCTTGGGTCAAGCGTTTTCCT 4 21 0 CTTGGGTCAA 0.98119 -146 TCTTTCTTTTCTAGGGTCAAGAGTAGCCAT 4 101 1 CTAGGGTCAA 0.989247 -66 ********** Masking position 10 Map Score: 3.66724 Number of sites scoring better than the average of aligned sites = 707 Number in coding regions = 635 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 9 ********** No masking Map Score: 1.77168e-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: 1.77168e-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: 1.77168e-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