AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i182_synecho_ctra_100.orf -o182_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 RCY15119 104 Synechocystis #2 RCY49636 271 Synechocystis #3 RCY36009 224 Synechocystis #4 RCY19918 108 Synechocystis #5 RCT00385 300 Chlamydia_trachomatis #6 RCT00699 41 Chlamydia_trachomatis #7 RCT00700 109 Chlamydia_trachomatis Motif number 1 GGAAATTACCGGGATAGGGCGATCGCCTCCC 1 4 0 GGTGGGAGCT 0.971058 -101 CCACAGCCCAGGCCATGGGGAAATTACCGGGATAGGGC 1 22 0 GGAGGGATCC 0.950945 -83 CCATGGCCTGGGCTGTGGGGGATAGCCCCGAAAAACTC 1 42 1 GGGGGGAGCC 0.996178 -63 GGATGGGGGCCAGCGGAACCAGGGCGCT 2 1 1 GGGGGGAGAA 0.984105 -271 GTTTCTTCGTCGTAGGGGATGAATTTCTCTAAAAAAGG 2 77 0 CGGGGAATCT 0.82235 -195 TGACAACGGTGGTCGCAGAAGATCGACTGTTGCAACAA 2 159 0 GGGAGAAGCT 0.91759 -113 AACTTAAGAAGCTGGAGGAAAATTGACAACGGTGGTCG 2 182 0 GCGGGAAGCA 0.990435 -90 AAATCGGACGGGATACGGGGGACAGAAACGTTCAAGGT 2 240 0 GGAGGGAGAA 0.946818 -32 GGGTGGTCAAGGTTAGGGAAACGAGTCTAGAGTTCCCT 3 116 0 GGAGGACGCT 0.938504 -109 CAATGCCATGGCTGGAGGGAGAGTTGCAGCTCGGGGTG 3 149 0 GCGGGGATCA 0.982712 -76 CAATTGTGCCAGTTGGGGGCCAATGCCATGGCTGGAGG 3 169 0 AGGGGGAGCA 0.972186 -56 GGCAGGGTAGGGAAATGGAATCTAGTCAAATCTACTGG 4 60 0 GGAGGACGCA 0.954559 -49 TCTGCGCACAGCGAGGGGATTATAGACAAAGAACGTTT 7 41 1 GCGGGAAGCA 0.990435 -69 GGAAAACTTAGCCAGTGGGAAACGTTCTTTGTCTATAA 7 60 0 GCGGGGATCT 0.976354 -50 ** * *** * * ** Masking position 8 Map Score: 21.1951 Number of sites scoring better than the average of aligned sites = 1628 Number in coding regions = 1504 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 2 CCACAGCCCAGGCCATGGGGAAATTACCGG 1 30 0 GGCCATGGGG 0.914335 -75 ATAGGACTATAGCCATGGCAGAATAAGTTT 2 46 1 AGCCATGGCA 0.546983 -226 CAGTACCCATTGTAAAGGTATTGACCGTTT 3 34 1 TGTAAAGGTA 0.73266 -191 GTTGACCGAAGGCAAAGGTATGCTTAATTG 3 70 1 GGCAAAGGTA 0.959173 -155 GACCAGATAATGCCAAGGGAACTCTAGACT 3 101 1 TGCCAAGGGA 0.933898 -124 AGCTCGGGGTGGTCAAGGTTAGGGAAACGA 3 130 0 GGTCAAGGTT 0.848692 -95 CTCTCCCTCCAGCCATGGCATTGGCCCCCA 3 164 1 AGCCATGGCA 0.546983 -61 TTTGGTCTGAGATCATGGCAGGGTAGGGAA 4 84 0 GATCATGGCA 0.860423 -25 CTCCGGATCTGATCAAGGCAAACAGCGGTT 5 201 0 GATCAAGGCA 0.906807 -100 GTCACGACCTAGCAAAGGTATTTAATTGTC 5 280 1 AGCAAAGGTA 0.901654 -21 ********** Masking position 5 Map Score: 7.80148 Number of sites scoring better than the average of aligned sites = 3089 Number in coding regions = 2827 Number in noncoding regions = 262 Number of orfs with sites within 600 bp upstream = 279 Fraction of orfs with sites within 600 bp upstream = 0.0448121 Motif number 3 GTAGATCAGAGTTTTTCGGGGCTATCCCCC 1 58 0 GTTTTTCGGG 0.993687 -47 CTATTTTAAAGCTTTTCTGGGAAGGCTTTG 2 115 0 GCTTTTCTGG 0.95475 -157 GGTATTGACCGTTTTCCGGGGTTGACCGAA 3 50 1 GTTTTCCGGG 0.982921 -175 CGTGTATCTAGTTTTTCAAGATTGCTAAAA 5 241 1 GTTTTTCAAG 0.957548 -60 TCGCTATCTGATTTTTCAGGTTGAGTAT 6 24 1 ATTTTTCAGG 0.957548 -18 AATCTACCCCGTTTTTGAGGAAAACTTAGC 7 86 0 GTTTTTGAGG 0.970956 -24 ********** Masking position 5 Map Score: 5.24295 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 170 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 4 GGGAAATTACCGGGATAGGGCGATCGCCTC 1 13 0 CGGGATAGGG 0.892241 -92 TCCCCATGGCCTGGGCTGTGGGGGATAGCC 1 39 1 CTGGGCTGTG 0.87361 -66 CAGAGTTTTTCGGGGCTATCCCCCACAGCC 1 52 0 CGGGGCTATC 0.876158 -53 TAAAGCTTTTCTGGGAAGGCTTTGGTTTCT 2 109 0 CTGGGAAGGC 0.956643 -163 GACCGTTTTCCGGGGTTGACCGAAGGCAAA 3 56 1 CGGGGTTGAC 0.974833 -169 AGTTGCAGCTCGGGGTGGTCAAGGTTAGGG 3 136 0 CGGGGTGGTC 0.987345 -89 TCGGGAATTGCTGGGTAATCCGTTGCTAAA 4 27 1 CTGGGTAATC 0.867879 -82 GAGATCATGGCAGGGTAGGGAAATGGAATC 4 76 0 CAGGGTAGGG 0.924772 -33 TGATCAGATCCGGAGAGGGCTTTTTCGTGT 5 216 1 CGGAGAGGGC 0.798304 -85 TCCTCAAAAACGGGGTAGATTGAGA 7 95 1 CGGGGTAGAT 0.889627 -15 ********** Masking position 1 Map Score: 5.63753 Number of sites scoring better than the average of aligned sites = 1830 Number in coding regions = 1727 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 5 GGGAGGCGATCGCCCTATCCCGGTA 1 6 1 GCGATCGCCC 0.937138 -99 TGGGCTGTGGGGGATAGCCCCGAAAAACTC 1 50 1 GGGATAGCCC 0.895849 -55 GATCGGGTTAGCGGTAGATCAGAGTTTTTC 1 71 0 GCGGTAGATC 0.968263 -34 GGTGTAGTTCCCTAGATCGG 1 95 0 GGTGTAGTTC 0.912256 -10 TTCTGCCATGGCTATAGTCCTATGATGGAA 2 39 0 GCTATAGTCC 0.911559 -233 CCATTGTAAAGGTATTGACCGTTTTCCGGG 3 40 1 GGTATTGACC 0.929877 -185 ACCGTTTTCCGGGGTTGACCGAAGGCAAAG 3 57 1 GGGGTTGACC 0.980668 -168 CCTCAAAAACGGGGTAGATTGAGA 7 96 1 GGGGTAGATT 0.847369 -14 ********** Masking position 5 Map Score: 4.68088 Number of sites scoring better than the average of aligned sites = 939 Number in coding regions = 877 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 6 GGGATGAATTTCTCTAAAAAAGGGAAACTT 2 70 0 TCTCTAAAAA 0.831836 -202 GGGTAATCCGTTGCTAAAAATCCAGTAGAT 4 39 1 TTGCTAAAAA 0.973717 -70 TAGGCGACTTTTGAAAAAAAATCACCACAA 5 33 0 TTGAAAAAAA 0.879647 -268 GTGTCTTGTGTTGAAAAGAACCTCTTCTTA 5 117 1 TTGAAAAGAA 0.85844 -184 AGAGAAAACCTTTCTAAGAAGAGGTTCTTT 5 131 0 TTTCTAAGAA 0.915085 -170 TTTTTCAAGATTGCTAAAAAGTATTGTTGT 5 252 1 TTGCTAAAAA 0.973717 -49 ********** Masking position 6 Map Score: 2.00259 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 174 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 7 ATGCCAAGGGAACTCTAGACTCGTTTCCCTAA 3 110 1 AACTCTACTC 0.863036 -115 TAACACAATTCTTGATTGTGATT 5 2 1 AACACAACTT 0.972218 -299 AAAAAAAATCACCACAAATCACAATCAAGAAT 5 18 0 ACCACAACAC 0.978742 -283 GGTTCTTTTCAACACAAGACACAGGATTTTAT 5 107 0 AACACAACAC 0.982312 -194 CTAGGTCGTGACAACAATACTTTTTAGCAATC 5 260 0 ACAACAACTT 0.817869 -41 CGCAGAGTATAACACAAACCTCTACTTTCTGC 7 15 0 AACACAACTC 0.990441 -95 ******* *** Masking position 7 Map Score: 1.50587 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 68 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 8 TCGTAGGGGATGAATTTCTCTAAAAAAGGG 2 76 0 TGAATTTCTC 0.884037 -196 GCTAAATTGTTGCAACAGTCGATCTTCTGC 2 153 1 TGCAACAGTC 0.925367 -119 CACCCCGAGCTGCAACTCTCCCTCCAGCCA 3 149 1 TGCAACTCTC 0.984266 -76 TATTCATTACTCACAGTCGGGA 4 3 1 TTCATTACTC 0.841779 -106 CCTTGCATCTCTCTCGCTATCTG 6 4 1 TGCATCTCTC 0.988967 -38 ********** Masking position 4 Map Score: 0.160501 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 53 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 9 ********** No masking Map Score: 3.21409e-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: 3.21409e-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: 3.21409e-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