AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i174_synecho_ctra_300.orf -o174_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 RCY43755 46 Synechocystis #2 RCY14039 107 Synechocystis #3 RCY51943 111 Synechocystis #4 RCT00118 300 Chlamydia_trachomatis Motif number 1 ATTACCCACCCCCCAATACAACAAAATACGA 2 85 0 CCCCAATACA 0.994099 -23 GACCCCGCGTCCCCATTCCCA 3 1 0 CCCCATTCCA 0.986994 -111 GCTTTCGTATCGCCAATGCAACATGTTCTAC 4 43 0 CGCCAATGCA 0.990747 -258 TCTTGAATCCCTCCATAGCAATCAGTGCTTT 4 69 0 CTCCATAGCA 0.974993 -232 GACAGGCACACCCCAAAGCGATTCTGCACTG 4 115 0 CCCCAAAGCA 0.997356 -186 ACTCTTAGTTCCCCAAAAATAATTGCCATTG 4 184 1 CCCCAAAAAA 0.963061 -117 ********* * Masking position 5 Map Score: 7.63391 Number of sites scoring better than the average of aligned sites = 608 Number in coding regions = 557 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 2 CAAAAGTTCACCCAACATTCTACTAGGGG 1 6 0 CCCACTCTCT 0.986462 -41 TTGGTCAGCTCAAGCTTTACTAATCGTATTTTGT 2 62 1 CAACTTCTAT 0.858529 -46 GTCAACAAAACCCGATATTCTACTAAAAGACTAA 3 52 1 CCCATTCTCT 0.995795 -60 ATCGCCAATGCAACATGTTCTACTCTGTCCTATA 4 32 0 CAAATTCTCT 0.974838 -269 CTAAGAGTTTCCCTCTATCCTCCTTTTCTCTTTA 4 158 0 CCCCTTCTCT 0.996515 -143 ATTGCCATTGTACACTCTCCTTCTTATCGTAGAG 4 205 1 TACCTTCTCT 0.974208 -96 GGCCTCTTCTCTCATTTCCTTCTGTAGAGATGA 4 278 0 TCTATTCTCT 0.925256 -23 *** ** * ** ** Masking position 8 Map Score: 5.56268 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 188 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 3 AGTAGAATGTTGGGTGAACTTTTGAGTCTT 1 16 1 TGGGTGAACT 0.932744 -31 CGTAGGCTCATTGGTCAGCTCAAGCTTTAC 2 52 1 TTGGTCAGCT 0.878769 -56 GTTGTATTGGGGGGTGGGTAATTC 2 94 1 GGGGTGGGTA 0.980923 -14 ATGGGGACGCGGGGTCAGTATATCGGCGAT 3 16 1 GGGGTCAGTA 0.961384 -96 ACGCTAGAGCTGGGTGGGCCA 3 101 1 TGGGTGGGCC 0.993363 -11 GAATCGCTTTGGGGTGTGCCTGTCGTGAAA 4 122 1 GGGGTGTGCC 0.988543 -179 ********** Masking position 5 Map Score: 3.41417 Number of sites scoring better than the average of aligned sites = 768 Number in coding regions = 717 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 4 GGAAGCCAAGGAAGACTCAAA 1 36 0 GAAGCCAAGG 0.880846 -11 TCTAGCGTTGGAAAACGATGTGTTTAGTCT 3 79 0 GAAAACGATG 0.891203 -33 TTGCATTGGCGATACGAAAGCACTGATTGC 4 53 1 GATACGAAAG 0.897965 -248 AGCACTGATTGCTATGGAGGGATTCAAGAA 4 71 1 GCTATGGAGG 0.898622 -230 TGCCTGTCGTGAAATGTATGTAAAGAGAAA 4 138 1 GAAATGTATG 0.939545 -163 TATGTAAAGAGAAAAGGAGGATAGAGGGAA 4 154 1 GAAAAGGAGG 0.982315 -147 AACCCTCTACGATAAGAAGGAGAGTGTACA 4 213 0 GATAAGAAGG 0.960203 -88 CCACAAGATTGAAGTGTATGTGCGTCATCT 4 254 1 GAAGTGTATG 0.88368 -47 TCTACAGAAGGAAATGAGAGAAGAGGCC 4 283 1 GAAATGAGAG 0.82543 -18 ********** Masking position 1 Map Score: 3.29365 Number of sites scoring better than the average of aligned sites = 1137 Number in coding regions = 1028 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 5 GGAAGCCAAGGAAGACTCAAAAG 1 34 0 AGCCAAGGAA 0.959761 -13 CCACCCCCCAATACAACAAAATACGATTAG 2 81 0 ATACAACAAA 0.95052 -27 GCGATCGCCTAGTCAACAAAACCCGATATT 3 41 1 AGTCAACAAA 0.977416 -71 CTATGGAGGGATTCAAGAAAATTCTTGTCT 4 82 1 ATTCAAGAAA 0.96387 -219 TGCACTGCGCAGACAAGAATTTTCTTGAAT 4 92 0 AGACAAGAAT 0.950292 -209 ********** Masking position 5 Map Score: 1.8456 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 209 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 6 GAAGACTCAAAAGTTCACCCAACATTCTAC 1 17 0 AAGTTCACCC 0.974563 -30 GGGTAGATGGATTTTAACCCGTAGGCTCAT 2 33 1 ATTTTAACCC 0.989574 -75 GTGGTCAAAAATTTTAACCCTCTACGATAA 4 228 0 ATTTTAACCC 0.989574 -73 ********** Masking position 7 Map Score: 0.59518 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 32 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 GATTAGTAAAGCTTGAGCTGACCAATGAGC 2 57 0 GCTTGAGCTG 0.996856 -51 GTTTTCCAACGCTAGAGCTGGGTGGGCCA 3 93 1 GCTAGAGCTG 0.996856 -19 ********** Masking position 6 Map Score: 0.0773379 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 9 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 8 ********** No masking Map Score: -1.01364e-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 9 ********** No masking Map Score: -1.01364e-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: -1.01364e-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