AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i160_synecho_ctra_100.orf -o160_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 RCY48177 106 Synechocystis #2 RCT00719 300 Chlamydia_trachomatis Motif number 1 CTCCTAGATAAATTTTTTTTGTAAAATTAC 1 82 0 AATTTTTTTT 0.812141 -25 GCATAAGATGTAGCTTTCTTTCGAACGAGG 2 52 0 TAGCTTTCTT 0.77634 -249 TATGCTATCCCCTATTTTTTATGCACCTAT 2 77 1 CCTATTTTTT 0.985292 -224 TTTTTATGCACCTATTTTTTATCAACTCCC 2 92 1 CCTATTTTTT 0.985292 -209 CCCAAAAAACCCTTTTTCTTAACCTCTCAA 2 120 1 CCTTTTTCTT 0.977084 -181 AAAATTTTCCTCTCTTTTTTTCTTTTTTTT 2 191 1 TCTCTTTTTT 0.986627 -110 TCTCTTTTTTTCTTTTTTTTGCTCATCCTA 2 201 1 TCTTTTTTTT 0.988888 -100 CTTCCTCTCTTCGATTTTTTTGTCGAAATT 2 233 1 TCGATTTTTT 0.970936 -68 TTGTCGAAATTCTTTTTTTTAGCGCTCCAA 2 252 1 TCTTTTTTTT 0.988888 -49 ********** Masking position 5 Map Score: 16.4009 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 284 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 2 CCAATCCTTGAGGATCAGGGGATTTAGTCTT 1 18 0 AGGATAGGGG 0.995475 -89 CTGATCCTCAAGGATTGGGGGCACCGGGGGA 1 31 1 AGGATGGGGG 0.997804 -76 GCCTCTTACGTGGATGAGAGGGCGCGATAG 2 10 0 TGGATAGAGG 0.974239 -291 CTTTCGAACGAGGGTTGAAGGAAGGCCTCTT 2 34 0 AGGGTGAAGG 0.975103 -267 AATAGGGGATAGCATAAGATGTAGCTTTCTT 2 62 0 AGCATAGATG 0.944308 -239 AAAAGTGTTAAGGATAGTGTGTGAGGGGATA 2 152 0 AGGATGTGTG 0.971454 -149 GAAGAGAGGAAGGGTAGGATGAGCAAAAAAA 2 214 0 AGGGTGGATG 0.991908 -87 ***** ***** Masking position 5 Map Score: 10.816 Number of sites scoring better than the average of aligned sites = 482 Number in coding regions = 413 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 3 CTTTGCTAGCTTATCATTTCCCCCGGTGCC 1 50 0 TTATCATTTC 0.903331 -57 ACATCTTATGCTATCCCCTATTTTTTATGC 2 71 1 CTATCCCCTA 0.950273 -230 CACCTATTTTTTATCAACTCCCCAAAAAAC 2 100 1 TTATCAACTC 0.956326 -201 ACCCTTTTTCTTAACCTCTCAATTTATCCC 2 128 1 TTAACCTCTC 0.982087 -173 ACCTCTCAATTTATCCCCTCACACACTATC 2 141 1 TTATCCCCTC 0.995453 -160 TAAAACAAAATTTTCCTCTCTTTTTTTCTT 2 185 1 TTTTCCTCTC 0.991371 -116 CTCATCCTACCCTTCCTCTCTTCGATTTTT 2 222 1 CCTTCCTCTC 0.959657 -79 ********** Masking position 9 Map Score: 8.57143 Number of sites scoring better than the average of aligned sites = 462 Number in coding regions = 384 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 4 AGATAAATTTTTTTTGTAAAATTACGCCTT 1 77 0 TTTTTGTAAA 0.965798 -30 TATCCCCTATTTTTTATGCACCTATTTTTT 2 82 1 TTTTTATGCA 0.929277 -219 ATGCACCTATTTTTTATCAACTCCCCAAAA 2 97 1 TTTTTATCAA 0.965277 -204 GAAAAAGGGTTTTTTGGGGAGTTGATAAAA 2 108 0 TTTTTGGGGA 0.921328 -193 CAAAAAACCCTTTTTCTTAACCTCTCAATT 2 122 1 TTTTTCTTAA 0.862557 -179 TCCTTAACACTTTTTATAAAACAAAATTTT 2 169 1 TTTTTATAAA 0.91513 -132 CTCTTCGATTTTTTTGTCGAAATTCTTTTT 2 239 1 TTTTTGTCGA 0.974396 -62 ********** Masking position 10 Map Score: 5.84327 Number of sites scoring better than the average of aligned sites = 337 Number in coding regions = 237 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 5 ********** No masking Map Score: -3.17312e-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 6 ********** No masking Map Score: -3.17312e-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 7 ********** No masking Map Score: -3.17312e-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