AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i201_synecho_ctra_100.orf -o201_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 RCY46170 157 Synechocystis #2 RCY38700 191 Synechocystis #3 RCT00557 198 Chlamydia_trachomatis #4 RCT00558 24 Chlamydia_trachomatis Motif number 1 GCTGGCGATCGCCATTTACTTAGAAATAGGCTTAAAAC 1 71 0 GCATTTTAAA 0.917546 -87 TCAATTAATCGAATATTTATATTAAGGAGATAAACAGC 2 11 0 GATATTTAAA 0.979765 -181 TTGAAGACAAGCAGAGTAATGCTAACAAAACACGGTGG 2 85 0 GCGAGTTAAA 0.976816 -107 GGATAATAGGGCTGATTAAAGATAACTATCGTGGCTGG 2 141 0 GCGATTAAAA 0.966018 -51 TCTTTAGAAAGATGATTGTTAGGAAGGATTATAGA 3 8 0 GAGATTTAAA 0.9901 -191 CCCTGAATCAGACTATTTTTAAAAAGCAGGCTTTAGGG 3 60 1 GATATTTAAA 0.979759 -139 GGCTTTAGGGGCTTATTTTTCGTAAAAATCCAGAGATG 3 88 1 GCTATTTAAA 0.987147 -111 AGCAAGGAGCGAGGTTTTTTCCCAAACAGGGTCCCGCC 3 158 1 GAGTTTTAAA 0.973413 -41 ** **** * ** * Masking position 14 Map Score: 7.46419 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 71 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 2 AAATGGCGATCGCCAGCCAAGATTAGCAAAGA 1 92 1 CCCAGCCAGA 0.945713 -66 TGGCCTGTCTGTCTCGCACAGTGCTTTATTGT 2 52 0 GCTCGCAAGT 0.985547 -140 AGACAGACAGGCCACCCACCGTGTTTTGTTAG 2 70 1 GCACCCACGT 0.964381 -122 TATCTTTGAAGACAAGCAGAGTAATGCTAACA 2 96 0 GCAAGCAAGT 0.97746 -96 ACCGCTGAATGGCCAGCCACGATAGTTATCTT 2 129 1 GCCAGCCCGA 0.994685 -63 ATCCAGAGATGTCTTGCATCGATAAATTAAGA 3 115 1 GCTTGCACGA 0.964565 -84 CCCAAACAGGGTCCCGCCTCGTGAGTCAGCT 3 178 1 GCCCGCCCGT 0.997397 -21 * ****** *** Masking position 7 Map Score: 5.0182 Number of sites scoring better than the average of aligned sites = 385 Number in coding regions = 361 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 3 AGGCTCTTAACTTTTCTTCACGATTTTAAA 1 127 0 CTTTTCTTCA 0.958542 -31 AGTTAAGAGCCTTGTCTCCCCCT 1 145 1 CTTGTCTCCC 0.979001 -13 CATTACTCTGCTTGTCTTCAAAGATACACC 2 102 1 CTTGTCTTCA 0.950417 -90 TTAATCAGCCCTATTATCCCAGACTATAGC 2 160 1 CTATTATCCC 0.950417 -32 TCTATAATCCTTCCTAACAAT 3 2 1 CTATAATCCT 0.869137 -197 CTTGCTTTTTCTTTAATTCTTAATTTATCG 3 134 0 CTTTAATTCT 0.887397 -65 ********** Masking position 7 Map Score: 1.38793 Number of sites scoring better than the average of aligned sites = 426 Number in coding regions = 355 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 4 GATCAAAAAAATCTGTATCAATTTCGTAAA 1 32 1 ATCTGTATCA 0.926233 -126 TGGGTGGCCTGTCTGTCTCGCACAGTGCTT 2 58 0 GTCTGTCTCG 0.972037 -134 GGGATAATAGGGCTGATTAAAGATAACTAT 2 150 0 GGCTGATTAA 0.936656 -42 TTTAAAAATAGTCTGATTCAGGGGCTATGT 3 53 0 GTCTGATTCA 0.986204 -146 AGCTGACTCACGAGGCGGGA 3 189 0 AGCTGACTCA 0.981473 -10 ********** Masking position 4 Map Score: 0.818832 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 107 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 TTAAAACCCAGAACAGTTTACGAAATTGAT 1 48 0 GAACAGTTTA 0.953039 -110 AAATCGTGAAGAAAAGTTAAGAGCCTTGTC 1 131 1 GAAAAGTTAA 0.970711 -27 CTTTATTGTTGATCAATTAATCGAATATTT 2 31 0 GATCAATTAA 0.97073 -161 GTCTTGCATCGATAAATTAAGAATTAAAGA 3 125 1 GATAAATTAA 0.955436 -74 ********** Masking position 5 Map Score: 0.698409 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 127 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 6 GCTGTTTATCTCCTTAATATAAAT 2 5 1 TTTATCTCCT 0.916941 -187 TATCCCAGACTATAGCTCCTTTGCCGCC 2 174 1 TATAGCTCCT 0.982914 -18 GATGATGTTACATAGCCCCTGAATCAGACT 3 44 1 CATAGCCCCT 0.98971 -155 TTTACGAAAAATAAGCCCCTAAAGCCTGCT 3 84 0 ATAAGCCCCT 0.914647 -115 TGGGAAAAAACCTCGCTCCTTGCTTTTTCT 3 152 0 CCTCGCTCCT 0.971214 -47 ********** Masking position 10 Map Score: 0.651255 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 184 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 7 AAATAGGCTTAAAACCCAGAACAGTTTACG 1 56 0 AAAACCCAGA 0.977694 -102 AAGACAGTTTAAAATCGTGAAGAAAAGTTA 1 120 1 AAAATCGTGA 0.975963 -38 ATTTTTCGTAAAAATCCAGAGATGTCTTGC 3 102 1 AAAATCCAGA 0.986794 -97 AAAATCTTAACAACTATCCA 4 1 1 AAAATCTTAA 0.873339 -24 ********** Masking position 4 Map Score: 0.260622 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 208 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 8 ********** No masking Map Score: 1.60826e-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: 1.60826e-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: 1.60826e-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