AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i217_synecho_ctra_300.orf -o217_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 RCY11650 125 Synechocystis #2 RCY51581 32 Synechocystis #3 RCY24462 49 Synechocystis #4 RCY49641 136 Synechocystis #5 RCT00240 300 Chlamydia_trachomatis #6 RCT00753 300 Chlamydia_trachomatis Motif number 1 GGGGAAGGAAAGGGAACAAATACA 1 4 1 GAAGGAAGGG 0.946778 -122 CCAGATGGTTGGGGGGCGGGGATTTTTCCCC 1 43 0 GGGGGGGGGG 0.992158 -83 TGTAGAAATAGGGGAAGATGGTATGGAGGCA 1 77 1 GGGGAAATGG 0.854117 -49 AGGTTGCCGGGAAGACTGGGGGGCTCAATGG 4 49 0 GAAGACGGGG 0.964134 -88 TTTTTGATGTAGAGAGGGGGGATGGTTATTT 5 56 1 AGAGAGGGGG 0.980011 -245 GCTCCGTTCGGAAGAGCAGAGTTGAATCTCT 5 144 1 GAAGAGAGAG 0.978986 -157 TTCTCGACAAGAAGTGGAGAGGTTTTGTCTT 5 191 1 GAAGTGAGAG 0.86764 -110 TTCTCCCTATGGGGAGGGAAGCCTCGTTCCT 5 264 0 GGGGAGGAAG 0.897273 -37 AGGAATGCGTAGAGAGCAGAGA 6 2 0 AGAGAGAGAG 0.962797 -299 GAGCCTTCCCGGATAAAGGAGGATTAACAAC 6 73 1 GGATAAGGAG 0.742989 -228 GTCAAAAAGTGAGGAAAAGGGTAAATTTTGT 6 111 0 GAGGAAAGGG 0.970082 -190 TCTGCCCCCAAGAGACTAGGGACGAGTTTAA 6 245 0 AGAGACAGGG 0.936122 -56 CCTAGTCTCTTGGGGGCAGAGTCCCTAGAGA 6 256 1 TGGGGGAGAG 0.853691 -45 ****** **** Masking position 11 Map Score: 12.2591 Number of sites scoring better than the average of aligned sites = 3352 Number in coding regions = 2904 Number in noncoding regions = 448 Number of orfs with sites within 600 bp upstream = 370 Fraction of orfs with sites within 600 bp upstream = 0.0594282 Motif number 2 GAACAAATACAATTTTAGTGGGGAAAAATCCCCGC 1 24 1 ATTATGGGGA 0.928433 -102 TACAATCCCAGATGGTTGGGGGGCGGGGATTTTTC 1 46 0 GTGTGGGGGG 0.869516 -80 CATCTGGGATTGTAGAAATAGGGGAAGATGGTATG 1 67 1 TTGATAGGGA 0.890064 -59 AGACTGTGTCTTTTTTTGTGGAGTAA 3 34 1 TTTTTGGAGA 0.954024 -16 ACCTTGGCAATATTTATCTAGAGAGCTTGTTAGCA 4 76 1 TTTTTAGAGG 0.938668 -61 ACATTAAACTTTTTGATGTAGAGAGGGGGGATGGT 5 47 1 TTGTTAGAGG 0.905532 -254 ACTTGGCGTCATTTTATAGAGGGTATCTTTTCCAT 5 96 0 ATTTGAGGGA 0.95385 -205 CTGCAAAGTTTTTTTGATTAGGGAATTAAAGCAAC 5 223 1 TTTATAGGGA 0.928194 -78 CGAGGTGGGTTCTCCCTATGGGGAGGGAAGCCTCG 5 269 0 TTCTTGGGGG 0.944139 -32 GTGCCTTAGGAATGCGTAGAGAGCAGAGA 6 5 0 ATCTGAGAGA 0.826997 -296 TGTTTGCAATTCTGTGTATGGAGCGTGGGCTAGTG 6 37 0 TTTTTGGAGG 0.954843 -264 ACTCGTCCCTAGTCTCTTGGGGGCAGAGTCCCTAG 6 249 1 ATTTGGGGGA 0.966165 -52 AGACTTCAAGAGTATTAGGAGAGTATT 6 284 1 ATTAGAGAGA 0.83731 -17 * * * * ***** * Masking position 3 Map Score: 8.65489 Number of sites scoring better than the average of aligned sites = 1312 Number in coding regions = 1155 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 3 ATTGCCAAGGTTGCCGGGAAGACTGGGGGGC 4 56 0 TTGCGGGAAG 0.903799 -81 CCAAAATCCATTGCTAACAAGCTCTCTAGAT 4 91 0 TTGCAACAAG 0.990819 -46 GAATCGTCTTTTGCTTACAAGAGATTCAACT 5 163 0 TTGCTACAAG 0.963801 -138 CAAAAGACGATTCTCGACAAGAAGTGGAGAG 5 181 1 TTCTGACAAG 0.945795 -120 GGAAGCCTCGTTCCTATCAAGGTTGCTTTAA 5 248 0 TTCCATCAAG 0.942414 -53 ATACACAGAATTGCAAACAAGAGCCTTCCCG 6 53 1 TTGCAACAAG 0.990819 -248 AAGTCTCTTATTGTCAAAAAGTGAGGAAAAG 6 123 0 TTGTAAAAAG 0.845489 -178 GTAGATAGAATTCTGAGCAAGTCTCTTATTG 6 141 0 TTCTAGCAAG 0.945795 -160 **** ****** Masking position 9 Map Score: 7.53759 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 88 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 4 CCCAGATGGTTGGGGGGCGGGGATTTTTCCC 1 44 0 TGGGGGGGGG 0.992172 -82 GAAGATGGTATGGAGGCATTTCACCCCCTGC 1 90 1 TGGAGGCTTT 0.860352 -36 CTTGTGCCATTGCAGGGGGTGAAATGCCTCC 1 101 0 TGCAGGGGTG 0.964462 -25 ATGATACAATTGGAGACTGTGTCTTTTTTTG 3 21 1 TGGAGACGTG 0.98227 -29 AATCAAGCACTGGAGCCATTGAGCCCCCCAG 4 34 1 TGGAGCCTTG 0.944054 -103 AATATTTATCTAGAGAGCTTGTTAGCAATGG 4 84 1 TAGAGAGTTG 0.843284 -53 AACTTTTTGATGTAGAGAGGGGGGATGGTTA 5 53 1 TGTAGAGGGG 0.946823 -248 CGACAAGAAGTGGAGAGGTTTTGTCTTTCTG 5 195 1 TGGAGAGTTT 0.843284 -106 GGGTTCTCCCTATGGGGAGGGAAGCCTCGTT 5 267 0 TATGGGGGGG 0.771451 -34 ATTCTGTGTATGGAGCGTGGGCTAGTGCCTT 6 33 0 TGGAGCGGGG 0.988424 -268 CCTAGTCTCTTGGGGGCAGAGTCCCTAGAGA 6 256 1 TGGGGGCGAG 0.934007 -45 ******* *** Masking position 1 Map Score: 10.908 Number of sites scoring better than the average of aligned sites = 2382 Number in coding regions = 2188 Number in noncoding regions = 194 Number of orfs with sites within 600 bp upstream = 202 Fraction of orfs with sites within 600 bp upstream = 0.0324446 Motif number 5 GTATTTGTTCCCTTTCCTTCCCC 1 3 0 CCTTTCCTCC 0.962978 -123 GGGGCGGGGATTTTTCCCCACTAAAATTGTA 1 31 0 TTTTTCCCAC 0.924766 -95 GGTATGGAGGCATTTCACCCCCTGCAATGGC 1 96 1 CATTTCACCC 0.863236 -30 CACTTCCAACCTTTTCAAACCAGATTTAATT 2 12 1 CTTTTCAACC 0.930953 -21 TAGAGGGTATCTTTTCCATGCACTTGGAAAA 5 84 0 CTTTTCCTGC 0.969263 -217 TTCAACTCTGCTCTTCCGAACGGAGCTTCAT 5 139 0 CTCTTCCAAC 0.928447 -162 CGAGAATCGTCTTTTGCTTACAAGAGATTCA 5 166 0 CTTTTGCTAC 0.920546 -135 AAAATTTACCCTTTTCCTCACTTTTTGACAA 6 113 1 CTTTTCCCAC 0.990997 -188 ******* *** Masking position 5 Map Score: 4.19604 Number of sites scoring better than the average of aligned sites = 651 Number in coding regions = 555 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 6 ********** No masking Map Score: -9.92328e-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: -9.92328e-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 8 ********** No masking Map Score: -9.92328e-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