AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i015_synecho_ctra_100.orf -o015_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 RCY49691 112 Synechocystis #2 RCY39030 187 Synechocystis #3 RCY05748 42 Synechocystis #4 RCY36146 300 Synechocystis #5 RCT00193 300 Chlamydia_trachomatis #6 RCT00195 29 Chlamydia_trachomatis #7 RCT00196 19 Chlamydia_trachomatis #8 RCT00197 38 Chlamydia_trachomatis #9 RCT00316 275 Chlamydia_trachomatis #10 RCT00317 96 Chlamydia_trachomatis Motif number 1 AGCAAAACTTCTTTGTGAGAATTCTTAAAAT 1 41 0 CTTGTGAGAA 0.765647 -72 GTGACGCCAACTGTGACAAAAGATGAATAAA 4 31 0 CTTGACAAAA 0.975624 -270 TTGGTCAAAACTATGACAAGAACT 4 287 1 CTTGACAAGA 0.885196 -14 TATTATAGATTTATGACAAAAAAAAGCATTA 5 28 0 TTTGACAAAA 0.748711 -273 GAAGGAAGGACTCTCAGAAAACGAGCAGGCC 5 163 0 CTTCAGAAAA 0.928189 -138 ACCTTCAAGCCTTTCACGGAAGGAAGGACTC 5 181 0 CTTCACGGAA 0.963753 -120 CATATAGAGTCGTTGACAGAAGATTTTTGGC 5 219 1 CGTGACAGAA 0.954411 -82 TGGCATGCTACGACCAGGAAATAATCGATTA 5 246 1 CGCCAGGAAA 0.75765 -55 GCCAAGATAGCTTCCACGGAATGACAGTCCT 9 96 0 CTCCACGGAA 0.945775 -180 TCTTGGCTATCTATGAGGAAATGTTTTCTCT 9 120 1 CTTGAGGAAA 0.956921 -156 GAAGTATCTACTGCGACAGAACCATCGGGGT 9 213 0 CTCGACAGAA 0.971265 -63 ** ******** Masking position 11 Map Score: 7.76568 Number of sites scoring better than the average of aligned sites = 426 Number in coding regions = 378 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 2 GGCAATTTTTCCCAATAGTCTGCACAGTTTGAT 2 20 0 CCCAATTCGC 0.956181 -168 GGAAAAATTGCCCAAAGCCCAGCCTACCATCGT 2 41 1 CCCAAACCGC 0.993485 -147 GAGAATATTTCCCTAACACCGCTTAAAAGCAGA 2 121 1 CCCTAACCCT 0.98965 -67 ATTTAACTGCCCCTAATTTCAGCCCATT 2 170 1 CCCTAATCGC 0.989638 -18 CATTCCCTTAATTCCTCCTCAGTAAGTT 3 6 1 CCTTAACCCC 0.964686 -37 CCGGCAAAAACCCTATGCCCCCCGTCCCAACCT 4 170 0 CCCTATCCCC 0.988957 -131 ATCTAATCACCCCAAAAATCCCTTTAAAAAACT 4 224 0 CCCAAATCCT 0.958847 -77 ATATTCTACTCACTAATACCGGTATCCCGATTT 10 74 1 CACTAACCGT 0.91437 -23 ****** ** ** Masking position 5 Map Score: 7.7626 Number of sites scoring better than the average of aligned sites = 714 Number in coding regions = 617 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 3 AGCAAACCCATCAAACTGTGCAGACTATTGGG 2 3 1 CAATCTGTGA 0.86229 -185 CTTACAGGGCCAACGATGGTAGGCTGGGCTTTGGGCAATT 2 46 0 CACGCTGGGT 0.966667 -142 TCCCTTAATTCCTCCTCAGTAAGTTGGACTAAAATTCCA 3 14 1 CCCGTTGGAT 0.772415 -29 CAGTTGGCGTCACACTTTTCCCCCTGGGGAGCAGATAAGA 4 49 1 CAATCTGGGA 0.965921 -252 TCACTCCTCACACCACACTCCGCCTGGATGATGTTCGGGC 4 96 0 CACTCTGGAG 0.935954 -205 AACCCTATGCCCCCCGTCCCAACCTGTACAATGAAGAGGG 4 155 0 CCCCCTGTAA 0.902499 -146 ATAGTTTTGACCAACCTTTATCTCTGGATTTCACTGGAAA 4 261 0 CCATCTGGAT 0.96464 -40 CGATTATTCACAAATCTTCAGAACTGGAGTAACTTTGACG 5 271 1 CAACCTGGAT 0.920076 -30 GGCTCCCTATAATTTTATCTGGATAAAAA 6 5 0 CCATCTGGAA 0.97879 -25 TCTCGGTACCCGAAGCAAGTCATCTGGACACCGTTATACA 9 27 1 CGAGCTGGAA 0.919963 -249 GAATGACAGTCCTCAAGCGCCTTCTGTAAAACCAGAAGGC 9 69 0 CCCGCTGTAA 0.946554 -207 TCCCATTAAGCATCCTTTTATCCCTGGGGAATCTGT 9 250 1 CACTCTGGGA 0.978309 -26 ** * * ***** * Masking position 15 Map Score: 5.99295 Number of sites scoring better than the average of aligned sites = 1258 Number in coding regions = 1161 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 4 CCGTTTCAGTTGCATCGGCTTACAGGGCCA 2 74 0 TGCATCGGCT 0.881374 -114 CCGATGCAACTGAAACGGCGATCGTGGCGG 2 86 1 TGAAACGGCG 0.926831 -102 GCAGATAAGAAGAAACCGCCCGAACATCAT 4 79 1 AGAAACCGCC 0.937091 -222 GCCGTAGCAGAGCAACGACCATGGAGCTCG 5 136 0 AGCAACGACC 0.976425 -165 GTCGTTGCTCTGCTACGGCCTGCTCGTTTT 5 147 1 TGCTACGGCC 0.985082 -154 ATTTTTGGCATGCTACGACCAGGAAATAAT 5 241 1 TGCTACGACC 0.962711 -60 TAGCCAAGATAGCTTCCACGGAATGACAGT 9 99 0 AGCTTCCACG 0.752252 -177 CAAAATATTTAGCAACCGCAATCG 10 5 0 AGCAACCGCA 0.925768 -92 ********** Masking position 6 Map Score: 4.00802 Number of sites scoring better than the average of aligned sites = 830 Number in coding regions = 784 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 5 GTGACAAAAGATGAATAAATTCTAAGTTTCACG 4 17 0 ATGAAAAACT 0.894647 -284 GGTGTGAGGAGTGAACGGAAACTTACGTCTCCG 4 122 1 GTGAAGGACT 0.976529 -179 CCTTTCACGGAAGGAAGGACTCTCAGAAAACGA 5 170 0 AAGGAGGACT 0.911224 -131 AATGAAGGGAAGCTCTTTAGTTAT 8 25 0 ATGAAGGACT 0.992659 -14 CCGGTCATGCAGGAAATCTCGGTACCCGA 9 7 1 ATGCAGAACT 0.959901 -269 TTCCCCAGGGATAAAAGGATGCTTAATGGGATT 9 248 0 ATAAAGGACT 0.946059 -28 AATATCCGAAATGAAAGAAGCCTTCAACTATAC 10 34 0 ATGAAGAACT 0.984955 -63 ***** *** ** Masking position 5 Map Score: 3.15366 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 28 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 AATAAATTCTAAGTTTCACGATATTT 4 7 0 AAGTTTCACG 0.917078 -294 GTGTGACGCCAACTGTGACAAAAGATGAAT 4 34 0 AACTGTGACA 0.974963 -267 CCAGGGGGAAAAGTGTGACGCCAACTGTGA 4 46 0 AAGTGTGACG 0.983669 -255 GGTTGGTCAAAACTATGACAAGAACT 4 285 1 AACTATGACA 0.93454 -16 GAACTGGAGTAACTTTGACG 5 291 1 AACTTTGACG 0.982676 -10 ********** Masking position 6 Map Score: 1.56857 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 32 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 TCTGCACAGTTTGATGGGTTTGCT 2 5 0 TTGATGGGTT 0.975323 -183 GTTAAGTTTTTTAAAGGGATTTTTGGGGTG 4 220 1 TTAAAGGGAT 0.946067 -81 CGTGAAAGGCTTGAAGGTTTGCACTCATAT 5 194 1 TTGAAGGTTT 0.934445 -107 AAAAGGATGCTTAATGGGATTGCCTGAAGT 9 239 0 TTAATGGGAT 0.924483 -37 TTTTGTATAGTTGAAGGCTTCTTTCATTTC 10 30 1 TTGAAGGCTT 0.954805 -67 ********** Masking position 4 Map Score: 0.883234 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 100 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 8 ********** No masking Map Score: 2.9725e-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: 2.9725e-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: 2.9725e-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