AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i297_synecho_ctra_300.orf -o297_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 RCY04992 300 Synechocystis #2 RCY11382 300 Synechocystis #3 RCT00464 88 Chlamydia_trachomatis #4 RCT00465 300 Chlamydia_trachomatis Motif number 1 TGTGCTTCAGAGAGTGCATTTAACCACGCTGAAA 1 105 0 AGAGCATTTC 0.981303 -196 CCCTGGCTGGAGAGGCAGTTTTTCCTATGTCCTT 1 203 1 AGAGAGTTTC 0.984056 -98 TGGGAAAGGAAGATAAAATTTAACCTATTGAATA 2 71 1 AGATAATTTC 0.926149 -230 GTTAAGATATAGAGACAATTTAGCTGAGTAAATT 2 119 0 AGAGAATTTC 0.993082 -182 CCCCCACAATAAAGCCAATTTGCGGGGCTTCATT 2 222 1 AAAGAATTTG 0.792522 -79 AGAAGAGGTAATTTCAAGTTACGGGTG 2 284 0 AGAGAATTTA 0.941277 -17 AGAGTGGATTTTTCTTTTCGAGCT 3 1 1 AGAGGATTTC 0.994618 -88 GGCAAAATAAAGAGCTGATTCTTCTATCAAGCAA 3 57 1 AGAGGATTCC 0.992457 -32 AATGATCCGCAGAGGAGGTTCAAGGTGAGGAATC 4 44 1 AGAGGGTTCG 0.945153 -257 TACCTATCCAAGAGCAGATTCCTCACCTTGAACC 4 60 0 AGAGGATTCC 0.992457 -241 **** ***** * Masking position 9 Map Score: 13.9089 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 142 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 2 TATGGGAAAGGAAGATAAAATTTAACCTAT 2 69 1 GAAGATAAAA 0.852555 -232 TGAATAAAGTAAATGTAAAAAATTTACTCA 2 99 1 AAATGTAAAA 0.679474 -202 TCAACAGCTCGAAAAGAAAAATCCACTCT 3 10 0 GAAAAGAAAA 0.835698 -79 AGCTGTTGACAAAGGTAAAAGTGGTTGGCA 3 31 1 AAAGGTAAAA 0.852555 -58 CTTTTCCCATAAAAAGAAATGATCCGCAGA 4 27 1 AAAAAGAAAT 0.889866 -274 TAGATGTTTGAAAAATAAAAATTATCTAAT 4 178 0 AAAAATAAAA 0.964926 -123 TCAAACATCTAAAAATAAAATCGATTTATT 4 197 1 AAAAATAAAA 0.964926 -104 TTATTGCATGAATAATAAATCGATTTTATT 4 210 0 AATAATAAAT 0.725538 -91 AATAATTTTAAAAAATAAATTATTAAAAAA 4 261 0 AAAAATAAAT 0.949471 -40 CGCCACCATAAAAAATAATTTTAAAAAATA 4 274 0 AAAAATAATT 0.725538 -27 ********** Masking position 7 Map Score: 7.42237 Number of sites scoring better than the average of aligned sites = 404 Number in coding regions = 302 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 3 GCAATTAGACTTATGGGAAAGGAAGATAAA 2 58 1 TTATGGGAAA 0.910967 -243 ATTTCCCCTCGGTTGGGAAAGTTGCACCTT 2 182 1 GGTTGGGAAA 0.977506 -119 CTTTTCGAGCTGTTGACAAAGGTAAAAGTG 3 24 1 TGTTGACAAA 0.957909 -65 AGGTAAAAGTGGTTGGCAAAATAAAGAGCT 3 43 1 GGTTGGCAAA 0.982782 -46 TCATTTCTTTTTATGGGAAAAGATTCTTAG 4 19 0 TTATGGGAAA 0.910967 -282 TCCACATCTTTGTTGGCATACCTATCCAAG 4 82 0 TGTTGGCATA 0.912556 -219 AATTATCTAATTTTGACAAAAAACGGACCC 4 159 0 TTTTGACAAA 0.93465 -142 ATTTTTAGATGTTTGAAAAATAAAAATTAT 4 183 0 GTTTGAAAAA 0.729237 -118 ********** Masking position 8 Map Score: 7.17279 Number of sites scoring better than the average of aligned sites = 699 Number in coding regions = 584 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 4 CCGAACCATTGCCTCGAATAGTT 1 1 1 CCGACCATCC 0.985131 -300 AAACTGCCTCTCCAGCCAGGGGCGATCGCCAAA 1 191 0 TCCACCAGGC 0.978528 -110 GTGCAACTTTCCCAACCGAGGGGAAATACCATG 2 176 0 CCCACCGGGG 0.950769 -125 TGGGGGCTAGCCGACCAAGGTGCAACTTTCCCA 2 195 0 CCGACAAGGC 0.988661 -106 TATAAACTATCGGAACCAAGACCGGGGAAATGA 2 251 0 CGGACCAGCC 0.99539 -50 TGTTGGCATACCTATCCAAGAGCAGATTCCTCA 4 69 0 CCTACCAGGC 0.992295 -232 TGACAAAAAACGGACCCATGCCCTTTATAGAGA 4 143 0 CGGACCAGCC 0.995389 -158 **** *** * ** Masking position 4 Map Score: 5.76735 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 305 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 5 CCGAACCATTGCCTCGAATAGTTCTTC 1 8 1 ATTGCCTCGA 0.959127 -293 GGTGTGGTGGCTTGACTGGCACTGATGCAT 1 45 1 CTTGACTGGC 0.673324 -256 GATCGCCAAACTGGCCCCGAAATATTAAGA 1 171 0 CTGGCCCCGA 0.967429 -130 CAGTTTGGCGATCGCCCCTGGCTGGAGAGG 1 188 1 ATCGCCCCTG 0.888327 -113 CATAGGAAAAACTGCCTCTCCAGCCAGGGG 1 202 0 ACTGCCTCTC 0.828314 -99 CCCTTCTGAGATTGCCTGGGCAGTCAGTGA 1 266 1 ATTGCCTGGG 0.897886 -35 AAATTGACCCTCCCATCACTGA 1 289 0 ATTGACCCTC 0.882447 -12 GACCCTAGTTCTGGCCTCAATTTTGTTAAG 2 147 0 CTGGCCTCAA 0.669609 -154 GGGTCATGGTATTTCCCCTCGGTTGGGAAA 2 172 1 ATTTCCCCTC 0.923488 -129 GCGGGGCTTCATTTCCCCGGTCTTGGTTCC 2 243 1 ATTTCCCCGG 0.945605 -58 CTGTCCCCGCCACCATAAAA 4 291 0 CTGTCCCCGC 0.949577 -10 ********** Masking position 6 Map Score: 5.46614 Number of sites scoring better than the average of aligned sites = 3751 Number in coding regions = 3447 Number in noncoding regions = 304 Number of orfs with sites within 600 bp upstream = 321 Fraction of orfs with sites within 600 bp upstream = 0.051558 Motif number 6 GGAGGCGTTTACCATGCTCCCCATGCATCA 1 67 0 ACCATGCTCC 0.962706 -234 GGCAGTTTTTCCTATGTCCTTTGTCGCCCT 1 216 1 CCTATGTCCT 0.946403 -85 CTATGTTTACCCTATCCTCTAAGCAATTAG 2 36 1 CCTATCCTCT 0.930732 -265 GAGGGGAAATACCATGACCCTAGTTCTGGC 2 162 0 ACCATGACCC 0.88608 -139 TTCTGACTCGCCTATGCTATTCCACATCTT 4 102 0 CCTATGCTAT 0.900655 -199 AAAAAACGGACCCATGCCCTTTATAGAGAT 4 142 0 CCCATGCCCT 0.993146 -159 ********** Masking position 5 Map Score: 1.16775 Number of sites scoring better than the average of aligned sites = 1140 Number in coding regions = 1048 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 7 GTGCCAGTCAAGCCACCACACCCCAGACTG 1 37 0 AGCCACCACA 0.995571 -264 TTGGTCGGCTAGCCCCCACAATAAAGCCAA 2 210 1 AGCCCCCACA 0.994736 -91 CTGTCCCCGCCACCATAAAAAATAATT 4 284 0 CGCCACCATA 0.985771 -17 ********** Masking position 8 Map Score: 0.858078 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 59 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 ********** No masking Map Score: 3.05066e-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 GTGGTTAAATGCACTCTCTGAAGCACACGCTAA 1 112 1 GCATCTTGAG 0.985222 -189 GACTGCCCAGGCAATCTCAGAAGGGATACTCCA 1 258 0 GCATCTAGAG 0.989643 -43 GATTGCCTGGGCAGTCAGTGATGGGAGGGTCAA 1 275 1 GCATCATGAG 0.989643 -26 AGAGGATAGGGTAAACATAGACGGTCAGAGTCA 2 23 0 GTAACAAGAG 0.948215 -278 GGATAGGTATGCCAACAAAGATGTGGAATAGCA 4 85 1 GCCACAAGAG 0.977297 -216 *** *** *** * Masking position 11 Map Score: 0.288306 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 27 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 10 ********** No masking Map Score: 3.05066e-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 11 ********** No masking Map Score: 3.05066e-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 12 ********** No masking Map Score: 3.05066e-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