AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i190_synecho_ctra_300.orf -o190_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 RCY49610 300 Synechocystis #2 RCY26651 230 Synechocystis #3 RCT00791 300 Chlamydia_trachomatis #4 RCT00792 37 Chlamydia_trachomatis Motif number 1 AAATAATAGTTGGGGGGGGGAACGAACCCA 1 20 1 TGGGGGGGGG 0.964563 -281 AAATTGTTATCAGGGCAATGGCTCACCCTG 1 60 1 CAGGGCAATG 0.859652 -241 TGGCTCACCCTGGGGTGATTTCAGACATTG 1 78 1 TGGGGTGATT 0.866335 -223 ACCCGATCCCCAGGGGGGTGGCCTATGATA 1 145 1 CAGGGGGGTG 0.98924 -156 GGGGACTTCGTAGGGTAGCGGAACAAACTG 1 265 0 TAGGGTAGCG 0.887166 -36 AAAAGACAGTCAGGGGGACTTCGTAGGGTA 1 278 0 CAGGGGGACT 0.986117 -23 TAAAAGATTGCGGGGCGGCGCCGAGCTAAA 2 44 1 CGGGGCGGCG 0.987485 -187 AAGAGTAATTTAGGTGGACTACTAAAGTCC 2 138 0 TAGGTGGACT 0.918921 -93 TGGGTTAGAATAGGTCGGTTCACAATTTTC 2 194 1 TAGGTCGGTT 0.84972 -37 TTTTGACGGATAGGGGGACTAGAGGCGTCT 3 232 1 TAGGGGGACT 0.984976 -69 ********** Masking position 4 Map Score: 10.505 Number of sites scoring better than the average of aligned sites = 2310 Number in coding regions = 2032 Number in noncoding regions = 278 Number of orfs with sites within 600 bp upstream = 259 Fraction of orfs with sites within 600 bp upstream = 0.0415997 Motif number 2 TCACCCCAGGGTGAGCCATTGCCCTGATAA 1 66 0 GTGAGCCATT 0.970413 -235 AGGGCCCAAAGTGAGAGCTTAGATAAATTA 1 226 0 GTGAGAGCTT 0.951779 -75 AGCTCTCACTTTGGGCCCTTGACCCTGTCA 1 237 1 TTGGGCCCTT 0.952286 -64 GTATAGAGTTGTGTGACCTTTGTCGAGATG 2 82 1 GTGTGACCTT 0.968945 -149 AACTATGTAAGAGGGACTTTAGTAGTCCAC 2 125 1 GAGGGACTTT 0.875817 -106 CTTTGAGTATGCGAGCCCCTAAAAACCCAA 3 152 0 GCGAGCCCCT 0.967074 -149 AAACGGTAGAGAGAGCCCTTATCTTATACT 3 202 0 GAGAGCCCTT 0.987574 -99 ********** Masking position 10 Map Score: 5.03975 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 128 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 3 GGCCTATGATAAAGTGCCAGATGTGGAGTA 1 164 1 AAAGTGCCAG 0.986576 -137 TCAAGGGCCCAAAGTGAGAGCTTAGATAAA 1 229 0 AAAGTGAGAG 0.978874 -72 GTAGCGGAACAAACTGACAGGGTCAAGGGC 1 251 0 AAACTGACAG 0.976625 -50 AGAAAAAGACAGTCAGGGGGAC 1 289 0 AAAAAGACAG 0.921572 -12 GTCGGTAGCGAAAGAGCCATAAAAAATTCT 2 15 1 AAAGAGCCAT 0.897137 -216 AAAATAGCATAAACTGCGATGAAAAATTTC 3 57 0 AAACTGCGAT 0.912883 -244 TTATACTTAAAAAATCAGAGCATTATCCTT 3 179 0 AAAATCAGAG 0.798119 -122 ********** Masking position 3 Map Score: 4.09366 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 230 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 4 GGGGGGGAACGAACCCAATCTTAACAAAAAT 1 33 1 GAACCCAATT 0.955396 -268 CCATTGCCCTGATAACAATTTTTGTTAAGAT 1 50 0 GATAACAATT 0.898027 -251 TAGGCATTTGGTAGCCAATTTAGCAACCCGA 1 120 1 GTAGCCAATT 0.927633 -181 ACAAGAACAAGAAAACTATGTAAGAGGGACT 2 112 1 GAAAACTATT 0.745741 -119 GAATAGGTCGGTTCACAATTTTCCTTACTGC 2 201 1 GTTCACAATT 0.969541 -30 CTCGGCTCTTGTATACCATATATAGAAGCTA 3 107 0 GTATACCATT 0.874583 -194 GAGCCGAGACGTTCACAATATCTTGGGTTTT 3 130 1 GTTCACAATT 0.969541 -171 AGAATAATGCGTATTCAATGTTTACAAGGAT 3 276 1 GTATTCAATT 0.848279 -25 ********* * Masking position 8 Map Score: 1.56173 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 163 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 5 CCCCAACTATTATTTCTTAAAAAA 1 3 0 TTTCTTAAAA 0.901499 -298 TGCCTAGAATTAATCCTTCAATGTCTGAAATC 1 94 0 TATCTTCAAT 0.94983 -207 ATGTAGGACATCATGCTTAAAAGTTTGCTCTC 3 20 1 TATCTTAAAA 0.954686 -281 GCAGTTTATGCTATTTTTCAATTGCAGGAAAC 3 70 1 CATTTTCAAT 0.747825 -231 AGCCCTTATCTTATACTTAAAAAATCAGAGCA 3 187 0 TATCTTAAAA 0.951213 -114 TCTAGTCCCCCTATCCGTCAAAAAAACGGTAG 3 223 0 CATCGTCAAA 0.94175 -78 CTAGAGGCGTCTTTGCTTCAAAATAGAGAATA 3 250 1 CTTCTTCAAA 0.958085 -51 * ** ******* Masking position 10 Map Score: 1.51761 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 162 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 6 AGGGTGAGCCATTGCCCTGATAACAATTTT 1 59 0 ATTGCCCTGA 0.942101 -242 TTGGCTACCAAATGCCTAGAATTAATCCTT 1 108 0 AATGCCTAGA 0.911238 -193 GACAGGGTCAAGGGCCCAAAGTGAGAGCTT 1 236 0 AGGGCCCAAA 0.970704 -65 GTTGATCAAGACTGCCCAAAGAAACTGGGT 2 169 1 ACTGCCCAAA 0.992424 -62 AATTTTCCTTACTGCCCAAATTCC 2 217 1 ACTGCCCAAA 0.992424 -14 ********** Masking position 1 Map Score: 2.53718 Number of sites scoring better than the average of aligned sites = 368 Number in coding regions = 333 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 AGATTGGGTTCGTTCCCCCCCCCAACTATT 1 24 0 CGTTCCCCCC 0.97393 -277 TCAATGTCTGAAATCACCCCAGGGTGAGCC 1 79 0 AAATCACCCC 0.732743 -222 ACTTTATCATAGGCCACCCCCCTGGGGATC 1 149 0 AGGCCACCCC 0.994375 -152 AGATCAGTGTCGGCCACACCATATCTGTGG 1 194 1 CGGCCACACC 0.970897 -107 CTACCCTACGAAGTCCCCCTGACTGTCTTT 1 277 1 AAGTCCCCCT 0.779213 -24 TTGTTTAGCTCGGCGCCGCCCCGCAATCTT 2 47 0 CGGCGCCGCC 0.839877 -184 ATCTCGACAAAGGTCACACAACTCTATACA 2 81 0 AGGTCACACA 0.889462 -150 GGACTTTAGTAGTCCACCTAAATTACTCTT 2 138 1 AGTCCACCTA 0.841778 -93 AGACGCCTCTAGTCCCCCTATCCGTCAAAA 3 232 0 AGTCCCCCTA 0.872603 -69 ********** Masking position 7 Map Score: 2.34441 Number of sites scoring better than the average of aligned sites = 2785 Number in coding regions = 2582 Number in noncoding regions = 203 Number of orfs with sites within 600 bp upstream = 200 Fraction of orfs with sites within 600 bp upstream = 0.0321234 Motif number 8 ********** No masking Map Score: -1.22681e-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: -1.22681e-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 CCCAATCTTAACAAAAATTGTTATCAGGGCA 1 46 1 ACAAAAATTT 0.786127 -255 GCCGAGCTAAACAAGAATTGTATAGAGTTGT 2 63 1 ACAAGAATTT 0.938777 -168 GATGACAAGAACAAGAAAACTATGTAAGAGG 2 108 1 ACAAGAAAAT 0.96201 -123 TCTTGATCAACCAAGAGTAATTTAGGTGGAC 2 149 0 CCAAGAGTAT 0.857396 -82 TCAAGACTGCCCAAAGAAACTGGGTTAGAAT 2 174 1 CCAAAGAAAT 0.797595 -57 TTTGCTCTCGAAAAGAAATTTTTCATCGCAG 3 43 1 AAAAGAAATT 0.723408 -258 CTCGCATACTCAAAGGATAATGCTCTGATTT 3 167 1 CAAAGGATAT 0.806937 -134 TTCAATGTTTACAAGGATAGTT 3 289 1 ACAAGGATAT 0.962469 -12 ATATAAATTAACAATAAAATTAACGGTTCTT 4 17 1 ACAATAAAAT 0.766588 -21 ********* * Masking position 4 Map Score: 2.2195 Number of sites scoring better than the average of aligned sites = 604 Number in coding regions = 510 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 11 ********** No masking Map Score: -1.22681e-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: -1.22681e-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 13 ********** No masking Map Score: -1.22681e-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