AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i111_synecho_ctra_100.orf -o111_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 RCY29694 187 Synechocystis #2 RCY03689 300 Synechocystis #3 RCY50298 300 Synechocystis #4 RCY17260 138 Synechocystis #5 RCT00147 300 Chlamydia_trachomatis #6 RCT00148 35 Chlamydia_trachomatis Motif number 1 AGTTTTAGCCAGGCCAAGTGACCTAGAAAAGC 2 201 0 AGGCAAGGAC 0.772731 -100 CAGGAAGGAAAGTCAATACCAGCCTTAGAATT 2 234 0 AGTCATACAG 0.68248 -67 CCGAATTAGCGGGCTAGGACAGGAAGGAAAGT 2 253 0 GGGCAGGCAG 0.986734 -48 AAAAACGATGCGAGGGAAGAATAGTACCG 2 282 0 ATGCAGGAAG 0.919902 -19 CCCTGCCTATAGCCAAGAACAGGTAGAAAT 3 9 0 AGCCAGACAG 0.982279 -292 GGCTATAGGCAGGGCAGGAAAGAAAAAAAAAC 3 27 1 AGGGAGGAAG 0.888381 -274 AAGAATTAATAGCCAAGGGCAGCGCATGGTGG 3 60 1 AGCCAGGCAG 0.988883 -241 AGTCAGAATTAGTCGAGATCAGCTAGGGGAAG 3 106 1 AGTCAGACAG 0.960941 -195 GAGATCAGCTAGGGGAAGTGAGCAAAAACTAT 3 120 1 AGGGAAGGAG 0.87131 -181 CTTAATCCTAGGGCCAGGGGCGGTCAAATTGA 4 69 1 GGGCAGGGCG 0.916886 -70 CTAGCTAAAGATCCTAGAACCGAGGTAACG 4 119 1 ATCCAGACCG 0.806616 -20 ATTTGATGCCAGGCAAAAAGAGTTGTTTTATC 5 21 0 AGGCAAAGAG 0.959157 -280 CTTTGAATAAATGCGAGAGCAGATCTTGATTA 5 218 1 ATGCAGACAG 0.976413 -83 TCTCAAGAAAATGCTAAATCAGCCCCTATGCT 5 267 0 ATGCAAACAG 0.922478 -34 **** *** *** Masking position 6 Map Score: 14.7103 Number of sites scoring better than the average of aligned sites = 1113 Number in coding regions = 968 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 2 CCGACATTTTCCCAGTCAAAAGACTCGAAT 1 97 1 CCCAGTCAAA 0.979246 -91 TTTTCCTTTCCCCAGGAATTATTGCCTCCT 1 144 1 CCCAGGAATT 0.983321 -44 GCAAAGAAGTCCAAGGAATTGATAAATTGT 2 27 0 CCAAGGAATT 0.852501 -274 CCTAGAAAAGCCCAGTAATATTGCTTTACC 2 182 0 CCCAGTAATA 0.982819 -119 TGGTGGTTTCTCCAGGCAAAAGTCAGAATT 3 86 1 TCCAGGCAAA 0.954962 -215 TGGGGGACTGCCCAGTAACAGGAACAATAG 3 176 0 CCCAGTAACA 0.962644 -125 TGGGCAGTCCCCCAGGAAAATTCTAGAACA 3 192 1 CCCAGGAAAA 0.991181 -109 AGTTGTTTTATCCAGTAATTTA 5 3 0 TCCAGTAATT 0.872829 -298 ATTATTTGATGCCAGGCAAAAAGAGTTGTT 5 26 0 GCCAGGCAAA 0.94687 -275 ********** Masking position 4 Map Score: 11.5376 Number of sites scoring better than the average of aligned sites = 936 Number in coding regions = 824 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 3 CAGGAACAATAGTGTTAATGG 1 2 1 AGGAACAATA 0.893318 -186 TGGAGCTAAAACGAACAAAAACTTAACAGT 1 34 0 ACGAACAAAA 0.831791 -154 TAATTCCTGGGGAAAGGAAAAATTTCAATG 1 135 0 GGAAAGGAAA 0.819611 -53 GGGGGTTTTTACGGAGAAAAAATGGACTGA 2 76 1 ACGGAGAAAA 0.888089 -225 GGGCTAGGACAGGAAGGAAAGTCAATACCA 2 245 0 AGGAAGGAAA 0.947152 -56 AACGATGCGAGGGAAGAATAGTACCGAATT 2 278 0 GGGAAGAATA 0.960472 -23 AGGCAGGGCAGGAAAGAAAAAAAAACTAAG 3 33 1 GGAAAGAAAA 0.913546 -268 GCCCAGTAACAGGAACAATAGCCTATCAAT 3 167 0 AGGAACAATA 0.893318 -134 CTTAGATGCTCGGGAGAAAATTTTAACTTA 4 43 1 CGGGAGAAAA 0.915622 -96 CTTTAGACACGGTGAGAAAATGATTTTTTG 5 97 0 GGTGAGAAAA 0.810126 -204 ********** Masking position 5 Map Score: 5.71508 Number of sites scoring better than the average of aligned sites = 1300 Number in coding regions = 1102 Number in noncoding regions = 198 Number of orfs with sites within 600 bp upstream = 203 Fraction of orfs with sites within 600 bp upstream = 0.0326052 Motif number 4 TTCCAGTGGAGCTAAAACGAACAAAAACTT 1 40 0 GCTAAAACGA 0.981295 -148 ACTTGGCCTGGCTAAAACTAAATTCTAAGG 2 214 1 GCTAAAACTA 0.97136 -87 GGGCAGGAAAGAAAAAAAAACTAAGAATTA 3 38 1 GAAAAAAAAA 0.736315 -263 GGGGAAGTGAGCAAAAACTATAATTATTAG 3 131 1 GCAAAAACTA 0.936525 -170 TAAATTACTGGATAAAACAACTCTTTTTGC 5 11 1 GATAAAACAA 0.959234 -290 TTCTCTTACACCTAAAACGACAAATAATTA 5 52 0 CCTAAAACGA 0.909792 -249 ATGATTTTTTGATAAAAAAATCTTTCTTCT 5 78 0 GATAAAAAAA 0.865209 -223 ********** Masking position 5 Map Score: 4.01091 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 217 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 5 AGGGGCTGGGGGGATGGGGAACAGA 1 173 0 GCTGGGGGGT 0.995799 -15 TTGCCAACTTGCTGGGGGTTTTTACGGAGAA 2 63 1 GCTGGGGGTT 0.973455 -238 CAAGGGCAGCGCATGGTGGTTTCTCCAGGCA 3 73 1 GCATGGTGGT 0.963994 -228 CTAGAATTTTCCTGGGGGACTGCCCAGTAAC 3 187 0 CCTGGGGGAT 0.958122 -114 TTTGAATCAAGCATGGGAGCTATCTAGAGCG 3 273 0 GCATGGGAGT 0.968846 -28 GGATGTATGGGGATTGCAGAAGGAG 4 5 1 GTATGGGGAT 0.87957 -134 AATCCTAGGGCCAGGGGCGGTCAAATTGAGC 4 72 1 CCAGGGGCGT 0.962777 -67 AATAGGTATAGCATAGGGGCTGATTTAGCAT 5 258 1 GCATAGGGGT 0.963994 -43 ********* * Masking position 11 Map Score: 6.71621 Number of sites scoring better than the average of aligned sites = 999 Number in coding regions = 862 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 6 TTAACAAAGTAACAAATAAGTTTACAAAAC 2 152 0 AACAAATAAG 0.816828 -149 GGCTAAAACTAAATTCTAAGGCTGGTATTG 2 223 1 AAATTCTAAG 0.906892 -78 GGAAAGAAAAAAAAACTAAGAATTAATAGC 3 43 1 AAAAACTAAG 0.906892 -258 AAAATTCTAGAACATCAAAGTCGTTATGAT 3 208 1 AACATCAAAG 0.929915 -93 TTTTCTCCCGAGCATCTAAGATAGAATCTC 4 33 0 AGCATCTAAG 0.978064 -106 GCTTTTATCTAGCTTCTAAGATTCCCAAGG 6 11 1 AGCTTCTAAG 0.959835 -25 ********** Masking position 8 Map Score: 1.24415 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 107 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 7 GCCTCCTCTGTTCCCCATCCCCCCAGCCCC 1 167 1 TTCCCCATCC 0.908035 -21 GATTCCAATCGTCCCTGTGCCAGTTGTCTT 2 105 0 GTCCCTGTGC 0.969518 -196 GCCTGGAGAAACCACCATGCGCTGCCCTTG 3 73 0 ACCACCATGC 0.899234 -228 GCTCTAGATAGCTCCCATGCTTGATTCAAA 3 274 1 GCTCCCATGC 0.96351 -27 TCCTTCTGCAATCCCCATACATCC 4 5 0 ATCCCCATAC 0.864558 -134 CAATTTGACCGCCCCTGGCCCTAGGATTAA 4 70 0 GCCCCTGGCC 0.912217 -69 TGCTAAATCAGCCCCTATGCTATACCTATT 5 258 0 GCCCCTATGC 0.989911 -43 ********** Masking position 5 Map Score: 1.31085 Number of sites scoring better than the average of aligned sites = 1117 Number in coding regions = 1009 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 8 CGTTACCTCGGTTCTAGGATCTTTA 4 124 0 ACCTCGTTCT 0.935082 -15 TGATAAAAAAATCTTTCTTCTCTTACACCTA 5 68 0 ATCTTTTTCT 0.950716 -233 TTCTAGCAATATCTTTTTTAATAAGACTATA 5 142 0 ATCTTTTTAA 0.755096 -159 CCAAGATCTTACCTAAATTCTAGCAATATCT 5 159 0 ACCTAATTCT 0.82473 -142 TTTAGGTAAGATCTTGGTTCAGAAAGTGCAA 5 173 1 ATCTTGTTCA 0.961294 -128 GCGAGAGCAGATCTTGATTATTTTTGAAAAT 5 230 1 ATCTTGTTAT 0.857654 -71 CCTATGCTATACCTATTTTCAAAAATAATCA 5 244 0 ACCTATTTCA 0.926286 -57 GAATGAACCTTTTCTCAAGAAAATGCT 5 284 0 ACCTTTCTCA 0.824866 -17 GCTTTTATCTAGCTTCTAAGATTCCCA 6 7 1 ATCTAGTTCT 0.950183 -29 ****** **** Masking position 4 Map Score: 2.76491 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 140 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 9 ********** No masking Map Score: -1.19839e-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: -1.19839e-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: -1.19839e-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