AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i254_synecho_ctra_100.orf -o254_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 RCY29546 300 Synechocystis #2 RCY03338 300 Synechocystis #3 RCY11382 300 Synechocystis #4 RCY49571 65 Synechocystis #5 RCY41531 22 Synechocystis #6 RCT00473 293 Chlamydia_trachomatis #7 RCT00554 300 Chlamydia_trachomatis #8 RCT00657 135 Chlamydia_trachomatis Motif number 1 ATATCCCTACTTCCGTCTTCTTCAAAAAGA 1 21 1 TTCCGTCTTC 0.968327 -280 TGCTTCAGAGTTCCGTTTTCCACGAGTGCG 1 173 1 TTCCGTTTTC 0.854193 -128 AGGGTTACTTTTGCCTGTTCCCTGGGGCCT 1 244 1 TTGCCTGTTC 0.980426 -57 CCCATTAATATTCCCTCTTCG 2 2 0 TTCCCTCTTC 0.98856 -299 GGGGCTTCATTTCCCCGGTCTTGGTTCCGA 3 245 1 TTCCCCGGTC 0.973344 -56 TAACTTGAAATTACCTCTTCT 3 290 1 TTACCTCTTC 0.943048 -11 TTCGTTCTATTTGCCCCGTCAAGCGCCTAG 4 38 1 TTGCCCCGTC 0.973344 -28 GATCGGGTGCTTGCCCGTTCTCATAGGCAT 6 104 1 TTGCCCGTTC 0.980038 -190 ********** Masking position 2 Map Score: 9.63698 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 144 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 2 CTACTTCCGTCTTCTTCAAAAAGAGAAGAT 1 27 1 CTTCTTCAAA 0.786548 -274 AAAATACGAATTTCTTAACATTCATGTAAG 1 120 1 TTTCTTAACA 0.956757 -181 ATTGTCTCTATATCTTAACAAAATTGAGGC 3 134 1 TATCTTAACA 0.777175 -167 ACAAGTTTATTCCCAAAAATTGACA 6 6 1 TTTATTCCCA 0.88879 -288 CCATTGTAAACTTCTTCCCATCGCCTGGTG 6 37 1 CTTCTTCCCA 0.975519 -257 CCTCATAGGTTTTCTTCTCAAAGTGTATCG 6 75 0 TTTCTTCTCA 0.973105 -219 ATGACATGGTTTTCTTCTTAATGGTTTACG 6 173 0 TTTCTTCTTA 0.801603 -121 GTCTTCGTTTTTTCTTAACAGATGACATGG 6 194 0 TTTCTTAACA 0.956757 -100 CTATACGATTTTTCTTCCCATGGTAGTTGC 7 49 1 TTTCTTCCCA 0.987882 -252 ********** Masking position 5 Map Score: 7.65677 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 125 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 3 TACTTTCTGTATCCATTTTTACGGTTTTTCAAG 1 65 1 ATCATTTTAG 0.976459 -236 CTTGGGGTCAATCGTTACTTAAGAACCATTTAC 2 31 0 ATCTTCTTAG 0.895821 -270 GACTCTGACCGTCTATGTTTACCCTATCCTCTA 3 24 1 GTCATTTTAC 0.946129 -277 TACAATGGCTGTCAATTTTTGGGAATAAACTTG 6 12 0 GTCATTTTGG 0.965725 -282 TCTCTTCGACGTCTTTTTTTACGCTTATGCTTG 6 234 0 GTCTTTTTAG 0.974904 -60 CAATTTAACTATCTATTTTTATGCCGATCTCTT 6 261 0 ATCATTTTAG 0.976459 -33 CGGTAGAAAAGTCTATTTTTAGGGATAAGTCTT 7 104 0 GTCATTTTAG 0.990664 -197 AACCTCATTCGTCCATGCTTATGGACAAATCAA 7 207 1 GTCATCTTAG 0.983631 -94 *** ** **** * Masking position 6 Map Score: 8.33577 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 31 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 GGCAAAAGTAACCCTTCTAGCAGATCGTTGGCA 1 226 0 ACCCCTAGAG 0.825483 -75 GCATAGGTTCCCCCCGCAATTAGAAAATATCTA 2 78 1 CCCCCAATAG 0.978474 -223 CGCCGCCATGACCCTTCGATCGCCA 2 286 1 ACCCCGATGC 0.964753 -15 GTGCAACTTTCCCAACCGAGGGGAAATACCATG 3 176 0 CCCACGAGGG 0.887674 -125 GGTCGGCTAGCCCCCACAATAAAGCCAATTTGC 3 212 1 CCCCCAATAA 0.875502 -89 GGAAATGAAGCCCCGCAAATTGGCTTTATTGTG 3 226 0 CCCCAAATGG 0.930981 -75 GTTCTATTTGCCCCGTCAAGCGCCTAGATAACC 4 41 1 CCCCCAAGGC 0.990884 -25 GCCGGCTTTCACCAGGCGATGGGAAGAAGTTTA 6 43 0 ACCACGATGG 0.897643 -251 GAGGCTTCCTCCCCTACAAGGGCTTCACCTCGT 7 271 1 CCCCCAAGGC 0.961728 -30 **** **** ** Masking position 9 Map Score: 5.19065 Number of sites scoring better than the average of aligned sites = 1057 Number in coding regions = 972 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 5 ATACAGAAAGTAAATCGTTCATCTTCTCTTTTTGAAGAA 1 38 0 TATTTATCTT 0.947074 -263 TTTTTGCTATTATTTTGTTTAGATATTTTCTAATTGCGG 2 91 0 TATTTATTTT 0.966182 -210 ATTTTGGATTTATATACTTGTATTTTTTGCTATTATTTT 2 114 0 TATTTTTTTG 0.789897 -187 AGACAAATATTAACTAATTGACTTGTTATGGCATTATTA 2 173 0 TATTTATTTT 0.966182 -128 TATATTTTAGTCTTTAGTTCAACTTTTAGAGAATTAAAC 2 220 0 TCTTTATTTG 0.834211 -81 TTTAGCTGAGTAAATTTTTTACATTTACTTTATTCAATA 3 96 0 TATTTATTAT 0.784027 -205 GGCATAAAAATAGATAGTTAAATTGTTTGGGTTCT 6 269 1 TATTTATTTG 0.963897 -25 ATCGTATAGTTAACTCGATGAGATTTTAGAGCCCTGGAC 7 19 0 TATATATTTG 0.772467 -282 GCTCTCCAGATACCTCTTTTCTATATTATTGGGTACAGT 7 144 0 TATTTCTTTT 0.856287 -157 AGAGCTTTCTTACTTTATTCATCTCCTTTAACCTCATTC 7 178 1 TATTTATCTT 0.947074 -123 CGCTCCTTTTTAGTTGCTTTAATTCCTTTATATTGATTT 7 233 0 TATTTATCTT 0.947074 -68 ** * ** * * ** * Masking position 9 Map Score: 5.13625 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 40 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 6 AAGTAAATGTAAAAAATTTACTCAGCTAAA 3 105 1 AAAAAATTTA 0.636065 -196 TGACACAATAACTTACTTCAGC 5 8 0 CAATAACTTA 0.816497 -15 AAGTCTTTTGAAAAGACTCAGCTAATGCCT 6 128 0 AAAAGACTCA 0.933598 -166 GAGTCTTTTCAAAAGACTTACCAATTATTC 6 139 1 AAAAGACTTA 0.961283 -155 TAAGAAAAAACGAAGACTTAAGATCGCCAA 6 207 1 CGAAGACTTA 0.912742 -87 TTCCGTTTACAAAAGACTTATCCCTAAAAA 7 92 1 AAAAGACTTA 0.961283 -209 ACTCAAGATACAAAATCTTATAATGCAAAT 8 54 0 CAAAATCTTA 0.816469 -82 CCCCAGAATACAAAAACTCAAGATACAAAA 8 69 0 CAAAAACTCA 0.933598 -67 ********** Masking position 3 Map Score: 3.30951 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 104 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 7 CACGAGTGCGAGGGAGATGGAACTTGGGCTG 1 193 1 AGGGAATGGA 0.981205 -108 TTAAGGCCCCAGGGAACAGGCAAAAGTAACC 1 246 0 AGGGACAGGC 0.984075 -55 TGGCGATCGAAGGGTCATGGCGGCGCACTAA 2 280 0 AGGGTATGGC 0.975185 -21 GGCCAGAACTAGGGTCATGGTATTTCCCCTC 3 161 1 AGGGTATGGT 0.908183 -140 TCTTTTGTAAACGGAACAGGATTACTGTAGC 7 77 0 ACGGACAGGA 0.894395 -224 GTCTATTTTTAGGGATAAGTCTTTTGTAAAC 7 96 0 AGGGAAAGTC 0.875623 -205 TATAGAAAAGAGGTATCTGGAGAGCTTTCTT 7 158 1 AGGTACTGGA 0.921285 -143 TGGACGAATGAGGTTAAAGGAGATGAATAAA 7 191 0 AGGTTAAGGA 0.881563 -110 ***** ***** Masking position 1 Map Score: 3.87403 Number of sites scoring better than the average of aligned sites = 871 Number in coding regions = 776 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 8 ATTTACTGATCATTCGGCTGGACTGCTTCAG 1 150 1 CATTGGCTGG 0.953151 -151 GGGAGATGGAACTTGGGCTGGATGCCAACGA 1 204 1 ACTTGGCTGG 0.953152 -97 ATGATCCATAAATTAGGCTAATAATGCCATA 2 155 1 AATTGGCTAA 0.938276 -146 ACTTTTAGAGAATTAAACTGAATTTCAGACA 2 207 0 AATTAACTGA 0.879697 -94 TCCTCTAAGCAATTAGACTTATGGGAAAGGA 3 50 1 AATTGACTTA 0.805705 -251 ATATAGAGACAATTTAGCTGAGTAAATTTTT 3 116 0 AATTAGCTGA 0.964036 -185 GAATACAACGAATTGGGCTGAGAATTAGGAA 8 109 1 AATTGGCTGA 0.989926 -27 **** ****** Masking position 4 Map Score: 2.07333 Number of sites scoring better than the average of aligned sites = 308 Number in coding regions = 258 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 9 TCAAGGAATGGTCAACAAAATACGAATTTCTT 1 104 1 GTCCAAAATA 0.982767 -197 ATTGCTTGCAGTCTTTAAAATAACCTCATTTC 1 278 1 GTCTAAAATA 0.950666 -23 GACGGTCAGAGTCATCAAAATTTTAA 3 5 0 GTCCAAAATT 0.93364 -296 TGGTCGGCTAGCCCCCACAATAAAGCCAATTT 3 211 1 GCCCACAATA 0.924423 -90 TCTACAGACCGTCCCCAGAATACAAAAACTCA 8 79 0 GTCCAGAATA 0.984016 -57 TCTGGGGACGGTCTGTAGAATACAACGAATTG 8 92 1 GTCTAGAATA 0.954133 -44 *** ******* Masking position 7 Map Score: 1.79157 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 28 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 10 TACTCCCCTTGGGGTCAATCGTTACTTAAG 2 41 0 GGGGTCAATC 0.941362 -260 TTCTAATTGCGGGGGGAACCTATGCTTTTT 2 73 0 GGGGGGAACC 0.985988 -228 GCTTTATTGTGGGGGCTAGCCGACCAAGGT 3 207 0 GGGGGCTAGC 0.983647 -94 GCCTATGAGAACGGGCAAGCACCCGATCCT 6 102 0 ACGGGCAAGC 0.915918 -192 GCCCTTGTAGGGGAGGAAGCCTCGCTCCTT 7 264 0 GGGAGGAAGC 0.97458 -37 GTTTATCACGAGGTGAAGCCCTTGTAGGG 7 282 0 GAGGTGAAGC 0.941365 -19 ********** Masking position 8 Map Score: 1.07876 Number of sites scoring better than the average of aligned sites = 516 Number in coding regions = 442 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 11 ********** No masking Map Score: 2.23354e-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: 2.23354e-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: 2.23354e-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