AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i066_synecho_ctra_300.orf -o066_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 RCY33655 258 Synechocystis #2 RCY27198 197 Synechocystis #3 RCY30985 201 Synechocystis #4 RCY15108 176 Synechocystis #5 RCY52095 117 Synechocystis #6 RCT00412 49 Chlamydia_trachomatis #7 RCT00414 300 Chlamydia_trachomatis Motif number 1 GTATTAAAAATCCCCCTGCCATGCTCTCCACTGAAA 1 159 1 TCCCCCCACC 0.998625 -100 TCCACTGAAATGCCCCTTCCAACCACCGGAAGCACC 1 185 1 TCCCCCCACC 0.998625 -74 CCTTATTAAAAACCCCGGCCTCCCCCTCCCCCAACC 1 219 1 ACCCCCCTCC 0.958157 -40 GGCCTCCCCCTCCCCCAACCAAAATCTTTTACCG 1 235 1 TCCCCCCAAC 0.997302 -24 GGGGCATTATTGTCCAGCCCAGCCCTTAGTTTTTGA 2 137 1 TTCCACCACT 0.829473 -61 TAACGTTCACTTCCCCTAACATCATCGTCC 2 178 1 TCCCCACAAC 0.96681 -20 GCTACGGAATTACCCAAGCCAGTGCCGAGGAACGAA 3 41 1 TCCCACCAGC 0.988567 -161 AACATGACTCTCTCCCTCCCTGGAGCAACCTAGTCT 4 70 1 TTCCCCCTAC 0.933913 -107 GAAACGATGCTTCCAAGACCATTACCAAGCGCCCCA 7 115 0 TCCAACCAAC 0.941419 -186 GCACTCTTTATCCTCTACCCACTCTCCCTTATCCTT 7 233 0 TCTCTCCACC 0.864699 -68 ATTTCCACCTCCACTGATTAAACCTTGC 7 283 0 TCCACCCAGT 0.879145 -18 * **** *** * * Masking position 10 Map Score: 14.1327 Number of sites scoring better than the average of aligned sites = 1362 Number in coding regions = 1250 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 2 CCAAAAAAGAAGGAAAACAATCATCCCTAA 1 23 1 AGGAAAACAA 0.929913 -236 TAAATCACTTAGGGCAACTAATCTAATATA 2 84 1 AGGGCAACTA 0.818643 -114 CGATGATGTTAGGGGAAGTGAACGTTAAAT 2 175 0 AGGGGAAGTG 0.891204 -23 CTAAATTGACAGGAAATAAGTTACATCT 3 184 1 AGGAAATAAG 0.702822 -18 TGCTCCAGGGAGGGAGAGAGTCATGTTATG 4 67 0 AGGGAGAGAG 0.79465 -110 TCAAAAATTAAGGACAAAAACTATTAGTAA 4 140 0 AGGACAAAAA 0.887167 -37 CAATTTTGTCAGGAAAAGAAAGAGAATTAC 5 17 0 AGGAAAAGAA 0.945732 -101 ATCAGGTTAGAGGGAAACTAAAGTCAGGCG 5 95 0 AGGGAAACTA 0.902294 -23 GCTTCCTACTAGGAAAAAAGCTT 7 4 0 AGGAAAAAAG 0.956941 -297 GTAAGCGACTAGGGAAAATGGGGCGCTTGG 7 97 1 AGGGAAAATG 0.939277 -204 TAAACTTTCTAGGAGAAAGAGGATTTATTT 7 172 0 AGGAGAAAGA 0.866407 -129 ATTCCCATAAAGGATAAGGGAGAGTGGGTA 7 224 1 AGGATAAGGG 0.862559 -77 GAGTGGGTAGAGGATAAAGAGTGCCTCTGC 7 245 1 AGGATAAAGA 0.807424 -56 ********** Masking position 1 Map Score: 8.18522 Number of sites scoring better than the average of aligned sites = 1546 Number in coding regions = 1292 Number in noncoding regions = 254 Number of orfs with sites within 600 bp upstream = 263 Fraction of orfs with sites within 600 bp upstream = 0.0422422 Motif number 3 TCGACTATCAACACTAACTTCCAGGGTAATCA 2 38 0 ACATAATTCC 0.972268 -160 CCAGTATATTAGATTAGTTGCCCTAAGTGATT 2 86 0 AGATAGTGCC 0.981112 -112 CGGCATGGTAACAGTAGGTTCCATTAACCAAC 3 100 1 ACATAGTTCC 0.992279 -102 TGGCTGGCTGAGACTAGGTTGCTCCAGGGAGG 4 84 0 AGATAGTTGC 0.974814 -93 CATTACACACAGAATAAATTTCAAACTTACTA 4 114 1 AGATAATTTC 0.876898 -63 CGATCGCCTGACTTTAGTTTCCCTCTAACCTG 5 91 1 ACTTAGTTCC 0.963875 -27 TCTCATCAAAAGATTAGATTCCCATAAAGGAT 7 207 1 AGATAGTTCC 0.994099 -94 *** *** **** Masking position 6 Map Score: 6.28464 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 17 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 4 TCAATCTTAGGGATGATTGTTTTCCTTCTTTTTTGGC 1 22 0 GGATTTTCCT 0.660385 -237 CGACCAGTCCGACTAAATTTTATCTGTATTAAAAATC 1 134 1 GACTATTCTT 0.781072 -125 GCGGAAATATGGCATTTTTATGGCCATTG 2 3 1 GGAAAGCTTT 0.778831 -195 AATCACTTAGGGCAACTAATCTAATATACTGGTTACA 2 86 1 GGCATTCATT 0.468472 -112 CCAGTGCCGAGGAACGAAATTATTTATAGACCACTGG 3 59 1 GGAAATTTTT 0.956551 -143 TAAATTGACAGGAAATAAGTTACATCT 3 185 1 GGAAATTATT 0.917759 -17 AAATACTGATGGCAATAGTTTCTTTATTATTCCCAAC 5 52 1 GGCAATTTTT 0.941904 -66 GCGATCGCCTGACTTTAGTTTCCCTCTAACCTGATCC 5 90 1 GACTATTCTT 0.781072 -28 TTCTGGAGCAGGAAACAGTTTCATTTTGGGAGAATCG 6 23 1 GGAAATTTTT 0.956645 -27 TTTCCTAGTAGGAAGCTTCTTGACTTTTGCTGTAAGA 7 18 1 GGAATTTCTT 0.950724 -283 TAATGGTCTTGGAAGCATCGTTTCTTTTTCTTATAGT 7 127 1 GGAAAGTCTT 0.968089 -174 AGGAGAAAGAGGATTTATTTTAACTATAACTATAAGA 7 155 0 GGATATTCTT 0.97462 -146 AGTGGGTAGAGGATAAAGAGTGCCTCTGCAAGGTCTT 7 246 1 GGATAGTCTT 0.950942 -55 **** * ** ** * Masking position 17 Map Score: 6.50347 Number of sites scoring better than the average of aligned sites = 640 Number in coding regions = 547 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 5 ACTGGTCGGACATCGGAGCTACAACAACCG 1 112 0 CATCGGAGCT 0.9361 -147 AGGGGCATTTCAGTGGAGAGCATGGCAGGG 1 172 0 CAGTGGAGAG 0.941024 -87 CCAGGGTAATCAATGGCCATAAAAATGCCA 2 20 0 CAATGGCCAT 0.806178 -178 ATACTGGTTACATCGGGGCTTATCATGGGG 2 111 1 CATCGGGGCT 0.818434 -87 TTACCCAAGCCAGTGCCGAGGAACGAAATT 3 50 1 CAGTGCCGAG 0.881395 -152 ATTTATAGACCACTGGCGATCGGCATGGTA 3 80 1 CACTGGCGAT 0.934645 -122 TAGTTAGAATCAATGCAGTTGGTTAATGGA 3 119 0 CAATGCAGTT 0.862837 -83 CGCCGTTGCCCAATGGAGTGATCTAGTTAG 3 142 0 CAATGGAGTG 0.910056 -60 CTCCATTGGGCAACGGCGTTAATGCACTGA 3 154 1 CAACGGCGTT 0.95251 -48 TTATTATTCCCAACGGCGATCGCCTGACTT 5 75 1 CAACGGCGAT 0.969858 -43 GCTTTAATACCATTGCAGCTTCAGTTGATC 7 59 0 CATTGCAGCT 0.860742 -242 AAGGTTTAATCAGTGGAGGTGGAAAT 7 285 1 CAGTGGAGGT 0.912629 -16 ********** Masking position 2 Map Score: 9.49302 Number of sites scoring better than the average of aligned sites = 2137 Number in coding regions = 1940 Number in noncoding regions = 197 Number of orfs with sites within 600 bp upstream = 216 Fraction of orfs with sites within 600 bp upstream = 0.0346932 Motif number 6 AGAGCATGGCAGGGGGATTTTTAATACAGA 1 156 0 AGGGGGATTT 0.895059 -103 CGGTGGTTGGAAGGGGCATTTCAGTGGAGA 1 183 0 AAGGGGCATT 0.973795 -76 GGTTTTTAATAAGGTGCTTCCGGTGGTTGG 1 203 0 AAGGTGCTTC 0.979753 -56 GGGGCTTATCATGGGGCATTATTGTCCAGC 2 125 1 ATGGGGCATT 0.90206 -73 AGCAAAAGTCAAGAAGCTTCCTACTAGGAA 7 19 0 AAGAAGCTTC 0.882181 -282 CGCTTACCATAAGGTGCTTTAATACCATTG 7 74 0 AAGGTGCTTT 0.980031 -227 AGAAAAAGAAACGATGCTTCCAAGACCATT 7 128 0 ACGATGCTTC 0.8737 -173 TTCTAGGAGAAAGAGGATTTATTTTAACTA 7 166 0 AAGAGGATTT 0.901166 -135 ********** Masking position 1 Map Score: 3.56762 Number of sites scoring better than the average of aligned sites = 486 Number in coding regions = 418 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 7 CCCCGATGTAACCAGTATATTAGATTAGTT 2 99 0 ACCAGTATAT 0.942878 -99 CCAGAATATTTCCAGAAAATTACCAT 3 7 0 TCCAGAAAAT 0.976585 -195 CCGTAGCATTTCCAGAATATTTCCAGAAAA 3 18 0 TCCAGAATAT 0.9906 -184 TGTTTCCTGCTCCAGAATATAAAAGATAT 6 10 0 TCCAGAATAT 0.9906 -40 ********** Masking position 4 Map Score: 3.15557 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 6 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 8 AATAACTCTTGTAATATCCCAGTTTATCAA 1 55 0 GTAATATCCC 0.846382 -204 TTATCTGTATTAAAAATCCCCCTGCCATGC 1 153 1 TAAAAATCCC 0.879805 -106 GCTCTCCACTGAAATGCCCCTTCCAACCAC 1 181 1 GAAATGCCCC 0.973018 -78 AGCACCTTATTAAAAACCCCGGCCTCCCCC 1 215 1 TAAAAACCCC 0.949306 -44 AATGCCCCATGATAAGCCCCGATGTAACCA 2 115 0 GATAAGCCCC 0.912029 -83 GGGCTGGACAATAATGCCCCATGATAAGCC 2 127 0 ATAATGCCCC 0.90076 -71 CAAACTTTGTTTAAAGTCCAACATAACATG 4 46 1 TTAAAGTCCA 0.676494 -131 TGCAATGGTATTAAAGCACCTTATGGTAAG 7 72 1 TTAAAGCACC 0.842512 -229 ********** Masking position 4 Map Score: 1.63085 Number of sites scoring better than the average of aligned sites = 1286 Number in coding regions = 1102 Number in noncoding regions = 184 Number of orfs with sites within 600 bp upstream = 176 Fraction of orfs with sites within 600 bp upstream = 0.0282686 Motif number 9 TGTAATATCCCAGTTTATCAATCTTAGGGA 1 46 0 CAGTTTATCA 0.869875 -213 TTATAGACCACTGGCGATCGGCATGGTAAC 3 82 1 CTGGCGATCG 0.977704 -120 AAAAGTCTTGCTGATGATCAAAAATTAAGG 4 157 0 CTGATGATCA 0.932463 -20 AAACTAAAGTCAGGCGATCGCCGTTGGGAA 5 81 0 CAGGCGATCG 0.984329 -37 ATTGCAGCTTCAGTTGATCATATTCTTACA 7 48 0 CAGTTGATCA 0.972133 -253 ********** Masking position 7 Map Score: 0.519967 Number of sites scoring better than the average of aligned sites = 1549 Number in coding regions = 1421 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 10 GTTTTTAATAAGGTGCTTCCGGTGGTTGGA 1 202 0 AGGTGCTTCC 0.973141 -57 CGATTCTCCCAAAATGAAAC 6 40 0 CGATTCTCCC 0.955896 -10 GCAAAAGTCAAGAAGCTTCCTACTAGGAAA 7 18 0 AGAAGCTTCC 0.821065 -283 GAAAAAGAAACGATGCTTCCAAGACCATTA 7 127 0 CGATGCTTCC 0.977338 -174 ********** Masking position 7 Map Score: 0.357535 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 64 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 11 ********** No masking Map Score: 2.93697e-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: 2.93697e-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: 2.93697e-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