AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i307_synecho_ctra_300.orf -o307_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 RCY48542 119 Synechocystis #2 RCY31870 49 Synechocystis #3 RCY18430 293 Synechocystis #4 RCY40674 143 Synechocystis #5 RCY05882 300 Synechocystis #6 RCY51246 183 Synechocystis #7 RCY38268 228 Synechocystis #8 RCY42426 99 Synechocystis #9 RCY52862 204 Synechocystis #10 RCT00577 197 Chlamydia_trachomatis Motif number 1 AAAATGCCTAGGGAAAATGGGAAGATTTTCTCG 1 13 1 GGGAAATGAA 0.786443 -107 ATTAATCCCTGGGAGCAAGACACGGTTCGGATG 1 75 0 GGGACAAGAC 0.971489 -45 GGTGGCTGGGGGGAAAGGGCTGCTCGGGGCCCG 3 58 1 GGGAAGGGGC 0.970012 -236 GTATAGTCTTGGGAGATAGTAACCGCAATACAG 3 118 0 GGGAATAGAC 0.930167 -176 CGGGTCATCCGGGGGAAGGCAACAGGTTGGTTT 3 235 1 GGGGAAGGAC 0.993673 -59 ACTTATATGAAGGATATGGTGACCAAAACCTAT 4 50 1 AGGAATGGAC 0.950214 -94 AAAATCTTGGGGAACAGGGGAATGTTAATGAA 5 279 0 GGGACAGGAA 0.979931 -22 ACCAAAAACAAGGATAAGGTAACCCATCCAACT 7 47 0 AGGAAAGGAC 0.976825 -182 AGCCAGTACCGGGGTAGGGAAACAAATTTTTGT 7 120 1 GGGGAGGGAC 0.987143 -109 TATGGGTATTGGGGCCAGGGCACAAAAATTTGT 7 141 0 GGGGCAGGAC 0.992799 -88 TAGGGAGTCAGGGAACAGGGAGCGGAAAAATCG 8 64 0 GGGACAGGGC 0.987122 -36 ATTAACCCAGAGGGTCTGGCTAATTTTTGTCCC 9 142 1 AGGGCTGGAA 0.800604 -63 **** **** ** Masking position 9 Map Score: 17.4084 Number of sites scoring better than the average of aligned sites = 825 Number in coding regions = 733 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 2 GGAAAATGCCTAGGGAAAATGGGAAGA 1 8 1 GCCTAGGGAA 0.972533 -112 GAGAGATTAATCCCTGGGAGCAAGACACGG 1 83 0 TCCCTGGGAG 0.815761 -37 ACTTTATTTTCATTGGGGAGAGATTAATC 1 101 0 TCATTGGGGA 0.935162 -19 CGAAATGGTGGCTGGGGGGAAAGGGCTGCT 3 52 1 GCTGGGGGGA 0.922867 -242 CTGCTTGCTTGCTTTGGGAACTGTATTGCG 3 98 1 GCTTTGGGAA 0.963482 -196 GTGGCGTATAGTCTTGGGAGATAGTAACCG 3 126 0 GTCTTGGGAG 0.81172 -168 CCCGTCTAGGGCATGGGGGTGGTAATAGGC 3 209 0 GCATGGGGGT 0.797846 -85 AGACGGGTCATCCGGGGGAAGGCAACAGGT 3 232 1 TCCGGGGGAA 0.976437 -62 CTTGATTTTTTCAGAGGGAAAAATTCCTCG 5 26 0 TCAGAGGGAA 0.923503 -275 TATATTTATCTCAGGGGGAATCATTGCTTT 5 217 1 TCAGGGGGAA 0.968637 -84 AAAATCTTGGGGAACAGGGGAATG 5 287 0 TCTTGGGGAA 0.956641 -14 TGGGAAGGACGTATTGGGAACTTTGGTTGA 6 44 0 GTATTGGGAA 0.864201 -140 GATTTGAGCAGAATTGGGAAGGACGTATTG 6 58 0 GAATTGGGAA 0.783029 -126 AGGGGCGAGATCCTAGGGAGTCAGGGAACA 8 80 0 TCCTAGGGAG 0.917614 -20 ********** Masking position 6 Map Score: 12.2174 Number of sites scoring better than the average of aligned sites = 2781 Number in coding regions = 2478 Number in noncoding regions = 303 Number of orfs with sites within 600 bp upstream = 311 Fraction of orfs with sites within 600 bp upstream = 0.0499518 Motif number 3 ATTTTTTCAGAGGGAAAAATTCCTCGGCTA 5 22 0 AGGGAAAAAT 0.733278 -279 AAAATCTTTAGGACAAAACTCGCCAGAGGT 5 61 0 GGACAAAACT 0.87595 -240 GCTCCATGGCGGCCAAAAATCTTTAGGACA 5 76 0 GGCCAAAAAT 0.952064 -225 GCGCTAATCTGGGCAAAAATTCGTTGGTTT 5 159 0 GGGCAAAAAT 0.990413 -142 GCCCAGATTAGCGCCAAAATTAAGCGGAGC 5 175 1 GCGCCAAAAT 0.951711 -126 GCGGAGCAGTGGGTCAAAATATATTTATCT 5 198 1 GGGTCAAAAT 0.832231 -103 CGAGTTAACTGGGCAAATATCTATGGATTA 6 87 1 GGGCAAATAT 0.935637 -97 TGGGGCCAGGGCACAAAAATTTGTTTCCCT 7 135 0 GCACAAAAAT 0.937587 -94 GGAACAGGGAGCGGAAAAATCGAATAGAAA 8 56 0 GCGGAAAAAT 0.933161 -44 AGTTTTTCGGGGACAAAAATTAGCCAGACC 9 154 0 GGACAAAAAT 0.971313 -51 ********** Masking position 6 Map Score: 11.0053 Number of sites scoring better than the average of aligned sites = 1149 Number in coding regions = 967 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 204 Fraction of orfs with sites within 600 bp upstream = 0.0327658 Motif number 4 GCAAGACACGGTTCGGATGTAAATCTTGGCACC 1 61 0 GTTGTGTAAA 0.831445 -59 GAGTTGAGAAGTCCCTATGTCAAGA 3 279 1 GTCCTGTCAA 0.976017 -15 TATTATTCGTGTTTCAATGACAAGCATCTTTCC 4 93 1 GTTCTGACAA 0.985832 -51 TGCTGGCTTTGTTGCCCTGTCAACCAAAGTTCC 6 25 1 GTTCTGTCAA 0.986275 -159 CCCGGTACTGGCTCCAATGTCAATGCAATCCCA 7 100 0 GCTCTGTCAA 0.950219 -129 TTTGACTAGTTTGATTGACAATTTGATACTT 8 9 1 GTTGTGACAA 0.977853 -91 TCCTTTGGATCTCTCTTTGACAAGGGAAACCTT 10 15 1 CTCCTGACAA 0.935054 -183 AAAAATCCCTTTGGATGACAAAAAAAAGAAA 10 177 0 CTTGTGACAA 0.939861 -21 *** * ****** Masking position 12 Map Score: 5.57137 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 93 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 CTATTGTAGTCAGTGGTGCCAAGATTTACAT 1 47 1 CAGTGGTGCA 0.972574 -73 AATCTCTGCCAGTGGTGAGGGCTTGTTACA 2 30 0 CAGTGGTGAG 0.976298 -20 TTGATTTTTTCAGAGGGAAAAATTCCTCGGC 5 24 0 CAGAGGGAAA 0.735534 -277 CAAAACTCGCCAGAGGTCAAGGCTTGATTTT 5 47 0 CAGAGGTCAG 0.920861 -254 TTAAGCGGAGCAGTGGGTCAAAATATATTTA 5 194 1 CAGTGGGTCA 0.873223 -107 TGGTGTAGCTCAGTGGTAGAGCAACTGATTT 9 85 0 CAGTGGTAGG 0.86827 -120 TATTCTGTATCAGAGATGCTGGTGTAGCTCA 9 104 0 CAGAGATGCG 0.938016 -101 AAGATTAACCCAGAGGGTCTGGCTAATTTTT 9 139 1 CAGAGGGTCG 0.967072 -66 AGGTTTCCAACAGGGTTGCTGTAGATCAAAA 10 67 0 CAGGGTTGCG 0.847205 -131 ACTCTCTATACAGAGGTGCTGTTTCTTTTTT 10 156 1 CAGAGGTGCG 0.993538 -42 ********* * Masking position 2 Map Score: 7.04657 Number of sites scoring better than the average of aligned sites = 682 Number in coding regions = 634 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 6 TTCATTGGGGAGAGATTAATCCCTGGGAGCAA 1 90 0 AGAGTAATCC 0.90492 -30 TGGTTTTCGGAAAGGTGAACCCGTAGCTAGCT 5 133 0 AAAGTAACCC 0.939031 -168 GAGAAATGGGAAGGAGTAATCCATAGATATTT 6 101 0 AAGGGAATCC 0.903184 -83 CTGATGGAAGGAAGATCGACCCAGTGAATGAC 6 155 1 GAAGTGACCC 0.974822 -29 TGTTTTTGGTGGGGGTTGACCCTGCCATGGTG 7 70 1 GGGGTGACCC 0.973758 -159 AGGGGCGAGATCCTAGGGAGTCA 8 87 0 GGGGGGATCC 0.928825 -13 CAGAATAGCAGAAGATTAACCCAGAGGGTCTG 9 128 1 GAAGTAACCC 0.960674 -77 TTCCCTTGTCAAAGAGAGATCCAAAGGAGATT 10 11 0 AAAGGGATCC 0.937874 -187 **** * ***** Masking position 9 Map Score: 4.2138 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 207 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 7 AATGTAACAAGCCCTCACCACTGGCAGAGA 2 28 1 GCCCTCACCA 0.979562 -22 CCCTTTCCCCCCAGCCACCATTTCGGCGAT 3 47 0 CCAGCCACCA 0.939923 -247 ATTGTTAGGGGCCGCCGCCAACGGGAACAT 3 169 0 GCCGCCGCCA 0.993602 -125 GGCAGGGTCAACCCCCACCAAAAACAAGGA 7 66 0 ACCCCCACCA 0.971154 -163 GGTGGGGGTTGACCCTGCCATGGTGGGATT 7 77 1 GACCCTGCCA 0.807075 -152 AGGTTCAAATCCCGTCACCAGCTTATTTTG 9 39 0 CCCGTCACCA 0.970505 -166 AATTCTTATCGCCGCTATCATCCTGCCCAT 10 126 1 GCCGCTATCA 0.890897 -72 ********** Masking position 10 Map Score: 3.32772 Number of sites scoring better than the average of aligned sites = 2156 Number in coding regions = 2096 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 8 CGAACCGTGTCTTGCTCCCAGGGATTAATC 1 79 1 CTTGCTCCCA 0.778485 -41 CAGAGCCTTTCGGGCCCCGAGCAGCCCTTT 3 71 0 CGGGCCCCGA 0.927527 -223 CCCGTTGGCGGCGGCCCCTAACAATCCGCT 3 174 1 GCGGCCCCTA 0.938439 -120 TTGCTCCATGGCGGCCAAAAATCTTTAGGA 5 78 0 GCGGCCAAAA 0.633056 -223 GCTAGCTTGTATTGCCCAAACCTAACTCAT 5 110 0 ATTGCCCAAA 0.868607 -191 CCAACGAATTTTTGCCCAGATTAGCGCCAA 5 162 1 TTTGCCCAGA 0.786026 -139 CCTTCCCAATTCTGCTCAAATCGAGTTAAC 6 66 1 TCTGCTCAAA 0.722142 -118 AACCCATCCAACTGCCCCAAGGTTAGGAAG 7 30 0 ACTGCCCCAA 0.952469 -199 TACCCCGGTACTGGCTCCAATGTCAATGCA 7 106 0 CTGGCTCCAA 0.938591 -123 TTTTTGTGCCCTGGCCCCAATACCCATAAT 7 146 1 CTGGCCCCAA 0.983919 -83 CCGCTATCATCCTGCCCATACTCTCTATAC 10 137 1 CCTGCCCATA 0.934014 -61 ********** Masking position 10 Map Score: 3.22396 Number of sites scoring better than the average of aligned sites = 2574 Number in coding regions = 2367 Number in noncoding regions = 207 Number of orfs with sites within 600 bp upstream = 218 Fraction of orfs with sites within 600 bp upstream = 0.0350145 Motif number 9 TTTTCTCGACTATTGTAGTCAGTGGTGCCA 1 38 1 TATTGTAGTC 0.902123 -82 GCTTGTTACATTTTGTAATCAAATTGCTC 2 10 0 TTTTGTAATC 0.958886 -40 GTTTCTCTGAATTTGAATTCTATGGACGAA 4 17 0 ATTTGAATTC 0.757617 -127 TATTGTAGTCATTCACTGGG 6 174 0 TATTGTAGTC 0.902123 -10 GATAATCTCGTTTTCTATTCGATTTTTCCG 8 45 1 TTTTCTATTC 0.794244 -55 CACCAGCTTATTTTGAATTCATTAACCTAT 9 24 0 TTTTGAATTC 0.895158 -181 AGAGCAACTGATTTGTAATCAGTCGGTCGC 9 69 0 ATTTGTAATC 0.895158 -136 TGTTTCTTTTTTTTGTCATCCAAAGGGATT 10 175 1 TTTTGTCATC 0.861009 -23 ********** Masking position 4 Map Score: 2.89646 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 99 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 10 GGGAAGGCAGGTTTTTTAGACGACGTTTCC 3 12 0 GTTTTTTAGA 0.85512 -282 TTGGTTTAGCGGTTTATTGAGTTGAGAAGT 3 261 1 GGTTTATTGA 0.872686 -33 TATAAGTCAAGTTTCTCTGAATTTGAATTC 4 27 0 GTTTCTCTGA 0.904558 -117 AAAATTCGTTGGTTTTCGGAAAGGTGAACC 5 144 0 GGTTTTCGGA 0.954675 -157 TTTGACTAGTTTGATTGACAATTTGATA 8 9 1 GTTTGATTGA 0.788343 -91 CGTTAAAAAAGTTTTTCGGGGACAAAAATT 9 163 0 GTTTTTCGGG 0.908083 -42 GTTTTACTAGGTTTTACGGATCGTTAAAAA 9 184 0 GTTTTACGGA 0.958654 -21 CCTGATTTTTGTTTTTTTGATCTACAGCAA 10 53 1 GTTTTTTTGA 0.951026 -145 ********** Masking position 4 Map Score: 1.46636 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 196 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 11 ********** No masking Map Score: -4.59478e-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: -4.59478e-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: -4.59478e-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