AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i139_synecho_ctra_300.orf -o139_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 RCY25830 300 Synechocystis #2 RCT00265 300 Chlamydia_trachomatis #3 RCT00604 21 Chlamydia_trachomatis #4 RCT00605 113 Chlamydia_trachomatis #5 RCT00710 142 Chlamydia_trachomatis #6 RCT00711 104 Chlamydia_trachomatis #7 RCT00712 250 Chlamydia_trachomatis #8 RCT00713 300 Chlamydia_trachomatis Motif number 1 AGAGATTTGTCTATCTTGTTGGCGGCGATG 2 65 0 CTATCTTGTT 0.963719 -236 ATAGACAAATCTCTCTTCCTGGAGCTTTAC 2 81 1 CTCTCTTCCT 0.950953 -220 GATGGCTCCCCTTTTTAGTCCGGAA 4 6 1 CTCCCCTTTT 0.761297 -108 TAATATTGCTCTTTTTTGTTATTCGGCGTA 4 39 0 CTTTTTTGTT 0.778405 -75 ATAATAAAATTTTTCTTGTTTTTTGTGATG 4 69 0 TTTTCTTGTT 0.885393 -45 AGGAATAAGGCTTTCTTGTT 6 1 0 CTTTCTTGTT 0.970349 -104 ATTGATCCCCCTATCTTCCTGTGTTAACCT 6 54 1 CTATCTTCCT 0.892175 -51 CTGTGTTAACCTATCCTTTTTAACCCTAAT 6 72 1 CTATCCTTTT 0.909349 -33 TTTTAGCGCTTTCTCTTTTTTATAGAGGGC 7 13 1 TTCTCTTTTT 0.901772 -238 ACAGGGCCCTCTTTCCTCTTCTCATTGATC 7 53 1 CTTTCCTCTT 0.910667 -198 CATTGATCCCTTCTCTTTTTTTTGTTATCC 7 75 1 TTCTCTTTTT 0.901772 -176 ATTCAAGTTGCTCTCCTGCTATCGTAACTG 7 191 1 CTCTCCTGCT 0.957879 -60 AAGGAGCTTGTTCTCTTGTTAGAAGATTC 8 10 0 TTCTCTTGTT 0.93628 -291 GAACAAGCTCCTTTCTTTCTTTTCTAAACA 8 27 1 CTTTCTTTCT 0.925143 -274 TTGTTTTAAACTATTTTTTTCAGTTTTAAT 8 261 0 CTATTTTTTT 0.640468 -40 ********** Masking position 7 Map Score: 18.0088 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 276 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 2 AATACTGACAGAAATTTATCGCAGTATTAT 1 253 0 GAAATTTATC 0.745729 -48 TCCAGGAAGAGAGATTTGTCTATCTTGTTG 2 74 0 GAGATTTGTC 0.85959 -227 AAGGACCGGAAATATTTGTCGAATAACAAA 2 121 1 AATATTTGTC 0.942908 -180 ATAGGATTCTAATATTTGTTATTCGACAAA 2 135 0 AATATTTGTT 0.803614 -166 ACAAATTATTAAAATTTTTACGAATAAAAA 2 177 0 AAAATTTTTA 0.590839 -124 AAAAATTTTAATAATTTGTTACGTTTTGAA 2 188 1 ATAATTTGTT 0.608641 -113 CAATGCTCGAAAAACTTGTCGATTCCCTTT 2 249 1 AAAACTTGTC 0.827826 -52 TTCCCTTTGGAAAATTTGTCGTAAAAGCAA 2 271 1 AAAATTTGTC 0.965459 -30 ATTTAATAATAAAATTTTTCTTGTTTTTTG 4 74 0 AAAATTTTTC 0.934508 -40 AGTTTTATAAAAAATTTTTCTATTAACAGA 8 110 1 AAAATTTTTC 0.934508 -191 TTATCAATAGGTTATTTTTCCTCTGTTAAT 8 131 0 GTTATTTTTC 0.615522 -170 ACAACTAGAGGATATTTTTTC 8 290 1 GATATTTTTT 0.637417 -11 ********** Masking position 4 Map Score: 8.23831 Number of sites scoring better than the average of aligned sites = 712 Number in coding regions = 562 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 3 TTCTGACCCCACTGCTCCTCCCGGCCACGG 1 198 1 ACTGCTCCTC 0.942662 -103 GGGTTAATTGCTCCCTACTCAATCAA 1 285 0 ATTGCTCCCT 0.989544 -16 GATGGCTCCCCTTTTTAGTCC 4 2 1 ATGGCTCCCC 0.983496 -112 GTGATGTAATATTGCTCTTTTTTGTTATTC 4 45 0 ATTGCTCTTT 0.875897 -69 CTGGAAAAGGATTGATCCCCCTATCTTCCT 6 44 1 ATTGATCCCC 0.981472 -61 TCCTCTTCTCATTGATCCCTTCTCTTTTTT 7 66 1 ATTGATCCCT 0.962284 -185 TAGGATTCAAGTTGCTCTCCTGCTATCGTA 7 187 1 GTTGCTCTCC 0.942666 -64 ********** Masking position 6 Map Score: 6.45087 Number of sites scoring better than the average of aligned sites = 506 Number in coding regions = 447 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 4 TTGACCGATTCAAGGGGGGGCGCGCCCTAT 1 49 1 CAAGGGGGGG 0.908936 -252 CAAATGCAGCAAAGGACCGGAAATATTTGT 2 110 1 AAAGGACCGG 0.96693 -191 TCCGGACTAAAAAGGGGAGCCATC 4 5 0 AAAGGGGAGC 0.750713 -109 GGCTTTGCTGAAAGGAGCTCGTTT 5 5 0 AAAGGAGCTC 0.955485 -138 AAGCAAAGCCCAAGGACCTGGGCTTTGCTG 5 25 0 CAAGGACCTG 0.966856 -118 TTAGGGTTAAAAAGGATAGGTTAACACAGG 6 71 0 AAAGGATAGG 0.742047 -34 CTTTTATTTGCAAGGACTTGCCTTTGCGAG 7 113 0 CAAGGACTTG 0.816665 -138 TTTTTCCTCCAAAGGAGGTGTGAGGTTGTA 7 143 0 AAAGGAGGTG 0.967464 -108 GAAAAGAAAGAAAGGAGCTTGTTCTCTTGT 8 21 0 AAAGGAGCTT 0.932779 -280 CAGAGCGGTACAAGGAGATGTCAAATAAAG 8 162 1 CAAGGAGATG 0.96263 -139 TAAGGATCCTAAAGCAGCTTTATTTGACAT 8 179 0 AAAGCAGCTT 0.61839 -122 ********** Masking position 3 Map Score: 7.27635 Number of sites scoring better than the average of aligned sites = 568 Number in coding regions = 496 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 5 ATATTCAACGTTTCTAAACACCTAGTACAA 2 11 1 TTTCTAAACA 0.881889 -290 ATATTAGAATCCTATAAACAACCGAGTTTT 2 150 1 CCTATAAACA 0.839327 -151 AACGTAACAAATTATTAAAATTTTTACGAA 2 183 0 ATTATTAAAA 0.571767 -118 TATAGGTTACTCTATAAAAAATCAACGGAG 5 78 0 TCTATAAAAA 0.939468 -65 AATTATAAAAATCCCTGGAAT 5 132 0 ATTATAAAAA 0.770028 -11 AAAAGTGCCCTCTATAAAAAAGAGAAAGCG 7 19 0 TCTATAAAAA 0.939468 -232 AGAGGGCACTTTTATCAACAGGGCCCTCTT 7 36 1 TTTATCAACA 0.834761 -215 CTTTCTTTCTTTTCTAAACAAGGTTCAGCG 8 37 1 TTTCTAAACA 0.881889 -264 TTCAGCGCTTTCTATTAAAAGAAACCCTAT 8 60 1 TCTATTAAAA 0.861746 -241 AGCACATAGTTTTATAAAAAATTTTTCTAT 8 103 1 TTTATAAAAA 0.921755 -198 AAAAAATTTTTCTATTAACAGAGGAAAAAT 8 118 1 TCTATTAACA 0.908902 -183 AAATAACCTATTGATAAACAGAGCGGTACA 8 144 1 TTGATAAACA 0.787771 -157 ********** Masking position 7 Map Score: 10.3244 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 116 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 CATTAGGAATAAGGCTTTCTTGTT 6 5 0 AAGGCTTTCT 0.939431 -100 TATTTTAGCGCTTTCTCTTTTTTATA 7 7 1 AGCGCTTTCT 0.987742 -244 TGTTGATAAAAGTGCCCTCTATAAAAAAGA 7 26 0 AGTGCCCTCT 0.970426 -225 TTTTATCAACAGGGCCCTCTTTCCTCTTCT 7 45 1 AGGGCCCTCT 0.988013 -206 AACAAGGTTCAGCGCTTTCTATTAAAAGAA 8 53 1 AGCGCTTTCT 0.987742 -248 ********** Masking position 8 Map Score: 3.63715 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 11 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 TTTTACGAATAAAAAACTCGGTTGTTTATA 2 162 0 AAAAAACTCG 0.898419 -139 AACAAAAATCTCGATCTTTTATT 4 101 0 AAAAATCTCG 0.898419 -13 AAACGAGCTCCTTTCAGCAAA 5 2 1 AACGAGCTCC 0.936158 -141 ATAAAACTTTAAAAAACTCCGTTGATTTTT 5 62 1 AAAAAACTCC 0.961536 -81 TAACCCTAATAAAAGGCACCTCG 6 92 1 AAAAGGCACC 0.851098 -13 TGAGGAGATGAACAGCCTCCACAGACGCCA 7 230 0 AACAGCCTCC 0.921025 -21 CTAACAAGAGAACAAGCTCCTTTCTTTCTT 8 18 1 AACAAGCTCC 0.982209 -283 GAAAAAATATCCTCTAGTTGTT 8 289 0 AAAAATATCC 0.736257 -12 ********** Masking position 2 Map Score: 2.51128 Number of sites scoring better than the average of aligned sites = 318 Number in coding regions = 245 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 8 AAATTTATCGCAGTATTATCAAGCCTACCA 1 242 0 CAGTATTATC 0.908631 -59 AAATTTCTGTCAGTATTATTTGATTGAGTA 1 266 1 CAGTATTATT 0.936623 -35 GAGTTTTTTAAAGTTTTATTACAAGGAAGC 5 51 0 AAGTTTTATT 0.861978 -92 TTATAGAGGGCACTTTTATCAACAGGGCCC 7 32 1 CACTTTTATC 0.905757 -219 TGTGAGGTTGTACTTTTATTTGCAAGGACT 7 125 0 TACTTTTATT 0.79576 -126 ATGCAGCACATAGTTTTATAAAAAATTTTT 8 99 1 TAGTTTTATA 0.730954 -202 GATCCTAAAGCAGCTTTATTTGACATCTCC 8 175 0 CAGCTTTATT 0.914693 -126 CTATTTTTTTCAGTTTTAATTTTTAATTAG 8 251 0 CAGTTTTAAT 0.878559 -50 ********** Masking position 8 Map Score: 1.47229 Number of sites scoring better than the average of aligned sites = 337 Number in coding regions = 247 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 9 AGTAAACGTATTTACGATAATCGTTGTACT 2 34 0 TTTACGATAA 0.842148 -267 TAATATTTGTTATTCGACAAATATTTCCGG 2 126 0 TATTCGACAA 0.848579 -175 ATCGACAAGTTTTTCGAGCATTGTGTCTGA 2 242 0 TTTTCGAGCA 0.93793 -59 GAAATTTGCTTTTACGACAAATTTTCCAAA 2 276 0 TTTACGACAA 0.9333 -25 GGATCAATCCTTTTCCAGAAGGAACAGCAT 6 32 0 TTTTCCAGAA 0.922007 -73 AGGACTTGCCTTTGCGAGAACGGAAAGGAT 7 101 0 TTTGCGAGAA 0.955949 -150 CATGCAACCATTTTCTAGAATCTAGGTAAG 8 205 0 TTTTCTAGAA 0.889625 -96 ********** Masking position 7 Map Score: 2.02092 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 104 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 ATATTCAACGTTTCTAAACACCTAGT 2 7 1 AACGTTTCTA 0.804783 -294 ACACGTTCAAAACGTAACAAATTATTAAAA 2 193 0 AACGTAACAA 0.795943 -108 AAAGGTTGAGAACGTTACACGTTCAAAACG 2 209 0 AACGTTACAC 0.963871 -92 TAACGTTCTCAACCTTTCTCTCAGACACAA 2 222 1 AACCTTTCTC 0.952037 -79 TTTATAGAGTAACCTATAACTTGACGCTAC 5 90 1 AACCTATAAC 0.760309 -53 ATAAAAGTACAACCTCACACCTCCTTTGGA 7 136 1 AACCTCACAC 0.940425 -115 TTGGAGGAAAAACCTTTCACTTTCTTTAGG 7 161 1 AACCTTTCAC 0.978554 -90 ********** Masking position 2 Map Score: 1.68092 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 120 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 11 AAATATTTCCGGTCCTTTGCTGCATTTGTA 2 108 0 GGTCCTTTGC 0.958061 -193 CCCAAGGACCTGGGCTTTGCTGAAAGGAGC 5 17 0 TGGGCTTTGC 0.993579 -126 CCCAGGTCCTTGGGCTTTGCTTCCTTGTAA 5 33 1 TGGGCTTTGC 0.993579 -110 TTGCAAGGACTTGCCTTTGCGAGAACGGAA 7 106 0 TTGCCTTTGC 0.974966 -145 ********** Masking position 6 Map Score: 1.9983 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 77 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 12 ********** No masking Map Score: -2.32047e-13 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: -2.32047e-13 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 14 ********** No masking Map Score: -2.32047e-13 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