AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i231_synecho_ctra_300.orf -o231_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 RCY26220 201 Synechocystis #2 RCY36788 79 Synechocystis #3 RCY02011 299 Synechocystis #4 RCY53113 300 Synechocystis #5 RCT00328 300 Chlamydia_trachomatis #6 RCT00675 166 Chlamydia_trachomatis #7 RCT00676 300 Chlamydia_trachomatis Motif number 1 TTGTGCCATATTCTCCGCTTCTAGGGATTGGGAGCC 2 17 0 TTCCTCTGGG 0.932532 -63 CCCGTTGGCCCAAATTACCCTTGGGGTGTCAGAGG 3 10 1 CCATCCTGGG 0.98406 -290 AACCTCCTGCCCTCCCTGTCCTAGGGCGTTAGTCCC 3 109 1 CCTCCCTGGG 0.990937 -191 TTACCTAGATTTACTTGAGCCTTGGGGGACTAACGC 3 134 0 TTATCCTGGG 0.949976 -166 AAAGTTTTTTTTCCCCACTCCTTGGACGCCGGCTTG 3 222 1 TTCCCCTGGA 0.838917 -78 TCCCATTCTCTCAAACCGGCCTGGGGGACCCCCCGG 4 23 1 TCACCCTGGG 0.985971 -278 GGGCGAGAATCTTTTCCCGCCGGGGGGTCCCCCAGG 4 42 0 CTTCCCGGGG 0.965421 -259 AAGCCGGGTGCCATTTTTTCCTAGGGCGAGAATCTT 4 65 0 CCATCCTGGG 0.984076 -236 TATGCTAGGTTCACTTAGACCGAGGGAAATGTTTCC 4 167 0 TCATCCGGGG 0.94036 -134 TCTAAGTGAACCTAGCATAACACGGGTAGAAGGGCC 4 184 1 CCTCACAGGG 0.716257 -117 TGCAGTCCTTCCCAGCCCTCCAGGGGTGAACTTAGT 4 234 1 CCCCCCAGGG 0.971983 -67 AATCCTTTGTCTAAATCAATCTAGGA 5 1 0 CTATTCTGGA 0.650258 -300 GCACACAACCCTTGCTCTTCCAAGGATTTTGAACTA 5 258 1 CTTTCCAGGA 0.553086 -43 AATTCTATGTTTAAGTGTCTCTTGGGTCAAGCGTTT 6 25 0 TTATTCTGGG 0.878159 -142 TTAGATGGGGTCTTTCTTTTCTAGGGTCAAGAGTAG 6 91 1 TCTCTCTGGG 0.958378 -76 AGAAGAGCATTCTAGATAATCTGGGGAGTTTTTCGC 7 165 0 TCTATCTGGG 0.667964 -136 ATCTAGAATGCTCTTCTTCTCGCGGGTGTAGCTCAG 7 184 1 CTCCTCGGGG 0.919867 -117 *** * *** *** Masking position 14 Map Score: 22.4001 Number of sites scoring better than the average of aligned sites = 1851 Number in coding regions = 1635 Number in noncoding regions = 216 Number of orfs with sites within 600 bp upstream = 224 Fraction of orfs with sites within 600 bp upstream = 0.0359782 Motif number 2 TCTGGAAATGCTACGGAATTACCCAAGCCAGTGCC 1 156 0 CTCTTACCCA 0.635765 -46 ACTACGGTAACAACACCATCTCCCC 2 65 1 CACTCTCCCC 0.875789 -15 GGCAGATTAACCTCCTGCCCTCCCTGTCCTAGGGC 3 101 1 CCCCCTCCCT 0.951176 -199 CCCTACCTTTCCCCGTACCTAACCC 3 285 1 CCCCTAACCC 0.932896 -15 GGGTTGACCGCCACAGGTCTTCCCCGAGCCATTGC 4 116 1 CCCCTTCCCC 0.997499 -185 AGACCGATTTCTGCAGTCCTTCCCAGCCCTCCAGG 4 223 1 CTCCTTCCCA 0.938353 -78 TGCCCACTGCCCCCATTGTTTCACCATCGAGATTT 4 269 1 CCCTTTCACC 0.947019 -32 GATAAAAACCCTGCTATACTTTCTCGTGTTAGATG 5 167 1 CTCCTTTCTC 0.772747 -134 CTCTCTTCTTCCTCTATTTTTCCCCTTTTTAAAGC 7 35 1 CCCTTTCCCC 0.992287 -266 TTTTTTACCACCTCTTCACCTTCTCAAAAAACCTT 7 91 1 CCCCCTTCTC 0.884717 -210 TGGCGCTCTACCACTGAGCTACACCCGCGAGAAGA 7 198 0 CCCCTACACC 0.951698 -103 GCCTCATCACCCGCTTCTCTTTCCCGGATAACTTA 7 262 1 CCCCTTTCCC 0.98998 -39 ** * ******* Masking position 4 Map Score: 13.0454 Number of sites scoring better than the average of aligned sites = 1351 Number in coding regions = 1220 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 3 TGCCCAATGGAGTGATCTAGTTAGAATCAA 1 57 1 AGTGATCTAG 0.801482 -145 TTTCCTTTACTTTGCTTTAGGTTAACTCAA 3 194 0 TTTGCTTTAG 0.910523 -106 TCATTGATTTAGTCCCATTCTC 4 3 1 ATTGATTTAG 0.97249 -298 TCCTAGATTGATTTAGACAAAGGATT 5 7 1 ATTGATTTAG 0.97249 -294 CGAATTAATTTTTGAATTAAAACGGTTTTA 5 45 0 TTTGAATTAA 0.691334 -256 TAAAGTCGGTTTTGATTTGGCGACAGCGAA 5 71 0 TTTGATTTGG 0.910523 -230 TTCCAAGGATTTTGAACTAGTTGCCCAAGG 5 275 1 TTTGAACTAG 0.91781 -26 GTAGGTGTATTTTGAATTAGATGGGGTCTT 6 75 1 TTTGAATTAG 0.958065 -92 CAAAATTTTCATTGATTTAGC 7 2 0 ATTGATTTAG 0.97249 -299 ********** Masking position 3 Map Score: 9.33803 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 79 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 4 ATCTGCCCTGTCAATTTACCTATTCCGGAG 3 78 0 TCAATTTACC 0.749928 -222 GGCAGGAGGTTAATCTGCCCTGTCAATTTA 3 90 0 TAATCTGCCC 0.753334 -210 CGACATGGTCTCATCTTACCTAGATTTACT 3 155 0 TCATCTTACC 0.957392 -145 AAGGAAAAGTTTTTTTTCCCCACTCCTTGG 3 217 1 TTTTTTTCCC 0.89385 -83 GCCTTTTTCTTAATTTTCCCTACCTTTCCC 3 268 1 TAATTTTCCC 0.912399 -32 GTTTTTCTATTCAACTTCTCTTTGCTGCAA 5 135 1 TCAACTTCTC 0.794301 -166 TAATATTACTTCTTCTTACCGATATACTAC 5 221 0 TCTTCTTACC 0.963005 -80 TTTGACCCTCTCTTCTTCCTCTATTTTTCC 7 28 1 TCTTCTTCCT 0.85642 -273 CTTCTTCCTCTATTTTTCCCCTTTTTAAAG 7 39 1 TATTTTTCCC 0.923465 -262 CCAATTTTTCTTTTTTTACCACCTCTTCAC 7 80 1 TTTTTTTACC 0.707642 -221 TACCACCTCTTCACCTTCTCAAAAAACCTT 7 96 1 TCACCTTCTC 0.85659 -205 TCTAGAATGCTCTTCTTCTCGCGGGTGTAG 7 185 1 TCTTCTTCTC 0.947449 -116 ATCACCCGCTTCTCTTTCCCGGATAACTTA 7 267 1 TCTCTTTCCC 0.949226 -34 ********** Masking position 6 Map Score: 10.367 Number of sites scoring better than the average of aligned sites = 1467 Number in coding regions = 1232 Number in noncoding regions = 235 Number of orfs with sites within 600 bp upstream = 255 Fraction of orfs with sites within 600 bp upstream = 0.0409573 Motif number 5 GTGCATTAACGCCGTTGCCCAATGGAGTGATC 1 42 1 GCGTGCCCAA 0.964984 -160 ACAGTAGGTTCCATTAACCAACTGCATTGATT 1 81 0 CCTTACCAAC 0.871482 -121 TCCCCTGGCTCCCAATCCCTAGAAG 2 4 1 CCGGTCCCAA 0.918046 -76 CCCGTTGGCCCAAATTACCCTTG 3 2 1 CCTTGCCCAA 0.987672 -298 TGATTTAGTCCCATTCTCTCAAACCGGCCTGG 4 15 1 CCTTTCTCAA 0.849977 -286 CGGTTATAATCCTTTGTCTAAATCAATCTAGG 5 12 0 CCTTTCTAAA 0.779727 -289 AAATTAATTCGCTGTCGCCAAATCAAAACCGA 5 64 1 GCGTGCCAAA 0.945107 -237 GGATTTTGAACTAGTTGCCCAAGGACAATT 5 281 1 CTGTGCCCAA 0.918053 -20 CGCAGGAAAACGCTTGACCCAAGAGACACTTA 6 18 1 CGTTACCCAA 0.802181 -149 CGTAAGCACACCTGTAACCAAATGATTTGAGA 6 133 1 CCGTACCAAA 0.969056 -34 TCTCAAAAAACCTTTTTCCAAAGTTTTTTTGT 7 112 1 CCTTTCCAAA 0.962232 -189 GGTAGAGCGCCACGTTGCCAACGTGAAGGTCG 7 221 1 CAGTGCCAAC 0.7081 -80 ** ** ****** Masking position 11 Map Score: 9.01392 Number of sites scoring better than the average of aligned sites = 1485 Number in coding regions = 1345 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 6 TAACGCCCTAGGACAGGGAGGGCAGGAGGTTA 3 108 0 GGACGGAGGG 0.99348 -192 ATTAAGAAAAAGGCGGACAGGGATCAAGCCGG 3 250 0 AGGCGAAGGG 0.91247 -50 TTAGGTACGGGGAAAGGTAGGGAAAATTAAGA 3 275 0 GGAAGGAGGG 0.983487 -25 GGGGACCCCCCGGCGGGAAAAGATTCTCGCCC 4 46 1 CGGCGGAAAG 0.840887 -255 TTGCGTTGCGGGGCTAGAAGGGAAACATTTCC 4 147 1 GGGCAGAGGG 0.994985 -154 TAGCATAACACGGGTAGAAGGGCCCACAGACC 4 196 1 CGGGAGAGGG 0.950485 -105 CACCCCTGGAGGGCTGGGAAGGACTGCAGAAA 4 230 0 GGGCGGAAGG 0.992233 -71 AACACGAGAAAGTATAGCAGGGTTTTTATCAA 5 165 0 AGTAAGAGGG 0.765967 -136 CAAAATCCTTGGAAGAGCAAGGGTTGTGTGCA 5 257 0 GGAAAGAAGG 0.908553 -44 **** ** **** Masking position 9 Map Score: 6.03621 Number of sites scoring better than the average of aligned sites = 929 Number in coding regions = 805 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 7 ATTCCGTAGCATTTCCAGAATATTTCCAGA 1 172 1 ATTTCCAGAA 0.931304 -30 TTTCCAGAATATTTCCAGAAAATTACCAT 1 183 1 ATTTCCAGAA 0.931304 -19 TAGAGGAGAAATCTCCGGAATAGGTAAATT 3 66 1 ATCTCCGGAA 0.971024 -234 GTTTTTATCAATTGCAGCAAAGAGAAGTTG 5 146 0 ATTGCAGCAA 0.917646 -155 ATACTACAAAATCGCAACAATTAGTGCATC 5 198 0 ATCGCAACAA 0.917645 -103 TTTTGATCGCAGGAAAACGCTTGAC 6 6 1 ATCGCAGGAA 0.971032 -161 ********** Masking position 2 Map Score: 1.39167 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 165 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 8 TCACTCCATTGGGCAACGGCGTTAATGCAC 1 42 0 GGGCAACGGC 0.957481 -160 TATAGACCACTGGCGATCGGCATGGTAACA 1 110 0 TGGCGATCGG 0.731784 -92 TCTAGGGATTGGGAGCCAGGGGA 2 4 0 GGGAGCCAGG 0.917298 -76 GGGTAATTTGGGCCAACGGG 3 1 0 GGCCAACGGG 0.972717 -299 TCAACTTTGTTGCCGACATGGTCTCATCTT 3 168 0 TGCCGACATG 0.859801 -132 CCCACTCCTTGGACGCCGGCTTGATCCCTG 3 235 1 GGACGCCGGC 0.774414 -65 TTAAGAAAAAGGCGGACAGGGATCAAGCCG 3 251 0 GGCGGACAGG 0.864786 -49 GAGAATCTTTTCCCGCCGGGGGGTCCCCCA 4 44 0 TCCCGCCGGG 0.823401 -257 TAGGAAAAAATGGCACCCGGCTTATATTAT 4 78 1 TGGCACCCGG 0.937573 -223 GGTTTTGATTTGGCGACAGCGAATTAATTT 5 64 0 TGGCGACAGC 0.96837 -237 AAAATTGGACTGCAAACAGCTTTAAAAAGG 7 58 0 TGCAAACAGC 0.724067 -243 AAAAAAACTTTGGAAAAAGGTTTTTTGAGA 7 112 0 TGGAAAAAGG 0.363908 -189 ACCTTCACGTTGGCAACGTGGCGCTCTACC 7 221 0 TGGCAACGTG 0.859801 -80 ********** Masking position 2 Map Score: 3.43989 Number of sites scoring better than the average of aligned sites = 4504 Number in coding regions = 4205 Number in noncoding regions = 299 Number of orfs with sites within 600 bp upstream = 301 Fraction of orfs with sites within 600 bp upstream = 0.0483456 Motif number 9 CCGCTTCTAGGGATTGGGAGCCAGGGGA 2 8 0 GGATTGGGGC 0.949678 -72 CCCCCAGGCCGGTTTGAGAGAATGGGACTAA 4 19 0 GGTTTGAGGA 0.880364 -282 ATGATCAATTGGGTTGACCGCCACAGGTCTT 4 106 1 GGGTTGACGC 0.969945 -195 TGCAGAAATCGGTCTGTGGGCCCTTCTACCC 4 207 0 GGTCTGTGGC 0.974435 -94 GAAACAATGGGGGCAGTGGGCACTAAGTTCA 4 260 0 GGGCAGTGGC 0.98002 -41 GGAAGAGCAAGGGTTGTGTGCACATGTTTAA 5 248 0 GGGTTGTGGC 0.994074 -53 TGTAGCTCAGTGGTAGAGCGCCACGTTGCCA 7 210 1 TGGTAGAGGC 0.904519 -91 ******** ** Masking position 6 Map Score: 3.1841 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 322 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 10 TCCATTGGGCAACGGCGTTAATGCACTGAC 1 38 0 AACGGCGTTA 0.78106 -164 AAAGTAAAGGAAAAGTTTTTTTTCCCCACT 3 211 1 AAAAGTTTTT 0.79234 -89 TTTGAATTAAAACGGTTTTAACGGTTATAA 5 35 0 AACGGTTTTA 0.945139 -266 TTCGATAAATAACAGTTTTTCTATTCAACT 5 121 1 AACAGTTTTT 0.942583 -180 TTGGACTGCAAACAGCTTTAAAAAGGGGAA 7 54 0 AACAGCTTTA 0.894557 -247 AACTTTGGAAAAAGGTTTTTTGAGAAGGTG 7 107 0 AAAGGTTTTT 0.908636 -194 AACCTTTTTCCAAAGTTTTTTTGTAAAACC 7 120 1 CAAAGTTTTT 0.726403 -181 ********** Masking position 2 Map Score: 0.953781 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 225 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 11 ********** No masking Map Score: -1.29076e-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: -1.29076e-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 TCGTTCCTCGGCACTGGCTTGGGTAATTCCGTA 1 147 1 GCATGCTGGG 0.994533 -55 GAAATATTCTGGAAATGCTACGGAATTACCCAA 1 165 0 GGAAGCTCGG 0.928232 -37 GGAGAATATGGCACAATCTAGGGAGAATACTAC 2 37 1 GCAATCTGGG 0.96848 -43 GCCCCGCAACGCAATGGCTCGGGGAAGACCTGT 4 128 0 GCATGCTGGG 0.994533 -173 GGTGTATTTTGAATTAGATGGGGTCTTTCTTTT 6 78 1 GAATGATGGG 0.967494 -89 AAAAATAGAGGAAGAAGAGAGGGTCAAAATTTT 7 23 0 GAAAGAGGGG 0.922631 -278 AAACCTACAAGCAAAGGATTGCGAAAAACTCCC 7 145 1 GCAAGATGCG 0.956614 -156 *** * *** *** Masking position 3 Map Score: 1.69041 Number of sites scoring better than the average of aligned sites = 511 Number in coding regions = 460 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 14 ********** No masking Map Score: -1.29076e-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 15 ********** No masking Map Score: -1.29076e-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