AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i014_synecho_ctra_300.orf -o014_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 Purged sequences: RCT00490 17 Chlamydia_trachomatis Input sequences: #1 RCY09935 80 Synechocystis #2 RCY34729 121 Synechocystis #3 RCY47122 38 Synechocystis #4 RCY53017 115 Synechocystis #5 RCY11182 235 Synechocystis #6 RCY06446 94 Synechocystis #7 RCY04603 188 Synechocystis #8 RCY37403 269 Synechocystis #9 RCT00313 295 Chlamydia_trachomatis #10 RCT00480 43 Chlamydia_trachomatis #11 RCT00481 65 Chlamydia_trachomatis #12 RCT00482 20 Chlamydia_trachomatis #13 RCT00483 21 Chlamydia_trachomatis #14 RCT00484 55 Chlamydia_trachomatis #15 RCT00485 22 Chlamydia_trachomatis #16 RCT00488 21 Chlamydia_trachomatis #17 RCT00489 27 Chlamydia_trachomatis #18 RCT00493 16 Chlamydia_trachomatis #19 RCT00495 32 Chlamydia_trachomatis #20 RCT00497 18 Chlamydia_trachomatis #21 RCT00499 23 Chlamydia_trachomatis #22 RCT00502 300 Chlamydia_trachomatis #23 RCT00660 160 Chlamydia_trachomatis #24 RCT00662 127 Chlamydia_trachomatis Motif number 1 GGGGGTAGAGTTTTTGCTATGATGTCGCTCA 8 79 0 TTTTGCTATG 0.927592 -191 GGCCTCTGGGTTTTGTCTATGCCTGGGGGTA 8 103 0 TTTTTCTATG 0.926318 -167 GCCCTCTCTGTTTTAGCTCAGTACATTTAAG 8 240 0 TTTTGCTCAG 0.860507 -30 CTTGTCTTACTTTTTTCTGTGAATTTGCTTA 9 38 0 TTTTTCTGTG 0.952655 -258 TCCAAGAGATTTATATCAAAGCAATAGAAAA 9 81 1 TTATTCAAAG 0.745168 -215 TTGGAAATGGTTTTCTGTGAGTTTCTTTGTC 9 216 0 TTTTTGTGAG 0.907902 -80 TTATAGCTAAGGAGTTTGGG 12 1 1 TTATGCTAAG 0.865527 -20 TAATTTTTAGGAGAGAGTGTT 13 5 1 TTTTGGAGAG 0.823021 -17 GTTTTTGCGATTTTTGGTGTGGGATTTCTTA 22 75 1 TTTTGGTGTG 0.865208 -226 AATTTTTTGTTTTTTTCTAAGATTTTTCACG 23 48 0 TTTTTCTAAG 0.951631 -113 TTGGGAGCATTTTTCTCAAAGACAATTAAAA 23 131 1 TTTTTCAAAG 0.901038 -30 ACTAAAAATGTTTTGTCTGAGTGATTCTTCA 24 31 1 TTTTTCTGAG 0.969221 -97 ACTCAAGCCTTTATCTCAGTGCCACATGAAG 24 57 0 TTATTCAGTG 0.749413 -71 **** ****** Masking position 4 Map Score: 11.7965 Number of sites scoring better than the average of aligned sites = 548 Number in coding regions = 454 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 2 TCTATCATCGCCCCCTGGCTGAGATCGGTG 2 32 1 CCCCCTGGCT 0.970274 -90 TCAATTCTTCCCTTTGTAAACCTGGAGG 3 9 1 TCCCTTTGTA 0.728944 -30 CCCTGGCGATCGCCATTGTAAACACTGATG 4 92 0 CGCCATTGTA 0.775113 -24 TGTCTCACTACCCCCATGATTTACCTTGGA 5 35 1 CCCCCATGAT 0.891873 -201 GTTATCTAATCCCCTTTGAAAAGGGTTGGG 5 84 0 CCCCTTTGAA 0.950874 -152 CTGCAAAAGATGCCCTTGATAATACCATCA 6 47 0 TGCCCTTGAT 0.786879 -48 GAATTAATGCCGCCCTGGCTTTCAATCTAG 7 50 0 CGCCCTGGCT 0.959209 -139 AAAAACTCTACCCCCAGGCATAGACAAAAC 8 95 1 CCCCCAGGCA 0.879621 -175 ATTCCCACCCCCCCTTTGAAATTCGGGATC 8 167 1 CCCCTTTGAA 0.950874 -103 TTGGTTTTAGCCCCTTTGTTAT 9 3 0 CCCCTTTGTT 0.950874 -293 GCCCATTCGCCGCCTTTGTTTGCTTTAAGG 22 153 1 CGCCTTTGTT 0.933207 -148 TCGTGGAAATCGCTCTTGCAGGATGGAGGG 22 199 1 CGCTCTTGCA 0.751512 -102 ********** Masking position 3 Map Score: 10.1159 Number of sites scoring better than the average of aligned sites = 1408 Number in coding regions = 1207 Number in noncoding regions = 201 Number of orfs with sites within 600 bp upstream = 199 Fraction of orfs with sites within 600 bp upstream = 0.0319627 Motif number 3 GATAGAATTTGCACAAGTTAATGGAAA 2 8 0 GCACAAGTTA 0.776441 -114 GGGGCTAAACTCACAGGTAAATCCCATTTC 4 26 1 TCACAGGTAA 0.85678 -90 TTTTCTCCTTTCCAAGGTAAATCATGGGGG 5 45 0 TCCAAGGTAA 0.856814 -191 AGGGCAGTTTTCAAAGGTTGTATTTACCGT 5 112 0 TCAAAGGTTG 0.873932 -124 GGCAGGAGTTGCCCCGGATGTTTTTGATGG 6 23 1 GCCCCGGATG 0.886133 -72 TATAAAGTCTGCAAAAGATGCCCTTGATAA 6 55 0 GCAAAAGATG 0.616542 -40 AAACCCAGAGGCCACGGTAAACAGCGACGG 8 121 1 GCCACGGTAA 0.883747 -149 CAAAATACATGCACAGGTTATTCAGCAAAT 9 174 1 GCACAGGTTA 0.945783 -122 GAGAAGGTGGGCCCAAGTTGGAAATGGTTT 9 234 0 GCCCAAGTTG 0.868929 -62 TGCTAAATCCCAGGTAGTCAGTGTTTT 10 27 0 TCCCAGGTAG 0.919499 -17 GCAACGGTTATGAGACGAAG 11 56 0 GCAACGGTTA 0.864392 -10 TAAGTTTTCTTCCAAGGAAGCTCCACTAGT 22 18 1 TCCAAGGAAG 0.792846 -283 ATAGGCCTAAGCAAAGGAAAACTCAAGCCT 24 78 0 GCAAAGGAAA 0.834596 -50 ********** Masking position 2 Map Score: 9.22761 Number of sites scoring better than the average of aligned sites = 2218 Number in coding regions = 2046 Number in noncoding regions = 172 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 4 AAAATAGTTGGAAAAATTAGTTGTTGACCA 5 207 0 GAAAAATTAG 0.944204 -29 CCTATTGCCTGAACACTTAGATCCCGAATT 8 186 0 GAACACTTAG 0.955742 -84 CAGTGTTTTCGAAAAATTAGCATCA 10 6 0 GAAAAATTAG 0.944204 -38 CACGCTAGAAAAAAATTTAGGGTTGGTCGT 11 25 1 AAAAATTTAG 0.847163 -41 CTAGAACTTTTAGGTAAAGTTT 15 4 1 GAACTTTTAG 0.834096 -19 TTCCTTGGAAGAAAACTTATAACGCT 22 7 0 GAAAACTTAT 0.809825 -294 TCGAGCGTGAAAAATCTTAGAAAAAAACAA 23 43 1 AAAATCTTAG 0.761514 -118 AGGCCTATAAGAAAATTTAGGTTAAGGATC 24 100 1 GAAAATTTAG 0.960374 -28 ********** Masking position 3 Map Score: 4.10242 Number of sites scoring better than the average of aligned sites = 312 Number in coding regions = 267 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 5 ATCATGGGGGTAGTGAGACAATTTTTAGACTTTTTA 5 19 0 TAGTGGTTTT 0.693115 -217 GAAAAGGGTTGGGTTTAAGAATTTTTCTCCTTTCCA 5 61 0 GGGTTATTTT 0.922513 -175 AGAGTTGATTGGGTGAGGATAGTTTTTATTGCTAAA 5 154 0 GGGTGGGTTT 0.968931 -82 TCTGATGTCAGGGTGAAGAGTTGATTGGGTGAGGAT 5 170 0 GGGTGATGTT 0.907905 -66 TTGAGTTTGGGGGTTAGTTCCTCGTTGGTTAATGGT 7 92 1 GGGTTGTCTT 0.907905 -97 CGTAAACTGGGGGTTGGCAAATTTTGTTGTGACCTT 7 143 1 GGGTTGTTTG 0.947761 -46 GTCTATGCCTGGGGGTAGAGTTTTTGCTATGATGTC 8 84 0 GGGGGATTTG 0.790954 -186 TTCAAAGGGGGGGTGGGAATCTTTTTCCCTTTCTCT 8 151 0 GGGTGGTTTT 0.993357 -119 TAGGTTATAAGGGTGTGTGAATTATT 19 17 1 GGGTGGTTTT 0.993357 -16 TTGCGATTTTTGGTGTGGGATTTCTTAGCGTCAAGA 22 79 1 TGGTGGTTTT 0.962758 -222 ***** * ** ** Masking position 15 Map Score: 4.69491 Number of sites scoring better than the average of aligned sites = 364 Number in coding regions = 323 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 6 GTTAAGTTTATTTGACATTTAGGAGGAAAAGGT 1 57 1 TTTGATTAGG 0.839007 -24 TCGCCCCCTGGCTGAGATCGGTGATATCGGTGG 2 39 1 GCTGATCGTG 0.94844 -83 GTTGGTCTGACTTTTGGGGCTAAACTCA 4 6 1 TCTGATTGGG 0.988092 -110 ACCAAGCCGGTCTGACATCAGTGTTTACAATGG 4 77 1 TCTGATCGTG 0.96471 -39 TGTTGACCAATCTGATGTCAGGGTGAAGAGTTG 5 183 0 TCTGATCGGG 0.990119 -53 GCTTCAAGCAGTTGAGTTTGGGGGTTAGTTCCT 7 81 1 GTTGATTGGG 0.964332 -108 CCACCCCCCCTTTGAAATTCGGGATCTAAGTGT 8 171 1 TTTGATTGGG 0.97569 -99 ***** ** *** Masking position 5 Map Score: 4.13706 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 82 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 CCTTTCACTGCCCCATACTCGTA 2 109 0 TTCACTGCCC 0.91469 -13 CACCTGCCGGTTCACCGCACCTGTAATTGA 8 52 1 TTCACCGCAC 0.861337 -218 GGGAAAAAGATTCCCACCCCCCCTTTGAAA 8 158 1 TTCCCACCCC 0.966937 -112 TTTAAGCAAATTCACAGAAAAAAGTAAGAC 9 36 1 TTCACAGAAA 0.696964 -260 AATAATTCACACACCCTTATAACCT 19 18 0 TTCACACACC 0.981375 -15 ACGCTAAGAAATCCCACACCAAAAATCGCA 22 80 0 ATCCCACACC 0.916127 -221 TTGACAACGCTTCACAGACCGCCCCCGGTG 22 258 0 TTCACAGACC 0.981375 -43 TAATTACCTTATCACACAACTTGACAACGC 22 278 0 ATCACACAAC 0.882903 -23 ********** Masking position 2 Map Score: 3.23169 Number of sites scoring better than the average of aligned sites = 327 Number in coding regions = 285 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 8 AAAACGCAATTTTTAGCAATAAAAACTATC 5 143 1 TTTTAGCAAT 0.896132 -93 TTGAGCGACATCATAGCAAAAACTCTACCC 8 78 1 TCATAGCAAA 0.919314 -192 AAACCAACTATTTAAGCAAATTCACAGAAA 9 26 1 TTTAAGCAAA 0.924126 -270 GAGATTTATATCAAAGCAATAGAAAATAAA 9 86 1 TCAAAGCAAT 0.919314 -210 CTCTGAGCCATCAAAGCAATTTGTTTTCGG 9 266 1 TCAAAGCAAT 0.919314 -30 TTATAGCTAAGGAGTTTGGG 12 1 1 TTATAGCTAA 0.607537 -20 AGGGCCTCCCTTAAAGTAATATAAGCATCT 14 32 0 TTAAAGTAAT 0.489783 -24 TAGTGGTTTAGCAATT 18 6 1 GTTTAGCAAT 0.642765 -11 ACGCGGCTCCTTAAAGCAAACAAAGGCGGC 22 161 0 TTAAAGCAAA 0.935388 -140 CTAATTACACTTTTAGCAAACGGCCATGCC 22 227 0 TTTTAGCAAA 0.911126 -74 TTCTTATAGGCCTAAGCAAAGGAAAACTCA 24 83 0 CCTAAGCAAA 0.703804 -45 ********** Masking position 5 Map Score: 6.02023 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 187 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 9 ATTCTTAAACCCAACCCTTTTCAAAGGGGA 5 75 1 CCAACCCTTT 0.948278 -161 ACTAATTTTTCCAACTATTTTTCCAATACC 5 216 1 CCAACTATTT 0.974161 -20 GGGGCTAAAACCAACTATTTAAGCAAATTC 9 19 1 CCAACTATTT 0.974161 -277 TCGTTACCGTCCTAATCTTTTAATTTG 17 8 0 CCTAATCTTT 0.844786 -20 CTATGTATCTCCTACTATTTGAAGGGGACC 23 13 1 CCTACTATTT 0.963385 -148 ********** Masking position 4 Map Score: 1.65275 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 39 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 10 GGATTGATTGCCTCCAGGTTTACAAAGGGAA 3 18 0 CCTCAGGTTT 0.949097 -21 GCCGGTCTGACATCAGTGTTTACAATGGCGA 4 82 1 CATCGTGTTT 0.957159 -34 TTTACCGTGGCCTCTGGGTTTTGTCTATGCC 8 111 0 CCTCGGGTTT 0.98668 -159 CCTTTCTCTCCGTCGCTGTTTACCGTGGCCT 8 129 0 CGTCCTGTTT 0.976805 -141 TTCGTCTTGCCCTCTCTGTTTTAGCTCAGTA 8 248 0 CCTCCTGTTT 0.983959 -22 AATCCCAGGTAGTCAGTGTTTTCGAAAAATT 10 18 0 AGTCGTGTTT 0.904417 -26 **** ****** Masking position 3 Map Score: 1.08339 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 64 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 11 ACTCACAGGTAAATCCCATTTCACCATGCA 4 34 1 AAATCCCATT 0.908667 -82 GCTTTGATATAAATCTCTTGGATATGCTAA 9 73 0 AAATCTCTTG 0.972613 -223 GTTATTCAGCAAATCTCATGTTTACAGACA 9 190 1 AAATCTCATG 0.972615 -106 TGCTAAATCCCAGGTAGTCAGTGT 10 30 0 AAATCCCAGG 0.91501 -14 AGCGTGTTGCATATCTCTTT 11 1 0 ATATCTCTTT 0.747516 -65 GCGTCAAGAAAAATCTCTTGTGTGGATGTC 22 106 1 AAATCTCTTG 0.972613 -195 ********** Masking position 4 Map Score: 1.84176 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 44 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 12 CGACAATGGAAAGCCCCAAA 1 1 0 AAGCCCCAAA 0.985521 -80 CCTGTGAGTTTAGCCCCAAAAGTCAGACCA 4 13 0 TAGCCCCAAA 0.943797 -103 ACGAGGAACTAACCCCCAAACTCAACTGCT 7 87 0 AACCCCCAAA 0.950816 -102 CGCTCCTCACAAGCCATAAATGTTAACGTC 8 16 1 AAGCCATAAA 0.883771 -254 TGTCATTAATAATCCTTAAATGTACTGAGC 8 226 1 AATCCTTAAA 0.719834 -44 CGCAAAAACAAAGCCTGAAAAATCGTTCTA 22 54 0 AAGCCTGAAA 0.918498 -247 ********** Masking position 8 Map Score: 0.130639 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 258 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 13 ********** No masking Map Score: 6.40442e-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 14 ********** No masking Map Score: 6.40442e-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: 6.40442e-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