AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i021_synecho_ctra_300.orf -o021_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 RCY10148 16 Synechocystis #2 RCY23515 146 Synechocystis #3 RCY19118 39 Synechocystis #4 RCY26516 95 Synechocystis #5 RCY51144 104 Synechocystis #6 RCY06801 171 Synechocystis #7 RCY33546 300 Synechocystis #8 RCT00785 69 Chlamydia_trachomatis Motif number 1 AGAGATAGACCGGAAAAACCAGGACTCAGCAAG 2 104 0 CGGAAAAAGG 0.98711 -43 GTGCCTCCGGAGGATAAAAGTTGTAGTTGCGAA 3 14 0 AGGATAATTG 0.766154 -26 AGAGGCTATTCGGAAAATTGAAGTCTATTTTTA 4 42 0 CGGAAAAAAG 0.975765 -54 GGATTATTAAAGGAAAACTGTGGCTTGATGCCC 5 78 0 AGGAAAATGG 0.98612 -27 TGGTGCTGCTAGGAAAAACCAAAAAACATTAGG 6 44 0 AGGAAAAAAA 0.940824 -128 CAATAACTTAAAAATAACCCAGGATTAAGGTGG 6 90 0 AAAATAAAGG 0.703552 -82 ATAAGATTTAAAGAAAATCTAGAAACCCCAG 7 9 0 AAGAAAAAGA 0.869711 -292 GAAGAGATTACGGAAAATTTAAGGAAAATAAGA 7 36 0 CGGAAAAAAG 0.975764 -265 CTCCCCTAACAAAAAAATCATGGTGAGCAAAGA 7 210 1 AAAAAAATGG 0.775892 -91 GACATGAGGTAGGAAAATAATGGAGAAAGGTCA 7 243 1 AGGAAAATGG 0.98612 -58 TGAAGTAAAAAGAATAATAAAAGATAAGGAGGA 8 29 1 AGAATAAAAG 0.84968 -41 AAAGATAAGGAGGAAAAATTAAAGGGTTATTT 8 48 1 AGGAAAAAAA 0.940824 -22 ******* *** Masking position 7 Map Score: 12.4932 Number of sites scoring better than the average of aligned sites = 1044 Number in coding regions = 863 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 214 Fraction of orfs with sites within 600 bp upstream = 0.034372 Motif number 2 CTATCAGTAGCGATCGCCGTTGATCCCCG 2 3 0 CACCGTGCCC 0.997441 -144 GGGTAGACCCCCATCACCAAAGCCCCCAATAATGAGG 2 42 1 CACCAAGCCC 0.997363 -105 TTTTTCCGGTCTATCTCTGCAGGCCTCCACCTTCCCC 2 119 1 CACCGAGCTC 0.99591 -28 GTATCGTCAACCAGAGCAAAATGTCCC 5 1 0 CAACAATCCC 0.941439 -104 TACAGTGAAGCTTGGACTGGTTGACCCCGATAGCTGC 5 35 1 CTGCGTTCCC 0.934558 -70 GGCTTGATGCCCTACTCCGCAGCTATCGGGGTCAACC 5 53 0 CTCCGAGATC 0.882954 -52 GACTCCAAGGGCAATAGTACTGAAATCGAAAT 6 6 1 CAGCAAGCTG 0.864338 -166 CCTAGCAGCACCACCACAATATGCCCCCACCTTAATC 6 64 1 CACCAATCCC 0.991996 -108 AGGCGATCGCCAAACTCAGTTGTGCCCTCAAGTGAGC 7 152 0 CACCGTGCCC 0.997441 -149 * * * * * ** *** Masking position 7 Map Score: 8.3074 Number of sites scoring better than the average of aligned sites = 680 Number in coding regions = 640 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 3 CGGGGATCAACGGCGATCGC 2 1 1 CGGGGATCAA 0.975713 -146 GCTTTGGTGATGGGGGTCTACCCCCCTATC 2 35 0 TGGGGGTCTA 0.934579 -112 TCCGCAGCTATCGGGGTCAACCAGTCCAAG 5 45 0 TCGGGGTCAA 0.929415 -60 GCTGCGGAGTAGGGCATCAAGCCACAGTTT 5 67 1 AGGGCATCAA 0.972448 -38 AACTGGAGGGAGTGGAGCAATAACTTAAAA 6 110 0 AGTGGAGCAA 0.937603 -62 TTTTGGGAGTAGGGGAGCAACTTTAAGAAG 7 65 0 AGGGGAGCAA 0.992623 -236 TGCCCTCAAGTGAGCAGCAGTAATGAAGTC 7 137 0 TGAGCAGCAG 0.858604 -164 GGGAGTTTTCTGGGCGGCAGAATATCAGGC 7 185 0 TGGGCGGCAG 0.978167 -116 AAAAAAATCATGGTGAGCAAAGAGACATGA 7 220 1 TGGTGAGCAA 0.954878 -81 ********** Masking position 8 Map Score: 8.20363 Number of sites scoring better than the average of aligned sites = 1840 Number in coding regions = 1647 Number in noncoding regions = 193 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 4 GATCGCTACTGATAGGGGGGTAGACCCCCA 2 25 1 GATAGGGGGG 0.958003 -122 GGGGGCTTTGGTGATGGGGGTCTACCCCCC 2 39 0 GTGATGGGGG 0.867689 -108 GCCCCCAATAATGAGGGAAGATGGTATGAC 2 63 1 ATGAGGGAAG 0.933003 -84 AGGGGAAGGTGGAGGCCTGCAG 2 135 0 GGGAAGGTGG 0.920139 -12 CAGAATTAACAGGAAGTAAGTTTTAGAGA 4 10 0 AGGAAGTAAG 0.637095 -86 ATAACCCAGGATTAAGGTGGGGGCATATTG 6 80 0 ATTAAGGTGG 0.791017 -92 ATCAACTGGAGGGAGTGGAGCAATAACTTA 6 113 0 GGGAGTGGAG 0.920749 -59 AGTTTTTGGGAGTAGGGGAGCAACTTTAAG 7 68 0 AGTAGGGGAG 0.968327 -233 AGTGAGCAGCAGTAATGAAGTCAAATTCCA 7 129 0 AGTAATGAAG 0.666601 -172 TGATTTTTTTGTTAGGGGAGTTTTCTGGGC 7 200 0 GTTAGGGGAG 0.963619 -101 GCAAAGAGACATGAGGTAGGAAAATAATGG 7 236 1 ATGAGGTAGG 0.708824 -65 GAGGTAGGAAAATAATGGAGAAAGGTCAGA 7 248 1 AATAATGGAG 0.597825 -53 AATAATAAAAGATAAGGAGGAAAAATTAAA 8 41 1 GATAAGGAGG 0.88226 -29 ********** Masking position 4 Map Score: 9.96936 Number of sites scoring better than the average of aligned sites = 3010 Number in coding regions = 2572 Number in noncoding regions = 438 Number of orfs with sites within 600 bp upstream = 380 Fraction of orfs with sites within 600 bp upstream = 0.0610344 Motif number 5 TATCTCTGCAGGCCTCCACCTTCCCCT 2 130 1 GGCCCCACCT 0.996187 -17 CACCACAATATGCCCCCACCTTAATCCTGGG 6 75 1 TGCCCCACCT 0.996837 -97 CAAGCAATTTTGCCATCAACTGGAGGGAGTG 6 126 0 TGCCTCAACT 0.985449 -46 AAGTCCTTTTTACCGCCGCCTAGTATGGAAT 7 104 1 TACCCCGCCT 0.975854 -197 AACTCAGTTGTGCCCTCAAGTGAGCAGCAGT 7 146 0 TGCCTCAAGT 0.939498 -155 AACTGAGTTTGGCGATCGCCTGATATTCTGC 7 168 1 GGCGTCGCCT 0.969311 -133 **** ****** Masking position 11 Map Score: 4.81348 Number of sites scoring better than the average of aligned sites = 429 Number in coding regions = 400 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 6 TGACTAAAAATAGACTTCAATTTTCCGAAT 4 38 1 TAGACTTCAA 0.882123 -58 AAGCCACAGTTTTCCTTTAATAATCCCCCC 5 85 1 TTTCCTTTAA 0.923344 -20 GCAAGCAATTTTGCCATCAACTGGAGGGAG 6 128 0 TTGCCATCAA 0.931208 -44 GTTTCTAGATTTTCTTTAAATCTTATTTTC 7 16 1 TTTCTTTAAA 0.731786 -285 TAAATCTTATTTTCCTTAAATTTTCCGTAA 7 32 1 TTTCCTTAAA 0.954435 -269 AGTATGGAATTTGACTTCATTACTGCTGCT 7 125 1 TTGACTTCAT 0.882123 -176 TATTATTCTTTTTACTTCAATCAACTTTGA 8 18 0 TTTACTTCAA 0.95073 -52 ********** Masking position 9 Map Score: 1.98413 Number of sites scoring better than the average of aligned sites = 690 Number in coding regions = 594 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 7 GGCTTTGGTGATGGGGGTCTACCCCCCTAT 2 36 0 ATGGGGGTCT 0.957043 -111 TCCCTCATTATTGGGGGCTTTGGTGATGGG 2 51 0 TTGGGGGCTT 0.98687 -96 AGGGGAAGGTGGAGGCCTGCAGAGATAG 2 129 0 GTGGAGGCCT 0.983805 -18 CAGGATTAAGGTGGGGGCATATTGTGGTGG 6 74 0 GTGGGGGCAT 0.995053 -98 TGCTGCTCACTTGAGGGCACAACTGAGTTT 7 148 1 TTGAGGGCAC 0.919586 -153 ********** Masking position 2 Map Score: 1.6824 Number of sites scoring better than the average of aligned sites = 585 Number in coding regions = 531 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 8 AGGACTCAGCAAGGTTTAGTTCCAGTCATAC 2 86 0 AAGGTTTAGT 0.944493 -61 CGGAGGATAAAAGTTGTAGTTGCGAAACC 3 9 0 AAGTTGTAGT 0.980474 -31 AACAGGAAGTAAGTTTTAGAGA 4 2 0 AAGTTTTAGG 0.974736 -94 GGTTATTTTTAAGTTATTGCTCCACTCCCTC 6 104 1 AAGTTATTGT 0.908017 -68 GACTTGAATCAAGTTTTTGGGAGTAGGGGAG 7 78 0 AAGTTTTTGG 0.953872 -223 TTAAAAAATGATGTTGTAGATAATTCTGACC 7 271 0 ATGTTGTAGT 0.925338 -30 ********* * Masking position 5 Map Score: 2.33471 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 89 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 9 GGTGATGGGGGTCTACCCCCCTATCAGTAG 2 30 0 GTCTACCCCC 0.94955 -117 CCCCCATCACCAAAGCCCCCAATAATGAGG 2 49 1 CAAAGCCCCC 0.933129 -98 CAGTCATACCATCTTCCCTCATTATTGGGG 2 65 0 ATCTTCCCTC 0.880084 -82 CTCAGCACCCTAAGAGTTAT 4 86 0 CTCAGCACCC 0.947386 -10 TTTTCCTTTAATAATCCCCCC 5 94 1 ATAATCCCCC 0.954626 -11 CACCACCACAATATGCCCCCACCTTAATCC 6 72 1 ATATGCCCCC 0.987816 -100 TCGCCTGATATTCTGCCGCCCAGAAAACTC 7 183 1 TTCTGCCGCC 0.927215 -118 ********** Masking position 6 Map Score: 1.91668 Number of sites scoring better than the average of aligned sites = 1844 Number in coding regions = 1614 Number in noncoding regions = 230 Number of orfs with sites within 600 bp upstream = 243 Fraction of orfs with sites within 600 bp upstream = 0.0390299 Motif number 10 ********** No masking Map Score: 1.21035e-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 11 ********** No masking Map Score: 1.21035e-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: 1.21035e-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