AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i327_synecho_ctra_300.orf -o327_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 RCY35517 107 Synechocystis #2 RCY39915 204 Synechocystis #3 RCY29136 46 Synechocystis #4 RCY29721 151 Synechocystis #5 RCY05183 198 Synechocystis #6 RCT00063 185 Chlamydia_trachomatis #7 RCT00064 300 Chlamydia_trachomatis Motif number 1 CCAACTGGTTGCCCTGTTATTGTAAACACC 1 73 0 GCCCTGTTAT 0.91365 -35 ACTTTTTTTGGCCCATCCGGCACCAACCTC 2 103 1 GCCCATCCGG 0.784206 -102 ATACCCTAAGGCCCTGTTTCGCCCCGTCCC 2 155 1 GCCCTGTTTC 0.921808 -50 GCCCTGTTTCGCCCCGTCCCGTCCTCCCAC 2 165 1 GCCCCGTCCC 0.985584 -40 GCCCCGTCCCGTCCTCCCACTGCTATCTAG 2 175 1 GTCCTCCCAC 0.684479 -30 CACTTCCATTGCCCTGCCCCCC 5 187 1 GCCCTGCCCC 0.994116 -12 CTAAAAAGAAGCCCCGTTCTATCTCGGACG 6 31 1 GCCCCGTTCT 0.967783 -155 CAAAAGAAAAGCCCCGTCCGAGATAGAACG 6 45 0 GCCCCGTCCG 0.982205 -141 CCGTTAACATGTCCTTTTCGAAGCAAAAAC 6 153 1 GTCCTTTTCG 0.821491 -33 TTCTCAGTGAGCCCTTCTGCTTGTTCAGCA 7 18 1 GCCCTTCTGC 0.965055 -283 TCAGCATACAGCCCTTTTCTATTGCCTTCC 7 42 1 GCCCTTTTCT 0.958213 -259 TTTTTATTCCGCCCTCCTGGGCTCCTTGAG 7 120 1 GCCCTCCTGG 0.964188 -181 AGGAGGAGATGCCCTCCACTCAAGGAGCCC 7 138 0 GCCCTCCACT 0.872711 -163 ********** Masking position 4 Map Score: 13.8995 Number of sites scoring better than the average of aligned sites = 2174 Number in coding regions = 2004 Number in noncoding regions = 170 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 2 CGTAAGCTTTCCCCATCAGGGATTTTTCTCTC 2 59 1 CCCATCGGGA 0.948796 -146 CTCCCACCAGTACCCTCCAAGACGGATACCCT 2 130 1 TCCCTCAAGA 0.952705 -75 GTCCTCCCACTGCTATCTAGGAGCTTGCCC 2 185 1 TCTATCAGGA 0.978306 -20 TACTTCAGAATACAATCGAGGAAATCTTAACG 4 35 1 TCAATCAGGA 0.985369 -117 GTTAGTTAAGTTCATTCAAGGACAAGAATATC 4 66 0 TCATTCAGGA 0.973097 -86 AGAAGCCCCGTTCTATCTCGGACGGGGCTTTT 6 37 1 TCTATCCGGA 0.945056 -149 CCTTTTCTATTGCCTTCCGAGACCTTTGGTGG 7 54 1 TCCTTCGAGA 0.897574 -247 GGAGATGCCCTCCACTCAAGGAGCCCAGGAGG 7 132 0 TCACTCAGGA 0.981208 -169 * ***** **** Masking position 12 Map Score: 5.9588 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 167 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 3 ATCAGGGATTTTTCTCTCGATCCATATGCT 2 73 1 TTTCTCTCGA 0.889122 -132 TAAGACTTTCTAAAAATTCTCTAAAA 6 7 1 TTTCTAAAAA 0.515076 -179 ACGGGGCTTCTTTTTAGAGAATTTTTAGAA 6 18 0 TTTTTAGAGA 0.788929 -168 GGCGAGGGGATTTTTAAAGACAAAAGAAAA 6 65 0 TTTTTAAAGA 0.833974 -121 CCCCTCGCCTTTTTTATAAACTCTTCTAGA 6 86 1 TTTTTATAAA 0.646818 -100 CTAGATTACTTTTCTCTAGATAGACAACTC 6 117 1 TTTCTCTAGA 0.933894 -69 AAATCAAAATTTTTTCACGACTTTTTAAAG 7 205 1 TTTTTCACGA 0.913979 -96 TTTTCACGACTTTTTAAAGAAATACTTTAA 7 216 1 TTTTTAAAGA 0.833974 -85 ********** Masking position 10 Map Score: 5.20261 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 123 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 CCTGTGCCATTGGGGGGAGAAGAATTAGCCA 1 27 1 TGGGGGAGAA 0.945168 -81 CCATTGCTGGTGGTGTGGGGTGTTTACAATA 1 55 1 TGGTGGGGGT 0.981768 -53 GAAAAATCCCTGATGGGGAAAGCTTACGAGA 2 56 0 TGATGGGAAA 0.789214 -149 GGTGGGAGGTTGGTGCCGGATGGGCCAAAAA 2 107 0 TGGTGCGGAT 0.939597 -98 TGGAGGGTACTGGTGGGAGGTTGGTGCCGGA 2 118 0 TGGTGGAGGT 0.902998 -87 GATAGCAGTGGGAGGACGGGACGGGGCGAAA 2 171 0 GGAGGCGGGA 0.970581 -34 AGTGGGGCCGGGAAAAATAGGGG 3 34 0 TGGGGCGGGA 0.993717 -13 TTTATAAAAAAGGCGAGGGGATTTTTAAAGA 6 75 0 AGGCGGGGGA 0.905667 -111 AAGGAGCCCAGGAGGGCGGAATAAAAAATGG 7 116 0 GGAGGCGGAA 0.933685 -185 TTCGATTACGTGAGGAGGAGATGCCCTCCAC 7 149 0 TGAGGGGAGA 0.945168 -152 ***** ***** Masking position 5 Map Score: 8.24171 Number of sites scoring better than the average of aligned sites = 2588 Number in coding regions = 2359 Number in noncoding regions = 229 Number of orfs with sites within 600 bp upstream = 251 Fraction of orfs with sites within 600 bp upstream = 0.0403148 Motif number 5 GATGGGCCAAAAAAAGTAGCATATGGATCG 2 90 0 AAAAAGTAGC 0.954188 -115 GTAATATACAAAAAAATATCTCATTTT 4 8 0 AAAAAATATC 0.804206 -144 ATGAACCAGAAATGAAAAGCTCCCTACATT 5 77 1 AATGAAAAGC 0.884058 -122 AAGTGTGATCAATAAATCGCCTTCACATTG 5 162 0 AATAAATCGC 0.831181 -37 AAAATTCTCTAAAAAGAAGCCCCGTTCTAT 6 23 1 AAAAAGAAGC 0.954188 -163 TTTAAAGACAAAAGAAAAGCCCCGTCCGAG 6 53 0 AAAGAAAAGC 0.954188 -133 GAAGAGTTTATAAAAAAGGCGAGGGGATTT 6 82 0 TAAAAAAGGC 0.816025 -104 AGGGCGGAATAAAAAATGGCAGAAATCCAA 7 105 0 AAAAAATGGC 0.961166 -196 ********** Masking position 5 Map Score: 2.82539 Number of sites scoring better than the average of aligned sites = 522 Number in coding regions = 435 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 6 TTCTCTCGATCCATATGCTACTTTTTTTGG 2 84 1 CCATATGCTA 0.938842 -121 GTCCCGTCCTCCCACTGCTATCTAGGAGCT 2 180 1 CCCACTGCTA 0.970201 -25 AACAACAGACCCCTATGATAAACCTTTTAC 4 120 0 CCCTATGATA 0.97104 -32 AGCACAAATGCCCGATGCAAGACTGTTGCT 5 42 1 CCCGATGCAA 0.959933 -157 CAGCATACAGCCCTTTTCTATTGCCTTCCG 7 43 1 CCCTTTTCTA 0.858667 -258 ATTTCACCCTCTGAAAAGCTTGTGTT 7 285 0 CCCTCTGAAA 0.950979 -16 ********** Masking position 6 Map Score: 1.79291 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 237 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 7 TTACCTGTGCCATTGGGGGGAGAAGAATTA 1 24 1 CATTGGGGGG 0.959979 -84 AAGAATTAGCCATTGCTGGTGGTGTGGGGT 1 46 1 CATTGCTGGT 0.987827 -62 TTGCATCGGGCATTTGTGCTTCAAATTGGG 5 32 0 CATTTGTGCT 0.937105 -167 GGGAGCTTTTCATTTCTGGTTCATCACTTA 5 71 0 CATTTCTGGT 0.972984 -128 CTTCCGAGACCTTTGGTGGTATACTCTTTT 7 67 1 CTTTGGTGGT 0.972919 -234 ********** Masking position 4 Map Score: 1.33537 Number of sites scoring better than the average of aligned sites = 352 Number in coding regions = 334 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 8 GGGAATTTATTTTAATCTGTTCCAGT 3 4 0 TTATCTTTCC 0.989979 -43 AAATCTTAACGATATTCTTGTCCTTGAATGAAC 4 56 1 GTATCTGTCC 0.952488 -96 GCCTTCACATTGTAATCCTTTCCTCGGTTAGAA 5 141 0 TTATCCTTCC 0.990702 -58 ACAGCCCTTTTCTATTGCCTTCCGAGACCTTTG 7 49 1 TTATGCTTCC 0.968037 -252 CCTTTGGTGGTATACTCTTTTCCTAAAGGTTGG 7 76 1 TTATCTTTCC 0.989979 -225 * ** *** **** Masking position 6 Map Score: 0.855921 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 20 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 9 AGCTTACGAGAATTTTAACGCAAATCAGCG 2 37 0 AATTTTAACG 0.91053 -168 AAATTCCCCTATTTTTCCCGGCCCCACT 3 29 1 ATTTTTCCCG 0.950025 -18 CAATCGAGGAAATCTTAACGATATTCTTGT 4 47 1 AATCTTAACG 0.872583 -105 GGAGTCCGCAATTCTAACCGAGGAAAGGAT 5 130 1 ATTCTAACCG 0.892124 -69 AGGCGAGGGGATTTTTAAAGACAAAAGAAA 6 66 0 ATTTTTAAAG 0.752068 -120 TGTTTTTAACCGAGTTTTTGCT 6 174 0 TTTTTAACCG 0.842426 -12 GAAATCAAAATTTTTTCACGACTTTTTAAA 7 204 1 TTTTTTCACG 0.872583 -97 ********** Masking position 5 Map Score: 0.0936732 Number of sites scoring better than the average of aligned sites = 715 Number in coding regions = 619 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 10 ********** No masking Map Score: -1.39734e-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: -1.39734e-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: -1.39734e-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