AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i223_synecho_ctra_300.orf -o223_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 RCY09567 185 Synechocystis #2 RCY24465 237 Synechocystis #3 RCY17780 95 Synechocystis #4 RCY18001 37 Synechocystis #5 RCY20929 300 Synechocystis #6 RCY27839 51 Synechocystis #7 RCY11822 42 Synechocystis #8 RCT00692 296 Chlamydia_trachomatis Motif number 1 TTTCTTCTCCCCCTCTGCTTCCCTAGCCC 1 7 0 CCCTGCTCCC 0.953463 -179 TCGTCCCATTGCCCTTTCTTCTCCCCCTCTGCT 1 21 0 GCCTTCTCTC 0.928663 -165 GGAGTAATTTGCTTTATCGTCCCATTGCCCTTT 1 37 0 GCTATCTCCC 0.967269 -149 TCTATCTGTGTCTTTTTCACCCTTGAAAAGGTG 1 155 1 TCTTTCCCCT 0.890653 -31 GTTGCTAAACCCCCTCCCATCCCCATGGACAAG 2 71 1 CCCCCCTCCC 0.978347 -167 CCAAATTATAGGTCTTTCCTCCCTTGTCCATGG 2 93 0 GGTTTCTCCC 0.912112 -145 ACATACAAAGGCTACTTCATCCCCGGTAAAAAA 3 31 0 GCTTTCTCCC 0.990681 -65 TCCTCCCATTTCCCATCCACCCTA 5 2 0 TCCTCCCCCT 0.925692 -299 CGATCATTTCCCCCTCTCCTCCCATTTCCCATC 5 18 0 CCCCTCTCCC 0.982118 -283 GCCAATTTCAGCCTATCCCTCCTTTTACTTTCG 5 136 1 GCCTCCTCCT 0.988695 -165 CGATAAATCCGCTGGTTCGTCCTAATTTTCCGG 5 211 0 GCTTTCTCCT 0.982813 -90 ATTACGAAAGGCTTCATCTTCCTTGTTTGCGGA 8 32 1 GCTATCTCCT 0.940814 -265 AATGAAGAGTTCCCCCCCTCCCTTATAAGGTAA 8 84 0 TCCCCCCCCT 0.886395 -213 *** *** **** Masking position 8 Map Score: 17.7467 Number of sites scoring better than the average of aligned sites = 1562 Number in coding regions = 1422 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 2 GAGAAGAAAGGGCAATGGGACGATAAAGCA 1 31 1 GGCAATGGGA 0.78879 -155 TGGCGTAACTGTCACCGGGCCA 2 3 0 GTCACCGGGC 0.980541 -235 TTCCTCCCTTGTCCATGGGGATGGGAGGGG 2 81 0 GTCCATGGGG 0.957374 -157 GAGTCACAACATCCCCGGGGATCATGGCCA 2 123 0 ATCCCCGGGG 0.988167 -115 GAAAAAAGGCGTCCCCGGAGTCACAACATC 2 140 0 GTCCCCGGAG 0.984053 -98 AACCCACCATGGCATCGGGGGAAACTTGAA 2 203 0 GGCATCGGGG 0.912828 -35 AGGCTACTTCATCCCCGGTAAAAAATCGTT 3 26 0 ATCCCCGGTA 0.825992 -70 TTCCGGTTGTATCCACGGAAACTCCCCTTT 5 260 1 ATCCACGGAA 0.882315 -41 CATGAAAGTTGACAAAGGGGAGTTTCCGTG 5 273 0 GACAAAGGGG 0.79401 -28 GGACTGAAGACCACGGACGGACAATTTT 6 9 1 GACCACGGAC 0.845714 -43 TCTCCGAAACAACACCGGGAACTCTCTTAG 8 206 0 AACACCGGGA 0.921419 -91 ********** Masking position 3 Map Score: 8.52333 Number of sites scoring better than the average of aligned sites = 2177 Number in coding regions = 2032 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 3 TAGGGAAGCAGAGGGGGAGAAGAAAGGGCA 1 15 1 GAGGGGGAGA 0.992756 -171 CTTAACGCATTAAGGGGAAACCAATCGCTA 1 69 1 TAAGGGGAAA 0.938266 -117 GCACCTTTTCAAGGGTGAAAAAGACACAGA 1 159 0 AAGGGTGAAA 0.913843 -27 CACCATGGCATCGGGGGAAACTTGAAACGA 2 199 0 TCGGGGGAAA 0.968868 -39 AATGGGAGGAGAGGGGGAAATGATCGCTTA 5 25 1 GAGGGGGAAA 0.995885 -276 AAAGGAGGGATAGGCTGAAATTGGCCATAA 5 131 0 TAGGCTGAAA 0.904597 -170 TCTCTGGATAGACGCGGAAAAAGCCCTGAA 5 172 0 GACGCGGAAA 0.942726 -129 CCTTATAAGGGAGGGGGGGAACTCTTCATT 8 87 1 GAGGGGGGGA 0.973261 -210 ********** Masking position 10 Map Score: 9.54791 Number of sites scoring better than the average of aligned sites = 739 Number in coding regions = 660 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 4 TAATGCGTTAAGGAGTAATTTGCTTTATCGTC 1 49 0 AGGATAATTG 0.973765 -137 TACTTTGAAGAGGTAAAATCGGTAGCGATTGG 1 89 0 AGGTAAATCG 0.723621 -97 CAGGCTAAGTCGGATTAATTGGTAGCAAACAT 2 31 1 CGGATAATTG 0.971308 -207 AATAAGAGCATTAATTATTGTTGTGGTG 4 7 1 AGCATAATTT 0.741152 -31 CCTAATTTTCCGGATTAATCTATCTCTGGATA 5 192 0 CGGATAATCA 0.819432 -109 GACGAACCAGCGGATTTATCGTCAAATTGCCC 5 223 1 CGGATTATCT 0.670916 -78 TGGATACAACCGGAAATATTGGGCAATTTGAC 5 243 0 CGGAATATTG 0.916164 -58 AGACCACGGACGGACAATTTTTACTAATTATT 6 18 1 CGGAAATTTT 0.795884 -34 AATAACCTCAGGAATAATTAGTAAAAATTGT 6 31 0 AGGATAATTG 0.974195 -21 TAGCAGGACAAATTATCGAGGTTGTT 7 27 0 AGGAAAATTT 0.953784 -16 CCTCTTTGAGAGGAGAACTTCTTCTGGACTCT 8 123 1 AGGAAACTTT 0.799942 -174 **** ***** * Masking position 9 Map Score: 4.70737 Number of sites scoring better than the average of aligned sites = 805 Number in coding regions = 710 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 5 ATCGGTAGCGATTGGTTTCCCCTTAATGCG 1 74 0 ATTGGTTTCC 0.793684 -112 AAGTCGGATTAATTGGTAGCAAACATCACA 2 37 1 AATTGGTAGC 0.817897 -201 GCTTCTTTGTTTAGCAACCCACCAT 2 223 0 TTTGTTTAGC 0.829403 -15 CAAAATAACGATTTTTTACCGGGGATGAAG 3 20 1 ATTTTTTACC 0.937727 -76 TATTAGAAGCAATGGTTAGCCTTTAAGAGT 5 61 1 AATGGTTAGC 0.940674 -240 GAGGTTGTTTATTTGTTAGCAAGGT 7 6 0 ATTTGTTAGC 0.973437 -37 CTTTGCAAAGATTTTTTACCTTATAAGGGA 8 69 1 ATTTTTTACC 0.937727 -228 GGAACTCTTCATTTGTGAGCCTCTTTGAGA 8 104 1 ATTTGTGAGC 0.895421 -193 GGGTCGTTTTTATTTTTACCCTTGAATCTA 8 179 1 TATTTTTACC 0.713971 -118 ********** Masking position 3 Map Score: 4.90619 Number of sites scoring better than the average of aligned sites = 466 Number in coding regions = 407 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 6 CTAGGGAAGCAGAGGGGGAGAAGAAAGGGC 1 14 1 AGAGGGGGAG 0.988811 -172 CCACCATGGCATCGGGGGAAACTTGAAACG 2 200 0 ATCGGGGGAA 0.973524 -38 AAATGGGAGGAGAGGGGGAAATGATCGCTT 5 24 1 AGAGGGGGAA 0.99588 -277 AAAAGGAGGGATAGGCTGAAATTGGCCATA 5 132 0 ATAGGCTGAA 0.868482 -169 ATCTCTGGATAGACGCGGAAAAAGCCCTGA 5 173 0 AGACGCGGAA 0.96661 -128 CTTATAAGGGAGGGGGGGAACTCTTCATTT 8 88 1 AGGGGGGGAA 0.990899 -209 ********** Masking position 9 Map Score: 6.40807 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 302 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 7 CCGATTTTACCTCTTCAAAGTATGCCAACG 1 99 1 CTCTTCAAAG 0.688524 -87 ATAAACGCACCTTTTCAAGGGTGAAAAAGA 1 165 0 CTTTTCAAGG 0.700322 -21 CAGACATTTACTCTTAAAGGCTAACCATTG 5 70 0 CTCTTAAAGG 0.930348 -231 TGCGGATTATCTTTGCAAAGATTTTTTACC 8 59 1 CTTTGCAAAG 0.499329 -238 TTGTGAGCCTCTTTGAGAGGAGAACTTCTT 8 116 1 CTTTGAGAGG 0.856893 -181 ********** Masking position 4 Map Score: 1.03635 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 46 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 AATAAACGCACCTTTTCAAGGGTG 1 172 0 AACGCACCTT 0.931865 -14 ATTTGTTGCTAAACCCCCTCCCATCCCCAT 2 67 1 AAACCCCCTC 0.96865 -171 TTTGTTTAGCAACCCACCATGGCATCGGGG 2 213 0 AACCCACCAT 0.859073 -25 CCCATTTCCCATCCACCCTA 5 1 0 ATCCACCCTA 0.782968 -300 ATTTCAGCCTATCCCTCCTTTTACTTTCGA 5 140 1 ATCCCTCCTT 0.848545 -161 TATCCACGGAAACTCCCCTTTGTCAACTTT 5 269 1 AACTCCCCTT 0.927702 -32 GCTAACAAATAAACAACCTCGATAATTTGT 7 16 1 AAACAACCTC 0.798321 -27 AATGAAGAGTTCCCCCCCTCCCTTATAAGG 8 87 0 TCCCCCCCTC 0.883873 -210 TAAAAATAAAAACGACCCTCCATCATATCA 8 167 0 AACGACCCTC 0.947899 -130 ********** Masking position 7 Map Score: 1.71505 Number of sites scoring better than the average of aligned sites = 1242 Number in coding regions = 1026 Number in noncoding regions = 216 Number of orfs with sites within 600 bp upstream = 190 Fraction of orfs with sites within 600 bp upstream = 0.0305172 Motif number 9 ACGCCTTTTTTCGCTCAGATGCCTTGGATG 2 158 1 TCGCTCAGAT 0.978414 -80 GGGGAAATGATCGCTTAGGTATTTATTAGA 5 38 1 TCGCTTAGGT 0.978414 -263 CACCGGGAACTCTCTTAGATTCAAGGGTAA 8 194 0 TCTCTTAGAT 0.980375 -103 GGAGAGAAGGTTTCTTAGATAGTCGCTTAT 8 231 1 TTTCTTAGAT 0.926327 -66 ********** Masking position 5 Map Score: 0.375438 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 12 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 10 ********** No masking Map Score: 3.15071e-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 11 ********** No masking Map Score: 3.15071e-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 12 ********** No masking Map Score: 3.15071e-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