AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i182_riboflafin_biosynthesis_synecho_reg_100.orf -o182_synecho_100.ace -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -g0.48 -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 = 0.48 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RCY15119 104 Synechocystis #2 RCY49636 271 Synechocystis #3 RCY36009 224 Synechocystis #4 RCY19918 108 Synechocystis Motif number 1 GGGAGGCGATCGCCCTATCCCGGTAATTTCC 1 5 1 GCTGCCCACC 0.98846 -100 CCCTATCCCGGTAATTTCCCCATGGCCTGGGCTGTGG 1 23 1 GATCCCCTCC 0.977655 -82 AGTTTTTCGGGGCTATCCCCCACAGCCCAGGCCATGG 1 42 0 GCTCCCCCCC 0.996138 -63 GCGCCCTGGTTCCGCTGGCCCCCATCC 2 1 0 TCTGCCCCCC 0.990206 -271 TGTTGCAACAGTCGATCTTCTGCGACCACCGTTGTCA 2 160 1 GCTTTCTCCC 0.951615 -112 GACCACCGTTGTCAATTTTCCTCCAGCTTCTTAAGTT 2 183 1 GCTTTCCCGC 0.983466 -89 CCTTGAACGTTTCTGTCCCCCGTATCCCGTCCGATTT 2 241 1 TCTCCCCTCC 0.97767 -31 GGGAACTCTAGACTCGTTTCCCTAACCTTGACCACCC 3 117 1 GCGTTCCTCC 0.976124 -108 ACCCCGAGCTGCAACTCTCCCTCCAGCCATGGCATTG 3 150 1 GATTCCCCGC 0.961453 -75 CTCCAGCCATGGCATTGGCCCCCAACTGGCACAATTG 3 170 1 GCTGCCCCCT 0.980931 -55 CAGTAGATTTGACTAGATTCCATTTCCCTACCCTGCC 4 61 1 GCGTTCCTCC 0.976093 -48 * * * **** * ** Masking position 10 Map Score: 17.7239 Number of sites scoring better than the average of aligned sites = 1455 Number in coding regions = 1338 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 2 CATGGGGAAATTACCGGGATAGGGCGATCGCC 1 15 0 TTCGGGATAG 0.97268 -90 ATTTCCCCATGGCCTGGGCTGTGGGGGATAGC 1 36 1 GGCGGGCTGT 0.983233 -69 GATCAGAGTTTTTCGGGGCTATCCCCCACAGC 1 53 0 TTCGGGCTAT 0.981695 -52 AAACTTATTCTGCCATGGCTATAGTCCTATGA 2 44 0 TGCTGGCTAT 0.943948 -228 TTTTAAAGCTTTTCTGGGAAGGCTTTGGTTTC 2 110 0 TTCGGGAAGG 0.962559 -162 ATTGACCGTTTTCCGGGGTTGACCGAAGGCAA 3 53 1 TTCGGGTTGA 0.942489 -172 AGCTCGGGGTGGTCAAGGTTAGGGAAACGAGT 3 128 0 GGCAGGTTAG 0.835702 -97 TGGGGGCCAATGCCATGGCTGGAGGGAGAGTT 3 162 0 TGCTGGCTGG 0.9814 -63 CAGTCGGGAATTGCTGGGTAATCCGTTGCTAA 4 24 1 TTCGGGTAAT 0.938686 -85 TCTGAGATCATGGCAGGGTAGGGAAATGGAAT 4 77 0 TGCGGGTAGG 0.987096 -32 ** * ******* Masking position 4 Map Score: 10.0766 Number of sites scoring better than the average of aligned sites = 1831 Number in coding regions = 1668 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 3 GGGCTGTGGGGGATAGCCCCGAAAAACTCT 1 51 1 GGATAGCCCC 0.965856 -54 GAAAAACTCTGATCTACCGCTAACCCGATC 1 71 1 GATCTACCGC 0.91263 -34 CCGATCTAGGGAACTACACC 1 95 1 GAACTACACC 0.955458 -10 TTCCATCATAGGACTATAGCCATGGCAGAA 2 39 1 GGACTATAGC 0.910377 -233 CGACGGACAAGAACAGTACCCATTGTAAAG 3 21 1 GAACAGTACC 0.879928 -204 CCCGGAAAACGGTCAATACCTTTACAATGG 3 40 0 GGTCAATACC 0.953733 -185 CTTTGCCTTCGGTCAACCCCGGAAAACGGT 3 57 0 GGTCAACCCC 0.988154 -168 AATCTTCTAAGGTTTGTCCCATT 3 212 1 GGTTTGTCCC 0.934822 -13 TTTTAGCAACGGATTACCCAGCAATTCCCG 4 28 0 GGATTACCCA 0.805525 -81 ********** Masking position 1 Map Score: 6.92971 Number of sites scoring better than the average of aligned sites = 2829 Number in coding regions = 2603 Number in noncoding regions = 226 Number of orfs with sites within 600 bp upstream = 241 Fraction of orfs with sites within 600 bp upstream = 0.0387086 Motif number 4 CCATCATAGGACTATAGCCATGGCAGAATAA 2 41 1 ACATAGCCAT 0.96767 -231 ATGGCAGAATAAGTTTCCCTTTTTTAGAGAA 2 60 1 AATTTCCCTT 0.795636 -212 CGACGAAGAAACCAAAGCCTTCCCAGAAAAG 2 103 1 ACAAAGCCTT 0.950844 -169 TTAAGTTTTAACTTTTTCCTTTTCTGCACCT 2 213 1 ACTTTTCCTT 0.86989 -59 ACGGACAAGAACAGTACCCATTGTAAAGGTA 3 23 1 ACGTACCCAT 0.961259 -202 AATTAAGCATACCTTTGCCTTCGGTCAACCC 3 68 0 ACTTTGCCTT 0.972137 -157 AAACGAGTCTAGAGTTCCCTTGGCATTATCT 3 105 0 AGGTTCCCTT 0.861752 -120 CCAGTTGGGGGCCAATGCCATGGCTGGAGGG 3 168 0 GCAATGCCAT 0.818826 -57 ATGATCTCAGACCAAACCCAT 4 98 1 ACAAACCCAT 0.940123 -11 ** ******** Masking position 11 Map Score: 3.48225 Number of sites scoring better than the average of aligned sites = 791 Number in coding regions = 712 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 5 GGGAGGCGATCGCCCTATCC 1 1 1 GGGAGGCGAT 0.929666 -104 TGGCCTGGGCTGTGGGGGATAGCCCCGAAA 1 45 1 TGTGGGGGAT 0.778801 -60 GTTTCTTCGTCGTAGGGGATGAATTTCTCT 2 85 0 CGTAGGGGAT 0.954508 -187 CTTAAGAAGCTGGAGGAAAATTGACAACGG 2 188 0 TGGAGGAAAA 0.847551 -84 AAACGTTCAAGGTGCAGAAAAGGAAAAAGT 2 223 0 GGTGCAGAAA 0.628685 -49 CGGGATACGGGGGACAGAAACGTTCAAGGT 2 240 0 GGGACAGAAA 0.902836 -32 CGGTAAATCGGACGGGATACGGGGGACA 2 254 0 CGGACGGGAT 0.953307 -18 ATCTCTTCGACGGACAAGAACAGTACCCAT 3 14 1 CGGACAAGAA 0.600351 -211 CGGGGTTGACCGAAGGCAAAGGTATGCTTA 3 66 1 CGAAGGCAAA 0.697319 -159 GGTGGTCAAGGTTAGGGAAACGAGTCTAGA 3 123 0 GTTAGGGAAA 0.756324 -102 ATGCCATGGCTGGAGGGAGAGTTGCAGCTC 3 155 0 TGGAGGGAGA 0.846648 -70 ATCATGGCAGGGTAGGGAAATGGAATCTAG 4 73 0 GGTAGGGAAA 0.977405 -36 ********** Masking position 9 Map Score: 4.46417 Number of sites scoring better than the average of aligned sites = 6256 Number in coding regions = 5522 Number in noncoding regions = 734 Number of orfs with sites within 600 bp upstream = 654 Fraction of orfs with sites within 600 bp upstream = 0.105043 Motif number 6 ********** No masking Map Score: 1.10377e-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 7 ********** No masking Map Score: 1.10377e-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 8 ********** No masking Map Score: 1.10377e-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