AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i015_Glycolysis_2_synecho_reg_100.orf -o015_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 RCY49691 112 Synechocystis #2 RCY39030 187 Synechocystis #3 RCY05748 42 Synechocystis #4 RCY36146 300 Synechocystis Motif number 1 TAAAATTGTCCTCAATCCTTAACCTACTTTTAAC 1 13 0 CTCACTTACC 0.845733 -100 GGAAAAATTGCCCAAAGCCCAGCCTACCATCGTT 2 41 1 CCCACCCACC 0.994779 -147 ATTTAACTGCCCCTAATTTCAGCCCATT 2 170 1 CCCATTCACC 0.988483 -18 CATTCCCTTAATTCCTCCTCAGTAAGTT 3 5 1 CCCTTTCCCC 0.983543 -38 CAGTTGGCGTCACACTTTTCCCCCTGGGGAGCAG 4 49 1 CACCTTCCCC 0.968552 -252 GAAGAAACCGCCCGAACATCATCCAGGCGGAGTG 4 87 1 CCCAATCACC 0.971404 -214 TCACTCCTCACACCACACTCCGCCTGGATGATGT 4 102 0 CACACTCCCC 0.9925 -199 ACGTAAGTTTCCGTTCACTCCTCACACCACACTC 4 116 0 CCGTCTCCCA 0.816939 -185 TGAACGGAAACTTACGTCTCCGCCCTCTTCATTG 4 133 1 CTTCCTCCCC 0.914537 -168 AACCCTATGCCCCCCGTCCCAACCTGTACAATGA 4 161 0 CCCCCCCACC 0.993677 -140 TTAACAAATACGGAACTCCCCACCGGCAAAAACC 4 191 0 CGGACCCCCC 0.949054 -110 *** * **** ** Masking position 13 Map Score: 13.9077 Number of sites scoring better than the average of aligned sites = 2015 Number in coding regions = 1823 Number in noncoding regions = 192 Number of orfs with sites within 600 bp upstream = 183 Fraction of orfs with sites within 600 bp upstream = 0.0293929 Motif number 2 AGTAGGTTAAGGATTGAGGACAATTTTAAGAATTCT 1 19 1 GGTGGGAATT 0.956445 -94 ATGGTAGGCTGGGCTTTGGGCAATTTTTCCCAATAG 2 35 0 GGTTGGGATT 0.99743 -153 GCTTTTAAGCGGTGTTAGGGAAATATTCTCATTATC 2 115 0 GGTTGGGAAT 0.989667 -73 AATGGGCTGAAATTAGGGGCAGTTAAATATAATA 2 164 0 GATTGGGATT 0.995966 -24 CCGCCTGGATGATGTTCGGGCGGTTTCTTCTTATCT 4 81 0 GATTGGGGTT 0.995138 -220 TTTTTAAAGGGATTTTTGGGGTGATTAGATCCATTT 4 227 1 GATTGGGGTT 0.995138 -74 ** ** *** * ** Masking position 5 Map Score: 6.49662 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 122 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 3 AATAAAACAGAACTATATCGGCAAGGAAAA 1 91 1 AACTATATCG 0.87814 -22 AAACCCATCAAACTGTGCAGACTATTGGGA 2 14 1 AACTGTGCAG 0.935364 -174 AAGCCGATGCAACTGAAACGGCGATCGTGG 2 83 1 AACTGAAACG 0.945385 -105 GTGTGACGCCAACTGTGACAAAAGATGAAT 4 34 0 AACTGTGACA 0.985948 -267 CCAGGGGGAAAAGTGTGACGCCAACTGTGA 4 46 0 AAGTGTGACG 0.979429 -255 GGTTGGTCAAAACTATGACAAGAACT 4 285 1 AACTATGACA 0.959529 -16 ********** Masking position 4 Map Score: 2.84908 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 231 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 4 ATATTCTCATTATCCGCCACGATCGCCGTT 2 99 0 TATCCGCCAC 0.969592 -89 CTATTATATTTAACTGCCCCTAATTTCAGC 2 163 1 TAACTGCCCC 0.99112 -25 CATTCCCTTAATTCCTCCTCAGTAAGTT 3 9 1 TAATTCCTCC 0.746107 -34 GGTTTCTTCTTATCTGCTCCCCAGGGGGAA 4 66 0 TATCTGCTCC 0.962306 -235 AGATAAGAAGAAACCGCCCGAACATCATCC 4 81 1 AAACCGCCCG 0.907727 -220 GAAACTTACGTCTCCGCCCTCTTCATTGTA 4 139 1 TCTCCGCCCT 0.907727 -162 GCAAAAACCCTATGCCCCCCGTCCCAACCT 4 170 0 TATGCCCCCC 0.965068 -131 AAAATGGATCTAATCACCCCAAAAATCCCT 4 234 0 TAATCACCCC 0.923374 -67 ********** Masking position 7 Map Score: 3.72155 Number of sites scoring better than the average of aligned sites = 2312 Number in coding regions = 2074 Number in noncoding regions = 238 Number of orfs with sites within 600 bp upstream = 247 Fraction of orfs with sites within 600 bp upstream = 0.0396723 Motif number 5 CAGTTAAAAGTAGGTTAAGG 1 1 1 CAGTTAAAAG 0.948343 -112 TTTGCTTCTACAAATAAAACAGAACTATAT 1 79 1 CAAATAAAAC 0.890095 -34 ACTATATCGGCAAGGAAAACC 1 102 1 CAAGGAAAAC 0.882839 -11 AAATTAGGGGCAGTTAAATATAATAGTTAA 2 159 0 CAGTTAAATA 0.862414 -29 CCCTGGGGAGCAGATAAGAAGAAACCGCCC 4 70 1 CAGATAAGAA 0.881816 -231 CCAACCTGTACAATGAAGAGGGCGGAGACG 4 147 0 CAATGAAGAG 0.8667 -154 ATCCATTTTCCAGTGAAATCCAGAGATAAA 4 255 1 CAGTGAAATC 0.939987 -46 CAGTGAAATCCAGAGATAAAGGTTGGTCAA 4 265 1 CAGAGATAAA 0.78927 -36 ********** Masking position 6 Map Score: 1.2263 Number of sites scoring better than the average of aligned sites = 1021 Number in coding regions = 878 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987 Motif number 6 TAAGGATTGAGGACAATTTTAAGAATTCTC 1 26 1 GGACAATTTT 0.981795 -87 GCTGGGCTTTGGGCAATTTTTCCCAATAGT 2 34 0 GGGCAATTTT 0.993248 -154 AGCGGTGTTAGGGAAATATTCTCATTATCC 2 114 0 GGGAAATATT 0.968338 -74 ********** Masking position 5 Map Score: 0.137889 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 130 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 ********** 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 8 ********** 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 9 ********** 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