AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i015_Glycolysis_2_synecho_reg_300.orf -o015_synecho_300.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 GTTAAAAGTAGGTTAAGGATTGAGGACAATTTTA 1 13 1 GGTAAGTGAG 0.869147 -100 AACGATGGTAGGCTGGGCTTTGGGCAATTTTTCC 2 41 0 GGTGGGTGGG 0.995687 -147 AATGGGCTGAAATTAGGGGCAGTTAAAT 2 170 0 GGTGAATGGG 0.990475 -18 AACTTACTGAGGAGGAATTAAGGGAATG 3 5 0 GGGGAAAGGG 0.986377 -38 CTGCTCCCCAGGGGGAAAAGTGTGACGCCAACTG 4 49 0 GGGGAAGGTG 0.973901 -252 CACTCCGCCTGGATGATGTTCGGGCGGTTTCTTC 4 87 0 GGTGATTGGG 0.976279 -214 ACATCATCCAGGCGGAGTGTGGTGTGAGGAGTGA 4 102 1 GGGGAGTGTG 0.993802 -199 GAGTGTGGTGTGAGGAGTGAACGGAAACTTACGT 4 116 1 TGGGAGACGG 0.843917 -185 CAATGAAGAGGGCGGAGACGTAAGTTTCCGTTCA 4 133 0 GGGGAGGAAG 0.928393 -168 TCATTGTACAGGTTGGGACGGGGGGCATAGGGTT 4 161 1 GGTGGGGGGG 0.994775 -140 GGTTTTTGCCGGTGGGGAGTTCCGTATTTGTTAA 4 191 1 GGGGGGTCCG 0.957573 -110 ** **** * *** Masking position 2 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 0.958669 -94 ATGGTAGGCTGGGCTTTGGGCAATTTTTCCCAATAG 2 35 0 GGTTGGGATT 0.997566 -153 GCTTTTAAGCGGTGTTAGGGAAATATTCTCATTATC 2 115 0 GGTTGGGAAT 0.990211 -73 AATGGGCTGAAATTAGGGGCAGTTAAATATAATA 2 164 0 GATTGGGATT 0.99618 -24 CCGCCTGGATGATGTTCGGGCGGTTTCTTCTTATCT 4 81 0 GATTGGGGTT 0.995395 -220 TTTTTAAAGGGATTTTTGGGGTGATTAGATCCATTT 4 227 1 GATTGGGGTT 0.995396 -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 0.88421 -22 AAACCCATCAAACTGTGCAGACTATTGGGA 2 14 1 AACTGTGCAG 0.938782 -174 AAGCCGATGCAACTGAAACGGCGATCGTGG 2 83 1 AACTGAAACG 0.948302 -105 GTGTGACGCCAACTGTGACAAAAGATGAAT 4 34 0 AACTGTGACA 0.986729 -267 CCAGGGGGAAAAGTGTGACGCCAACTGTGA 4 46 0 AAGTGTGACG 0.980565 -255 GGTTGGTCAAAACTATGACAAGAACT 4 285 1 AACTATGACA 0.961721 -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 CTATTGGGAAAAATTGCCCAAAGCCCAGCC 2 35 1 AAATTGCCCA 0.831895 -153 ATATTCTCATTATCCGCCACGATCGCCGTT 2 99 0 TATCCGCCAC 0.909176 -89 CTATTATATTTAACTGCCCCTAATTTCAGC 2 163 1 TAACTGCCCC 0.993429 -25 CATTCCCTTAATTCCTCCTCAGTAAGTT 3 9 1 TAATTCCTCC 0.877346 -34 GGTTTCTTCTTATCTGCTCCCCAGGGGGAA 4 66 0 TATCTGCTCC 0.939823 -235 AGATAAGAAGAAACCGCCCGAACATCATCC 4 81 1 AAACCGCCCG 0.931971 -220 GCAAAAACCCTATGCCCCCCGTCCCAACCT 4 170 0 TATGCCCCCC 0.935024 -131 AACAAATACGGAACTCCCCACCGGCAAAAA 4 193 0 GAACTCCCCA 0.86738 -108 AAAATGGATCTAATCACCCCAAAAATCCCT 4 234 0 TAATCACCCC 0.921698 -67 ********** Masking position 2 Map Score: 4.28572 Number of sites scoring better than the average of aligned sites = 2815 Number in coding regions = 2479 Number in noncoding regions = 336 Number of orfs with sites within 600 bp upstream = 329 Fraction of orfs with sites within 600 bp upstream = 0.0528429 Motif number 5 ********** 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 6 ********** 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 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