AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i278_synecho_ctra_300.orf -o278_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 RCY43725 156 Synechocystis #2 RCY30220 162 Synechocystis #3 RCY29761 69 Synechocystis #4 RCY18164 234 Synechocystis Motif number 1 GGTCGGCCCATCTTCAAGGGATTCCAT 1 6 1 GCCCATTCAA 0.954416 -151 TTTCCCTTTCCCCCATGGGCCAATAGCTTTTA 1 97 1 CCCCATGCCA 0.990017 -60 ACCCCGTACTCCCCAAAATTTGATCTTGAATG 2 114 0 CCCCAATTTG 0.98241 -49 ACAAATTCACCCCCAAACGTTAACAACAGGAG 3 41 1 CCCCAAGTTA 0.972812 -29 CAGGGATTTCCCCCAAGTTCAACGACAGACAG 4 20 0 CCCCAATCAA 0.987253 -215 GGAAATCCCTGCCCAAAGTATGGCAGAAAACC 4 41 1 GCCCAATATG 0.919296 -194 CTTCCCAATGCCCCAACTTCCGGTAACCCGAT 4 78 1 CCCCAATCCG 0.996623 -157 CTAACTTTTAGCCCATTTTTCGGTTCCCCAAC 4 163 1 GCCCATTTCG 0.968927 -72 TTTTTCGGTTCCCCAACGGCCAAGATTAACAA 4 178 1 CCCCAAGCCA 0.994739 -57 ****** **** Masking position 5 Map Score: 13.826 Number of sites scoring better than the average of aligned sites = 897 Number in coding regions = 800 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 2 TGGCCCATGGGGGAAAGGGAAAATTCGGCT 1 89 0 GGGAAAGGGA 0.995813 -68 ACTAGACCCAGGCCAAGGGAGTGGCGAGGA 2 32 0 GGCCAAGGGA 0.985042 -131 ATCATTGCTGGGGAACCAGAGGAAGTGACA 2 75 1 GGGAACCAGA 0.933567 -88 GGTTGGCCCTGGACAAGGGATACTACCCCG 2 140 0 GGACAAGGGA 0.97799 -23 GCCATACTTTGGGCAGGGATTTCCCCCAAG 4 35 0 GGGCAGGGAT 0.968912 -200 TTGGGGCATTGGGAAGGGAAAGGTTTTCTG 4 64 0 GGGAAGGGAA 0.99202 -171 TTGGCCGTTGGGGAACCGAAAAATGGGCTA 4 171 0 GGGAACCGAA 0.981293 -64 ********** Masking position 5 Map Score: 8.36033 Number of sites scoring better than the average of aligned sites = 1572 Number in coding regions = 1399 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 3 AACCAGTCCTTAAAATTTATTGGAATTTAAC 1 52 0 TAAAATTTAT 0.977809 -105 GGATTGGGTATAAAAGCTATTGGCCCATGGG 1 108 0 TAAAAGCTAT 0.978207 -49 AAAAATGGGCTAAAAGTTAGGACGTGGTCTC 4 152 0 TAAAAGTTAG 0.978207 -83 AGTTAATATCTAAAATTTAATTTTGTTAATC 4 201 0 TAAAATTTAT 0.977887 -34 GGGAAAACTTAAAAGTTAATATCTAAAATT 4 215 0 TAAAAGTTAT 0.990061 -20 ********* * Masking position 5 Map Score: 5.32231 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 8 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 4 GAGATAGCCGAATTTTCCCTTTCCCCCATG 1 84 1 AATTTTCCCT 0.920941 -73 GGTCTAGTTGAAGTTACCGCCATCATTGCT 2 54 1 AAGTTACCGC 0.979039 -109 AATAATTACAAATTCACCCCCAAACGTTAA 3 34 1 AATTCACCCC 0.988944 -36 TTTGGGCAGGGATTTCCCCCAAGTTCAACG 4 28 0 GATTTCCCCC 0.958577 -207 CGTCGGTAACAATTCACCGCGGAACTCCAC 4 120 0 AATTCACCGC 0.979059 -115 ATTAACTTTTAAGTTTTCCC 4 225 1 AAGTTTTCCC 0.906167 -10 ********** Masking position 4 Map Score: 2.95298 Number of sites scoring better than the average of aligned sites = 1382 Number in coding regions = 1216 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 170 Fraction of orfs with sites within 600 bp upstream = 0.0273049 Motif number 5 TAAATTTTAAGGACTGGTTGGAGATAGCCG 1 64 1 GGACTGGTTG 0.972316 -93 GTTCAAAACTGGATTGGGTATAAAAGCTAT 1 119 0 GGATTGGGTA 0.97665 -38 CCACTCCCTTGGCCTGGGTCTAGTTGAAGT 2 38 1 GGCCTGGGTC 0.991775 -125 ATTTTGGGGAGTACGGGGTAGTATCCCTTG 2 127 1 GTACGGGGTA 0.978321 -36 CTAAAAGTTAGGACGTGGTCTCACCGTCGG 4 144 0 GGACGTGGTC 0.985561 -91 ********** Masking position 9 Map Score: 2.59456 Number of sites scoring better than the average of aligned sites = 490 Number in coding regions = 452 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 6 ACTGATTATTTTAAGGATGGAATCCCTTGA 1 24 0 TTAAGGATGG 0.91301 -133 CCAATAAATTTTAAGGACTGGTTGGAGATA 1 60 1 TTAAGGACTG 0.944678 -97 CCCCCAAACGTTAACAACAGGAGTAAAGTC 3 50 1 TTAACAACAG 0.95114 -20 TCCCCCAAGTTCAACGACAGACAGGCAAGC 4 14 0 TCAACGACAG 0.979486 -221 CGGTGAATTGTTACCGACGGTGAGACCACG 4 131 1 TTACCGACGG 0.990791 -104 ATTTTTCGGTTCCCCAACGGCCAAGATTAA 4 177 1 TCCCCAACGG 0.916824 -58 ********** Masking position 7 Map Score: 2.13043 Number of sites scoring better than the average of aligned sites = 389 Number in coding regions = 352 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 7 GGCCCATCTTCAAGGGATTCCATCCTTAAAAT 1 15 1 CAGGATTCCA 0.974184 -142 AAGGCCTTTCCTCGCCACTCCCTTGGCCTGGG 2 24 1 CCGCACTCCC 0.995395 -139 AGGGATACTACCCCGTACTCCCCAAAATTTGA 2 123 0 CCCGACTCCC 0.995393 -40 ATACTTTGGGCAGGGATTTCCCCCAAGTTCAA 4 30 0 CGGGTTTCCC 0.974555 -205 AACAATTCACCGCGGAACTCCACTGTAGCTCA 4 111 0 CCGGACTCCA 0.99703 -124 * *** ****** Masking position 9 Map Score: 2.01129 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 158 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 ********** No masking Map Score: 1.63668e-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: 1.63668e-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 10 ********** No masking Map Score: 1.63668e-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