AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i005_synecho_ctra_100.orf -o005_synecho_ctra_100.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 RCY08561 119 Synechocystis #2 RCY27506 300 Synechocystis #3 RCY30833 46 Synechocystis #4 RCY01603 300 Synechocystis #5 RCY37071 155 Synechocystis Motif number 1 TAGCAAAGTTGGGCAACCTTTCCGGATTCTGGGGGTTAAC 1 39 0 GGGCTCCGTT 0.921342 -81 GGGGATTTTTGTGCCGTCGTTCCCCCGAGGTTAAAAGGTT 1 88 1 GTGCGCCCGG 0.987442 -32 CTAACTAATGGGGCCGTTGTCACCAAGCTTCCTAATAGAA 2 23 1 GGGCGACCGT 0.973912 -278 CCTTTGACTATGACCACCGCAACCCATTTGCTGAAACTTG 2 72 0 TGACGACCTG 0.768092 -229 CCCATGTATTTAGCTAAAAGTCCGTGGTATTCTGAAATGC 2 147 0 TAGCACCGGT 0.873358 -154 GCTACACTAGGGAGGAACGTTCCCATGTATTTAGCTAAAA 2 168 0 GGAGGCCCGT 0.905047 -133 TTGCATTAACTGGCGATCGCCCCCAATATGGATCCCTGGG 2 219 1 TGGCGCCCTG 0.989696 -82 GATATGGGGCAGGCGGTAGTCCCCAGGGATCCATATTGGG 2 240 0 AGGCGCCCGT 0.986607 -61 CCAGGTTTATTGACCAAAAATCCGGGTCCGAATC 3 5 0 TGACACCGTG 0.838065 -42 TATCCGTAAAAGACCTCTGCACCGCCGACGGGTCTGGATT 4 60 1 AGACGCCGGG 0.972005 -241 AATCACAGTCGAGCCAGACTACCCCTGGAGGTAAACTCCG 4 109 1 GAGCCCCCGG 0.97243 -192 CTAATCTTTATGGCTCCAGCCCCGGAGTTTACCTCCAGGG 4 131 0 TGGCGCCGGT 0.994586 -170 TCACCCTGCCGGACAGTGGGGGCGTGGTATGATCTAGAAC 4 199 0 GGACGGCGGT 0.923517 -102 AACAACTTTTTGGCATCGGTGCAGGTGGTGAGCC 4 277 1 TGGCGCAGGG 0.962755 -24 AACCACATATTAGCAGATTCGCCCCTGTCGTCTGTTCCAC 5 29 0 TAGCTCCCGG 0.917269 -127 CTGTGCTCCTTTGCCCGGCCGCCGCCGAATCAACCACATA 5 60 0 TTGCCCCGGT 0.915152 -96 AGCTGGAATAGGACCATTCGGCCGTAGTGGGAAAAAGTTA 5 123 0 GGACCCCGGG 0.98798 -33 **** * *** * * Masking position 13 Map Score: 20.8541 Number of sites scoring better than the average of aligned sites = 3336 Number in coding regions = 3159 Number in noncoding regions = 177 Number of orfs with sites within 600 bp upstream = 182 Fraction of orfs with sites within 600 bp upstream = 0.0292323 Motif number 2 ACCTCGGGGGAACGACGGCACAAAAATCCC 1 89 0 AACGACGGCA 0.958263 -31 GAAGCTTGGTGACAACGGCCCCATTAGTTA 2 24 0 GACAACGGCC 0.966674 -277 CTTTGACTATGACCACCGCAACCCATTTGC 2 81 0 GACCACCGCA 0.935674 -220 GGTGGTCATAGTCAAAGGCAGTCAAATTAG 2 94 1 GTCAAAGGCA 0.956622 -207 GATCCCTGGGGACTACCGCCTGCCCCATAT 2 249 1 GACTACCGCC 0.946894 -52 CCCCATATCTATCTAAGGCAATCTAAGGCA 2 271 1 ATCTAAGGCA 0.975232 -30 ATCTAAGGCAATCTAAGGCAATCTAAGGCA 2 281 1 ATCTAAGGCA 0.975232 -20 ATCTAAGGCAATCTAAGGCA 2 291 1 ATCTAAGGCA 0.975232 -10 TTGGAGTCTTATCCAAGGCTGTGCTCCTTT 5 88 0 ATCCAAGGCT 0.846163 -68 AACTTTTTCCCACTACGGCCGAATGGTCCT 5 124 1 CACTACGGCC 0.949845 -32 ********** Masking position 5 Map Score: 12.9364 Number of sites scoring better than the average of aligned sites = 689 Number in coding regions = 631 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 3 ATTGGCTCAACCCAAAAGTACAGTTAACCCC 1 17 1 CCCAAAGTAC 0.948659 -103 TACAGTTAACCCCCAGAATCCGGAAAGGTTG 1 35 1 CCCCAAATCC 0.993828 -85 ACAAAAATCCCCCTAAAATCCTAGCAAAGTT 1 69 0 CCCTAAATCC 0.975919 -51 GGAACGACGGCACAAAAATCCCCCTAAAATC 1 80 0 CACAAAATCC 0.944613 -40 CATGTATTTAGCTAAAAGTCCGTGGTATTCT 2 154 0 GCTAAAGTCC 0.863299 -147 GGCGGTAGTCCCCAGGGATCCATATTGGGGG 2 238 0 CCCAGGATCC 0.952152 -63 AGGTTTATTGACCAAAAATCCGGGTCCGAAT 3 12 0 ACCAAAATCC 0.956138 -35 TGTGATTATTGCCCATAATCCAGACCCGTCG 4 85 0 GCCCAAATCC 0.980018 -216 CATACCACGCCCCCACTGTCCGGCAGGGTGA 4 208 1 CCCCATGTCC 0.969004 -93 CCCACTACGGCCGAATGGTCCTATTCCAGCT 5 132 1 CCGAAGGTCC 0.937581 -24 ***** ***** Masking position 9 Map Score: 12.4876 Number of sites scoring better than the average of aligned sites = 904 Number in coding regions = 793 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 4 CTTCCTAATAGAACTGTCGCGGCAAGTTTC 2 50 1 GAACTGTCGC 0.938653 -251 AGACTTGCATTAACTGGCGATCGCCCCCAA 2 215 1 TAACTGGCGA 0.977989 -86 TGGGCAATAATCACAGTCGAGCCAGACTAC 4 101 1 TCACAGTCGA 0.966803 -200 TTAAGAAATGTAACAATCGACGTTCTAGAT 4 178 1 TAACAATCGA 0.924686 -123 CCGGCAGGGTGAACAGAGGAGACTTTCCCC 4 227 1 GAACAGAGGA 0.971149 -74 ACTGACACTGTAACAGGGGAAAGTCTCCTC 4 242 0 TAACAGGGGA 0.977331 -59 GACATTAGTGGAACAGACGACAGGGGCGAA 5 22 1 GAACAGACGA 0.98762 -134 ********** Masking position 3 Map Score: 5.55179 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 195 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 5 ACTGTACTTTTGGGTTGAGCCAATCAGCGC 1 10 0 TGGTTGAGCC 0.968801 -110 TCCGGATTCTGGGGGTTAACTGTACTTTTGG 1 28 0 GGGGTTAACT 0.955039 -92 ATGCGCCAACGGTGTTTAGCTTTTGCCCTAA 2 120 0 GGGTTTAGCT 0.992576 -181 AACGTTCCCATGTATTTAGCTAAAAGTCCGT 2 162 0 TGATTTAGCT 0.874837 -139 CTCCAGCCCCGGAGTTTACCTCCAGGGGTAG 4 127 0 GGGTTTACCT 0.974342 -174 CATCGGTGCAGGTGGTGAGCC 4 290 1 GGGGTGAGCC 0.987035 -11 ** ******** Masking position 6 Map Score: 2.67064 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 223 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 6 AGGTTGCCCAACTTTGCTAGGATTTTAGGG 1 60 1 ACTTTGCTAG 0.423653 -60 TTTTGTGCCGTCGTTCCCCCGAGGTTAAAA 1 94 1 TCGTTCCCCC 0.97031 -26 ACTAATGGGGCCGTTGTCACCAAGCTTCCT 2 26 1 CCGTTGTCAC 0.683336 -275 CGGTGTTTAGCTTTTGCCCTAATTTGACTG 2 112 0 CTTTTGCCCT 0.92437 -189 ATACATGGGAACGTTCCTCCCTAGTGTAGC 2 178 1 ACGTTCCTCC 0.920635 -123 TAATGCAAGTCTTTTCCTCGCTACACTAGG 2 197 0 CTTTTCCTCG 0.877244 -104 CCGTTCCCATATCCAGGTTT 3 37 0 CCGTTCCCAT 0.964598 -10 AAAGTCTCCTCTGTTCACCCTGCCGGACAG 4 223 0 CTGTTCACCC 0.855478 -78 AACAGAGGAGACTTTCCCCTGTTACAGTGT 4 238 1 ACTTTCCCCT 0.937075 -63 CCCCTGTCGTCTGTTCCACTAATGTCAAAT 5 18 0 CTGTTCCACT 0.789411 -138 AGGCTGTGCTCCTTTGCCCGGCCGCCGCCG 5 73 0 CCTTTGCCCG 0.970245 -83 AGGACTTAACTTTTTCCCACTACGGCCGAA 5 117 1 TTTTTCCCAC 0.748814 -39 ********** Masking position 5 Map Score: 6.81739 Number of sites scoring better than the average of aligned sites = 5740 Number in coding regions = 5155 Number in noncoding regions = 585 Number of orfs with sites within 600 bp upstream = 538 Fraction of orfs with sites within 600 bp upstream = 0.0864118 Motif number 7 GGTATTCTGAAATGCGCCAACGGTGTTTAG 2 132 0 AATGCGCCAA 0.979145 -169 AATGCTCCAATCGCCTTGAT 4 1 1 AATGCTCCAA 0.990799 -300 CCTAATCTTTATGGCTCCAGCCCCGGAGTT 4 142 0 ATGGCTCCAG 0.938247 -159 AGCCTTGGATAAGACTCCAAGGACTTAACT 5 98 1 AAGACTCCAA 0.957156 -58 ACTACGGCCGAATGGTCCTATTCCAGCTAC 5 135 1 AATGGTCCTA 0.90318 -21 ********** Masking position 1 Map Score: 0.534117 Number of sites scoring better than the average of aligned sites = 338 Number in coding regions = 300 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 8 ********** No masking Map Score: -1.02785e-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: -1.02785e-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: -1.02785e-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