AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i142_synecho_ctra_300.orf -o142_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 RCY15025 300 Synechocystis #2 RCY37398 88 Synechocystis Motif number 1 CGGAGCTTTGGGGGAATAGTCTGCTACCAG 1 29 1 GGGGAATAGT 0.969223 -272 AGGATTAGGGAGGGATTAGCAACAGAAAAC 1 70 1 AGGGATTAGC 0.983674 -231 TCGCTGATAAAGGGGATTTCTACCCCTGCA 1 109 0 AGGGGATTTC 0.980777 -192 ACCCCGCTCTGGAGAATTGCTTTACCCTGT 1 236 1 GGAGAATTGC 0.983261 -65 TTTACCCTGTAGGGGATTGTAATTTTTGTT 1 256 1 AGGGGATTGT 0.991107 -45 TCCGAGAGATAGAGGTTTGCT 1 290 1 AGAGGTTTGC 0.983531 -11 ********** Masking position 7 Map Score: 7.17282 Number of sites scoring better than the average of aligned sites = 960 Number in coding regions = 858 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 2 AATAGTCTGCTACCAGTTTTGAGAACCAGGA 1 43 1 TACAGTTTTG 0.96855 -258 CCTGTTTTTATGATAAATTTGTTCTATGGCA 1 149 0 TGTAAATTTG 0.952474 -152 CAGAGTTCTTTAACAATCTTGCCGTCTCCTT 1 185 0 TACAATCTTG 0.919527 -116 TAAAGAACTCTGAAGAATTTGGCTGGAGCTT 1 204 1 TGAGAATTTG 0.915783 -97 TGTAGGGGATTGTAATTTTTGTTGTTTTCCG 1 263 1 TGAATTTTTG 0.933247 -38 GAGTCGTACTGGTCAGTTTTGCTTTAAAACC 2 33 1 GGCAGTTTTG 0.97202 -56 CTGTAAATTTTGACAAATTTGGTAGAAAACT 2 64 1 TGCAAATTTG 0.990529 -25 ** ******** Masking position 9 Map Score: 2.97923 Number of sites scoring better than the average of aligned sites = 1248 Number in coding regions = 1094 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 166 Fraction of orfs with sites within 600 bp upstream = 0.0266624 Motif number 3 GCAGACTATTCCCCCAAAGCTCCGTGCGATAATG 1 19 0 CCCCCAGCCG 0.999136 -282 TTGCTAATCCCTCCCTAATCCTGGTTCTCAAAAC 1 58 0 CTCCCATCGG 0.991327 -243 GGGATTTCTACCCCTGCAGCAACGAATGTTTTCT 1 93 0 CCCCTAGCCG 0.998646 -208 GGGTAGAAATCCCCTTTATCAGCGAAGACAATGA 1 114 1 CCCCTATCCG 0.997735 -187 GTAAAGCAATTCTCCAGAGCGGGGTCAAGCTCCA 1 227 0 TCTCCAGCGG 0.969329 -74 AGCAAACCTCTATCTCTCGGAAAACAACAA 1 281 0 CCTCTCTCGG 0.981227 -20 ***** *** ** Masking position 10 Map Score: 7.5322 Number of sites scoring better than the average of aligned sites = 409 Number in coding regions = 362 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 4 GCTCCGTGCGATAATGGGTAACTG 1 5 0 ATAATGGGTA 0.863551 -296 ACATTCGTTGCTGCAGGGGTAGAAATCCCC 1 98 1 CTGCAGGGGT 0.984588 -203 GTCTTCGCTGATAAAGGGGATTTCTACCCC 1 113 0 ATAAAGGGGA 0.955091 -188 CAGCCAAATTCTTCAGAGTTCTTTAACAAT 1 199 0 CTTCAGAGTT 0.889419 -102 TTACAATCCCCTACAGGGTAAAGCAATTCT 1 248 0 CTACAGGGTA 0.994188 -53 TTGTCAAAATTTACAGGGTTTTAAAGCAAA 2 50 0 TTACAGGGTT 0.977299 -39 ********** Masking position 2 Map Score: 3.27209 Number of sites scoring better than the average of aligned sites = 508 Number in coding regions = 442 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 5 GGGGGAATAGTCTGCTACCAGTTTTGAGAA 1 38 1 TCTGCTACCA 0.983116 -263 TTCTACCCCTGCAGCAACGAATGTTTTCTG 1 92 0 GCAGCAACGA 0.941956 -209 GCGGGGTCAAGCTCCAGCCAAATTCTTCAG 1 213 0 GCTCCAGCCA 0.98833 -88 AAGGTTAGGTGTTCCAACCAAA 2 3 0 GTTCCAACCA 0.988157 -86 AAAAAGTTTTCTACCAAATTTGTCAA 2 73 0 TTTTCTACCA 0.904534 -16 ********** Masking position 10 Map Score: 0.887261 Number of sites scoring better than the average of aligned sites = 531 Number in coding regions = 477 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 6 AACGAATGTTTTCTGTTGCTAATCCCTCCC 1 77 0 TTCTGTTGCT 0.96941 -224 TAAAGGGGATTTCTACCCCTGCAGCAACGA 1 102 0 TTCTACCCCT 0.973032 -199 GATAAATTTGTTCTATGGCAATCATTGTCT 1 139 0 TTCTATGGCA 0.960291 -162 TGCCGTCTCCTTCTGTGCCTGTTTTTATGA 1 167 0 TTCTGTGCCT 0.988566 -134 AGCAAACCTCTATCTCTCGGAAAACAA 1 284 0 CTCTATCTCT 0.929717 -17 ********** Masking position 4 Map Score: 0.676645 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 165 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 7 ********** No masking Map Score: 7.84029e-13 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: 7.84029e-13 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: 7.84029e-13 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