AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i142_synecho_ctra_100.orf -o142_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 RCY15025 300 Synechocystis #2 RCY37398 88 Synechocystis Motif number 1 CGGAGCTTTGGGGGAATAGTCTGCTACCAG 1 29 1 GGGGAATAGT 0.964765 -272 AGGATTAGGGAGGGATTAGCAACAGAAAAC 1 70 1 AGGGATTAGC 0.981268 -231 TCGCTGATAAAGGGGATTTCTACCCCTGCA 1 109 0 AGGGGATTTC 0.977955 -192 ACCCCGCTCTGGAGAATTGCTTTACCCTGT 1 236 1 GGAGAATTGC 0.980797 -65 TTTACCCTGTAGGGGATTGTAATTTTTGTT 1 256 1 AGGGGATTGT 0.989785 -45 TCCGAGAGATAGAGGTTTGCT 1 290 1 AGAGGTTTGC 0.981106 -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 TCCTGGTTCTCAAAACTGGTAGCAGACTATT 1 43 0 CAAAACTGTA 0.964938 -258 TGCCATAGAACAAATTTATCATAAAAACAGG 1 149 1 CAAATTTACA 0.947116 -152 AAGGAGACGGCAAGATTGTTAAAGAACTCTG 1 185 1 CAAGATTGTA 0.910808 -116 AAGCTCCAGCCAAATTCTTCAGAGTTCTTTA 1 204 0 CAAATTCTCA 0.906692 -97 CGGAAAACAACAAAAATTACAATCCCCTACA 1 263 0 CAAAAATTCA 0.925894 -38 GGTTTTAAAGCAAAACTGACCAGTACGACTC 2 33 0 CAAAACTGCC 0.968793 -56 AGTTTTCTACCAAATTTGTCAAAATTTACAG 2 64 0 CAAATTTGCA 0.989413 -25 ******** ** Masking position 3 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 0.99899 -282 TTGCTAATCCCTCCCTAATCCTGGTTCTCAAAAC 1 58 0 CTCCCATCGG 0.989867 -243 GGGATTTCTACCCCTGCAGCAACGAATGTTTTCT 1 93 0 CCCCTAGCCG 0.998416 -208 GGGTAGAAATCCCCTTTATCAGCGAAGACAATGA 1 114 1 CCCCTATCCG 0.997395 -187 GTAAAGCAATTCTCCAGAGCGGGGTCAAGCTCCA 1 227 0 TCTCCAGCGG 0.96871 -74 AGCAAACCTCTATCTCTCGGAAAACAACAA 1 281 0 CCTCTCTCGG 0.978674 -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 0.852404 -296 ACATTCGTTGCTGCAGGGGTAGAAATCCCC 1 98 1 CTGCAGGGGT 0.983136 -203 GTCTTCGCTGATAAAGGGGATTTCTACCCC 1 113 0 ATAAAGGGGA 0.950998 -188 CAGCCAAATTCTTCAGAGTTCTTTAACAAT 1 199 0 CTTCAGAGTT 0.880093 -102 TTACAATCCCCTACAGGGTAAAGCAATTCT 1 248 0 CTACAGGGTA 0.993634 -53 TTGTCAAAATTTACAGGGTTTTAAAGCAAA 2 50 0 TTACAGGGTT 0.975178 -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 TTCTCAAAACTGGTAGCAGACTATTCCCCC 1 38 0 TGGTAGCAGA 0.98135 -263 CAGAAAACATTCGTTGCTGCAGGGGTAGAA 1 92 1 TCGTTGCTGC 0.936163 -209 CTGAAGAATTTGGCTGGAGCTTGACCCCGC 1 213 1 TGGCTGGAGC 0.987101 -88 TTTGGTTGGAACACCTAACCTT 2 3 1 TGGTTGGAAC 0.986911 -86 TTGACAAATTTGGTAGAAAACTTTTT 2 73 1 TGGTAGAAAA 0.89542 -16 ********** Masking position 1 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 GGGAGGGATTAGCAACAGAAAACATTCGTT 1 77 1 AGCAACAGAA 0.967408 -224 TCGTTGCTGCAGGGGTAGAAATCCCCTTTA 1 102 1 AGGGGTAGAA 0.971258 -199 AGACAATGATTGCCATAGAACAAATTTATC 1 139 1 TGCCATAGAA 0.957748 -162 TCATAAAAACAGGCACAGAAGGAGACGGCA 1 167 1 AGGCACAGAA 0.987802 -134 TTGTTTTCCGAGAGATAGAGGTTTGCT 1 284 1 AGAGATAGAG 0.925314 -17 ********** Masking position 7 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