AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i288_synecho_ctra_300.orf -o288_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 RCY23271 201 Synechocystis #2 RCY11277 49 Synechocystis #3 RCY18066 196 Synechocystis Motif number 1 GTCCGAGAAAATCTTTGGAAAAGCGTCGTACC 1 30 1 ATCTTTGGAA 0.931592 -172 AAAGCGTCGTACCATTGAAAAATCTATCGGAA 1 49 1 ACCATTGAAA 0.984513 -153 AGACTGACTGCCCAGGGAAAAATTCACTTTCA 1 125 0 CCCAGGGAAA 0.917608 -77 GGTTGAGTATATCATGGGCATATAAGACGTTT 1 180 1 ATCATGGGAA 0.973306 -22 CTAGTTCTCGACCAGTGGAGCAGATATT 2 7 0 ACCAGTGGGA 0.98412 -43 CCATTGGTTCACCATTGATGGATAAAAAGCAG 3 72 0 ACCATTGAGA 0.972612 -125 TCAATGGTGAACCAATGGGATTCGCAAATACA 3 86 1 ACCAATGGAT 0.877906 -111 ATACACAGTCACCTTGGGCACATCGGGTGAGG 3 113 1 ACCTTGGGAA 0.983153 -84 ******** * * Masking position 7 Map Score: 6.72989 Number of sites scoring better than the average of aligned sites = 1567 Number in coding regions = 1413 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 2 TTGGTCTTTAACCTAGTCCGAGAAAATCTT 1 15 1 ACCTAGTCCG 0.986582 -187 CTCTATCACACCCTAGACTGACTGCCCAGG 1 141 0 CCCTAGACTG 0.992079 -61 GCCCATGATATACTCAACCGCCTTTTCTCT 1 169 0 TACTCAACCG 0.874358 -33 ACTGGTCGAGAACTAGACTGTCCCCAATCA 2 23 1 AACTAGACTG 0.975518 -27 CTTTTACTGTACCTCACCCGATGTGCCCAA 3 126 0 ACCTCACCCG 0.982511 -71 ATCCAAATCCCCCTAGCCTGCGGCGCTATG 3 169 1 CCCTAGCCTG 0.992782 -28 ********** Masking position 4 Map Score: 5.76789 Number of sites scoring better than the average of aligned sites = 414 Number in coding regions = 356 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 3 ACGCTTTTCCAAAGATTTTCTCGGACTAGG 1 26 0 AAAGATTTTC 0.938143 -176 TCAATGGTACGACGCTTTTCCAAAGATTTT 1 37 0 GACGCTTTTC 0.894637 -165 GAAGTTTTGTGAAAATTCTCCTTTGCAAAG 1 84 0 GAAAATTCTC 0.742477 -118 GAATTTTCACAAAACTTCTTGACCGGGGTT 1 96 1 AAAACTTCTT 0.818258 -106 CTGCCCAGGGAAAAATTCACTTTCAACCCC 1 120 0 AAAAATTCAC 0.88998 -82 TTGAGTAAAGAAAGTTTTACCCACAAAGTT 3 12 1 AAAGTTTTAC 0.902323 -185 TTTTACCCACAAAGTTTCTGGTAAATTGAT 3 26 1 AAAGTTTCTG 0.885038 -171 TTGATTGCCAAAAGCTTTTCCCTGCTTTTT 3 51 1 AAAGCTTTTC 0.981309 -146 ********** Masking position 2 Map Score: 4.9048 Number of sites scoring better than the average of aligned sites = 898 Number in coding regions = 722 Number in noncoding regions = 176 Number of orfs with sites within 600 bp upstream = 183 Fraction of orfs with sites within 600 bp upstream = 0.0293929 Motif number 4 AAACTTGGTCTTTAACCTAGTCCGAGA 1 8 1 GTCTTTAACC 0.789541 -194 GCTTTTCCAAAGATTTTCTCGGACTAGGTT 1 24 0 AGATTTTCTC 0.912718 -178 GTTGAAAGTGAATTTTTCCCTGGGCAGTCA 1 123 1 AATTTTTCCC 0.928328 -79 ATACTCAACCGCCTTTTCTCTCTATCACAC 1 160 0 GCCTTTTCTC 0.965467 -42 GAGTAAAGAAAGTTTTACCCACAAAGTTTC 3 14 1 AGTTTTACCC 0.961026 -183 GATTGCCAAAAGCTTTTCCCTGCTTTTTAT 3 53 1 AGCTTTTCCC 0.992888 -144 GCTTTTCCCTGCTTTTTATCCATCAATGGT 3 64 1 GCTTTTTATC 0.841046 -133 ACAAATTAACAGCTTTTACTGTACCTCACC 3 138 0 AGCTTTTACT 0.85903 -59 ********** Masking position 5 Map Score: 4.72793 Number of sites scoring better than the average of aligned sites = 2848 Number in coding regions = 2471 Number in noncoding regions = 377 Number of orfs with sites within 600 bp upstream = 388 Fraction of orfs with sites within 600 bp upstream = 0.0623193 Motif number 5 ATCTATCGGAATTCCTTTGCAAAGGAGAATTT 1 70 1 ATTCCTTCAA 0.945743 -132 CCAGGGAAAAATTCACTTTCAACCCCGGTCAA 1 114 0 ATTCACTCAA 0.960992 -88 CACACCCTAGACTGACTGCCCAGGGAAAAATT 1 133 0 ACTGACTCCA 0.953773 -69 TTTCTGGTAAATTGATTGCCAAAAGCTTTTCC 3 40 1 ATTGATTCAA 0.977419 -157 TGCGAATCCCATTGGTTCACCATTGATGGATA 3 80 0 ATTGGTTCCA 0.986573 -117 AAAGCTGTTAATTTGTTATCCAAATCCCCCTA 3 152 1 ATTTGTTCCA 0.948699 -45 ******* *** Masking position 7 Map Score: 1.1167 Number of sites scoring better than the average of aligned sites = 320 Number in coding regions = 285 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 6 ********** No masking Map Score: -3.81261e-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 7 ********** No masking Map Score: -3.81261e-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: -3.81261e-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