AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i047_tpal_bbur_100.orf -o047_tpal_bbur_100.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/synecho.fna -g0.40 -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 = 0.4 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTP00396 118 AE000520 #2 RTP01065 39 AE000520 #3 RTP00398 40 AE000520 #4 RTP00833 104 AE000520 #5 RTP01019 170 AE000520 Motif number 1 CGACGTGCCACTTGAGCTAACAGCTCAACA 1 44 1 CTTGAGCTAA 0.80269 -75 TTTTGCAGGAGGCGCGCGGCTACGATGTTG 1 69 0 GGCGCGCGGC 0.651232 -50 TGTTCCTCCTCCTGCGCGGTGTTCGTTGCT 1 98 0 CCTGCGCGGT 0.929926 -21 GTTGATCTTGCGCGCGCGGTCTGTCGTGT 2 10 0 CGCGCGCGGT 0.987769 -30 CGGTTCAGCACTGGCGCAGCTGGC 3 5 0 CTGGCGCAGC 0.918803 -36 GGGGTTTGAGCGCGAGCGGCTTTGGGGCTG 4 13 0 CGCGAGCGGC 0.99417 -92 AGCGGCACTTCTTGCGCAGTGGTTTTTGTA 4 47 0 CTTGCGCAGT 0.948937 -58 GGGGTTATTCCCCGCGTCGAGTATTC 4 89 1 CCCGCGTCGA 0.953312 -16 GCTCGCGCGGACCTGCTGTGG 5 2 1 CTCGCGCGGA 0.930974 -169 CATAACCACGCTCGAGCTGAATGCCAATTG 5 44 1 CTCGAGCTGA 0.977075 -127 ATGCCAATTGCCTGAGCGGAAAAAGCATGA 5 64 1 CCTGAGCGGA 0.993308 -107 CCGCCCCATACCGGAGCGAATTGACGGCTT 5 97 1 CCGGAGCGAA 0.967601 -74 TGGCGCCGGGCTTGAGTGGCTCTACAATGT 5 138 0 CTTGAGTGGC 0.933758 -33 CCACTCAAGCCCGGCGCCAAAAAGAAAATA 5 149 1 CCGGCGCCAA 0.90785 -22 ********** Masking position 6 Map Score: 32.2716 Number of sites scoring better than the average of aligned sites = 597 Number in coding regions = 189 Number in noncoding regions = 408 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 2 CGTCTCCATATGGACGTGCAGGTGAAAGTCGTTC 1 12 0 TGGCTGCGGG 0.989573 -107 AGGAGGCGCGCGGCTACGATGTTGAGCTGTTAGC 1 59 0 CGGTCGAGTG 0.986141 -60 CGGTGTTCGTTGCTTTTGCAGGAGGCGCGCGGCT 1 78 0 TGCTTGCGGG 0.959139 -41 GCAACGAACACCGCGCAGGAGGAGGAACAA 1 99 1 CCGGAGGGGG 0.912999 -20 TGGTTTTGATGTTGATCTTGCGCG 2 26 0 TGGTTGAGTG 0.98867 -14 CCACTTATATCGGTTCAGCACTGGCGCAGCTGGC 3 11 0 CGGTAGCCTG 0.962038 -30 TGAGCGCGAGCGGCTTTGGGGCTGTG 4 3 0 CGGTTGGGCG 0.98849 -102 TTTGTACCAGGGGGTTTGAGCGCGAGCGGCTTTG 4 19 0 GGGTTGACGG 0.946242 -86 GCTCGCGCGGACCTGCTGTGGACCCATCCCC 5 8 1 CGGCTGCGTG 0.99124 -163 AGCTCGAGCGTGGTTATGAAGGGGATGGGTCCAC 5 28 0 TGGTTGAGGG 0.992865 -143 TCAATTCGCTCCGGTATGGGGCGGCGTTCATGCT 5 87 0 CCGTTGGGCG 0.97273 -84 ATTTTCTTTTTGGCGCCGGGCTTGAGTGGCTCTA 5 144 0 TGGGCGGCTG 0.898671 -27 *** * *** ** * Masking position 8 Map Score: 16.5465 Number of sites scoring better than the average of aligned sites = 3222 Number in coding regions = 931 Number in noncoding regions = 2291 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 3 TGGAGACGACGTGCCACTTGAGCTAACAGC 1 38 1 GTGCCACTTG 0.988588 -81 TCGTAGCCGCGCGCCTCCTGCAAAAGCAAC 1 74 1 GCGCCTCCTG 0.98731 -45 TTGTTCCTCCTCCTGCGCGGTG 1 107 0 GTTCCTCCTC 0.90882 -12 AACACCCCACTTATATCGGTTCA 3 28 0 ACCCCACTTA 0.850838 -13 TCGGCAAATAGCGGCACTTCTTGCGCAGTG 4 56 0 GCGGCACTTC 0.984576 -49 GCGGGGAATAACCCCTCTTCGGCAAATAGC 4 74 0 ACCCCTCTTC 0.967498 -31 CTCGAGCTGAATGCCAATTGCCTGAGCGGA 5 54 1 ATGCCAATTG 0.790848 -117 CCGGGCTTGAGTGGCTCTACAATGTGGGGT 5 133 0 GTGGCTCTAC 0.878037 -38 ********** Masking position 5 Map Score: 4.9546 Number of sites scoring better than the average of aligned sites = 1045 Number in coding regions = 323 Number in noncoding regions = 722 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 4 ACGTGCAGGTGAAAGTCGTTCA 1 3 0 GAAAGTCGTT 0.88083 -116 AGCTCAAGTGGCACGTCGTCTCCATATGGA 1 32 0 GCACGTCGTC 0.988208 -87 GCTAACAGCTCAACATCGTAGCCGCGCGCC 1 59 1 CAACATCGTA 0.414753 -60 CATCGTAGCCGCGCGCCTCCTGCAAAAGCA 1 72 1 GCGCGCCTCC 0.937543 -47 CAAAAGCAACGAACACCGCGCAGGAGGAGG 1 94 1 GAACACCGCG 0.89436 -25 TTGATCTTGCGCGCGCGGTCTGTCGTGT 2 9 0 GCGCGCGGTC 0.959588 -31 CACAGCCCCAAAGCCGCTCGCGCTCAAA 4 9 1 CAAAGCCGCT 0.900534 -96 CATTCAGCTCGAGCGTGGTTATGAAGGGGA 5 37 0 GAGCGTGGTT 0.834321 -134 GAAAAAGCATGAACGCCGCCCCATACCGGA 5 82 1 GAACGCCGCC 0.995479 -89 TGGGGTCTATCAAAGCCGTCAATTCGCTCC 5 109 0 CAAAGCCGTC 0.953279 -62 AGCCACTCAAGCCCGGCGCCAAAAAGAAAA 5 147 1 GCCCGGCGCC 0.931834 -24 ********** Masking position 8 Map Score: 9.76623 Number of sites scoring better than the average of aligned sites = 3848 Number in coding regions = 1128 Number in noncoding regions = 2720 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 5 ********** No masking Map Score: 9.53751e-15 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 6 ********** No masking Map Score: 9.53751e-15 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: 9.53751e-15 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