AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i152_tpal_bbur_300.orf -o152_tpal_bbur_300.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 RTP00395 300 AE000520 #2 RTP00396 118 AE000520 #3 RTP01065 39 AE000520 #4 RTP00398 40 AE000520 Motif number 1 CCGACGCGCCAGTCACTCCT 1 1 1 CCGACGCGCC 0.990851 -300 TCACTCCTCCCCCCTGCTCCACCGCGCGCA 1 23 1 CCCCTGCTCC 0.993472 -278 CCCCTGCTCCACCGCGCGCAAAGACAACAC 1 33 1 ACCGCGCGCA 0.975592 -268 GCGCAAAGACAACACGCTCAAAAGCGGTTG 1 48 1 AACACGCTCA 0.576575 -253 GCGGTTGGTACACCCCCGCCAGCAGCAATA 1 71 1 CACCCCCGCC 0.984044 -230 AGCATTGCCGCCGCCGCTAGCGCCCCTGCG 1 127 1 CCGCCGCTAG 0.890922 -174 GCCGCTAGCGCCCCTGCGCACACGGTCGCC 1 139 1 CCCCTGCGCA 0.996139 -162 TACTACTGCACACACGCGCGGATTTGTGGC 1 166 0 CACACGCGCG 0.973592 -135 TCTGCGACCGCCCCTGCGTCTGTTCAGACT 1 207 0 CCCCTGCGTC 0.990603 -94 CGTGACGCATCCTCTGCGACCGCCCCTGCG 1 219 0 CCTCTGCGAC 0.874924 -82 GAGGATGCGTCACGCGCGTGCTGCATGCGA 1 235 1 CACGCGCGTG 0.499634 -66 GAACGACTTTCACCTGCACGTCCATATGGA 2 12 1 CACCTGCACG 0.956164 -107 CAACATCGTAGCCGCGCGCCTCCTGCAAAA 2 69 1 GCCGCGCGCC 0.962945 -50 TTGTTCCTCCTCCTGCGCGGTGTTCGTTG 2 100 0 CTCCTGCGCG 0.985413 -19 ACACGACAGACCGCGCGCGCAAGATCAAC 3 10 1 ACCGCGCGCG 0.984785 -30 GCCAGCTGCGCCAGTGCTGAAC 4 3 1 CAGCTGCGCC 0.990167 -38 ********** Masking position 7 Map Score: 36.4393 Number of sites scoring better than the average of aligned sites = 1023 Number in coding regions = 279 Number in noncoding regions = 744 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 2 GGTACACCCCCGCCAGCAGCAATACCAATGA 1 77 1 CGCAGCAGCA 0.884128 -224 GGGGCGCTAGCGGCGGCGGCAATGCTCACGC 1 122 0 CGCGGCGGCA 0.990778 -179 ACCGTGTGCGCAGGGGCGCTAGCGGCGGCGG 1 134 0 CAGGGCGCTA 0.987205 -167 CCCCTGCGCACACGGTCGCCACAAATCCGCG 1 149 1 CAGGTCGCCA 0.980706 -152 TCTGTTCAGACTACGGCGGTCCTTACTACTG 1 188 0 CTCGGCGGTC 0.961181 -113 TGAACAGACGCAGGGGCGGTCGCAGAGGATG 1 211 1 CAGGGCGGTC 0.987826 -90 ATGCGTCACGCGCGTGCTGCATGCGAGAAAA 1 239 1 CGGTGCTGCA 0.971427 -62 TCAAGTGGCACGTCGTCTCCATATGGACGTG 2 28 0 CGCGTCTCCA 0.970556 -91 ATCTTGCGCGCGCGGTCTGTCGTGT 3 5 0 CGGGTCTGTC 0.936714 -35 GCCAGCTGCGCCAGTGCTGAACC 4 3 1 CACTGCGCCA 0.972724 -38 ** ******** Masking position 7 Map Score: 14.7857 Number of sites scoring better than the average of aligned sites = 1863 Number in coding regions = 544 Number in noncoding regions = 1319 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 3 GGAGCAGGGGGGAGGAGTGACTGGCGCGTCG 1 12 0 GGAGAGTGAC 0.917431 -289 CTTTGCGCGCGGTGGAGCAGGGGGGAGGAGT 1 25 0 GGTGAGCAGG 0.881265 -276 TGCTGGCGGGGGTGTACCAACCGCTTTTGAG 1 64 0 GGTGACCAAC 0.971273 -237 CCCGCCAGCAGCAATACCAATGAACCGGAAA 1 85 1 GCAAACCAAT 0.908552 -216 GCGCGTGTGTGCAGTAGTAAGGACCGCCGTA 1 177 1 GCAGAGTAAG 0.975674 -124 ACAAACCCAAGCAGCACAAAGAAAATAA 1 283 1 GCAGACAAAG 0.964475 -18 ATATGGACGTGCAGGTGAAAGTCGTTCA 2 8 0 GCAGTGAAAG 0.835962 -111 CGCGCCTCCTGCAAAAGCAACGAACACCGCG 2 83 1 GCAAAGCAAC 0.9817 -36 ACACCGCGCAGGAGGAGGAACAA 2 106 1 GGAGAGGAAC 0.960524 -13 GACCGCGCGCGCAAGATCAACATCAAAACCA 3 19 1 GCAAATCAAC 0.874423 -21 CTGCGCCAGTGCTGAACCGATATAAGTGGGG 4 16 1 GCTGACCGAT 0.859768 -25 **** ****** Masking position 1 Map Score: 7.70082 Number of sites scoring better than the average of aligned sites = 1308 Number in coding regions = 389 Number in noncoding regions = 919 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 4 CCGGTTCATTGGTATTGCTGCTGGCGGGGGT 1 82 0 GGATTGCTGC 0.968737 -219 ACACACGCGCGGATTTGTGGCGACCGTGTGC 1 156 0 GGTTTGTGGC 0.994393 -145 TGTGCTGCTTGGGTTTGTGGCAGTGTGTGCG 1 270 0 GGTTTGTGGC 0.994398 -31 GGAGGCGCGCGGCTACGATGTTGAGCTGTTA 2 61 0 GGTACGATGT 0.911718 -58 CTCCTGCGCGGTGTTCGTTGCTTTTGCAGGA 2 89 0 GTTTCGTTGC 0.964866 -30 TGGTTTTGATGTTGATCTTGCG 3 28 0 GGTTTGATGT 0.98058 -12 ** ******** Masking position 7 Map Score: 4.54626 Number of sites scoring better than the average of aligned sites = 588 Number in coding regions = 182 Number in noncoding regions = 406 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 ********** No masking Map Score: 4.35863e-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 6 ********** No masking Map Score: 4.35863e-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: 4.35863e-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