AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i341_tpal_bbur_300.orf -o341_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 RTP00846 300 AE000520 #2 RTP00843 73 AE000520 #3 RTP00621 74 AE000520 #4 RTP00622 104 AE000520 #5 RBB00024 66 3615 Motif number 1 GAACCCCCACACACAGAACCAG 1 1 1 GACCCCCACC 0.985759 -300 TTGTGTAATGGTAGCACCGCAGATTCTGGTTC 1 26 0 GAGCACCGCG 0.984102 -275 ACGTGTCGTACTAGCCTGGGCCTCCCTCCCTG 1 59 0 CAGCCTGGGC 0.832354 -242 AGCAGATAACGAACACTCACTCAGATCAAAAA 1 102 1 GACACTCACC 0.920495 -199 CTTGACCGACGCAGACTGGCAGCTGCCATCAG 1 151 1 GAGACTGGCG 0.911326 -150 GCTGCCATCAGCAGCCCCACAGCACACGCGCA 1 172 1 GAGCCCCACG 0.980732 -129 CGATACAATTGTGCAGTCGCTCCTTCCAGTCA 1 234 1 GGCAGTCGCC 0.836202 -67 TATTGCAAAGCGCGCCTGGCTGCGATACAAGG 1 273 1 CCGCCTGGCG 0.962414 -28 TGGAAAAAACGACGCCCCACACTGAGGAAGTG 2 22 0 GCGCCCCACC 0.993689 -52 CGAGGCGCATCGCGCAAAAGCTGAA 2 59 0 GCGCATCGCC 0.9924 -15 AAGGCCTGGACAGCCCTCGCACTTGCAGTGGA 3 24 1 CGCCCTCGCC 0.98408 -51 TACGTTTCAGGCCGCACTGCCCAGATTTCCAC 3 51 0 GCGCACTGCC 0.929111 -24 AAAAAGACTCACGCGCCGCTCCCTCGATCTG 4 10 1 CCGCGCCGCC 0.987672 -95 TAGGCCTGTGCTACACCCGCACGTGGCATCGC 4 76 1 CACACCCGCC 0.972416 -29 ACACCCGCACGTGGCATCGCGCGTGGA 4 88 1 GGGCATCGCC 0.984734 -17 * ******** * Masking position 10 Map Score: 24.9071 Number of sites scoring better than the average of aligned sites = 1931 Number in coding regions = 581 Number in noncoding regions = 1350 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 2 TACGTGTCGTACTAGCCTGGGCCTCCCTCC 1 62 0 ACTAGCCTGG 0.884421 -239 CTTTGCCGGAATGCGCGTGTGCTGTGGGGC 1 185 0 ATGCGCGTGT 0.940566 -116 CTATTGCAAAGCGCGCCTGGCTGCGATACA 1 272 1 GCGCGCCTGG 0.992789 -29 GAGGAAGTGTACGGGCGTGT 2 1 0 ACGGGCGTGT 0.601044 -73 CTTTTGCGCGATGCGCCTCG 2 64 1 ATGCGCCTCG 0.982508 -10 TTGAACTTCAGAAGGCCTGGACAGCCCTCG 3 13 1 GAAGGCCTGG 0.863434 -62 GAAGGCCTGGACAGCCCTCGCACTTGCAGT 3 23 1 ACAGCCCTCG 0.853733 -52 AAAAAGACTCACGCGCCGCTCCCTCGATCT 4 11 1 ACGCGCCGCT 0.936811 -94 TTTTCTCCGTATAGGCCTGTGCTACACCCG 4 65 1 ATAGGCCTGT 0.616379 -40 GCACGTGGCATCGCGCGTGGA 4 94 1 TCGCGCGTGG 0.966157 -11 ********** Masking position 6 Map Score: 10.0399 Number of sites scoring better than the average of aligned sites = 977 Number in coding regions = 285 Number in noncoding regions = 692 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 3 TCTGGTTCTGTGTGTGGGGGTTC 1 4 0 TGTGTGGGGG 0.955564 -297 CCTCCCTGGTTGTGTAATGGTAGCACCGCA 1 37 0 TGTGTAATGG 0.938644 -264 GGAATGCGCGTGTGCTGTGGGGCTGCTGAT 1 178 0 TGTGCTGTGG 0.987939 -123 GTATCGGCAATGTGCAGTTGTGTGTCTTTG 1 210 0 TGTGCAGTTG 0.990794 -91 CCGATACAATTGTGCAGTCGCTCCTTCCAG 1 233 1 TGTGCAGTCG 0.989067 -68 CCAGGCGCGCTTTGCAATAGCGCTACTGAC 1 262 0 TTTGCAATAG 0.70297 -39 AGCCCTCGCACTTGCAGTGGAAATCTGGGC 3 35 1 CTTGCAGTGG 0.974343 -40 AGTGGAAATCTGGGCAGTGCGGCCTGAAAC 3 50 1 TGGGCAGTGC 0.930526 -25 CGCGATGCCACGTGCGGGTGTAGCACAGGC 4 79 0 CGTGCGGGTG 0.93574 -26 ********** Masking position 4 Map Score: 9.31853 Number of sites scoring better than the average of aligned sites = 1021 Number in coding regions = 296 Number in noncoding regions = 725 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 4 AAGCTGAAAAATCTGGAAAAAACGACGCCCCACACT 2 31 0 ATGAAAAGAC 0.992415 -43 CGCTCCCTCGATCTGAAAGAAAAGAGTTTGTGGTGT 4 27 1 ATGAGAAGAG 0.979535 -78 GCACAGGCCTATACGGAGAAAAGGACACCACAAACT 4 51 0 ATGAAAAGAC 0.99242 -54 TATATTTAATATTATTATATAAGGAG 5 1 0 ATTAATAGAG 0.929663 -66 AATATTAAATATACGAAAAAACTGAGAGTTGAGTCA 5 24 1 ATGAAAAGAG 0.99242 -43 GCACCATATAAATATATTGACTCAACTCTCA 5 46 0 ATAAATAGAC 0.930729 -21 ** * * *** *** Masking position 7 Map Score: 2.68305 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 9 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 5 GCAATGTGCAGTTGTGTGTCTTTGCCGGAATGC 1 201 0 GTTGGTGTTT 0.979441 -100 TCCTCAGTGTGGGGCGTCGTTTTTTCCAGATTT 2 26 1 GGGGGTCTTT 0.99491 -48 GGGAGCGGCGCGTGAGTCTTTTT 4 1 0 CGTGGTCTTT 0.980926 -104 AAAAGAGTTTGTGGTGTCCTTTTCTCCGTATAG 4 46 1 GTGGGTCTTT 0.994508 -59 AAAACTGAGAGTTGAGTCAATATATTTATATGG 5 41 1 GTTGGTCTAT 0.980762 -26 **** *** *** Masking position 7 Map Score: 2.44568 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 7 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 6 ********** No masking Map Score: 2.93755e-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: 2.93755e-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: 2.93755e-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