AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i341_tpal_bbur_100.orf -o341_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 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 0.987218 -300 TTGTGTAATGGTAGCACCGCAGATTCTGGTTC 1 26 0 GAGCACCGCG 0.985725 -275 ACGTGTCGTACTAGCCTGGGCCTCCCTCCCTG 1 59 0 CAGCCTGGGC 0.847092 -242 AGCAGATAACGAACACTCACTCAGATCAAAAA 1 102 1 GACACTCACC 0.928158 -199 CTTGACCGACGCAGACTGGCAGCTGCCATCAG 1 151 1 GAGACTGGCG 0.919794 -150 GCTGCCATCAGCAGCCCCACAGCACACGCGCA 1 172 1 GAGCCCCACG 0.982699 -129 CGATACAATTGTGCAGTCGCTCCTTCCAGTCA 1 234 1 GGCAGTCGCC 0.839922 -67 TATTGCAAAGCGCGCCTGGCTGCGATACAAGG 1 273 1 CCGCCTGGCG 0.96616 -28 TGGAAAAAACGACGCCCCACACTGAGGAAGTG 2 22 0 GCGCCCCACC 0.994341 -52 CGAGGCGCATCGCGCAAAAGCTGAA 2 59 0 GCGCATCGCC 0.993121 -15 AAGGCCTGGACAGCCCTCGCACTTGCAGTGGA 3 24 1 CGCCCTCGCC 0.985095 -51 TACGTTTCAGGCCGCACTGCCCAGATTTCCAC 3 51 0 GCGCACTGCC 0.935333 -24 AAAAAGACTCACGCGCCGCTCCCTCGATCTG 4 10 1 CCGCGCCGCC 0.988911 -95 TAGGCCTGTGCTACACCCGCACGTGGCATCGC 4 76 1 CACACCCGCC 0.975208 -29 ACACCCGCACGTGGCATCGCGCGTGGA 4 88 1 GGGCATCGCC 0.985551 -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 GGAGGGAGGCCCAGGCTAGTACGACACGTA 1 62 1 CCAGGCTAGT 0.884445 -239 GCCCCACAGCACACGCGCATTCCGGCAAAG 1 185 1 ACACGCGCAT 0.94057 -116 TGTATCGCAGCCAGGCGCGCTTTGCAATAG 1 272 0 CCAGGCGCGC 0.992789 -29 ACACGCCCGTACACTTCCTC 2 1 1 ACACGCCCGT 0.601026 -73 CGAGGCGCATCGCGCAAAAG 2 64 0 CGAGGCGCAT 0.982512 -10 CGAGGGCTGTCCAGGCCTTCTGAAGTTCAA 3 13 0 CCAGGCCTTC 0.86346 -62 ACTGCAAGTGCGAGGGCTGTCCAGGCCTTC 3 23 0 CGAGGGCTGT 0.853762 -52 AGATCGAGGGAGCGGCGCGTGAGTCTTTTT 4 11 0 AGCGGCGCGT 0.936825 -94 CGGGTGTAGCACAGGCCTATACGGAGAAAA 4 65 0 ACAGGCCTAT 0.616364 -40 TCCACGCGCGATGCCACGTGC 4 94 0 CCACGCGCGA 0.966163 -11 ********** Masking position 5 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 AGTGTGGGGCGTCGTTTTTTCCAGATTTTTCAGCTT 2 31 1 GTCTTTTCAT 0.993359 -43 ACACCACAAACTCTTTTCTTTCAGATCGAGGGAGCG 4 27 0 CTCTTCTCAT 0.982055 -78 AGTTTGTGGTGTCCTTTTCTCCGTATAGGCCTGTGC 4 51 1 GTCTTTTCAT 0.993365 -54 CTCCTTATATAATAATATTAAATATA 5 1 1 CTCTATTAAT 0.937645 -66 TGACTCAACTCTCAGTTTTTTCGTATATTTAATATT 5 24 0 CTCTTTTCAT 0.993364 -43 TGAGAGTTGAGTCAATATATTTATATGGTGC 5 46 1 GTCTATTTAT 0.938874 -21 *** *** * * ** Masking position 10 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 0.981281 -100 TCCTCAGTGTGGGGCGTCGTTTTTTCCAGATTT 2 26 1 GGGGGTCTTT 0.995372 -48 GGGAGCGGCGCGTGAGTCTTTTT 4 1 0 CGTGGTCTTT 0.982636 -104 AAAAGAGTTTGTGGTGTCCTTTTCTCCGTATAG 4 46 1 GTGGGTCTTT 0.995006 -59 AAAACTGAGAGTTGAGTCAATATATTTATATGG 5 41 1 GTTGGTCTAT 0.982486 -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