AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -ifis_tpal_opreg_100.orf -g0.528 -x5 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 = 0.528 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 TP0410 264 protein-export membrane protein (secD) #2 TP1008 126 ribonucleoside-diphosphate reductase, subunit alpha (nrdA) Motif number 1 CCTGTCGTTACTATCGGCGGTATCCACGGGGT 1 66 1 CTATCGGGGA 0.983689 -199 CGGCGGTATCCACGGGGTGGTAAGCGTGGTGC 1 80 1 CACGGGGGGA 0.986401 -185 GGGTGGTAAGCGTGGTGCGGGAGCACAGCCTT 1 94 1 CGTGGTGGGA 0.972138 -171 GAGCATGGCACGCTCGAAGTCAGCCGCAGTGC 1 141 1 CGCTCGAGTA 0.867727 -124 GTCGTTTATGCGCGCAATCGCACTGCGGCTGA 1 160 0 CGCGCAACGA 0.934433 -105 TTGTCCACACCTGTCAGGGGCACGCCGGGCTT 1 231 0 CTGTCAGGGA 0.951956 -34 CCCACAGAGACGCGCGGAAGAAAACACCCCCG 2 13 0 CGCGCGGAGA 0.987236 -114 TTCCGCGCGTCTCTGTGGGGGAAGCGTAAAGA 2 26 1 CTCTGTGGGA 0.976089 -101 AAGAACGAGTCTAGGAGTGGAAGTGAGAACTC 2 54 1 CTAGGAGGGA 0.962189 -73 CCATAATCCGCGTTCGGACGGAGAGATAT 2 108 1 CGTTCGGCGA 0.973039 -19 ******* ** * Masking position 12 Map Score: 9.25052 Number of sites scoring better than the average of aligned sites = 1077 Number in coding regions = 993 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 2 GCCGATAGTAACGACAGGATCACCCTTTTT 1 54 0 ACGACAGGAT 0.94785 -211 TCCTGTCGTTACTATCGGCGGTATCCACGG 1 65 1 ACTATCGGCG 0.965901 -200 TGAGCATGGCACGCTCGAAGTCAGCCGCAG 1 140 1 ACGCTCGAAG 0.976372 -125 GCGCGCATAAACGACAGGAGAGGTGTTTCG 1 177 1 ACGACAGGAG 0.99156 -88 TTGCGATTCGAAGCCCGGCGTGCCCCTGAC 1 221 1 AAGCCCGGCG 0.981192 -44 CCCCACAGAGACGCGCGGAAGAAAACACCC 2 16 0 ACGCGCGGAA 0.966577 -111 GTAAAGAACGAGTCTAGGAGTGGAAGTGAG 2 51 1 AGTCTAGGAG 0.906016 -76 ********** Masking position 1 Map Score: 4.46272 Number of sites scoring better than the average of aligned sites = 583 Number in coding regions = 533 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 3 CGGCGGTATCCACGGGGTGGTAAGCGTGGT 1 80 1 CACGGGGTGG 0.993723 -185 CGCATAAACGACAGGAGAGGTGTTTCGAAT 1 180 1 ACAGGAGAGG 0.94879 -85 CGATTCGAAGCCCGGCGTGCCCCTGACAGG 1 224 1 CCCGGCGTGC 0.978945 -41 CGTGCCCCTGACAGGTGTGGACAAGGAGAT 1 239 1 ACAGGTGTGG 0.960164 -26 CAGGTGTGGACAAGGAGATCGCCAG 1 250 1 CAAGGAGATC 0.806535 -15 CACGGGGGTGTTTTCTTCCG 2 1 1 CACGGGGGTG 0.968719 -126 TTCCGCGCGTCTCTGTGGGGGAAGCGTAAA 2 26 1 CTCTGTGGGG 0.872964 -101 AAGAACGAGTCTAGGAGTGGAAGTGAGAAC 2 54 1 CTAGGAGTGG 0.985274 -73 ********** Masking position 5 Map Score: 5.43997 Number of sites scoring better than the average of aligned sites = 740 Number in coding regions = 653 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 4 ********** No masking Map Score: -6.86222e-14 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 5 ********** No masking Map Score: -6.86222e-14 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: -6.86222e-14 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