AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -icspA_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 TP0005 126 DNA gyrase, subunit A (gyrA) #2 TP0848 32 ribosomal protein L20 (rplT) #3 TP0849 52 ribosomal protein L35 (rpmI) #4 TP0850 162 translation initiation factor 3 (infC) Motif number 1 GTCGTGCATAGGCTGCACGCAAGAAAAACC 1 58 0 GGCTGCACGC 0.983947 -69 CTTTGCGTTAGAATGCCCGCCCT 1 114 1 GAATGCCCGC 0.997421 -13 TCTCCCTTTTGGATGCCCACTATAGGTGGT 4 11 1 GGATGCCCAC 0.994933 -152 CCACTTCTAATGCACGCTAAAAAACAA 4 146 0 TAATGCACGC 0.989665 -17 ********** Masking position 4 Map Score: 6.29519 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 70 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 2 CAAGGAGAGACACAGTCGTGCATAGGCTGCA 1 71 0 CCAGTCGTGC 0.994505 -56 TCTCCTTGAACGCAGTATGGCTTTGCGTTAG 1 94 1 CCAGTATGGC 0.989655 -33 CCTCCGTCCTCTCACGCTTGCCAC 2 4 0 CCACGCTTGC 0.99202 -29 CTTTTGGATGCCCACTATAGGTGGTGAATTT 4 16 1 CCACTATAGG 0.95758 -147 AAGACTGGGCCCCAATCTAGCCATTCCTAAT 4 117 0 CCAATCTAGC 0.98844 -46 TAGATTGGGGCCCAGTCTTGTTTTTTAGCGT 4 129 1 CCAGTCTTGT 0.985127 -34 * ********* Masking position 4 Map Score: 5.51388 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 117 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 3 TTTTGCGGATGGGATTCGACGGA 1 4 1 TGCGGATGGG 0.995906 -123 TCCATAGGACTGCGGTTTTTCTTGCGTGCA 1 45 1 TGCGGTTTTT 0.973028 -82 GTCGGGTAACTGCAGTTCGTGTTGTTGGAT 3 17 1 TGCAGTTCGT 0.958479 -36 AATAAGGAATTGGGGTTGTGATGGGGATGG 4 56 1 TGGGGTTGTG 0.990674 -107 GGGGTTGTGATGGGGATGGTGATTTCCTGC 4 67 1 TGGGGATGGT 0.993578 -96 ********** Masking position 7 Map Score: 4.48337 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 118 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 GCATAGGCTGCACGCAAGAAAAACCGCAGT 1 53 0 CACGCAAGAA 0.994237 -74 CTATAGTGGGCATCCAAAAGGGAGA 4 6 0 CATCCAAAAG 0.949793 -157 TCCTTATTTACATGTAAAAATTCACCACCT 4 34 0 CATGTAAAAA 0.965947 -129 GTCAAGTAAACATGCAGGAAATCACCATCC 4 80 0 CATGCAGGAA 0.986298 -83 ACTTCTAATGCACGCTAAAAAACAAGACTG 4 141 0 CACGCTAAAA 0.979829 -22 ********** Masking position 2 Map Score: 3.12288 Number of sites scoring better than the average of aligned sites = 145 Number in coding regions = 126 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 CACGACTGTGTCTCTCCTTGAACGCAGTAT 1 82 1 TCTCTCCTTG 0.985133 -45 TCCTCCGTCCTCTCACGCTTGCCAC 2 6 0 TCTCACGCTT 0.972976 -27 ATACTTTCTCCCCTTTATCCAACAAC 3 37 0 TCTCCCCTTT 0.996765 -16 TCTCCCTTTTGGATGCCCAC 4 1 1 TCTCCCTTTT 0.991225 -162 ********** Masking position 3 Map Score: 2.83925 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 39 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 ACGGATCTGTTCAAAGTCCATAGGACTGCG 1 29 1 TCAAAGTCCA 0.797242 -98 GCAAGAAAAACCGCAGTCCTATGGACTTTG 1 40 0 CCGCAGTCCT 0.991009 -87 TCAAGGAGAGACACAGTCGTGCATAGGCTG 1 73 0 ACACAGTCGT 0.940886 -54 ACCACGCTCCTCCGTCCTCTC 2 22 0 CCACGCTCCT 0.971447 -11 TGCAGTTACCCGACACTCCA 3 1 0 CGACACTCCA 0.943152 -52 CCATCACAACCCCAATTCCTTATTTACATG 4 50 0 CCCAATTCCT 0.957903 -113 GCCCCAATCTAGCCATTCCTAATATGTCAT 4 110 0 AGCCATTCCT 0.922006 -53 CTAGATTGGGGCCCAGTCTTGTTTTTTAGC 4 128 1 GCCCAGTCTT 0.915993 -35 ********** Masking position 7 Map Score: 2.83877 Number of sites scoring better than the average of aligned sites = 571 Number in coding regions = 520 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 7 ********** No masking Map Score: -7.57276e-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 8 ********** No masking Map Score: -7.57276e-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 9 ********** No masking Map Score: -7.57276e-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