AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -iada_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 TP0141 171 methylated-DNA-protein-cysteine S-methyltransferase (dat) #2 TP0881 78 ABC transporter, ATP-binding protein (natA) #3 TP0884 29 conserved hypothetical integral membrane protein #4 TP0886 147 polyribonucleotide nucleotidyltransferase (pnp) Motif number 1 AGCTCAAGTCTCTGTCTGTATAGGGAGGGTGCACGAGCGA 1 30 1 TTTTGAGGGT 0.996697 -142 ATCGTGTTCGTATATGCGTACGAGCTCGCTCGTGCACCCT 1 55 0 TTTCGAAGGT 0.958517 -117 AGATGTAGTTTTTCTTTGAAAAACGAGGATATCTGTGTTC 1 119 1 TTTTGAACGT 0.980757 -53 TATAAAAATCTGTGTATTAACTGCAGTGGTGTGTCTGCTG 2 23 1 TTTTTAGCGT 0.938443 -56 TTACCTAGATGTGGAGAAGAGTGCTTTTT 3 6 1 TGTTGAAGGT 0.992207 -24 GGGCTTTGCATGGGGAAGTTTCGCAGTGCG 4 1 1 GGTTGAGGGT 0.994762 -147 TGCCGCCGAGGGGTTGTGCATAGGACGGTTGTCCGTTCTG 4 41 1 GGTTGAGGGT 0.994762 -107 TCCGTTCTGCTTTCTTTGTCTAGCTTCGCAGGTGGCTGTG 4 72 1 TTTTGCGCGA 0.922975 -76 GCTTCGCAGGTGGCTGTGCCAGGGCTTGGTGCGGCCTGCG 4 94 1 TGTTGCGGGT 0.994762 -54 * * * ** * ** * * Masking position 5 Map Score: 11.6318 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 100 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 2 TATGCGTACGAGCTCGCTCGTGCACCCTCCCTATA 1 48 0 AGCCTTGCAC 0.995509 -124 CAAGACAGCAGACACACCACTGCAGTTAATACACA 2 33 0 GACCCTGCAG 0.977208 -46 AAAAAGCACTCTTCTCCACATCTAGGTAA 3 11 0 AGCCTTCCAC 0.977072 -19 CGCACTGCGAAACTTCCCCATGCAAAGCCC 4 6 0 AACCCTGCAA 0.989475 -142 CCTATGCACAACCCCTCGGCGGCACGCACTGCGAA 4 30 0 ACCCGGGCAC 0.992074 -118 CAGAACGGACAACCGTCCTATGCACAACCCCTCGG 4 46 0 AACCCTGCAC 0.998357 -102 CGCAGGCCGCACCAAGCCCTGGCACAGCCACCTGC 4 99 0 ACCCCGGCAC 0.99774 -49 *** ** ***** Masking position 14 Map Score: 7.62434 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 142 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 3 TATTTTTCAGGAGAGCTCAAGTCTCTGTCT 1 17 1 GAGAGCTCAA 0.964027 -155 GGGTGCACGAGCGAGCTCGTACGCATATAC 1 56 1 GCGAGCTCGT 0.672318 -116 GTACGCATATACGAACACGATAAGAACACA 1 74 1 ACGAACACGA 0.952381 -98 CGAACACGATAAGAACACATAGGTCGTAAA 1 85 1 AAGAACACAT 0.981711 -87 ATAGGTCGTAAAGATCAGATGTAGTTTTTC 1 103 1 AAGATCAGAT 0.832411 -69 CTCCCCCTCCACGAACACAGATATCCTCGT 1 141 0 ACGAACACAG 0.945299 -31 GATTTTTATAGAAAACACATCC 2 3 0 GAAAACACAT 0.909906 -76 ACCGTCAAAAAAGAATTCAAGACAGCAGAC 2 55 0 AAGAATTCAA 0.724264 -24 GCTAGACAAAGAAAGCAGAACGGACAACCG 4 66 0 GAAAGCAGAA 0.819935 -82 ACGTTTCCTAAGAACAGAATGTATCGCAG 4 129 0 AAGAACAGAA 0.967187 -19 ********** Masking position 4 Map Score: 7.12106 Number of sites scoring better than the average of aligned sites = 595 Number in coding regions = 544 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 4 GAAACTTCCCCATGCAAAGCCC 4 3 0 CATGCAAAGC 0.978962 -145 GGCGGCACGCACTGCGAAACTTCCCCATGC 4 18 0 ACTGCGAAAC 0.99133 -130 GGCACAGCCACCTGCGAAGCTAGACAAAGA 4 84 0 CCTGCGAAGC 0.992255 -64 CTTGGTGCGGCCTGCGATACATTCTGTTCT 4 118 1 CCTGCGATAC 0.994686 -30 ********** Masking position 7 Map Score: 5.41633 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 63 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 5 GTCTCTGTCTGTATAGGGAGGGTGCACGAGC 1 37 1 GATAGGGAGG 0.992289 -135 CTGTGTTCGTGGAGGGGGAGAGAGACAGGCA 1 151 1 GAGGGGGAGA 0.988584 -21 TTACCTAGATGTGGAGAAGAGTGCTTT 3 7 1 AATGTGGAGA 0.819934 -23 GGGCTTTGCATGGGGAAGTTTCGCAGTG 4 8 1 GATGGGGAAG 0.986483 -140 GAGGGGTTGTGCATAGGACGGTTGTCCGTTC 4 48 1 GATAGGACGG 0.952735 -100 GTCTAGCTTCGCAGGTGGCTGTGCCAGGGCT 4 89 1 GAGGTGGCTG 0.941785 -59 CTGTGCCAGGGCTTGGTGCGGCCTGCGATAC 4 107 1 GTTGGTGCGG 0.938802 -41 * ********* Masking position 3 Map Score: 3.36794 Number of sites scoring better than the average of aligned sites = 823 Number in coding regions = 691 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 6 ********** No masking Map Score: -7.8627e-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: -7.8627e-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: -7.8627e-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