AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i214_bsub_mtub_100.orf -o214_bsub_mtub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 rplM 162 ribosomal protein L13 #2 rplM 233 rplM Motif number 1 CAACACAATAAGTTCCGGGGCTTATCGTGG 1 83 0 AGTTCCGGGG 0.979027 -80 TTCCGGGCCCCGGAGCGCGCAACAG 2 6 1 GGCCCCGGAG 0.996545 -228 ACCCCTGTGTGGTCCCGACGGGGGAGAGCC 2 36 1 GGTCCCGACG 0.99869 -198 ATGACTGTGTGGTCCCGACGGCTCTCCCCC 2 55 0 GGTCCCGACG 0.99869 -179 ATTGACCCGAGGTCCCGGCGTACCGCACGC 2 125 0 GGTCCCGGCG 0.999667 -109 ACGGCGGGTTGGTCTCGGCGAACCGACATT 2 152 0 GGTCTCGGCG 0.998052 -82 CGCCTGACCGGCGCCCGGGGCACCCCGGGA 2 185 1 GCGCCCGGGG 0.995502 -49 CTCTCGGGTGGATCCCGGGGTGCCCCGGGC 2 197 0 GATCCCGGGG 0.997944 -37 ********** Masking position 6 Map Score: 27.9039 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 52 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 2 GTATGTATTTCAACCCCACGATAAGCCCCG 1 68 1 CAACCCCACG 0.956858 -95 TCCGGGCCCCGGAGCGCGCAACAGACCCCT 2 12 1 GGAGCGCGCA 0.977087 -222 TCCCCCGTCGGGACCACACAGGGGTCTGTT 2 31 0 GGACCACACA 0.982941 -203 AGAGCCGTCGGGACCACACAGTCATTTTGA 2 60 1 GGACCACACA 0.982941 -174 TACCGACGAGCATCCACGCAGGTCAAAATG 2 82 0 CATCCACGCA 0.916761 -152 TACCGCACGCCAACCGAGCAGCTTACCGAC 2 105 0 CAACCGAGCA 0.775569 -129 AGGTCCCGGCGTACCGCACGCCAACCGAGC 2 116 0 GTACCGCACG 0.964142 -118 CGGTACGCCGGGACCTCGGGTCAATGTCGG 2 130 1 GGACCTCGGG 0.962251 -104 GGTCAGGCGTGAACGGCGGGTTGGTCTCGG 2 164 0 GAACGGCGGG 0.906903 -70 TGGATCCCGGGGTGCCCCGGGCGCCGGTCA 2 189 0 GGTGCCCCGG 0.735728 -45 GGCACCCCGGGATCCACCCGAGAGAAAAGA 2 203 1 GATCCACCCG 0.957794 -31 ********** Masking position 7 Map Score: 10.7752 Number of sites scoring better than the average of aligned sites = 1248 Number in coding regions = 1108 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 3 AATAAACTTCGATTACGTTCTATTTCACAA 1 110 0 GATTACGTTC 0.917498 -53 CCCGACGGGGGAGAGCCGTCGGGACCACAC 2 49 1 GAGAGCCGTC 0.977075 -185 CAACCGAGCAGCTTACCGACGAGCATCCAC 2 95 0 GCTTACCGAC 0.990089 -139 TGCTCGGTTGGCGTGCGGTACGCCGGGACC 2 115 1 GCGTGCGGTA 0.951568 -119 GTTGGTCTCGGCGAACCGACATTGACCCGA 2 145 0 GCGAACCGAC 0.988262 -89 AGCGCTTACCTTCTTTTCTCTCG 2 221 0 GCTTACCTTC 0.98437 -13 ********** Masking position 6 Map Score: 4.70177 Number of sites scoring better than the average of aligned sites = 719 Number in coding regions = 679 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 4 ACATATGGTATGTATTTCAACCCCACGATA 1 61 1 TGTATTTCAA 0.94596 -102 TCGATTACGTTCTATTTCACAACACAATAA 1 102 0 TCTATTTCAC 0.982896 -61 AAATGATCTGTCATTTTCAATAAACTTCGA 1 128 0 TCATTTTCAA 0.962271 -35 TGAATTTCCCCTCCTAAATG 1 153 0 TGAATTTCCC 0.962206 -10 GACCACACAGTCATTTTGACCTGCGTGGAT 2 71 1 TCATTTTGAC 0.942266 -163 ********** Masking position 5 Map Score: 1.5512 Number of sites scoring better than the average of aligned sites = 748 Number in coding regions = 641 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 5 ********** No masking Map Score: -5.80213e-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 6 ********** No masking Map Score: -5.80213e-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: -5.80213e-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