AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -imalT_ctra_opreg_300.orf -g0.413 -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 = 0.413 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 sycE 37 Secretion Chaperone #2 yscU 256 YopS Translocation Protein U #3 glgP 155 Glycogen Phosphorylase Motif number 1 GAAGTGCGCTCTTTTTATTACAGTTTTTAC 1 14 0 CTTTTTATTA 0.856963 -24 GTTGTACAGCTTTTTCTTAAGGCTAACACA 2 21 1 TTTTTCTTAA 0.97496 -236 CTAACACAGCCTTTTTATTATTAAGGAAAA 2 43 1 CTTTTTATTA 0.856963 -214 TAGAATTTCTTTTTCCTTAATAATAAAAAG 2 53 0 TTTTCCTTAA 0.943634 -204 CTAATCTTGCTTTTTCTTTAGAATTTCTTT 2 71 0 TTTTTCTTTA 0.97958 -186 TTAAAGAGCGTTTTTCATGAAGCACTAATC 2 95 0 TTTTTCATGA 0.966203 -162 GAACGGAATATTTTTTTTAAAGAGCGTTTT 2 111 0 TTTTTTTTAA 0.934661 -146 AACCCCTTACTCTTTGTTTATAAATGGGAT 2 148 1 TCTTTGTTTA 0.821942 -109 TCTGCCACCTTCTTTCTTGAGAAAAACATT 2 183 1 TCTTTCTTGA 0.951247 -74 TGTTCGCCTTTTTTAGTTAAGGAGGCTTT 3 10 0 TTTTAGTTAA 0.825264 -146 AAGGCGAACATTTTACTTGATTTTTTACCG 3 30 1 TTTTACTTGA 0.960936 -126 GAATAGAAATCTTTCTTTTAATATTAATAT 3 93 1 CTTTCTTTTA 0.847669 -63 CAAACAAACTCTTTACATGAGAAGCCTCT 3 137 1 CTTTACATGA 0.893188 -19 ********** Masking position 10 Map Score: 17.4483 Number of sites scoring better than the average of aligned sites = 505 Number in coding regions = 505 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 2 AAAGGAAGTGCGCTCTTTTTATTACAGTTTTTA 1 15 0 CCTTTTTATT 0.985977 -23 AAGAAGTTGTACAGCTTTTTCTTAAGGCTAACA 2 16 1 ACTTTTTCTT 0.974985 -241 AAGGCTAACACAGCCTTTTTATTATTAAGGAAA 2 39 1 CCTTTTTATT 0.985977 -218 TTTCTTTAGAATTTCTTTTTCCTTAATAATAAA 2 56 0 ACTTTTTCCT 0.965219 -201 AAGCACTAATCTTGCTTTTTCTTTAGAATTTCT 2 73 0 CCTTTTTCTT 0.992813 -184 TAAAGAACCCCTTACTCTTTGTTTATAAATGGG 2 143 1 CCTCTTTGTT 0.971683 -114 GAGCATCTGCCACCTTCTTTCTTGAGAAAAACA 2 178 1 CTTCTTTCTT 0.936191 -79 CTAAAAAAGGCGAACATTTTACTTGATTTTTTA 3 24 1 CCATTTTACT 0.875683 -132 TGTTGAGAATAGAAATCTTTCTTTTAATATTAA 3 87 1 AATCTTTCTT 0.805422 -69 CACAAGCAAACAAACTCTTTACATGAGAAGCCT 3 131 1 CCTCTTTACA 0.884145 -25 * ********* Masking position 8 Map Score: 13.7124 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 376 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 3 TTTAAAAAAAATATTCCGTTCTCTAAAGAA 2 120 1 ATATTCCGTT 0.975437 -137 AAAAACATTTATATACGGTAACTTGCGAAG 2 204 1 ATATACGGTA 0.964618 -53 AACTTGCGAAGTATTCCTTATAGCGCTTAA 2 223 1 GTATTCCTTA 0.96313 -34 GAGGGTCTTGATATTCGGTAAAAAATCAAG 3 45 0 ATATTCGGTA 0.988974 -111 TTTAATATTAATATTTCTTATTCACAAGCA 3 109 1 ATATTTCTTA 0.917436 -47 ********** Masking position 4 Map Score: 2.84092 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 26 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 4 TAAGGAATACTTCGCAAGTTACCGTATATA 2 213 0 TTCGCAAGTT 0.973694 -44 AGATGGCCAGTTGCTTAAGCGC 2 245 0 ATGGCCAGTT 0.9821 -12 AAGTAAAATGTTCGCCTTTTTTAGTTAAGG 3 18 0 TTCGCCTTTT 0.973699 -138 CCTCTGCAGTATCGTCTGTTGAGAATAGAA 3 71 1 ATCGTCTGTT 0.973631 -85 ********** Masking position 2 Map Score: 0.0295814 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 17 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: 5.92755e-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: 5.92755e-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 7 ********** No masking Map Score: 5.92755e-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