AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -imalT_ctra_opreg_100.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 GTAAAAACTGTAATAAAAAGAGCGCACTTC 1 14 1 TAATAAAAAG 0.852577 -24 TGTGTTAGCCTTAAGAAAAAGCTGTACAAC 2 21 0 TTAAGAAAAA 0.974083 -236 TTTTCCTTAATAATAAAAAGGCTGTGTTAG 2 43 0 TAATAAAAAG 0.852577 -214 CTTTTTATTATTAAGGAAAAAGAAATTCTA 2 53 1 TTAAGGAAAA 0.941725 -204 AAAGAAATTCTAAAGAAAAAGCAAGATTAG 2 71 1 TAAAGAAAAA 0.978861 -186 GATTAGTGCTTCATGAAAAACGCTCTTTAA 2 95 1 TCATGAAAAA 0.96503 -162 AAAACGCTCTTTAAAAAAAATATTCCGTTC 2 111 1 TTAAAAAAAA 0.93247 -146 ATCCCATTTATAAACAAAGAGTAAGGGGTT 2 148 0 TAAACAAAGA 0.816711 -109 AATGTTTTTCTCAAGAAAGAAGGTGGCAGA 2 183 0 TCAAGAAAGA 0.949582 -74 AAAGCCTCCTTAACTAAAAAAGGCGAACA 3 10 1 TTAACTAAAA 0.820111 -146 CGGTAAAAAATCAAGTAAAATGTTCGCCTT 3 30 0 TCAAGTAAAA 0.959588 -126 ATATTAATATTAAAAGAAAGATTTCTATTC 3 93 0 TAAAAGAAAG 0.84305 -63 AGAGGCTTCTCATGTAAAGAGTTTGTTTG 3 137 0 TCATGTAAAG 0.88977 -19 ********** Masking position 7 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 GGAAAAAGAAATTCTAAAGAAAAAGCAAGA 2 67 1 ATTCTAAAGA 0.983793 -190 CGGAATATTTTTTTTAAAGAGCGTTTTTCA 2 108 0 TTTTTAAAGA 0.802929 -149 AATATTCCGTTCTCTAAAGAACCCCTTACT 2 129 1 TCTCTAAAGA 0.811126 -128 GCTCATCCCATTTATAAACAAAGAGTAAGG 2 152 0 TTTATAAACA 0.918936 -105 TATAAATGTTTTTCTCAAGAAAGAAGGTGG 2 187 0 TTTCTCAAGA 0.989499 -70 TTTTTTACCGAATATCAAGACCCTCTGCAG 3 50 1 AATATCAAGA 0.862143 -106 AAAGATTTCTATTCTCAACAGACGATACTG 3 77 0 ATTCTCAACA 0.969379 -79 ********** Masking position 7 Map Score: 7.55637 Number of sites scoring better than the average of aligned sites = 273 Number in coding regions = 273 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 3 TAAAAAGAGCGCACTTCCTTT 1 27 1 GCCTTCCTTT 0.883636 -11 AAAAAGCTGTACAACTTCTTAGGTA 2 5 0 ACACTTCTTA 0.930509 -252 CTTTTTCTTTAGAATTTCTTTTTCCTTAATA 2 61 0 AGATTTCTTT 0.94449 -196 ATGAAGCACTAATCTTGCTTTTTCTTTAGAA 2 78 0 AACTTGCTTT 0.894933 -179 CTTTAAAAAAAATATTCCGTTCTCTAAAGAA 2 119 1 AAATTCCGTT 0.83905 -138 CGTTCTCTAAAGAACCCCTTACTCTTTGTTT 2 136 1 AGACCCCTTA 0.80085 -121 TGAGCATCTGCCACCTTCTTTCTTGAGAAAA 2 177 1 CCCCTTCTTT 0.816624 -80 TAACTTGCGAAGTATTCCTTATAGCGCTTAA 2 222 1 AGATTCCTTA 0.958042 -35 AAAGCCTCCTTAACTAAAAAAG 3 2 1 AACCTCCTTA 0.966927 -154 TGAGAATAGAAATCTTTCTTTTAATATTAAT 3 90 1 AACTTTCTTT 0.95884 -66 TTTTAATATTAATATTTCTTATTCACAAGCA 3 108 1 AAATTTCTTA 0.935929 -48 ** ******** Masking position 10 Map Score: 8.02314 Number of sites scoring better than the average of aligned sites = 538 Number in coding regions = 538 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 GCTTTTTCTTAAGGCTAACACAGCCTTTTT 2 29 1 AAGGCTAACA 0.990784 -228 TTAACTAAAAAAGGCGAACATTTTACTTGA 3 20 1 AAGGCGAACA 0.993763 -136 TTCTTATTCACAAGCAAACAAACTCTTTAC 3 123 1 CAAGCAAACA 0.9707 -33 ********** Masking position 7 Map Score: 0.239186 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 13 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