AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -igalR_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 CT309 166 hypothetical protein #2 CT495 211 ADP/ATP Translocase Motif number 1 AGGATCTTTGGCTTAAGGGGCTATGT 1 7 1 TTTGGCTTAA 0.92099 -160 AAGGGGCTATGTTGGTTAAATCGTTATTGG 1 25 1 GTTGGTTAAA 0.943223 -142 TTAAATCGTTATTGGGAAAATTCGTTGACG 1 40 1 ATTGGGAAAA 0.983456 -127 TTTTGTATGCGTTGAGAAAAGAAGAACTAT 1 96 1 GTTGAGAAAA 0.961933 -71 TCTGTTGAAATTTGGGATAATTACTGGATG 2 122 0 TTTGGGATAA 0.987687 -90 TATTGAAGACTTTGGGAAAAATTTTTGTGA 2 169 0 TTTGGGAAAA 0.990017 -43 ********** Masking position 3 Map Score: 7.64979 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 110 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 CGAGTTTGCGGAGCTTCCATCGTCAACGAAT 1 59 0 GAGCTTCCAC 0.943485 -108 CGCAAACTCGGAGTTTTTTTGTATGCGTTGA 1 80 1 GAGTTTTTTG 0.968959 -87 TATCTCTGGAGAGCTGTCTAGAGAGTTTCTT 1 123 1 GAGCTGTCTG 0.978225 -44 GCTGTCTAGAGAGTTTCTTAGTTGAAGGTGT 1 135 1 GAGTTTCTTG 0.989291 -32 TGCGGTATTCTAGTTCCCTGGATTTCATAAA 2 66 1 TAGTTCCCTG 0.950133 -146 AACAGAGTGCGAGGTTCCTCGCATCACAAAA 2 146 1 GAGGTTCCTG 0.993803 -66 ********* * Masking position 5 Map Score: 2.83128 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 148 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 ACAAAAAAACTCCGAGTTTGCGGAGCTTCC 1 72 0 TCCGAGTTTG 0.94579 -95 CAGAGATAGTTCTTCTTTTCTCAACGCATA 1 101 0 TCTTCTTTTC 0.902624 -66 AATCCGCTCTTACACCTTCAAC 1 155 0 TCCGCTCTTA 0.978815 -12 TCACTCCGCCTCCTCTTTTCTTTGGGCAC 2 10 0 TCCTCTTTTC 0.9862 -202 GAACTAGAATACCGCACTTGCTGCTAAAAT 2 52 0 ACCGCACTTG 0.912017 -160 AGTGCGAGGTTCCTCGCATCACAAAAATTT 2 151 1 TCCTCGCATC 0.950836 -61 ACACTCCTTCCTAATTTAATAAATATTG 2 194 0 TCCTAATTTA 0.85792 -18 ********** Masking position 9 Map Score: 2.27417 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 346 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 GCTTCCATCGTCAACGAATTTTCCCAATAA 1 48 0 TCAACGAATT 0.906401 -119 TAGACAGCTCTCCAGAGATAGTTCTTCTTT 1 113 0 TCCAGAGATA 0.912314 -54 TGGAGAGCTGTCTAGAGAGTTTCTTAGTTG 1 129 1 TCTAGAGAGT 0.947392 -38 TCTTACACCTTCAACTAAGAAACTCTCTAG 1 140 0 TCAACTAAGA 0.855532 -27 GGCGGAGTGATCAAGAACTTGAATTTTAGC 2 30 1 TCAAGAACTT 0.902813 -182 TTCATAAAAATCTTGTAATTATGCATTGCC 2 89 1 TCTTGTAATT 0.720655 -123 TTGCCAAGCATCCAGTAATTATCCCAAATT 2 114 1 TCCAGTAATT 0.957022 -98 ATCCCAAATTTCAACAGAGTGCGAGGTTCC 2 134 1 TCAACAGAGT 0.953817 -78 ********** Masking position 1 Map Score: 2.09832 Number of sites scoring better than the average of aligned sites = 373 Number in coding regions = 372 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 5 ATTTTCCCAATAACGATTTAACCAACATAGCCC 1 28 0 TAATTTAACC 0.878119 -139 CTTCCATCGTCAACGAATTTTCCCAATAACGAT 1 44 0 CAAATTTTCC 0.988603 -123 TGATCAAGAACTTGAATTTTAGCAGCAAGTGCG 2 37 1 CTATTTTAGC 0.928702 -175 TCATAAAAATCTTGTAATTATGCATTGCCAAGC 2 90 1 CTAATTATGC 0.960532 -122 TGCCAAGCATCCAGTAATTATCCCAAATTTCAA 2 115 1 CAAATTATCC 0.988392 -97 CCTCGCATCACAAAAATTTTTCCCAAAGTCTTC 2 162 1 CAATTTTTCC 0.984285 -50 * * ******** Masking position 6 Map Score: 1.70576 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 105 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: 7.41397e-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: 7.41397e-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: 7.41397e-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