AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00053_ctra_reg_300.orf -o00053_ctra_300.ace -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -g0.41 -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 = 0.41 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 dhnA 300 Predicted 1,6-Fructose biphosphate aldolase (dehydrin family) #2 ydaO 153 PP-Loop Superfamily ATPase #3 surE 100 SurE-like Acid Phosphatase #4 ubiA 111 4-hydroxybenzoate octaphenyltransferase Motif number 1 CTCACCTTCTCAAAGATCTTAACTAAAGAC 1 122 1 CAAAGATCTT 0.982631 -179 ACCTCAAGATAAACGATCTTTCCTGGAGTC 1 149 0 AAACGATCTT 0.989813 -152 TTTTGCACAGAAAAGGGCTTTGTAAAGAAG 2 15 1 AAAAGGGCTT 0.962159 -139 TCTTAGAAAGAAAAGAGCTTCTTTACAAAG 2 32 0 AAAAGAGCTT 0.987978 -122 TATTATTTTAAAAAGATCTAATAGCTCATT 3 69 1 AAAAGATCTA 0.947108 -32 CTGTACGTTGAAACGAACTTCAACGTACTT 4 15 1 AAACGAACTT 0.981303 -97 AAACGAACTTCAACGTACTTTTTTCAGCAA 4 25 1 CAACGTACTT 0.860561 -87 TTATAGGTGTAAAAGATCTTGTATTGTAAT 4 70 0 AAAAGATCTT 0.989995 -42 ********** Masking position 3 Map Score: 13.9955 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 110 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 2 GATAAACGATCTTTCCTGGAGTCTTTAGTT 1 142 0 CTTTCCTGGA 0.995518 -159 GTCTATAAATCTTTCTTAGCATGCAAACAT 1 196 0 CTTTCTTAGC 0.972104 -105 GTGTGTTGCGCTTTTTTGGGTTTTCACCAT 1 258 1 CTTTTTTGGG 0.965674 -43 TTACAAAGCCCTTTTCTGTGCAAAAGAAT 2 10 0 CTTTTCTGTG 0.889344 -144 AAGCTCTTTTCTTTCTAAGACTTACCTGGA 2 42 1 CTTTCTAAGA 0.882802 -112 CTTTCTAAGACTTACCTGGATTTCTAATTC 2 52 1 CTTACCTGGA 0.97549 -102 TCCTTTCCTAGATTTAAATAAA 3 3 1 CTTTCCTAGA 0.990786 -98 TCAGAAGGAGCTTTTCTTGCTGAAAAAAGT 4 41 0 CTTTTCTTGC 0.932394 -71 ********** Masking position 3 Map Score: 8.28592 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 194 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 GATCAGTTATATTAAAATAACCTTGGTGTT 1 50 0 ATTAAAATAA 0.758284 -251 TTTTTCCCCGTTCTAAAGATCAGTTATATT 1 67 0 TTCTAAAGAT 0.890965 -234 TGAGAAGGTGAGGTAAAGAAAATGAAAGAC 1 104 0 AGGTAAAGAA 0.839788 -197 GATGCTCCTATTTTAAATATGGTGAAAACC 1 276 0 TTTTAAATAT 0.846574 -25 CCCTTTTCTGTGCAAAAGAAT 2 2 0 TGCAAAAGAA 0.883752 -152 GAAAAGGGCTTTGTAAAGAAGCTCTTTTCT 2 24 1 TTGTAAAGAA 0.954297 -130 ATGAGGGAAATTTTAAAGATTTGCGAATTA 2 76 0 TTTTAAAGAT 0.937469 -78 CCTTTCCTAGATTTAAATAAAAATTTGTAT 3 12 1 ATTTAAATAA 0.788477 -89 ATTAGATCTTTTTAAAATAATAAGAAAAAT 3 61 0 TTTAAAATAA 0.887335 -40 TATCTGTACGTTGAAACGAACTTCAACGTA 4 12 1 TTGAAACGAA 0.769045 -100 GGATTATAGGTGTAAAAGATCTTGTATTGT 4 73 0 TGTAAAAGAT 0.887844 -39 ********** Masking position 5 Map Score: 8.27489 Number of sites scoring better than the average of aligned sites = 622 Number in coding regions = 622 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 CACATTGAACACCAAGGTTATTTTAATATAA 1 43 1 ACCAAGGTTT 0.90005 -258 CGGGGAAAAATCGCAGAGTCTTTCATTTTCT 1 87 1 TCGCAGAGTT 0.989681 -214 GGATGCGACATGGCAGATTGTCTATAAATCT 1 214 0 TGGCAGATTT 0.93853 -87 ATCCGCTCTGACGGAGAGTGTGTTGCGCTTT 1 241 1 ACGGAGAGTT 0.964882 -60 TCGAAGATGCTCCTATTTTAA 1 290 0 TCGAAGATGT 0.939544 -11 ATAGCTCATTACGCAGGTTTTT 3 89 1 ACGCAGGTTT 0.986605 -12 CCCATAATATTCGAAGGGTTT 4 101 1 TCGAAGGGTT 0.986605 -11 ********* * Masking position 5 Map Score: 3.72803 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 81 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 AATAAAAATTAAAAAGAGAAAATAGTT 1 6 0 AAAGAGAAAA 0.948287 -295 ACTGATCTTTAGAACGGGGAAAAATCGCAGAG 1 73 1 AAAGGGGAAA 0.978603 -228 GGTGAGGTAAAGAAAATGAAAGACTCTGCGAT 1 96 0 AAAATGAAAG 0.73786 -205 CCTATTTTAAATATGGTGAAAACCCAAAAAAG 1 268 0 AATGTGAAAA 0.927523 -33 TGTAGTGTAAACATGAGGGAAATTTTAAAGAT 2 86 0 AATAGGGAAA 0.974275 -68 TCCATGGACAAAATTAGGGAAACGTGTTGAAA 2 127 1 AATAGGGAAA 0.974275 -27 ATTTTTATTTAAATCTAGGAAAGGA 3 4 0 AATTAGGAAA 0.879819 -97 TCTTTTTAAAATAATAAGAAAAATAAACCAAG 3 53 0 AAAAAGAAAA 0.938215 -48 * ** ******* Masking position 3 Map Score: 4.72102 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 141 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: -6.15168e-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: -6.15168e-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 8 ********** No masking Map Score: -6.15168e-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