AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00940_ctra_reg_300.orf -o00940_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 GTCTTTAGTTAAGATCTTTGAGAAGGTGAG 1 122 0 AAGATCTTTG 0.980559 -179 GACTCCAGGAAAGATCGTTTATCTTGAGGT 1 149 1 AAGATCGTTT 0.988606 -152 CTTCTTTACAAAGCCCTTTTCTGTGCAAAA 2 15 0 AAGCCCTTTT 0.957769 -139 CTTTGTAAAGAAGCTCTTTTCTTTCTAAGA 2 32 1 AAGCTCTTTT 0.986556 -122 AATGAGCTATTAGATCTTTTTAAAATAATA 3 69 0 TAGATCTTTT 0.941051 -32 AAGTACGTTGAAGTTCGTTTCAACGTACAG 4 15 0 AAGTTCGTTT 0.979076 -97 TTGCTGAAAAAAGTACGTTGAAGTTCGTTT 4 25 0 AAGTACGTTG 0.846199 -87 ATTACAATACAAGATCTTTTACACCTATAA 4 70 1 AAGATCTTTT 0.988813 -42 ********** Masking position 2 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 GAAAGACTCTGCGATTTTTCCCCGTTCTAA 1 81 0 GCGATTTTTC 0.783537 -220 CTCCAGGAAAGATCGTTTATCTTGAGGTTT 1 151 1 GATCGTTTAT 0.820491 -150 CGTTTATCTTGAGGTTTTCTCCTACGAAAT 1 164 1 GAGGTTTTCT 0.938267 -137 AGAGTGTGTTGCGCTTTTTTGGGTTTTCAC 1 255 1 GCGCTTTTTT 0.98283 -46 TCTTTACAAAGCCCTTTTCTGTGCAAAAGA 2 13 0 GCCCTTTTCT 0.971079 -141 TTGTAAAGAAGCTCTTTTCTTTCTAAGACT 2 34 1 GCTCTTTTCT 0.986761 -120 TGAGCTATTAGATCTTTTTAAAATAATAAG 3 67 0 GATCTTTTTA 0.853363 -34 TAATCAGAAGGAGCTTTTCTTGCTGAAAAA 4 44 0 GAGCTTTTCT 0.989228 -68 TACAATACAAGATCTTTTACACCTATAATC 4 72 1 GATCTTTTAC 0.917204 -40 ********** Masking position 6 Map Score: 8.35999 Number of sites scoring better than the average of aligned sites = 324 Number in coding regions = 324 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 AACTATTTTCTCTTTTTAATTTTTATTC 1 6 1 TTTTCCTTTA 0.951034 -295 CTCTGCGATTTTTCCCCGTTCTAAAGATCAGTT 1 72 0 TTTCCCTTTA 0.96856 -229 ATCGCAGAGTCTTTCATTTTCTTTACCTCACCT 1 96 1 CTTTCTTTTT 0.872661 -205 CTTTTTTGGGTTTTCACCATATTTAAAATAGGA 1 268 1 TTTTCCATTT 0.968904 -33 ATCTTTAAAATTTCCCTCATGTTTACACTACAA 2 86 1 TTTCCTATTT 0.976148 -68 TTTCAACACGTTTCCCTAATTTTGTCCATGGAG 2 126 0 TTTCCTATTT 0.976148 -28 TCCTTTCCTAGATTTAAATAAAAATT 3 4 1 TTTCCAATTA 0.885765 -97 CTTGGTTTATTTTTCTTATTATTTTAAAAAGAT 3 53 1 TTTTCTTTTT 0.962689 -48 ***** * ** ** Masking position 10 Map Score: 6.20364 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 134 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 0.880405 -258 CGGGGAAAAATCGCAGAGTCTTTCATTTTCT 1 87 1 TCGCAGAGTT 0.987406 -214 GGATGCGACATGGCAGATTGTCTATAAATCT 1 214 0 TGGCAGATTT 0.925825 -87 ATCCGCTCTGACGGAGAGTGTGTTGCGCTTT 1 241 1 ACGGAGAGTT 0.957377 -60 TCGAAGATGCTCCTATTTTAA 1 290 0 TCGAAGATGT 0.927033 -11 ATAGCTCATTACGCAGGTTTTT 3 89 1 ACGCAGGTTT 0.983663 -12 CCCATAATATTCGAAGGGTTT 4 101 1 TCGAAGGGTT 0.983663 -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 TTCTCTTTTTAATTTTTATTCTGCACACAT 1 18 1 AATTTTTATT 0.935193 -283 AAAATCGCAGAGTCTTTCATTTTCTTTACC 1 93 1 AGTCTTTCAT 0.939371 -208 TCTTTCCTGGAGTCTTTAGTTAAGATCTTT 1 133 0 AGTCTTTAGT 0.891425 -168 ATTGTCTATAAATCTTTCTTAGCATGCAAA 1 199 0 AATCTTTCTT 0.973214 -102 CTAATTCGCAAATCTTTAAAATTTCCCTCA 2 75 1 AATCTTTAAA 0.641051 -79 GATTAATACAAATTTTTATTTAAATCTAGG 3 17 0 AATTTTTATT 0.935193 -84 ATACTTGGTTTATTTTTCTTATTATTTTAA 3 50 1 TATTTTTCTT 0.804124 -51 AATCAGAAGGAGCTTTTCTTGCTGAAAAAA 4 43 0 AGCTTTTCTT 0.856402 -69 ********** Masking position 5 Map Score: 3.58449 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 246 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