AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i021_Succinyl-CoA_Synthetase_ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 sdhC 300 succinate dehydrogenase, cytochrome b556 #2 BIME45 63 BIME #3 sucC 85 succinyl-CoA synthetase, beta subunit Motif number 1 GCAGGGTGTTCCGGAGACCTGGCGGCAGTATA 1 77 0 CCGGAGACTG 0.993619 -224 GTTTTCGCATCTGGAAGCAGTGTTTTGCATGA 1 140 1 CTGGAAGCGG 0.987652 -161 CGCAAGCAGACCGGAGGAAGGAAATCCCGACG 1 203 1 CCGGAGGAGA 0.992399 -98 TTTCTGTTACCTGGAGACGTCGGGATTTCCTT 1 220 0 CTGGAGACTG 0.989867 -81 TTATTATTCCCTGGGGACTACGGGCACAGAGG 1 257 0 CTGGGGACAG 0.953209 -44 TTCACCTGCACTGTAGACCGGATAAGGCATTA 2 21 1 CTGTAGACGA 0.98139 -43 TTCAATTGCCGGAGAAGGCGATAATGCCTT 2 44 0 CCGGAGAAGG 0.994823 -20 CCGACAATGCCCGGAAGCGATACGAAATATTC 3 17 1 CCGGAAGCAA 0.948173 -69 ATCTTTTAAACCGTAGACCGAATATTTCGTAT 3 36 0 CCGTAGACGA 0.988249 -50 ATAACGATTACTGAAGGATGGACAGAACAC 3 66 1 CTGAAGGAGA 0.901401 -20 ******** * * Masking position 1 Map Score: 17.1822 Number of sites scoring better than the average of aligned sites = 1894 Number in coding regions = 1593 Number in noncoding regions = 301 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 2 CTGTTCAGGATAAAACCCGACAAACTATAT 1 15 1 TAAAACCCGA 0.856848 -286 GGATTGCAGGGTGTTCCGGAGACCTGGCGG 1 84 0 GTGTTCCGGA 0.91314 -217 GGAACACCCTGCAATCCCGAGCCACCCAGC 1 97 1 GCAATCCCGA 0.988082 -204 TGACCCGCAAGCAGACCGGAGGAAGGAAAT 1 198 1 GCAGACCGGA 0.994192 -103 CCGGAGGAAGGAAATCCCGACGTCTCCAGG 1 213 1 GAAATCCCGA 0.981685 -88 CTCTGTGCCCGTAGTCCCCAGGGAATAATA 1 258 1 GTAGTCCCCA 0.975435 -43 CACCTGCACTGTAGACCGGATAAGGCATTA 2 23 1 GTAGACCGGA 0.995182 -41 CTTTTAAACCGTAGACCGAATATTTCGTAT 3 36 0 GTAGACCGAA 0.964018 -50 ********** Masking position 10 Map Score: 12.0485 Number of sites scoring better than the average of aligned sites = 627 Number in coding regions = 434 Number in noncoding regions = 193 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 3 AAATCATTACAATTAACCTACATATAGTTTGT 1 34 0 ATAACCTACA 0.588876 -267 CAGGTCTCCGGAACACCCTGCAATCCCGAGCC 1 88 1 GCACCCTGCA 0.93193 -213 GCAGTGTTTTGCATGACGCGCAGTTATAGAAA 1 156 1 GTGACGCGCA 0.990911 -145 AAAGGACGCTGTCTGACCCGCAAGCAGACCGG 1 185 1 GTGACCCGCA 0.993829 -116 TATTCCCTGGGGACTACGGGCACAGAGGTTAA 1 253 0 GCTACGGGCA 0.964698 -48 GAATAACGCCCACATGCTGTTC 1 289 0 GTAACGCCCA 0.91984 -12 TAGTTTAAGTTTCACCTGCACTGTAGACCG 2 9 1 GTCACCTGCA 0.985978 -55 GGCATTATCGCCTTCTCCGGCAATTGAA 2 46 1 CTCTCCGGCA 0.887985 -18 GGGTGACCGACAATGCCCGGAA 3 1 1 GTGACCGACA 0.976556 -85 TATTTCGTATCGCTTCCGGGCATTGTCGGTCA 3 14 0 CTTCCGGGCA 0.904418 -72 * ********* Masking position 12 Map Score: 6.72202 Number of sites scoring better than the average of aligned sites = 3005 Number in coding regions = 2836 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 4 TCACTGTTCAGGATAAAACCCGACAAACTAT 1 12 1 GATAAAACCC 0.816172 -289 TTTGTGAACAGCCTATACTGCCGCCAGGTCT 1 64 1 GCTATACTGC 0.941067 -237 CAGGTCTCCGGAACACCCTGCAATCCCGAGC 1 88 1 GACACCCTGC 0.863686 -213 GCAGTGTTTTGCATGACGCGCAGTTATAGAA 1 156 1 GATGACGCGC 0.73133 -145 AAAGGACGCTGTCTGACCCGCAAGCAGACCG 1 185 1 GCTGACCCGC 0.971307 -116 CAGACCGGAGGAAGGAAATCCCGACGTCTCC 1 209 1 GAGGAAATCC 0.742024 -92 TAACCTCTGTGCCCGTAGTCCCCAGGGAATA 1 254 1 GCCGTAGTCC 0.91242 -47 GAATAACGCCCACATGCTGTT 1 290 0 GATAACGCCC 0.91721 -11 GCCTTATCCGGTCTACAGTGCAGGTGAAACT 2 18 0 GCTACAGTGC 0.9153 -46 TGCCGGAGAAGGCGATAATGCCTTATCCGGT 2 37 0 GCGATAATGC 0.892582 -27 TCCGGGCATTGTCGGTCACCC 3 1 0 GCGGTCACCC 0.936693 -85 GTGTTCTGTCCATCCTTCAGTAATCGTT 3 68 0 GCCATCCTTC 0.733011 -18 * ********* Masking position 11 Map Score: 6.39361 Number of sites scoring better than the average of aligned sites = 5785 Number in coding regions = 5478 Number in noncoding regions = 307 Number of orfs with sites within 600 bp upstream = 279 Fraction of orfs with sites within 600 bp upstream = 0.0448121 Motif number 5 GTTGTAACGTGTCGTTTTCGCATCTGGAAG 1 127 1 GTCGTTTTCG 0.978466 -174 TTATAGAAAGGACGCTGTCTGACCCGCAAG 1 179 1 GACGCTGTCT 0.941108 -122 AGGAAATCCCGACGTCTCCAGGTAACAGAA 1 221 1 GACGTCTCCA 0.859877 -80 ATAAGGCATTATCGCCTTCTCCGGCAATTG 2 42 1 ATCGCCTTCT 0.972142 -22 AATATTTCGTATCGCTTCCGGGCATTGTCG 3 18 0 ATCGCTTCCG 0.97414 -68 TCCTTCAGTAATCGTTATCTTTTAAACCGT 3 54 0 ATCGTTATCT 0.890546 -32 ********** Masking position 4 Map Score: 0.539334 Number of sites scoring better than the average of aligned sites = 1374 Number in coding regions = 1278 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 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 Motif number 8 ********** 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