AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -ipdhR_aful_opreg_300.orf -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 AF0396 154 A. fulgidus predicted coding region AF0396 #2 AF0400 84 NADH oxidase (noxA-3) #3 AF2216 131 methylmalonyl-CoA decarboxylase, biotin carboxyl carrier subunit (mmdC) #4 AF2219 137 methylmalonyl-CoA mutase, subunit alpha, C-terminus (mcmA2) Motif number 1 TTTTATCTTAAAGAAAAATTTAAATATCGTCAGTG 1 42 0 AAAAATTAAT 0.946373 -113 TTTCTTTAAGATAAAAACTTAAAACTAATTTGCTT 1 61 1 AAAAATTAAC 0.963005 -94 AAGCTACAAACTTAAAAAGCAAATTAGTTTTAAGT 1 77 0 CAAAAGCAAT 0.960986 -78 TTCCGACGTACAGAAAAATTCAAGCTACAAACTTA 1 98 0 CAAAATTAAC 0.99252 -57 TTCTGTACGTCGGAAAATTTATATTGCAATATTGC 1 118 1 CAAAATTTAT 0.96832 -37 TTCAGCTTACCCAAAAATGTTAAGTTTTCGAGCCG 2 21 0 CAAAAGTAAT 0.980529 -64 AAGTTCATTCCAAATAATTTTAAATAAGTTGGCTC 4 23 0 CATAATTAAT 0.941647 -115 CTTCTCATCGCCCAAAATTCAAACCTCACAGAAGG 4 55 1 CAAAATCAAC 0.984821 -83 GGAATTAATCCGAAAAATTTTTACCTATATGACAA 4 98 1 CAAAATTTAC 0.975085 -40 * **** ** ** * Masking position 7 Map Score: 12.0525 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 54 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 2 CCTATCCCCTCCGCACTGCTACT 1 1 1 CCCCCCTCCG 0.996848 -154 CGCACTGCTACTGTGCCTCTCACTGACGATATT 1 22 1 CTCCTCTCAC 0.991563 -133 ACCACTCCCTCCTTCTCTCTCAGATAGCGATTT 3 58 0 CCTCTCTCAG 0.931034 -74 ATTCCCTGAGCTCAACCACTCCCTCCTTCTCTC 3 72 0 CTCCACTCCC 0.992436 -60 TCTCTCAACCTCGCCGCCATCTTCCA 3 116 0 CTCCTCGCCG 0.997385 -16 TTGGAATGAACTTCTCATCGCCCAAAATTCAAA 4 45 1 CTCATCGCCC 0.974145 -93 TATATGACAACTACTCCCCTACGGG 4 123 1 CTCCCCTACG 0.983863 -15 ** ******** Masking position 9 Map Score: 7.65279 Number of sites scoring better than the average of aligned sites = 773 Number in coding regions = 743 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 3 TATTGCAATATTGCCACTTGCTCACA 1 139 1 TTGCCATTGC 0.959909 -16 ATTATATGGCTTGCTATTTTCAGCTTACCCA 2 43 0 TTGCTATTTC 0.855084 -42 GGACCCCCGACTGCAGCGCTTATT 2 71 0 CCCCCGCTGC 0.984302 -14 GCCTGAAGAGTTTCTGGCTGCGGTAGCTGCG 3 25 1 TTTCTGCTGC 0.852081 -107 CTGCGATAAATCGCTATCTGAGAGAGAAGGA 3 51 1 TCGCTACTGA 0.907418 -81 AGCTCAACCACTCCCTCCTTCTCTCTCAGAT 3 66 0 CTCCCTCTTC 0.849962 -66 CTCAACCTCGCCGCCATCTTCCAGTTTCTTG 3 108 0 CCGCCACTTC 0.988547 -24 CGGATTAATTCCGCTAAATGCCTTCTGTGAG 4 79 0 CCGCTAATGC 0.955629 -59 ****** **** Masking position 9 Map Score: 1.46423 Number of sites scoring better than the average of aligned sites = 1585 Number in coding regions = 1494 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 4 ********** No masking Map Score: 4.64285e-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 5 ********** No masking Map Score: 4.64285e-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 6 ********** No masking Map Score: 4.64285e-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