AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00440_aful_reg_100.orf -o00440_aful_100.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 AF0140 123 ubiquinone/menaquinone biosynthesis methyltransferase (ubiE) #2 AF0727 97 cobalamin biosynthesis precorrin-2 methyltransferase (cbiL) #3 AF1215 101 cell division protein, putative #4 AF1778 105 stage V sporulation protein (spoVG) #5 AF1779 57 2-hydroxyacid dehydrogenase, putative Motif number 1 CAAAGGAGCGAAAATTTAAAA 1 2 0 AAAATTTAAA 0.952659 -122 TGGTAAACGAAAGGTATAAATGAATCCTTA 1 90 1 AAGGTATAAA 0.948152 -34 GAAAATCCAAAAAATTTAAATAAAGTCAAT 2 42 0 AAAATTTAAA 0.952659 -56 GATTTTCAGTAAGATTTATTTAACTGAGTT 2 65 1 AAGATTTATT 0.894119 -33 CGATAAAGGCAAGTTTAAAAACAGCAACGC 3 24 0 AAGTTTAAAA 0.917555 -78 AGTTGGGAAAAAGGTTTAAATAAAAAGCGT 3 63 1 AAGGTTTAAA 0.983013 -39 CTCAACGCTAAGATTTAATACGCTTTTTA 3 83 0 AAGATTTAAT 0.981685 -19 CAGGAAACGTTAGATTAAATTACCACGCTC 4 24 0 TAGATTAAAT 0.815939 -82 GAACCCAGAAAAGATAAAAAGGTTTTGAAG 5 29 0 AAGATAAAAA 0.944257 -29 ********** Masking position 5 Map Score: 10.9508 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 100 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 2 AATTTTCGCTCCTTTGCTTAAATCGCCCATTG 1 16 1 CCTTTTTAAA 0.956433 -108 AACATGCAGCCTGTAAATTCAATGGGCGATTT 1 35 0 CTGTATTCAA 0.778169 -89 ATCCTGGCATCTTTTTACCCAAAAAACATGCA 1 59 0 CTTTTCCCAA 0.954669 -65 TTCATTTATACCTTTCGTTTACCATCCTGGCA 1 82 0 CCTTTTTTAC 0.820734 -42 TGTCAGATTGACTTTATTTAAATTTTTTGGAT 2 36 1 ACTTTTTAAA 0.657298 -62 TTTATTTAAACCTTTTTCCCAACTTTGCAATC 3 55 0 CCTTTCCCAA 0.970934 -47 ATTTAATACGCTTTTTATTTAAACCTTTTTCC 3 68 0 CTTTTTTTAA 0.932617 -34 TTTAATCTAACGTTTCCTGCAATCAAAATTCT 4 35 1 CGTTTTGCAA 0.93019 -71 TTTCAAATTTCGTTACTCTCAAACAAAGTGGT 4 72 0 CGTTACTCAA 0.908501 -34 AAGAGTTTGGCTTTTGCTTCAAAACCTTTTTA 5 13 1 CTTTTTTCAA 0.983743 -45 ***** ***** Masking position 4 Map Score: 5.57448 Number of sites scoring better than the average of aligned sites = 705 Number in coding regions = 627 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 3 GCATCTTTTTACCCAAAAAACATGCAGCCT 1 55 0 ACCCAAAAAA 0.99397 -69 CTTACTGAAAATCCAAAAAATTTAAATAAA 2 48 0 ATCCAAAAAA 0.983722 -50 ACAGAATTGAACCCAGAAAAGATAAAAAGG 5 37 0 ACCCAGAAAA 0.992834 -21 ********** Masking position 5 Map Score: 2.73802 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 8 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 4 TTTTAAATTTTCGCTCCTTTGCTTAAAT 1 9 1 TTTCGCTCCT 0.984832 -115 TACCTTTCGTTTACCATCCTGGCATCTTTT 1 76 0 TTACCATCCT 0.982186 -48 TTTAAACCTTTTTCCCAACTTTGCAATCTC 3 53 0 TTTCCCAACT 0.943687 -49 TTAGATTAAATTACCACGCTCTCATAATAA 4 15 0 TTACCACGCT 0.902585 -91 TCCTTTCAAATTTCGTTACTCTCAAACAAA 4 77 0 TTTCGTTACT 0.878835 -29 TTCTAACCCTCCTTTCAAATTTC 4 93 0 TAACCCTCCT 0.968402 -13 ********** Masking position 1 Map Score: 1.79612 Number of sites scoring better than the average of aligned sites = 469 Number in coding regions = 439 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 5 CAAAAAACATGCAGCCTGTAAATTCAATGGGC 1 40 0 GCACCTTAAA 0.931078 -84 CTTTCGTTTACCATCCTGGCATCTTTTTACCC 1 71 0 CCACCTGCAT 0.992733 -53 AACCTTTTTCCCAACTTTGCAATCTCGATAAA 3 47 0 CCACTTGCAA 0.975268 -55 GATTAAATTACCACGCTCTCATAATAAGCCC 4 10 0 CCAGCTTCAT 0.97908 -96 TTCTAACCCTCCTTTCAAATTTCGTTAC 4 88 0 CCCCCTTCAA 0.991183 -18 GAAGCAAAAGCCAAACTCTTAA 5 1 0 CCAACTTTAA 0.918633 -57 *** *** **** Masking position 7 Map Score: 1.03563 Number of sites scoring better than the average of aligned sites = 429 Number in coding regions = 399 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 6 ********** No masking Map Score: -6.37056e-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: -6.37056e-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: -6.37056e-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