AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00950_aful_reg_100.orf -o00950_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 AF1418 49 glycerol-3-phosphate cytidyltransferase (taqD) #5 AF1419 24 ribose-phosphate pyrophosphokinase (prsA-2) #6 AF1420 216 membrane protein #7 AF1778 105 stage V sporulation protein (spoVG) #8 AF1779 57 2-hydroxyacid dehydrogenase, putative Motif number 1 AATGGGCGATTTAAGCAAAGGAGCGAAAATT 1 16 0 TTAAGCAAAG 0.934644 -108 GCATGTTTTTTGGGTAAAAAGATGCCAGGAT 1 60 1 TGGGTAAAAG 0.914903 -64 GCCAGGATGGTAAACGAAAGGTATAAATGAA 1 83 1 TAAACGAAAG 0.81329 -41 AGAAGAAAAGGGCTTAAGGAT 1 113 0 AGAAGAAAAG 0.957872 -11 GATTGCAAAGTTGGGAAAAAGGTTTAAATAA 3 55 1 TTGGGAAAAG 0.925861 -47 GAAAAAGGTTTAAATAAAAAGCGTATTAAAT 3 69 1 TAAATAAAAG 0.903701 -33 GGATTGGAGATGAAGAAAAGGGTC 4 36 1 TGAAGAAAAG 0.990242 -14 GCAGAATAACTTGACAAAACGAATAGCCCTG 6 101 0 TTGACAAAAG 0.916495 -116 ATTGAGATATTGCAGAAAACGAATCCACGAA 6 149 0 TGCAGAAAAG 0.982896 -68 GAATTTTGATTGCAGGAAACGTTAGATTAAA 7 35 0 TGCAGGAAAG 0.961103 -71 AAAAAGGTTTTGAAGCAAAAGCCAAACTCTT 8 13 0 TGAAGCAAAG 0.977596 -45 GAACCCAGAAAAGATAAAAAGGTTTTGAAGC 8 28 0 AAGATAAAAG 0.694933 -30 ********* * Masking position 7 Map Score: 11.7854 Number of sites scoring better than the average of aligned sites = 738 Number in coding regions = 665 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 2 TTTTAAATTTTCGCTCCTTTGCTTAAAT 1 2 1 TTAAATTCTT 0.964956 -122 CCCATTGAATTTACAGGCTGCATGTTTTTTGGGTAAA 1 41 1 TTCAGTGCGT 0.975041 -83 GTTTTTTGGGTAAAAAGATGCCAGGATGGTAAACGAA 1 64 1 TAAAATGCGT 0.752666 -60 AAGAAAAGGGCTTAAGGATTCATTTATACCTTTCGTT 1 95 0 CTAAGTTCTT 0.941748 -29 AACACCTCCAGATTTCTTGAGCTTGTGTCAGA 2 6 1 CTCAGTTCGC 0.776899 -92 ATTGACTTTATTTAAATTTTTTGGATTTTCAGTAAGA 2 42 1 TTAAATTTGT 0.866255 -56 CGTTGCTGTTTTTAAACTTGCCTTTATCGAGATTGCA 3 25 1 TTAAATGCTT 0.938998 -77 AAAACTTTTATGCCTACCTGAATTTGGATTGGA 4 7 1 TTATGTACGT 0.81129 -43 GTCACTCAGCTTCAAAGCTTCCCGGATAGTCTATTTC 6 55 1 TTAAATTCGT 0.98083 -162 CTGGCAACGCTTCAAGACTTCGTGGATTCGTTTTCTG 6 131 1 TTAAGTTCGT 0.989601 -86 AATAAGGTTTTTCATGAGTTTGATATTGAGATATTGC 6 167 0 TTATGTTTTT 0.675262 -50 CTAACCCTCCTTTCAAATTTCGTTACTCTCAAACAAA 7 77 0 TTCAATTCTT 0.952873 -29 CTTTTTATCTTTTCTGGGTTCAATTCTGTC 8 38 1 TTCTGTTCTT 0.923478 -20 ** *** *** * * Masking position 9 Map Score: 8.29666 Number of sites scoring better than the average of aligned sites = 617 Number in coding regions = 552 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 3 ACATGCAGCCTGTAAATTCAATGGGCGATT 1 36 0 TGTAAATTCA 0.9418 -88 TAAATCTTACTGAAAATCCAAAAAATTTAA 2 53 0 TGAAAATCCA 0.832948 -45 TGCTGCAACTCTAAACTCAGTTAAATAAA 2 79 0 TCTAAACTCA 0.963596 -19 TCATCTCCAATCCAAATTCAGGTAGGCATA 4 19 0 TCCAAATTCA 0.988805 -31 CTGTCCAAATTCAACTGCGGGCT 6 4 1 TCCAAATTCA 0.988805 -213 TTTCCTGCAATCAAAATTCTTATATACCAC 7 47 1 TCAAAATTCT 0.944755 -59 TGAAGCAAAAGCCAAACTCTTAA 8 4 0 GCCAAACTCT 0.888686 -54 ********** Masking position 5 Map Score: 5.87766 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 82 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 4 AGGCGTTGCTGTTTTTAAACTTGCCTTTAT 3 22 1 GTTTTTAAAC 0.789399 -80 TATCCGGGAAGCTTTGAAGCTGAGTGACAG 6 53 0 GCTTTGAAGC 0.745254 -164 AATCCACGAAGTCTTGAAGCGTTGCCAGCA 6 129 0 GTCTTGAAGC 0.982693 -88 AGATAAAAAGGTTTTGAAGCAAAAGCCAAA 8 18 0 GTTTTGAAGC 0.895712 -40 ********** Masking position 5 Map Score: 3.45672 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 27 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 ATTTTCGCTCCTTTGCTTAAATCGCCCATTGA 1 17 1 CTTGCTTAAT 0.873378 -107 TTGAGCTTGTGTCAGATTGACTTTATTTAAAT 2 27 1 GTAGATTACT 0.979347 -71 TGGATTTTCAGTAAGATTTATTTAACTGAGTT 2 63 1 GTAGATTATT 0.922685 -35 ACAGCAACGCCTCAGCTTGACCG 3 2 0 CTAGCTTACC 0.969018 -100 CTCAACGCTAAGATTTAATACGCTTTTTA 3 83 0 CTAGATTAAT 0.97515 -19 ACAGAGTATCGTGAGATTTTCCGAGCCCGCAG 6 25 0 GTAGATTTCC 0.851122 -192 TACTCTGTCACTCAGCTTCAAAGCTTCCCGGA 6 49 1 CTAGCTTAAA 0.904721 -168 TGCAGGAAACGTTAGATTAAATTACCACGCTC 7 24 0 GTAGATTAAT 0.974985 -82 ** ***** *** Masking position 7 Map Score: 4.25416 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 87 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 CATGTTTTTTGGGTAAAAAGATGCCAGGAT 1 61 1 GGGTAAAAAG 0.923983 -63 GTAAACGAAAGGTATAAATGAATCCTTAAG 1 92 1 GGTATAAATG 0.953914 -32 TTGGGAAAAAGGTTTAAATAAAAAGCGTAT 3 65 1 GGTTTAAATA 0.762154 -37 AATTCAGGTAGGCATAAAAGTTTT 4 5 0 GGCATAAAAG 0.976598 -45 AATAACAAGAGGCTAATAAGGTTTTTCATG 6 188 0 GGCTAATAAG 0.923012 -29 CAAACAAAGTGGTATATAAGAATTTTGATT 7 55 0 GGTATATAAG 0.953914 -51 ********** Masking position 6 Map Score: 1.54891 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 100 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 7 CTTTCGTTTACCATCCTGGCATCTTTTTAC 1 73 0 CCATCCTGGC 0.99409 -51 GTGAAATAGACTATCCGGGAAGCTTTGAAG 6 64 0 CTATCCGGGA 0.984045 -153 ATTTCACACTCCATCAGGGCTATTCGTTTT 6 87 1 CCATCAGGGC 0.99409 -130 ********** Masking position 3 Map Score: 0.132478 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 37 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 ********** No masking Map Score: 6.91659e-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 9 ********** No masking Map Score: 6.91659e-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 10 ********** No masking Map Score: 6.91659e-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