AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00950_aful_reg_300.orf -o00950_aful_300.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 AF1421 49 conserved hypothetical protein #8 AF1422 35 aspartate racemase #9 AF1423 112 conserved hypothetical protein #10 AF1778 105 stage V sporulation protein (spoVG) #11 AF1779 57 2-hydroxyacid dehydrogenase, putative Motif number 1 ATTTTCGCTCCTTTGCTTAAATCGCCCATT 1 17 1 CTTTGCTTAA 0.890646 -107 TCCTTAAGCCCTTTTCTTCT 1 114 1 CTTTTCTTCT 0.92444 -10 ACAGCAACGCCTCAGCTTGACCG 3 4 0 CTCAGCTTGA 0.914294 -98 GACCCTTTTCTTCATCTCCAATCC 4 36 0 CTTTTCTTCA 0.97443 -14 AGCCCTTCCTCTTTTTTTGATTC 5 12 1 CTTTTTTTGA 0.938177 -13 TACTCTGTCACTCAGCTTCAAAGCTTCCCG 6 49 1 CTCAGCTTCA 0.885063 -168 GCTAATAAGGTTTTTCATGAGTTTGATATT 6 177 0 TTTTTCATGA 0.829699 -40 CCAAAGCTTTATCTTGTTAGGCGATTA 8 8 1 TTTATCTTGT 0.692822 -28 TGGATTTTGCTTGAAGTTGAGGTT 9 5 1 TTTTGCTTGA 0.95447 -108 GGGCTTATTATGAGAGCGTGGTA 10 4 1 CTTATTATGA 0.692822 -102 TTATATACCACTTTGTTTGAGAGTAACGAA 10 66 1 CTTTGTTTGA 0.954475 -40 AGAGTTTGGCTTTTGCTTCAAAACCTTTTT 11 14 1 TTTTGCTTCA 0.938014 -44 GCTTCAAAACCTTTTTATCTTTTCTGGGTT 11 28 1 CTTTTTATCT 0.530306 -30 ********** Masking position 8 Map Score: 11.984 Number of sites scoring better than the average of aligned sites = 909 Number in coding regions = 822 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 2 TTGACTTTATTTAAATTTTTTGGATTTTCAG 2 43 1 TTAAATTTTT 0.681237 -55 CAAAGTTGGGAAAAAGGTTTAAATAAAAAGC 3 60 1 AAAAAGTTTA 0.775493 -42 TCAGGTAGGCATAAAAGTTTT 4 1 0 ATAAAATTTT 0.956216 -49 CAAGAGGCTAATAAGGTTTTTCATGAGTTTG 6 182 0 ATAAGGTTTT 0.92817 -35 CTTTGAATGTTAAAAAGTTTGCTGTGCTACC 7 17 0 TAAAAATTTG 0.814778 -33 GCCTAACAAGATAAAGCTTTGG 8 2 0 ATAAAGTTTG 0.952991 -34 GAAGTTGAGGTTAAAATTTTTTAGGTTGGGT 9 23 1 TTAAAATTTT 0.913907 -90 GGTTGGGCCGATAAAAATTTACCGCTAAAAG 9 80 0 ATAAAATTTA 0.892177 -33 AAAGTGGTATATAAGAATTTTGATTGCAGGA 10 49 0 ATAAGATTTT 0.932873 -57 TTAAGAGTTTGGCTTTTGCTT 11 1 1 TTAAGATTTG 0.874314 -57 CAGAAAAGATAAAAAGGTTTTGAAGCAAAAG 11 23 0 AAAAAGTTTT 0.893273 -35 ****** **** Masking position 4 Map Score: 9.21942 Number of sites scoring better than the average of aligned sites = 257 Number in coding regions = 118 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 3 TTTGCTTAAATCGCCCATTGAATTTACAGGCTGCA 1 28 1 TCCCCTAATT 0.958379 -96 AACCTTTTTCCCAACTTTGCAATCTCGATAAAGGC 3 44 0 CCACTTAACT 0.870951 -58 CTTTTCTTCATCTCCAATCCAAATTCAGGTAGGCA 4 21 0 TCCCATAATT 0.965247 -29 ATTTTCCGAGCCCGCAGTTGAATTTGGACAG 6 7 0 CCGCATAATT 0.991096 -210 TGAAGCGTTGCCAGCAGAATAACTTGACAAAACGA 6 110 0 CCGCAAAATT 0.972357 -107 AATGCAATTCTGCTTTGAATGTTAAAAAGTTTG 7 27 0 TCGCTTATTT 0.815384 -23 AGCGCATCACCCAACCTAAAAAATTTTAACCTCAA 9 27 0 CCACCAAATT 0.907866 -86 TCTAACGTTTCCTGCAATCAAAATTCTTATATACC 10 40 1 CCGCATAATT 0.991096 -66 TTCTAACCCTCCTTTCAAATTTCGTTACTCTC 10 84 0 CCCCTTAATT 0.984868 -22 ** *** * ** ** Masking position 11 Map Score: 5.97813 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 87 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 AACACCTCCAGATTTCTTGAG 2 1 1 AACACCTCCG 0.981857 -97 TAAAAACAGCAACGCCTCAGCTTGACCG 3 8 0 AACGCCTCAC 0.93526 -94 GCGGGCTCGGAAAATCTCACGATACTCTGTC 6 27 1 AAAATCTCAG 0.865904 -190 ACTCAGCTTCAAAGCTTCCCGGATAGTCTAT 6 58 1 AAAGCTTCCG 0.985589 -159 TTCTGCTGGCAACGCTTCAAGACTTCGTGGA 6 126 1 AACGCTTCAG 0.988895 -91 TGAATGTTAAAAAGTTTGCTGTGCTACCAAT 7 14 0 AAAGTTTGCG 0.815649 -36 TGATGCGCTAAATACTTCAAGACAGGCCTTT 9 53 1 AATACTTCAG 0.869625 -60 AATTTAATCTAACGTTTCCTGCAATCAAAAT 10 33 1 AACGTTTCCG 0.98221 -73 ********* * Masking position 2 Map Score: 4.94434 Number of sites scoring better than the average of aligned sites = 386 Number in coding regions = 356 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 TTTACAGGCTGCATGTTTTTTGGGTAAAAA 1 50 1 GCATGTTTTT 0.924189 -74 TACCATCCTGGCATCTTTTTACCCAAAAAA 1 65 0 GCATCTTTTT 0.941219 -59 GCTGAGGCGTTGCTGTTTTTAAACTTGCCT 3 18 1 TGCTGTTTTT 0.888745 -84 AAGCCCTTCCTCTTTTTTTGATTC 5 8 1 TCCTCTTTTT 0.912987 -17 AACCTTATTAGCCTCTTGTTATTTATTTGC 6 195 1 GCCTCTTGTT 0.975905 -22 CCAAAGCTTTATCTTGTTAGGCGATTAG 8 9 1 TTATCTTGTT 0.754198 -27 TGGATTTTGCTTGAAGTTGAG 9 2 1 GGATTTTGCT 0.838607 -111 TGATGTTGTTCTGGTTGGGC 9 103 0 TGATGTTGTT 0.924189 -10 TTAAGAGTTTGGCTTTTGCTTCAAAACCTT 11 11 1 GGCTTTTGCT 0.869955 -47 ********** Masking position 6 Map Score: 4.47069 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 294 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 CCAATCCAAATTCAGGTAGGCATAAAAGTT 4 13 0 TTCAGGTAGG 0.881436 -37 TGTCAAGTTATTCTGCTGGCAACGCTTCAA 6 116 1 TTCTGCTGGC 0.945785 -101 AATGCAATTCTGCTTTGAATGTTAAAA 7 33 0 TTCTGCTTTG 0.944548 -17 TGGATTTTGCTTGAAGTTGAGGTT 9 5 1 TTTTGCTTGA 0.847981 -108 GTTAAAATTTTTTAGGTTGGGTGATGCGCT 9 32 1 TTTAGGTTGG 0.933322 -81 TGATGTTGTTCTGGTTGGGCCGATAAAA 9 95 0 TTCTGGTTGG 0.98988 -18 TATATAAGAATTTTGATTGCAGGAAACGTT 10 43 0 TTTTGATTGC 0.847983 -63 TTTTTATCTTTTCTGGGTTCAATTCTGTC 11 39 1 TTCTGGGTTC 0.818979 -19 ********** Masking position 2 Map Score: 2.41054 Number of sites scoring better than the average of aligned sites = 523 Number in coding regions = 464 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 7 GGGCGATTTAAGCAAAGGAGCGAAAATTTAA 1 13 0 AGCAAAGGAC 0.892063 -111 AGAAGAAAAGGGCTTAAGGATTCA 1 110 0 AGAAAAGGGT 0.988015 -14 TGCAAAGTTGGGAAAAAGGTTTAAATAAAAA 3 58 1 GGAAAAAGGT 0.918423 -44 TTGGAGATGAAGAAAAGGGTC 4 39 1 AGAAAAGGGC 0.982293 -11 GAATAACTTGACAAAACGAATAGCCCTGATG 6 98 0 ACAAAACGAT 0.862696 -119 GAGATATTGCAGAAAACGAATCCACGAAGTC 6 146 0 AGAAAACGAT 0.964792 -71 CCCAGAAAAGATAAAAAGGTTTTGAAGCAAA 11 25 0 ATAAAAAGGT 0.849858 -33 ********* * Masking position 6 Map Score: 1.45678 Number of sites scoring better than the average of aligned sites = 267 Number in coding regions = 239 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 ********** No masking Map Score: -6.51267e-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: -6.51267e-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: -6.51267e-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