AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00730_aful_reg_300.orf -o00730_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 AF0734 50 conserved hypothetical protein #2 AF2075 61 hydroxyethylthiazole kinase (thiM) #3 AF2079 33 A. fulgidus predicted coding region AF2079 #4 AF2081 111 A. fulgidus predicted coding region AF2081 #5 AF2082 90 A. fulgidus predicted coding region AF2082 #6 AF2083 121 conserved hypothetical protein #7 AF2086 41 protease inhibitor, putative #8 AF2089 111 conserved hypothetical protein #9 AF2207 300 formylmethanofuran:tetrahydromethanopterin formyltransferase (ftr-2) Motif number 1 GCACAATCAGTGAGCAAAAGTTCTTAATCCTTGACGCA 2 25 1 TAAAACTTAT 0.859456 -37 GGTCGAAATGTTATATATAATATTTGAAAATAAAATCA 4 43 0 TAATATTTAA 0.792246 -69 CTGCGTGAGAATATTTAAAGAATTCGAAGAATGGCTAC 5 23 0 AAAAATTCAA 0.955981 -68 GTTAAGAGATATTGACAAACTCCTTGAA 5 73 1 ATAAACTTAA 0.82039 -18 CTTATTGTTATTATTACAATATTTCGAAATTCGTGAAT 6 52 0 TACAATTCAA 0.883255 -70 AAAACCAAAGCTTTTTAATCATAAAGTT 7 1 1 AAAAATTTAA 0.97925 -41 ATTATGGTCATTAGCTAAAAGCTTTAATATAGCGTAAT 8 29 0 TAAAATTTAT 0.870541 -83 CATAATAGTTATAAGGCAACCTTTTGAAAAGCGTTTTT 8 61 1 AACAATTTAA 0.955913 -51 ACGTTACTCAACAAACAAAAGCCTCAAATTCTATCTAA 9 45 0 AAAAACTCAA 0.951815 -256 ATGTTGTATCTCACCGCAAGCCTTTCAACCTTGCTCAT 9 87 1 TACAATTTAA 0.942827 -214 ATTGAGTCCATCAGAGAGATAACTTCAAAGGATTTTGA 9 129 0 TAAGACTTAA 0.837133 -172 GGTTTATTACAAAGTTAAATCACTTCAATCTTTAAAAA 9 209 1 AAAAACTTAA 0.977233 -92 TATTTTTGCAAGCTGGAAAATTTTTAAAGATTGAAGTG 9 229 0 ACAAATTTAA 0.881564 -72 CCAGCTTGCAAAAATAAAAAGATTTAAATCGCTTCTAC 9 251 1 AAAAATTTAA 0.97925 -50 * * *** *** ** Masking position 9 Map Score: 11.8926 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 113 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 2 ATGGAGCAAAAAAGTTTAAGTTCTTTTCTC 1 24 0 AAAGTTTAAG 0.94022 -27 ATTGTGCAAAAAAATTGAAAA 2 2 0 AAAATTGAAA 0.898982 -60 AAGTTGCGTCAAGGATTAAGAACTTTTGCT 2 37 0 AAGGATTAAG 0.882409 -25 TTTCCTCATAAAAAATTAAATTTGAGAGC 3 10 0 AAAAATTAAA 0.793645 -24 AAATCAGGGTAAAAATTAAGGAGGA 4 6 0 AAAAATTAAG 0.837696 -106 ACTGCGTGAGAATATTTAAAGAATTCGAAG 5 32 0 AATATTTAAA 0.691911 -59 TTTTAATCATAAAGTTTAGGAGGAGAAGG 7 23 1 AAAGTTTAGG 0.72973 -19 CATTAGCTAAAAGCTTTAATATAGCGTAAT 8 29 0 AAGCTTTAAT 0.630539 -83 AAGCGTTTTTAAACTTGAAATCGAAATCCG 8 89 1 AAACTTGAAA 0.83442 -23 AAGCATGAGCAAGGTTGAAAGGCTTGCGGT 9 99 0 AAGGTTGAAA 0.928258 -202 AAAATTTTTAAAGATTGAAGTGATTTAACT 9 221 0 AAGATTGAAG 0.941269 -80 CAAAAATAAAAAGATTTAAATCGCTTCTAC 9 259 1 AAGATTTAAA 0.935555 -42 ********** Masking position 8 Map Score: 10.6152 Number of sites scoring better than the average of aligned sites = 416 Number in coding regions = 279 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 3 GGAATATTGGTCGAAATGTTATATATAATA 4 59 0 TCGAAATGTT 0.902919 -53 CAGATACGCCTCAAAATGCGATGATTAAC 6 10 0 TCAAAATGCG 0.981003 -112 TTACAATATTTCGAAATTCGTGAATAAATA 6 47 0 TCGAAATTCG 0.953352 -75 AACTTTATGATTAAAAAGCTTTGGTTTT 7 9 0 TTAAAAAGCT 0.847003 -33 AGGCAACCTTTTGAAAAGCGTTTTTAAACT 8 74 1 TTGAAAAGCG 0.957382 -38 AAACTTGAAATCGAAATCCGGCT 8 99 1 TCGAAATCCG 0.982377 -13 ATGAGCAAGGTTGAAAGGCTTGCGGTGAGA 9 95 0 TTGAAAGGCT 0.922505 -206 GCTCATGCTTTCAAAATCCTTTGAAGTTAT 9 119 1 TCAAAATCCT 0.932146 -182 ********** Masking position 5 Map Score: 6.46206 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 223 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 4 GAAAATAAAATCAGAAGCCAAAATCAGGGT 4 26 0 TCAGAAGCCA 0.979182 -86 TGATTTGCCTCAGTAGCCATTCTTCGAAT 5 10 1 TCAGTAGCCA 0.991648 -81 AGATGAATTATCTTTAGCTATATTTATAGA 6 101 0 TCTTTAGCTA 0.951586 -21 ACTATTATGGTCATTAGCTAAAAGCTTTAA 8 40 0 TCATTAGCTA 0.980257 -72 ********** Masking position 6 Map Score: 2.00916 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 15 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 5 AAAATCAGAAGCCAAAATCAGGGTAAAAATT 4 19 0 GCAAAATCAG 0.960717 -93 AATATTTGAAAATAAAATCAGAAGCCAAAAT 4 32 0 AAAAAATCAG 0.92057 -80 TTCCTTGTCGGCAGAATGCCGAGTAAGAGGT 4 85 1 GCGAATGCCG 0.921706 -27 GTGAATAAATAAAAAAAGCAGATACGCCTCA 6 27 0 AAAAAAGCAG 0.957931 -95 ATGGTCATTAGCTAAAAGCTTTAATATAGCG 8 33 0 GCAAAAGCTT 0.741987 -79 TAAACTTGAAATCGAAATCCGGCT 8 98 1 ATGAAATCCG 0.780522 -14 TTACTCAACAAACAAAAGCCTCAAATTCTAT 9 49 0 AAAAAAGCCT 0.876725 -252 CAGCCTCTTAACGAAATTCCGGTTTATTACA 9 189 1 ACAAATTCCG 0.936946 -112 CTTCTACCAAACAAAAAGCAGGTGATAGT 9 282 1 ACAAAAGCAG 0.983123 -19 ** ******** Masking position 6 Map Score: 3.30873 Number of sites scoring better than the average of aligned sites = 543 Number in coding regions = 498 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 6 AGAGGAAATGGAGCAAAAAAG 1 40 0 GAGGAAATGG 0.963505 -11 AATTTTTTATGAGGAAAGTAA 3 23 1 GAGGAAAGTA 0.922937 -11 GCAGAATGCCGAGTAAGAGGTGAAAAA 4 95 1 GAGTAAGAGG 0.930252 -17 ATAACAATAAGAGTAGAGGAAATCTATAAA 6 79 1 GAGTAGAGGA 0.949205 -43 TAAAGTTTAGGAGGAGAAGG 7 32 1 GAGGAGAAGG 0.974745 -10 TTTGTTTGTTGAGTAACGTGATAATGTTGT 9 64 1 GAGTAACGTG 0.910347 -237 ********** Masking position 5 Map Score: 0.312322 Number of sites scoring better than the average of aligned sites = 1099 Number in coding regions = 1054 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 ********** No masking Map Score: -1.58918e-12 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: -1.58918e-12 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: -1.58918e-12 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