AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00750_mthe_reg_100.orf -o00750_mthe_100.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 MTH147 23 phenylacrylic acid decarboxylase #2 MTH148 47 conserved protein #3 MTH150 75 conserved protein #4 MTH248 195 conserved protein #5 MTH249 64 conserved protein #6 MTH250 23 tRNA intron endonuclease #7 MTH251 54 tryptophanyl-tRNA synthetase #8 MTH252 22 conserved protein #9 MTH253 75 threonine synthase Motif number 1 CCGTTAATCTGTTCCAGGAGGTTTCTGTCC 2 20 0 GTTCCAGGAG 0.968529 -28 TCGCCACCGGCTCCATGAATATATACTAG 3 10 1 GCTCCATGAA 0.769954 -66 AGAGTGTTGAGTTCCTGAGGAATATTATAC 4 22 1 GTTCCTGAGG 0.895171 -174 GAATATTATACCTTGAGGGGCCCCGGGTCC 4 41 1 CCTTGAGGGG 0.914027 -155 GGGCATCACGGGACCCGGGGCCCCTCAAGG 4 51 0 GGACCCGGGG 0.934681 -145 ACACGGAAGGCCTCCCGGGCATCACGGGAC 4 67 0 CCTCCCGGGC 0.990541 -129 GGCCTTCCGTGTTCCTGGGGAATATTCCGC 4 85 1 GTTCCTGGGG 0.991715 -111 AACCAGCACCCCTCCAGCGGAATATTCCCC 4 101 0 CCTCCAGCGG 0.985075 -95 CCCAGATAGAGTTCCCTGGAAAACCAGCAC 4 122 0 GTTCCCTGGA 0.935467 -74 CCAGGGAACTCTATCTGGGGTGTCAGCGCC 4 133 1 CTATCTGGGG 0.843816 -63 CAGGGGAAATCCTTCAGGGCGCTGACACCC 4 150 0 CCTTCAGGGC 0.969325 -46 AAACCCTGACCCTCCAGGGGAAATCCTTCA 4 164 0 CCTCCAGGGG 0.997751 -32 TTAAAGGGGTCTTCCATGGATGACTGCAGC 5 13 0 CTTCCATGGA 0.953507 -52 ACCTCCCGTGAGTGCTGGTTG 6 13 0 CCTCCCGTGA 0.933101 -11 ********** Masking position 5 Map Score: 22.688 Number of sites scoring better than the average of aligned sites = 2954 Number in coding regions = 2852 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 2 CCTGGAACAGATTAACGGGGCAAGAC 2 32 1 ATTAACGGGG 0.996586 -16 GGCTGCATCTGTTAAAGGGGTCTTCCATGG 5 24 0 GTTAAAGGGG 0.983156 -41 GAAATGACTTAATAACGGTGATATGA 7 39 1 AATAACGGTG 0.944454 -16 AACCAGGGAAATTAAACGGGGT 9 3 0 ATTAAACGGG 0.988883 -73 ATGTACCTGAATTAACCAGGGAAATTAAAC 9 16 0 ATTAACCAGG 0.974622 -60 ********** Masking position 5 Map Score: 5.02112 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 71 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 3 AAAAAATCAGGACAGAAACCTCCT 2 5 1 AATCAGGACA 0.974034 -43 TTCCCTGGAAAACCAGCACCCCTCCAGCGG 4 111 0 AACCAGCACC 0.985932 -85 CTTTAATCAGTACTTGTGTATGGC 5 51 0 AATCAGTACT 0.951711 -14 CTCAACCAGCACTCACGGGAGGT 6 4 1 AACCAGCACT 0.984824 -20 AAATGAGAAATAAGAAGGTCA 8 2 1 AATGAGAAAT 0.763875 -21 TACCTGAATTAACCAGGGAAATTAAACGGG 9 13 0 AACCAGGGAA 0.870966 -63 TGATAAGGTGAATCAGAAACTTTATTCTTA 9 48 1 AATCAGAAAC 0.947824 -28 ********** Masking position 5 Map Score: 3.6392 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 216 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 GTCTTGCCCCGTTAATCTGT 2 38 0 GTCTTGCCCC 0.963082 -10 TCAACACTCTGTCTGACCTCA 4 2 0 GTCTGACCTC 0.964276 -194 CCAGGAACACGGAAGGCCTCCCGGGCATCA 4 73 0 GGAAGGCCTC 0.98266 -123 GCGCCCTGAAGGATTTCCCCTGGAGGGTCA 4 158 1 GGATTTCCCC 0.952566 -38 GGTCTTCCATGGATGACTGCAGCGA 5 6 0 GGATGACTGC 0.972102 -59 AGTCATCCATGGAAGACCCCTTTAACAGAT 5 18 1 GGAAGACCCC 0.98772 -47 CAGTACTTGTGTATGGCTGCATCTGTTAAA 5 38 0 GTATGGCTGC 0.963788 -27 ********** Masking position 7 Map Score: 6.70094 Number of sites scoring better than the average of aligned sites = 775 Number in coding regions = 740 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 5 TCATGTGGGTAACATTCAGAAGA 1 9 0 TGGGTAACAT 0.981679 -15 GTTGAGTTCCTGAGGAATATTATACCTTGA 4 27 1 TGAGGAATAT 0.972695 -169 TCCGTGTTCCTGGGGAATATTCCGCTGGAG 4 90 1 TGGGGAATAT 0.992984 -106 TTTGGCTACTATGACGGCTTAA 7 3 1 TGGCTACTAT 0.952413 -52 ********** Masking position 6 Map Score: 1.02264 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 56 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 6 ********** No masking Map Score: 1.3033e-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: 1.3033e-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: 1.3033e-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