AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00290_ctra_reg_300.orf -o00290_ctra_300.ace -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -g0.41 -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 = 0.41 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ileS 300 Isoleucyl-tRNA Synthetase #2 leuS 196 Leucyl tRNA Synthetase #3 pdhA 221 Pyruvate Dehydrogenase Alpha #4 valS 126 Valyl tRNA Synthetase #5 atpK 41 ATP Synthase Subunit K #6 CT309 166 hypothetical protein #7 atpE 108 ATP Synthase Subunit E #8 ldh 247 Leucine Dehydrogenase Motif number 1 CAGGATCGCATTAAAAAAAAGATGATGGAT 2 54 1 TTAAAAAAAA 0.916384 -143 GAGAAAACCTTAAAAATAACAACAGGTTAG 2 172 1 TAAAAATAAC 0.778736 -25 AAGTCTATGCTACAAAAAAAAACTTTTCGG 3 54 0 TACAAAAAAA 0.963674 -168 TAGAATGTCTTTCAAATAAATCTTTTGAAT 3 168 0 TTCAAATAAA 0.871829 -54 TTCTATTTTTTTCAAAAAAACGCACATCAA 5 21 0 TTCAAAAAAA 0.955618 -21 TCTCAACGCATACAAAAAAACTCCGAGTTT 6 83 0 TACAAAAAAA 0.963674 -84 AACGTTTATCTTAAAAAAACGATCAATTAT 7 70 0 TTAAAAAAAC 0.900398 -39 AGGCTGCCGATAAAATAAAAGTTTTACTGC 8 97 0 TAAAATAAAA 0.680363 -151 TCGTCTTTCGTACAAAAAACCTGTCTGAAA 8 187 0 TACAAAAAAC 0.956297 -61 ********** Masking position 5 Map Score: 9.66704 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 81 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 2 ATTCGCCTTTTAAACCGTTAATTAAAATATGCTTATCGAGCG 1 151 0 TACCTAAAAC 0.986206 -150 GAATCGATCATAATCCGTTAGTTAAGAAATACCTGTTTAGGA 1 189 1 TACCTAAGAC 0.996199 -112 AATTTTTCAGGAACCCTTTATCCAAGAGAATCT 3 199 1 GACCTAAGAC 0.986555 -23 TTAACCAACATAGCCCCTTAAGCCAAAGATCCT 6 2 0 TACCTAAAAC 0.986182 -165 AGTTTTTTTGTATGCGTTGAGAAAAGAAGAACTATCTCTGGA 6 91 1 TACGTAAGAC 0.980539 -76 AATCCGCTCTTACACCTTCAACTAAGAAACTCTCTAGACAGC 6 135 0 TACCTAAGAC 0.996101 -32 ATGATCCGGTTAGCCCCTAAGGTTAGATCATAACAACGTTTA 7 30 0 TACCTAAGAA 0.970292 -79 ** ** * * *** * Masking position 10 Map Score: 6.69808 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 4 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 3 TTGTTCATTAAAAGCGGATTGTGGTCGAGG 1 26 1 AAAGCGGATT 0.94328 -275 TGGTCGAGGCAAAGGGAAATGAAAGAGAGG 1 47 1 AAAGGGAAAT 0.964574 -254 GAAATGAAAGAGAGGGGATTCAGGCGATTA 1 62 1 AGAGGGGATT 0.977237 -239 TAACGGTTTAAAAGGCGAATCGATCATAAT 1 173 1 AAAGGCGAAT 0.835888 -128 AAGATTGGGGAAAGGGAAGTGTATACCAGG 2 28 1 AAAGGGAAGT 0.908724 -169 ACTATGTCTGAGATCGAAATCAAGTCCTCT 2 95 0 AGATCGAAAT 0.799702 -102 CCTTGCACTTAGAGAGAAATAAGCGTCAAA 2 130 0 AGAGAGAAAT 0.911119 -67 TTGCATAGCCAGAGTGAAATTCAAAAGATT 3 150 1 AGAGTGAAAT 0.911119 -72 TGAAGGTGTAAGAGCGGATT 6 157 1 AGAGCGGATT 0.970312 -10 ********** Masking position 3 Map Score: 5.93172 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 119 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 4 GGATTCAGGCGATTATATGGGGTTGGCCTAGGAGTAA 1 77 1 GTATAGTGGC 0.970375 -224 TTAACTAACGGATTATGATCGATTCGCCTTTTAAACC 1 177 0 GTATGGTCGC 0.995719 -124 GGAAAGGGAAGTGTATACCAGGATCGCATTAAAAAAA 2 36 1 GTATAGACGC 0.958649 -161 GCATTAAAAAAAAGATGATGGATTCGCAGACTGGAGA 2 61 1 AGATGGTCGC 0.967925 -136 ATTTCACTCTGGCTATGCAAGGCCGGCGCGGAAAAGT 3 133 0 GTATGGCGGC 0.981258 -89 AATAGTCACAACATATGGAAGTAAGGC 4 110 1 ATATGGAGGC 0.934423 -17 AAAATTCGTTGACGATGGAAGCTCCGCAAACTCGGAG 6 56 1 GGATGGTCGC 0.992421 -111 CTATCTGGACGAATAAGCCGGATGCGCAGGATAATTG 8 42 0 GTAAGGTCGC 0.976603 -206 * **** * * *** Masking position 5 Map Score: 6.31391 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 15 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 5 TTTATTGTGCTCTCTTCCGCTCGCTCGATAAGCATA 1 130 1 TCTCTTCGCC 0.979609 -171 AGTCCTCTCCAGTCTGCGAATCCATCATCTTTTTTT 2 67 0 AGTCTGCACC 0.946514 -130 ACAAAAAAAAACTTTTCGGCACTACCCAGAAAAATG 3 37 0 ACTTTTCGCC 0.988058 -185 CTTTCCGGTTACTTTTCCGCGCCGGCCTTGCATAGC 3 123 1 ACTTTTCGCC 0.988058 -99 AAAAACTCCGAGTTTGCGGAGCTTCCATCGTCAACG 6 62 0 AGTTTGCGCC 0.99009 -105 AGAAGAACTATCTCTGGAGAGCTGTCTAGAGAGTTT 6 115 1 TCTCTGGGCC 0.926535 -52 AGATAGTTTTAGTCTTCTGTTCTCGCAGTAAAACTT 8 73 1 AGTCTTCGCC 0.99009 -175 GGCTCATATTATTTTGCAGTACAATCACTCTCGTCT 8 211 0 ATTTTGCGCC 0.961755 -37 ******* * * * Masking position 5 Map Score: 6.1107 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 30 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 6 GCACAATAAATGGAGGAACCACTCTTTTACTC 1 108 0 TGGAGACCAC 0.862656 -193 TAACGGATTATGATCGATTCGCCTTTTAAACC 1 177 0 TGATGTTCGC 0.983354 -124 TTCGAAAGTTTGATCGATCTGCTTACAAAGTT 1 247 0 TGATGTCTGC 0.983354 -54 AAAAAAAAGATGATGGATTCGCAGACTGGAGA 2 66 1 TGATGTTCGC 0.983354 -131 TCGTTGACGATGGAAGCTCCGCAAACTCGGAG 6 61 1 TGGAGTCCGC 0.984385 -106 AAAACCTGTCTGAAAGGATTGCCACAAGTAAC 8 170 0 TGAAGATTGC 0.944039 -78 AAGACGAGAGTGATTGTACTGCAAAATAATAT 8 210 1 TGATGACTGC 0.978433 -38 **** * ***** Masking position 1 Map Score: 4.43929 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 31 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 ATTAAAATATGCTTATCGAGCGAGCGGAAGA 1 142 0 GCTATCGAGC 0.974886 -159 GGTTTAAAAGGCGAATCGATCATAATCCGTT 1 177 1 GCGATCGATC 0.993254 -124 AACTTTGTAAGCAGATCGATCAAACTTTCGA 1 247 1 GCAATCGATC 0.984925 -54 TCTCCAGTCTGCGAATCCATCATCTTTTTTT 2 67 0 GCGATCCATC 0.990204 -130 TCAAAAAAACGCACATCAACCTTCTGGAT 5 9 0 GCAATCAACC 0.906081 -33 CAATTATCCTGCGCATCCGGCTTATTCGTCC 8 42 1 GCGATCCGGC 0.97551 -206 *** ******* Masking position 6 Map Score: 3.90428 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 16 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: -1.63892e-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: -1.63892e-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 10 ********** No masking Map Score: -1.63892e-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