AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00360_tpal_reg_100.orf -o00360_tpal_100.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -g0.53 -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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 TP0223 267 aspartate aminotransferase (tpaaT) #2 TP0251 153 DNA-binding protein II #3 TP0417 26 apolipoprotein N-acyltransferase (cutE) Motif number 1 GGAAGCTCATCCGTGTGGCTGCGCGGGCTTGTGTGC 1 37 1 CTGTGCGCGG 0.952941 -231 GGCTTGTGTGCTCTGAAGTCGGGCTGTCGATTCACT 1 62 1 CTGCGGGCTG 0.990668 -206 CATAAATTGACAGGGTCAGGGGGCGTGTCTACACTG 1 104 1 CGGGGGGCGT 0.994256 -164 ACATGGACCTCTCTGAAGGCGCGCGTGCGTTAAACG 1 144 1 CTGCGCGCGT 0.999273 -124 TTGAAGGAACGGTGGTGCACGCGCTGTTATCTCCTC 1 186 1 GGGCGCGCTG 0.994351 -82 GTTATCTCCTCTTGGTTTGCGCGCGTATTTTCCCCA 1 211 1 CGGCGCGCGT 0.999258 -57 TTGTTGCACAGAATGCAGAGGCGCGG 1 252 1 GTGGGCGCGG 0.997301 -16 TTCTCTTCACCCGAGGTGGTGCGCGTTTGAGGCGGC 2 103 1 CAGTGCGCGT 0.988962 -51 CGTTTGAGGCGGCTGTTTGCCCGCGTGTGTTTCTTG 2 126 1 GTGCCCGCGT 0.990379 -28 * ** ******* Masking position 14 Map Score: 20.3274 Number of sites scoring better than the average of aligned sites = 479 Number in coding regions = 447 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 2 ACAAGCCCGCGCAGCCACACGGATGAGCTTCCTGCGGC 1 31 0 GAACACGTGC 0.996093 -237 AAGTCGGGCTGTCGATTCACTGGGGTGCATAAATTGAC 1 77 1 GCTCACGGGC 0.995869 -191 GTCAGGGGGCGTGTCTACACTGTGAGACATGGACCTCT 1 118 1 GGACACGGAC 0.988007 -150 TAACGCACGCGCGCCTTCAGAGAGGTCCATGTCTCACA 1 138 0 GGTCAGGGGC 0.994886 -130 GAAGGCGCGCGTGCGTTAAACGCTGCTCTTGAAGGAAC 1 158 1 GGTAAAGTGC 0.890691 -110 CGCTGCTCTTGAAGGAACGGTGGTGCACGCGCTGTTAT 1 178 1 GAACGGGTGC 0.966273 -90 AGCGACTTGACACCGCTGCCCGGAAAGGTGT 2 4 1 GCACACGTGC 0.997476 -150 CTCGGGTGAAGAGAACACACCGTTGTACAGTCTACACA 2 80 0 GGACACGTGC 0.998678 -74 * * **** * ** * Masking position 12 Map Score: 11.2983 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 124 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 3 TGCGCGGGCTTGTGTGCTCTGAAGTCGGGC 1 56 1 TGTGTGCTCT 0.979826 -212 GTGCACGCGCTGTTATCTCCTCTTGGTTTG 1 200 1 TGTTATCTCC 0.930516 -68 ATCTCCTCTTGGTTTGCGCGCGTATTTTCC 1 214 1 GGTTTGCGCG 0.962802 -54 TTTGCGCGCGTATTTTCCCCACGGGATTGT 1 226 1 TATTTTCCCC 0.900354 -42 CCCGGAAAGGTGTTTTCGCTAGAAAGGCTG 2 29 1 TGTTTTCGCT 0.984739 -125 TGTACAACGGTGTGTTCTCTTCACCCGAGG 2 89 1 TGTGTTCTCT 0.975732 -65 TTGAGGCGGCTGTTTGCCCGCGTGTGTTTC 2 129 1 TGTTTGCCCG 0.988252 -25 ********** Masking position 3 Map Score: 6.66186 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 191 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 GATGAGCTTCCTGCGGCAAATGGTTACACAAAC 1 15 0 CTGCGAAAGG 0.988799 -253 GAAGGCGCGCGTGCGTTAAACGCTGCTCTTGAA 1 158 1 GTGCGAAAGC 0.935942 -110 AAACGCTGCTCTTGAAGGAACGGTGGTGCACGC 1 175 1 CTTGAGAAGG 0.889638 -93 CACGGGATTGTTGCACAGAATGCAGAGGCGCGG 1 245 1 TTGCAGAAGC 0.947586 -23 CTTGACACCGCTGCCCGGAAAGGTGTTTTCGCT 2 16 1 CTGCCGAAGG 0.997037 -138 GAAAGGTGTTTTCGCTAGAAAGGCTGTGGCTCG 2 33 1 TTCGCGAAGG 0.958538 -121 AAGGCTGTGGCTCGCCAGAAGTCCCGAATGTGT 2 52 1 CTCGCGAATC 0.920062 -102 CGCGCACCACCTCGGGTGAAGAGAACACACCGT 2 95 0 CTCGGGAAAG 0.876151 -59 GGGCAAACAGCCGCCTCAAACGCGCACCACCTC 2 115 0 CCGCCAAAGC 0.967688 -39 AACTTTCCCCTGCCAGAAAAGCATTT 3 5 0 CTGCCAAAGC 0.993086 -22 ***** *** ** Masking position 9 Map Score: 7.86112 Number of sites scoring better than the average of aligned sites = 685 Number in coding regions = 634 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 5 ACACAAGCCCGCGCAGCCACACGGATGAGCT 1 40 0 GCGAGCCACA 0.944627 -228 AATCGACAGCCCGACTTCAGAGCACACAAGC 1 63 0 CCGCTTCAGA 0.943362 -205 ATGCACCCCAGTGAATCGACAGCCCGACTTC 1 76 0 GTGATCGACA 0.946069 -192 GTCAGGGGGCGTGTCTACACTGTGAGACATG 1 118 1 GTGCTACACT 0.885328 -150 TAACGCACGCGCGCCTTCAGAGAGGTCCATG 1 145 0 GCGCTTCAGA 0.982041 -123 CCGCGCCTCTGCATTCTGTGCAA 1 255 0 GCGCTCTGCA 0.938408 -13 AGCGACTTGACACCGCTGCCCG 2 2 1 GCGCTTGACA 0.991019 -152 TAGAAAGGCTGTGGCTCGCCAGAAGTCCCGA 2 48 1 GTGCTCGCCA 0.959451 -106 CACCGTTGTACAGTCTACACATTCGGGACTT 2 70 0 CAGCTACACA 0.855153 -84 *** ******* Masking position 3 Map Score: 5.04828 Number of sites scoring better than the average of aligned sites = 584 Number in coding regions = 534 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 6 ********** No masking Map Score: -3.81261e-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: -3.81261e-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: -3.81261e-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