AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i034_Pyruvate_Synthase_2_tpal_reg_300.orf -o034_tpal_300.ace -a/home/amcguire/alignace/lib/ORF_tpal.txt -z/skink1/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 RTP01203 38 AE000520 #2 RTP00707 76 AE000520 #3 RTP00709 48 AE000520 #4 RTP00710 170 AE000520 #5 RTP00711 151 AE000520 Motif number 1 AACTGGAACAGCGCGCCGATCCGCCCTTCCAC 2 19 0 GCGCGCCGCC 0.998688 -58 ACGGGGGGCTGTGCACCGCGCCTGTAATTTTA 3 24 0 GTGCACCGCC 0.995123 -25 GCGGTGCACAGCCCCCCGTTCG 3 37 1 GCCCCCCGCG 0.965142 -12 GCAGTGCACCGCGCACCCTTTCTG 4 3 0 GCGCACCCTC 0.995521 -168 CTGCATGCGCGCGCAGTGCACCGCGCACCCTT 4 15 0 GCGCAGTGCC 0.991664 -156 CTGCGCGCGCATGCAGCGAGTGCATCGCACGC 4 31 1 ATGCAGCGTG 0.964924 -140 TCGCTGATGCGTGCAGCGTGCGATGCACTCGC 4 46 0 GTGCAGCGCG 0.992058 -125 CTAAGGACGCACGCGCCGAGTCGCTGATGCGT 4 66 0 ACGCGCCGTC 0.99407 -105 CGGGCACTACTTGCGCTGTACCGAGTCACGCG 4 100 0 TTGCGCTGCC 0.88082 -71 CGCAAGTAGTGCCCGCTCATCGAGGCCGAACG 4 117 1 GCCCGCTCCG 0.940815 -54 GAGGCCGAACGTGCAGCGGGTGAGCCCTTTGA 4 138 1 GTGCAGCGTG 0.987273 -33 CACGCAGCCGCTCCACCACCCGC 5 2 1 ACGCAGCCTC 0.983644 -150 GGGCACTCTGACGCACTCAGCGCAGTGGACAC 5 52 0 ACGCACTCCG 0.95547 -100 GCCGGGAAAAACGCAGCTCGTCATTCCCCTTT 5 86 0 ACGCAGCTTC 0.904996 -66 GCTGCGTTTTTCCCGGCCACTGATCGAAACGG 5 101 1 TCCCGGCCTG 0.846116 -51 CGTCGGTATTGCGCGCCGTTTCGATCAGTGGC 5 116 0 GCGCGCCGTC 0.997892 -36 ******** ** Masking position 4 Map Score: 37.6388 Number of sites scoring better than the average of aligned sites = 3117 Number in coding regions = 2871 Number in noncoding regions = 246 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 2 GAACAGCGCGCCGATCCGCCCTTCCACGATGGAGG 2 8 0 CCGGCTCACG 0.973283 -69 AAAATTACAGGCGCGGTGCACAGCCCCCCGTTCG 3 25 1 GCGGCACCCC 0.862358 -24 CGCTGCATGCGCGCGCAGTGCACCGCGCACCCTTTCTG 4 11 0 GCGGCAGCGC 0.580682 -160 GATGCGTGCAGCGTGCGATGCACTCGCTGCATGCGCGC 4 35 0 GCGACACGCT 0.967372 -136 GACGCACGCGCCGAGTCGCTGATGCGTGCAGCGTGCGA 4 55 0 CCGGGACGTG 0.962525 -116 CGAGTCACGCGTGCTAAGGACGCACGCGCCGAGTCGCT 4 73 0 GTGGCGCGCG 0.968119 -98 GGCACTACTTGCGCTGTACCGAGTCACGCGTGCTAAGG 4 92 0 GCGAGACACG 0.946238 -79 GCACGTTCGGCCTCGATGAGCGGGCACTACTTGCGCTG 4 114 0 CCTGCGCACT 0.731242 -57 TTTCTGACAAGCGGGTGGTGGAGCGGCTGCGTG 5 6 0 GCGGGAGGCT 0.989245 -146 GACGCACTCAGCGCAGTGGACACCGGCGCCATTTCTGA 5 37 0 GCGGCAGGCG 0.996258 -115 GTCAGAGTGCCCGGAAAGGGGAATGACGAGCTGCGTTT 5 72 1 CCGGGAGACG 0.990333 -80 GTATTGCGCGCCGTTTCGATCAGTGGCCGGGAAAAACG 5 105 0 CCGGCAGGCC 0.996246 -47 GCGCGCAATACCGACGTGCTCGGGGGAGAG 5 132 1 CCGGCGGGAG 0.963767 -20 *** * ** **** Masking position 2 Map Score: 17.7263 Number of sites scoring better than the average of aligned sites = 1870 Number in coding regions = 1741 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 3 CCTCCATCGTGGAAGGGCGGATCGGCGC 2 9 1 GTGGAAGGGC 0.990698 -68 CTTCCAAAAACTGGAACAGCGCGCCGATCC 2 29 0 CTGGAACAGC 0.93581 -48 AATTTTAAGAGACGGACGGC 3 1 0 GACGGACGGC 0.980729 -48 CGAACGGGGGGCTGTGCACCGC 3 37 0 AACGGGGGGC 0.894635 -12 CAGAAAGGGTGCGCGGTGCA 4 1 1 CAGAAAGGGT 0.770071 -170 CGCGCGCATGCAGCGAGTGCATCGCACGCT 4 34 1 CAGCGAGTGC 0.829956 -137 CACGTTCGGCCTCGATGAGCGGGCACTACT 4 121 0 CTCGATGAGC 0.797723 -50 CGAAGGTATCCTCAAAGGGCTCACCCGCTG 4 151 0 CTCAAAGGGC 0.979025 -20 CAAGCGGGTGGTGGAGCGGCTGCGTG 5 7 0 GTGGAGCGGC 0.974917 -145 ACCCGCTTGTCAGAAATGGCGCCGGTGTCC 5 28 1 CAGAAATGGC 0.839031 -124 CGCTGAGTGCGTCAGAGTGCCCGGAAAGGG 5 62 1 GTCAGAGTGC 0.900836 -90 AAAGGGGAATGACGAGCTGCGTTTTTCCCG 5 86 1 GACGAGCTGC 0.916451 -66 ********** Masking position 9 Map Score: 10.773 Number of sites scoring better than the average of aligned sites = 1119 Number in coding regions = 998 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 4 AATCGGTTCATCTGCCAAGATGA 1 26 1 TCTGCCAAGA 0.77526 -13 GCCGATCCGCCCTTCCACGATGGAGG 2 7 0 CCTTCCACGA 0.991965 -70 ACGTGCCAAACCTTCCAAAAACTGGAACAG 2 40 0 CCTTCCAAAA 0.985393 -37 CCTTGCAAAACTTCAAGACG 2 67 0 CCTTGCAAAA 0.915449 -10 CTCTCCCCCGAGCACGTCGGT 5 141 0 TCTCCCCCGA 0.954201 -11 ********** Masking position 3 Map Score: 2.83111 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 83 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 ********** No masking Map Score: -6.37056e-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 6 ********** No masking Map Score: -6.37056e-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: -6.37056e-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