AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i301_mixed16_tpal_reg_300.orf -o301_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 RTP00110 135 AE000520 #2 RTP00774 72 AE000520 #3 RTP00775 171 AE000520 Motif number 1 ATATCGCAGAGCACCGTTTTTAA 1 2 0 GCACGTTTTA 0.954824 -134 ACGCAGCATTGCACGCCATTCGGCACCATATG 1 36 1 GCACCCTTCG 0.960045 -100 ACGCCATTCGGCACCATATGCAAGAGGCAGAT 1 48 1 GCACATTGCA 0.971881 -88 AGAGGCAGATGCGCAGAATGCGCTCATTGCGC 1 70 1 GCGCGATGCG 0.995146 -66 AAACAGCGCAACGCAGCGCGCAATGAGCGCAT 1 87 0 ACGCGCCGCA 0.977034 -49 GCGCTGCGTTGCGCTGTTTGCGGCACAGGATA 1 100 1 GCGCGTTGCG 0.997883 -36 TTAGGCAAGCGCGCAGCCTGCACACCCGCGGG 2 32 0 GCGCGCTGCA 0.998864 -41 CGCCTCTTCTGCACTGAATCCACTGATACTC 3 10 0 GCACGATCCA 0.982385 -162 GCGCTGCGCAGCGCGGTTTTCAGATTTTGCGC 3 39 0 GCGCGTTTCA 0.994959 -133 AAACCGCGCTGCGCAGCGCCTGGTTAAACGTT 3 52 1 GCGCGCCCTG 0.985408 -120 TCTATTTCAAGCGCAACGTTTAACCAGGCGCT 3 66 0 GCGCACTTTA 0.912156 -106 AGAGTATTCGGCAGGGTACGCGCGCGCTGGTG 3 133 1 GCAGGTCGCG 0.947838 -39 ACCGCGCACAGCCCCCACACCAGCGCG 3 155 0 GCACGCCCCA 0.994446 -17 **** ** **** Masking position 2 Map Score: 29.1762 Number of sites scoring better than the average of aligned sites = 2196 Number in coding regions = 2049 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 2 TTAAAAACGGTGCTCTGCGATATACACG 1 9 1 GGTGCTCTGC 0.943866 -127 CTCTGCGATATACACGCAGCATTGCACGCC 1 23 1 TACACGCAGC 0.907595 -113 GCGCAATGAGCGCATTCTGCGCATCTGCCT 1 72 0 CGCATTCTGC 0.925174 -64 ATGCGCTCATTGCGCGCTGCGTTGCGCTGT 1 87 1 TGCGCGCTGC 0.99877 -49 CCCGCGGGTGTGCAGGCTGCGCGCTTGCCT 2 32 1 TGCAGGCTGC 0.990824 -41 AAATCTGAAAACCGCGCTGCGCAGCGCCTG 3 44 1 ACCGCGCTGC 0.970644 -128 AACGTTTAACCAGGCGCTGCGCAGCGCGGT 3 54 0 CAGGCGCTGC 0.989054 -118 CCAGCGCGCGCGTACCCTGCCGAATACTCT 3 133 0 CGTACCCTGC 0.955125 -39 GCAGGGTACGCGCGCGCTGGTGTGGGGGCT 3 143 1 CGCGCGCTGG 0.994204 -29 CGCGCTGGTGTGGGGGCTGTGCGCGGT 3 155 1 TGGGGGCTGT 0.897704 -17 ********** Masking position 7 Map Score: 15.027 Number of sites scoring better than the average of aligned sites = 1913 Number in coding regions = 1790 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 3 TTTCCCCGCGGGTGTGCAGGCTGCGCGCTT 2 28 1 GGTGTGCAGG 0.992131 -45 AAATCAGCAGGTTGTCGGGGCGAGTATGGG 3 98 1 GTTGTCGGGG 0.966784 -74 TGTCGGGGCGAGTATGGGGGAAGAGAGTAT 3 110 1 AGTATGGGGG 0.981526 -62 TATTCGGCAGGGTACGCGCGCGCTGGTGTG 3 137 1 GGTACGCGCG 0.981265 -35 CGCGCGCGCTGGTGTGGGGGCTGTGCGCGG 3 151 1 GGTGTGGGGG 0.998783 -21 GTGTGGGGGCTGTGCGCGGT 3 162 1 TGTGCGCGGT 0.952465 -10 ********** Masking position 3 Map Score: 6.13953 Number of sites scoring better than the average of aligned sites = 781 Number in coding regions = 687 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 4 GCGCATCTGCCTCTTGCATATGGTGCCGAA 1 54 0 CTCTTGCATA 0.810042 -82 ATGAGCGCATTCTGCGCATCTGCCTCTTGC 1 67 0 TCTGCGCATC 0.763503 -69 AAGGCAGTATCCTGTGCCGCAAACAGCGCA 1 109 0 CCTGTGCCGC 0.982995 -27 CAGGATACTGCCTTTTCCTAC 1 125 1 CCTTTTCCTA 0.51042 -11 AATCGTTTTTCTTTCCCCGCGGGTGTGCAG 2 17 1 CTTTCCCCGC 0.954696 -56 GCAGGCTGCGCGCTTGCCTAAGGTGGAGCC 2 43 1 CGCTTGCCTA 0.919203 -30 GTTTTCAGATTTTGCGCCTCTTCTGCACTG 3 26 0 TTTGCGCCTC 0.923132 -146 TGAAAACCGCGCTGCGCAGCGCCTGGTTAA 3 49 1 GCTGCGCAGC 0.490936 -123 TTCCCCCATACTCGCCCCGACAACCTGCTG 3 102 0 CTCGCCCCGA 0.971201 -70 GCCGAATACTCTCTTCCCCCATACTCGCCC 3 115 0 CTCTTCCCCC 0.777807 -57 CCCACACCAGCGCGCGCGTACCCTGCCGAA 3 139 0 CGCGCGCGTA 0.900503 -33 ACCGCGCACAGCCCCCACACCA 3 160 0 CGCGCACAGC 0.864234 -12 ********** Masking position 7 Map Score: 5.20162 Number of sites scoring better than the average of aligned sites = 6302 Number in coding regions = 5795 Number in noncoding regions = 507 Number of orfs with sites within 600 bp upstream = 274 Fraction of orfs with sites within 600 bp upstream = 0.044009 Motif number 5 ********** No masking Map Score: 1.65857e-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: 1.65857e-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: 1.65857e-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