AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i254_soj_tpal_reg_300.orf -o254_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 RTP00369 300 AE000520 #2 RTP00372 39 AE000520 #3 RTP00841 132 AE000520 #4 RTP00712 151 AE000520 Motif number 1 GTGAAGCGTGCAATACACCGGCGTAGTCT 1 6 0 CACACGGCGT 0.808274 -295 AATCGTCACAGAAATCCCCACTGCCACACCAAAA 1 67 1 GACCCACTGC 0.88828 -234 CCGCCACTGAGTACGAAGGAGCGCGCGATAGTTT 1 99 0 GTAAGAGCGC 0.88605 -202 CGTACTCAGTGGCGGTAGCTCCGCGCCAGGAATA 1 118 1 GGTACTCCGC 0.856082 -183 CTCCGCGCCAGGAATAATCAGCGCCCACCATGTC 1 136 1 GGAACAGCGC 0.995485 -165 GTGCATTCCCGATAGTAACGCTGCTCTCTTTTAT 1 218 0 GATACGCTGC 0.897567 -83 TTTTGAAGCGCTGTCCATCGGTGCATTCCCGATA 1 238 0 CTCACGGTGC 0.889132 -63 CTTCTCATAGGGGGCAAGCAGAGCACAA 2 22 1 GGAACAGAGC 0.971383 -18 CACGTTATGAGGTTACCTCGGCGCGTAGTTCCTT 3 20 1 GGCCCGGCGC 0.995445 -113 TACCACGCACAACATAATCAGCGCTAAAGGAAAT 3 66 1 AAAACAGCGC 0.921814 -67 CCCGGCCACTGATCGAAACGGCGCGCAATACCGA 4 27 0 GAAACGGCGC 0.996737 -125 ATCAGTGGCCGGGAAAAACGCAGCTCGTCATTCC 4 48 1 GGAACGCAGC 0.962921 -104 CGGGCACTCTGACGCACTCAGCGCAGTGGACACC 4 88 1 GAACCAGCGC 0.986947 -64 ACTCAGCGCAGTGGACACCGGCGCCATTTCTGAC 4 103 1 GTCACGGCGC 0.994641 -49 ** ** ****** Masking position 13 Map Score: 19.9237 Number of sites scoring better than the average of aligned sites = 1284 Number in coding regions = 1199 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 2 CGGTGTATTGCACGCTTCACTGCACGATACGTCA 1 20 1 CCGCTTCGCA 0.954979 -281 TCAATTAATCCAATCGTCACAGAAATCCCCACTG 1 56 1 CATCGTCGAA 0.949978 -245 CAAAAACTATCGCGCGCTCCTTCGTACTCAGTGG 1 96 1 CCGCGCCTCG 0.867758 -205 TGGCGCGGAGCTACCGCCACTGAGTACGAAGGAG 1 112 0 CACCGCCGAG 0.963774 -189 TAATCAGCGCCCACCATGTCGGAGGCTTTGTCGA 1 150 1 CACCATCGAG 0.971767 -151 GAGGCTTTGTCGACCATTGCTGAATAAGACGTAT 1 171 1 CACCATCGAA 0.976713 -130 TCATAGGGGGCAAGCAGAGCACAA 2 26 1 CAGCAGCCAA 0.856479 -14 ATGATGCTACCACGCACAACATAATCAGCGCTAA 3 59 1 CCGCACCTAA 0.94024 -74 AAAAGTTTAGCCATCATTGCGGCATTTCCTTTAG 3 89 0 CATCATCGCA 0.949979 -44 CTCTCCCCCGAGCACGTCGGTATTGCGCGCCG 4 9 1 CAGCACCGTA 0.965337 -143 CACTCTGACGCACTCAGCGCAGTGGACACCGGCG 4 92 1 CCTCAGCGTG 0.819735 -60 CGCTCCACCACCCGCTTGTCAGAAATGGCGCCGG 4 120 0 CCGCTTCGAA 0.96752 -32 * ***** * *** Masking position 5 Map Score: 9.78221 Number of sites scoring better than the average of aligned sites = 1073 Number in coding regions = 991 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 3 GTAGCTCCGCGCCAGGAATAATCAGCGCCC 1 132 1 GCCAGGAATA 0.975003 -169 CAGCGTTACTATCGGGAATGCACCGATGGA 1 229 1 ATCGGGAATG 0.953242 -72 ACACTCATGCACCTGAAAAGTTTAGCCATC 3 108 0 ACCTGAAAAG 0.881995 -25 TCGATCAGTGGCCGGGAAAAACGCAGCTCG 4 45 1 GCCGGGAAAA 0.983696 -107 GCGTCAGAGTGCCCGGAAAGGGGAATGACG 4 73 0 GCCCGGAAAG 0.989798 -79 CCACCCGCTTGTCAGAAATGGCGCCGGTGT 4 117 0 GTCAGAAATG 0.929477 -35 ********** Masking position 7 Map Score: 2.81642 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 160 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 4 ACGAAGGAGCGCGCGATAGTTTTTGGTGTG 1 91 0 GCGCGATAGT 0.905925 -210 ACTATCGCGCGCTCCTTCGTACTCAGTGGC 1 101 1 GCTCCTTCGT 0.94495 -200 CGGAGCTACCGCCACTGAGTACGAAGGAGC 1 111 0 GCCACTGAGT 0.926189 -190 AGCGCCTCCGTCTTCTCATAG 2 2 1 GCGCCTCCGT 0.986806 -38 AACTTTTCAGGTGCATGAGTGTGGACT 3 116 1 GTGCATGAGT 0.859302 -17 TGCGCTGAGTGCGTCAGAGTGCCCGGAAAG 4 83 0 GCGTCAGAGT 0.965977 -69 GTCAGAAATGGCGCCGGTGTCCACTGCGCT 4 107 0 GCGCCGGTGT 0.974331 -45 GGGTGGTGGAGCGGCTGCGTG 4 141 1 GCGGCTGCGT 0.986806 -11 ********** Masking position 10 Map Score: 4.8888 Number of sites scoring better than the average of aligned sites = 709 Number in coding regions = 654 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 5 CCCACCATGTCGGAGGCTTTGTCGACCATT 1 159 1 CGGAGGCTTT 0.938272 -142 TTGTATCGTTTTGAAGCGCTGTCCATCGGT 1 250 0 TTGAAGCGCT 0.898591 -51 TATGAGAAGACGGAGGCGCT 2 1 0 CGGAGGCGCT 0.998042 -39 GCGCGCAATACCGACGTGCTCGGGGGAGAG 4 11 0 CCGACGTGCT 0.953049 -141 TCCGGGCACTCTGACGCACTCAGCGCAGTG 4 86 1 CTGACGCACT 0.967677 -66 CACGCAGCCGCTCCACCACCCG 4 140 0 CGCAGCCGCT 0.963875 -12 ********** Masking position 4 Map Score: 1.3763 Number of sites scoring better than the average of aligned sites = 428 Number in coding regions = 406 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 ACTGAGTACGAAGGAGCGCGCGATAGTTTT 1 98 0 AAGGAGCGCG 0.931147 -203 GTCTTCTCATAGGGGGCAAGCAGAGCACAA 2 20 1 AGGGGGCAAG 0.984602 -20 CTAAACTTTTCAGGTGCATGAGTGTGGACT 3 113 1 CAGGTGCATG 0.975531 -20 CCGACGTGCTCGGGGGAGAG 4 1 0 CGGGGGAGAG 0.981626 -151 AGTGCCCGGAAAGGGGAATGACGAGCTGCG 4 66 0 AAGGGGAATG 0.951669 -86 GGTGGTGGAGCGGCTGCGTG 4 142 1 CGGCTGCGTG 0.958418 -10 ********** Masking position 6 Map Score: 1.92879 Number of sites scoring better than the average of aligned sites = 566 Number in coding regions = 515 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 7 ATTGACGTGACGTATCGTGCAGTGAAGCGTGC 1 29 0 CGTTCTGCAG 0.993306 -272 TGACATCATACGTCTTATTCAGCAATGGTCGA 1 180 0 CGTTTTTCAG 0.965244 -121 CAGAAAGAATTGTATCGTTTTGAAGCGCTGTC 1 257 0 TGTTCTTTTG 0.904456 -44 AACCTCATAACGTGCCCTGTTGC 3 2 0 CGTCCTGTTG 0.948848 -131 ATCATTGCGGCATTTCCTTTAGCGCTGATTAT 3 79 0 CATTCTTTAG 0.946417 -54 TATTGCGCGCCGTTTCGATCAGTGGCCGGGAA 4 31 1 CGTTCATCAG 0.977897 -121 *** ** ***** Masking position 3 Map Score: 0.0822464 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 194 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 ********** No masking Map Score: 1.58694e-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: 1.58694e-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: 1.58694e-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