AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i299_mixed14_tpal_reg_100.orf -o299_tpal_100.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 RTP00961 300 AE000520 #2 RTP00429 59 AE000520 #3 RTP00462 131 AE000520 Motif number 1 AGACCTCCAGCCTATCGACCTTGTAGTGTG 1 67 1 CCTATCGACC 0.904415 -234 CCTGAAGACTCCTTGCACACTACAAGGTCG 1 82 0 CCTTGCACAC 0.956337 -219 AGCGGTTATCCCTTCCGAACATAGCTACCC 1 169 1 CCTTCCGAAC 0.955752 -132 CCAGCACGTACCCTTGGCAGGATAACTGGT 1 197 1 CCCTTGGCAG 0.946595 -104 CCACTTCGGTCCTCTCGTACTAAAAGCAGC 1 242 1 CCTCTCGTAC 0.983786 -59 AAAAGCAGCTCCTCTCACATATCCAACGCC 1 263 1 CCTCTCACAT 0.936241 -38 ATATCCAACGCCCATAGCAGATAGGGACCG 1 281 1 CCCATAGCAG 0.86664 -20 TTTACCTCCGACAGTTTTGTATAA 2 5 1 CCTCCGACAG 0.89801 -55 CTATCACAGCCCTATCGCACCGCGCA 3 7 0 CCTATCGCAC 0.996096 -125 TATTCGAAAGCCTATCACAGCCCTATCGCA 3 18 0 CCTATCACAG 0.984485 -114 TTACTCGAGACCTTTCGTACCTAATATTCG 3 42 0 CCTTTCGTAC 0.980485 -90 ********** Masking position 2 Map Score: 13.9905 Number of sites scoring better than the average of aligned sites = 585 Number in coding regions = 516 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 2 ACCTTACGGTACGTAGACCTCCAGCCTATCGACCT 1 53 1 ACGAGCCAGC 0.995461 -248 GAAGGCATCTAAGTGGGAAGCCCGCCTCAAGATTA 1 134 0 AAGGGCCCGC 0.993872 -167 TCCCTTCCGAACATAGCTACCCAGCACGTACCCTT 1 177 1 ACAAGCCAGC 0.994522 -124 TAAAGGCATTTCGGGGAGAACCAGCT 2 44 1 TCGGGCCAGC 0.989145 -16 TGACGTTCTCACAACGCCTCCGAGCGCGCGTATAC 3 73 1 ACACGCGAGC 0.995344 -59 GCGCGACTATACACCGTATACGCGCGCTCGGAGGC 3 88 0 ACACGCGCGC 0.99612 -44 TCCCTCAGAAATGGAGATCGCGCGACTATACAC 3 109 0 AAAGGCGCGC 0.990352 -23 *** ** ***** Masking position 6 Map Score: 10.0411 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 128 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 3 AGTACTAATAAGTCGTGAGGCTTGACCATA 1 11 0 AGTCGTGAGG 0.984961 -290 GAGGTCTACGTACCGTAAGGTATTAAGCCG 1 44 0 TACCGTAAGG 0.892424 -257 CAAGGTCGATAGGCTGGAGGTCTACGTACC 1 60 0 AGGCTGGAGG 0.947423 -241 GTGTGCAAGGAGTCTTCAGGAAGGTCAACC 1 92 1 AGTCTTCAGG 0.991428 -209 CAGGAAGGTCAACCTTCAGGGATATGTAAT 1 108 1 AACCTTCAGG 0.989404 -193 AGGGATATGTAATCTTGAGGCGGGCTTCCC 1 125 1 AATCTTGAGG 0.978359 -176 CCCACTTAGATGCCTTCAGCGGTTATCCCT 1 152 1 TGCCTTCAGC 0.961006 -149 CTCCCCGAAATGCCTTTAGGGACAGCCTTA 2 32 0 TGCCTTTAGG 0.974011 -28 ********** Masking position 8 Map Score: 10.0684 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 141 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 4 TCAAGCCTCACGACTTATTAGTACTGGTCGGCTT 1 16 1 CGACATGTAC 0.981267 -285 TCCAGCCTATCGACCTTGTAGTGTGCAAGGAGTC 1 72 1 CGACTTGTGT 0.991158 -229 CCGAAGTGGACGAACCTCTGGTGTACCAGTTATC 1 217 0 CGAATTGTGT 0.980324 -84 TCGTCCACTTCGGTCCTCTCGTACTAAAAGCAGC 1 238 1 CGGTTTGTAC 0.951445 -63 TTTACCTCCGACAGTTTTGTATAAGGCTGTCC 2 9 1 CGACTTGTAT 0.992657 -51 GATAGGCTTTCGAATATTAGGTACGAAAGGTCTC 3 32 1 CGAATAGTAC 0.958864 -100 **** * * **** Masking position 12 Map Score: 2.53173 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 29 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 5 TCTTCAGGAAGGTCAACCTTCAGGGATATG 1 104 1 GGTCAACCTT 0.85703 -197 GCTTCCCACTTAGATGCCTTCAGCGGTTAT 1 148 1 TAGATGCCTT 0.910647 -153 TATGTGAGAGGAGCTGCTTTTAGTACGAGA 1 254 0 GAGCTGCTTT 0.972223 -47 ATGCCTTTAGGGACAGCCTTATACAAAACT 2 23 0 GGACAGCCTT 0.974842 -37 GGTTCTCCCCGAAATGCCTTTAGGGACAGC 2 36 0 GAAATGCCTT 0.977058 -24 ATAGGGCTGTGATAGGCTTTCGAATATTAG 3 22 1 GATAGGCTTT 0.89409 -110 ********** Masking position 9 Map Score: 0.330442 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 179 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 ********** No masking Map Score: 6.2771e-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: 6.2771e-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: 6.2771e-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