AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i299_mixed14_tpal_reg_300.orf -o299_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 RTP00961 300 AE000520 #2 RTP00429 59 AE000520 #3 RTP01176 165 AE000520 #4 RTP00462 131 AE000520 Motif number 1 GGCTTAATACCTTACGGTACGTAGACCTCC 1 45 1 CTTACGGTAC 0.472361 -256 AGACCTCCAGCCTATCGACCTTGTAGTGTG 1 67 1 CCTATCGACC 0.815605 -234 CCTGAAGACTCCTTGCACACTACAAGGTCG 1 82 0 CCTTGCACAC 0.90916 -219 CACTTAGATGCCTTCAGCGGTTATCCCTTC 1 154 1 CCTTCAGCGG 0.637211 -147 AGCGGTTATCCCTTCCGAACATAGCTACCC 1 169 1 CCTTCCGAAC 0.905948 -132 AACATAGCTACCCAGCACGTACCCTTGGCA 1 186 1 CCCAGCACGT 0.552663 -115 CCAGCACGTACCCTTGGCAGGATAACTGGT 1 197 1 CCCTTGGCAG 0.914414 -104 AGTGGACGAACCTCTGGTGTACCAGTTATC 1 217 0 CCTCTGGTGT 0.629979 -84 CCACTTCGGTCCTCTCGTACTAAAAGCAGC 1 242 1 CCTCTCGTAC 0.964038 -59 AAAAGCAGCTCCTCTCACATATCCAACGCC 1 263 1 CCTCTCACAT 0.847979 -38 ATATCCAACGCCCATAGCAGATAGGGACCG 1 281 1 CCCATAGCAG 0.836584 -20 TTTACCTCCGACAGTTTTGTATAA 2 5 1 CCTCCGACAG 0.784727 -55 ATGATCGCTCATCGCACCGCTCCATAG 3 8 1 CTCATCGCAC 0.874179 -158 ACACACATACCCTATGGAGCGGTGCGATGA 3 19 0 CCTATGGAGC 0.899395 -147 CTATCACAGCCCTATCGCACCGCGCA 4 7 0 CCTATCGCAC 0.993576 -125 TATTCGAAAGCCTATCACAGCCCTATCGCA 4 18 0 CCTATCACAG 0.951018 -114 TTACTCGAGACCTTTCGTACCTAATATTCG 4 42 0 CCTTTCGTAC 0.954183 -90 CACAACGCCTCCGAGCGCGCGTATACGGTG 4 82 1 CCGAGCGCGC 0.876842 -50 ********** Masking position 1 Map Score: 13.6958 Number of sites scoring better than the average of aligned sites = 2764 Number in coding regions = 2502 Number in noncoding regions = 262 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 2 TATGGTCAAGCCTCACGACTTATTAGTA 1 9 1 AGCCTCACGA 0.980342 -292 GTGGGAAGCCCGCCTCAAGATTACATATCC 1 127 0 CGCCTCAAGA 0.898304 -174 TACCCTATGGAGCGGTGCGATGAGCGATCA 3 12 0 AGCGGTGCGA 0.992264 -154 GCGAGTCGCTCGTGGTACGCACAGGCGTTA 3 50 1 CGTGGTACGC 0.969649 -116 GCGAACAAAAAGCGTTACGCTTTTGTGCCC 3 107 0 AGCGTTACGC 0.971769 -59 AAAAAGCGCGGCACGTAAAATAAACG 3 150 0 CGCGGCACGT 0.987838 -16 TGCGCGGTGCGATAGGGCTGTG 4 3 1 CGCGGTGCGA 0.995109 -129 TACGGTGTATAGTCGCGCGATCTCCATTTC 4 105 1 AGTCGCGCGA 0.966215 -27 ********** Masking position 2 Map Score: 10.0688 Number of sites scoring better than the average of aligned sites = 803 Number in coding regions = 747 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 3 AGGCTGGAGGTCTACGTACCGTAAGGTATT 1 50 0 TCTACGTACC 0.964297 -251 GGTGTACCAGTTATCCTGCCAAGGGTACGT 1 202 0 TTATCCTGCC 0.904341 -99 ATGATCGCTCATCGCACCGCTCCATAGG 3 9 1 TCATCGCACC 0.956906 -157 AACTAACGCCTGTGCGTACCACGAGCGACT 3 53 0 TGTGCGTACC 0.915605 -113 AAGCGTTACGCTTTTGTGCCCTTCTCCAAA 3 98 0 CTTTTGTGCC 0.909337 -68 AAGCGTTTATTTTACGTGCCGCGCTTTTT 3 147 1 TTTACGTGCC 0.975502 -19 TATCACAGCCCTATCGCACCGCGCA 4 6 0 CTATCGCACC 0.97001 -126 TACTCGAGACCTTTCGTACCTAATATTCGA 4 41 0 CTTTCGTACC 0.989182 -91 ********** Masking position 9 Map Score: 5.80481 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 220 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 TATGGTCAAGCCTCACGACTTATTAGTACT 1 11 1 CCTCACGACT 0.967901 -290 CGGCTTAATACCTTACGGTACGTAGACCTC 1 44 1 CCTTACGGTA 0.798662 -257 GGTACGTAGACCTCCAGCCTATCGACCTTG 1 60 1 CCTCCAGCCT 0.94649 -241 GGTTGACCTTCCTGAAGACTCCTTGCACAC 1 92 0 CCTGAAGACT 0.987809 -209 ATTACATATCCCTGAAGGTTGACCTTCCTG 1 108 0 CCTGAAGGTT 0.985494 -193 GGGAAGCCCGCCTCAAGATTACATATCCCT 1 125 0 CCTCAAGATT 0.952871 -176 AGGGATAACCGCTGAAGGCATCTAAGTGGG 1 152 0 GCTGAAGGCA 0.949432 -149 TAAGGCTGTCCCTAAAGGCATTTCGGGGAG 2 32 1 CCTAAAGGCA 0.961182 -28 AACGCTTCATCCTGCAGGCGAACAAAAAGC 3 124 0 CCTGCAGGCG 0.973719 -42 ********** Masking position 3 Map Score: 10.1023 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 198 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 GAGGCGGGCTTCCCACTTAGATGCCTTCAGCGG 1 141 1 TCCCCAGATG 0.99024 -160 CGGTCCCTATCTGCTATGGGCGTTGG 1 285 0 TCCCATGCTA 0.89398 -16 AGCTGGTTCTCCCCGAAATGCCTTTAGGGA 2 40 0 TCTCCAAATG 0.976264 -20 TTTGTGCCCTTCTCCAAATGCTGAAAGAGAAAG 3 83 0 TCTCATGCTG 0.971962 -83 GTACGAAAGGTCTCGAGTAACTGACGTTCTCAC 4 52 1 TCTCAAACTG 0.976266 -80 TCCCTCAGAAATGGAGATCGCGC 4 119 0 TCCCCAAATG 0.984773 -13 **** * ***** Masking position 12 Map Score: 1.52412 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 64 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 ********** No masking Map Score: -1.70998e-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 7 ********** No masking Map Score: -1.70998e-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 8 ********** No masking Map Score: -1.70998e-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