AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i316_mixed3_tpal_reg_300.orf -o316_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 RTP01026 91 AE000520 #2 RTP00753 300 AE000520 Motif number 1 ACGCTCAGCGCGCCGCTCATGCAGA 1 77 0 CAGCGCGCCG 0.711512 -15 ACATGAATTGTGCACGTTGCAGGAAGA 2 8 1 TTGTGCACGT 0.914762 -293 GGTCATCGTGCAGCGCACGATTGGTTTTCT 2 58 1 CAGCGCACGA 0.903208 -243 GATTGGTTTTCTGTACACCACACGTGTTCT 2 76 1 CTGTACACCA 0.944375 -225 CTACCATGCACTGTGCTCGAAACTGGCGTG 2 104 1 CTGTGCTCGA 0.939359 -197 GAGCGCAACGTTGCGCACCGAAAGTTGCTC 2 178 0 TTGCGCACCG 0.645661 -123 GTGCGCAACGTTGCGCTCATTCAATCTTTG 2 190 1 TTGCGCTCAT 0.802903 -111 GGGCAGTAAACTGTGCACCAAACTCCAACG 2 221 0 CTGTGCACCA 0.706403 -80 AGAGAAAGGACAGCGCGCCGAGTATCATTG 2 278 0 CAGCGCGCCG 0.711512 -23 ********** Masking position 6 Map Score: 17.6668 Number of sites scoring better than the average of aligned sites = 1224 Number in coding regions = 1143 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 2 ATTGGTTGTATCCGCTGGGAGTTACATGCTT 1 36 0 TCGCTGGGAG 0.990795 -56 AATTCTGAAATGGTCTGCATGAGCGGCGCGC 1 64 1 TGTCTGCATG 0.959405 -28 GCATGAGCGGCGCGCTGAGCGT 1 80 1 CGGCTGAGCG 0.543077 -12 AGGAAGAAGATCAGCTGCTTGCAAGCAGGTC 2 31 1 TCGCTGCTTG 0.982451 -270 CGCTGCACGATGACCTGCTTGCAAGCAGCTG 2 42 0 TGCCTGCTTG 0.980729 -259 AAACCAATCGTGCGCTGCACGATGACCTGCT 2 54 0 TGGCTGCACG 0.840715 -247 GAAACTGGCGTGGTCAGGGAGTATTTTTTCT 2 122 1 TGTCAGGGAG 0.882275 -179 CGTGACGTCTTCCCCTGCGAGAAAAAATACT 2 141 0 TCCCTGCGAG 0.994878 -160 CGCACCCGTCTCCCCTGAGAGGGCAGTAAAC 2 240 0 TCCCTGAGAG 0.982388 -61 ** ******** Masking position 5 Map Score: 12.1524 Number of sites scoring better than the average of aligned sites = 756 Number in coding regions = 688 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 3 ACATGAATTGTGCACGTTGCAG 2 1 1 ACTAATTGTG 0.947575 -300 ACGTGTTCTACCATGCACTGTGCTCGAAACTG 2 97 1 CCTCACTGTG 0.997724 -204 CCTGAGAGGGCAGTAAACTGTGCACCAAACTC 2 226 0 CATAACTGTG 0.986045 -75 GGCGCGCTGTCCTTTCTCTGTG 2 289 1 CCTCTCTGTG 0.994301 -12 ** * ******* Masking position 4 Map Score: 0.543343 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 59 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 4 CTGCATGAGCGGCGCGCTGAGCGT 1 78 1 GGCGCGCTGA 0.991733 -14 TTGTGCACGTTGCAGGAAGAAGATCAGCTG 2 18 1 TGCAGGAAGA 0.971046 -283 AATCGTGCGCTGCACGATGACCTGCTTGCA 2 50 0 TGCACGATGA 0.995595 -251 AGGGGAAGACGTCACGATGATTGAGCAACT 2 156 1 GTCACGATGA 0.988818 -145 ********** Masking position 10 Map Score: 2.39036 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 68 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 5 ACAGAAAACCAATCGTGCGCTGCACGATGA 2 60 0 AATCGTGCGC 0.958722 -241 GCATGGTAGAACACGTGTGGTGTACAGAAA 2 83 0 ACACGTGTGG 0.979082 -218 TGTGCTCGAAACTGGCGTGGTCAGGGAGTA 2 115 1 ACTGGCGTGG 0.988104 -186 CTCAGGGGAGACGGGTGCGGGTAAGTCAAT 2 252 1 ACGGGTGCGG 0.994155 -49 ********** Masking position 1 Map Score: 0.601655 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 146 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 6 ********** No masking Map Score: -4.02005e-14 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: -4.02005e-14 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: -4.02005e-14 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