AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i321_mixed6_tpal_reg_300.orf -o321_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 RTP00893 262 AE000520 #2 RTP00740 47 AE000520 #3 RTP00743 169 AE000520 Motif number 1 GCGGGTGCGCATGTGCTGCAGGGCCTC 1 3 0 AGGCTGCACC 0.995288 -260 AATATGCTGACGCTGCTTCCAGCCCCTGTGCAAGT 1 38 1 CCGCTTCCCC 0.995632 -225 GTGCAAGGGACAGCGCTGCAAAACCCACTTGCACA 1 64 0 CGGCTGCACC 0.997051 -199 CTTGCACATCCACGGCTTCCTTTGGAGAGACGCGG 1 92 1 CCGCTTCCGG 0.983513 -171 ATATCGGGCAAACACCTGCTCTACCCCGCGTCTCT 1 117 0 ACCCTGCTCC 0.979714 -146 TTCGAACGATAGGTGGTGCTTACGGTGCATTCACC 1 180 1 AGGGTGCTGG 0.846091 -83 CACTAACTTACCGCGATCCAAATCCGC 1 246 1 CGGATCCACC 0.883277 -17 GCAGCGGCGCCTCGGCTGCACCTCGCGCTCGAGGC 2 12 0 CCGCTGCACG 0.995844 -36 GCAGCCGAGGCGCCGCTGCCACTGGCGCAG 2 28 1 CCGCTGCCGG 0.995865 -20 GTGATAGGTAAAGCGCTTCTTTTCCCGGAAATCCC 3 16 0 AGGCTTCTCC 0.975716 -154 CGCTTTACCTATCACCTGTCCTCCCGCGACGGCAT 3 36 1 ACCCTGTCCC 0.898632 -134 TCGTGTACATACCAGATGCCGTCGCGGGAGGACAG 3 51 0 ACGATGCCGC 0.978406 -119 * * ****** ** Masking position 7 Map Score: 17.1114 Number of sites scoring better than the average of aligned sites = 1384 Number in coding regions = 1305 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 2 CGCATGTGCTGCAGGGCCTC 1 1 0 GCAGGGCCTC 0.857752 -262 AGGCCCTGCAGCACATGCGCACCCGCAATA 1 12 1 GCACATGCGC 0.949878 -251 GCTGCAAAACCCACTTGCACAGGGGCTGGA 1 55 0 CCACTTGCAC 0.966356 -208 GCTGTCCCTTGCACATCCACGGCTTCCTTT 1 85 1 GCACATCCAC 0.978388 -178 CCGCGTCTCTCCAAAGGAAGCCGTGGATGT 1 97 0 CCAAAGGAAG 0.643577 -166 ATTCACCCTGCCAGATCCAGTACATGGCAT 1 208 1 CCAGATCCAG 0.971611 -55 TTACCGCGATCCAAATCCGC 1 253 1 CCAAATCCGC 0.975027 -10 GCGAGGTGCAGCCGAGGCGCCGCTGCCACT 2 21 1 GCCGAGGCGC 0.946346 -27 GGCGCCGCTGCCACTGGCGCAG 2 36 1 CCACTGGCGC 0.964475 -12 CGTGTACATACCAGATGCCGTCGCGGGAGG 3 55 0 CCAGATGCCG 0.955737 -115 CATTCTGTTCCCAAATTCTCAACTACGTAA 3 86 0 CCAAATTCTC 0.88398 -84 ACTTTTAGTCGCAGATGATCCCGTTTCGGT 3 124 1 GCAGATGATC 0.904127 -46 TTTTCAAATACCAGATTCACCGAAACGGGA 3 142 0 CCAGATTCAC 0.973836 -28 ********** Masking position 2 Map Score: 14.907 Number of sites scoring better than the average of aligned sites = 1618 Number in coding regions = 1523 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 3 CGTCAGCATATTGCGGGTGCGCATGTGCTG 1 20 0 TTGCGGGTGC 0.8989 -243 CCGCAATATGCTGACGCTGCTTCCAGCCCC 1 34 1 CTGACGCTGC 0.971032 -229 AAACACCTGCTCTACCCCGCGTCTCTCCAA 1 113 0 TCTACCCCGC 0.972746 -150 ATAGGTGGTGCTTACGGTGCATTCACCCTG 1 188 1 CTTACGGTGC 0.976937 -75 TTACGGTGCATTCACCCTGCCAGATCCAGT 1 199 1 TTCACCCTGC 0.887432 -64 TCCTCACTAACTTACCGCGATCCAAATCCG 1 242 1 CTTACCGCGA 0.956769 -21 CGCCTCGAGCGCGAGGTGCAGCCG 2 5 1 TCGAGCGCGA 0.747716 -43 GGCAGCGGCGCCTCGGCTGCACCTCGCGCT 2 18 0 CCTCGGCTGC 0.949267 -30 TATCACCTGTCCTCCCGCGACGGCATCTGG 3 45 1 CCTCCCGCGA 0.94013 -125 ********** Masking position 9 Map Score: 5.82729 Number of sites scoring better than the average of aligned sites = 1904 Number in coding regions = 1754 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 4 GAGCAGGTGTTTGCCCGATATCTAAGTACT 1 131 1 TTGCCCGATA 0.979806 -132 GTTCGAATTTTTTCCCAAAACGGCTCAGTA 1 157 0 TTTCCCAAAA 0.95751 -106 AAGCGCTTCTTTTCCCGGAAATCCCGGTAC 3 11 0 TTTCCCGGAA 0.81083 -159 AAATACCAGATTCACCGAAACGGGATCATC 3 137 0 TTCACCGAAA 0.960828 -33 ********** Masking position 2 Map Score: 0.86585 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 36 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 5 GAGGCCCTGCAGCACATGCGCAC 1 4 1 GCCCTGCAGC 0.976551 -259 TGCAGCACATGCGCACCCGCAATATGCTGA 1 18 1 GCGCACCCGC 0.958547 -245 GGGTTTTGCAGCGCTGTCCCTTGCACATCC 1 73 1 GCGCTGTCCC 0.995964 -190 GCAAACACCTGCTCTACCCCGCGTCTCTCC 1 115 0 GCTCTACCCC 0.962699 -148 TCCCAAAACGGCTCAGTACTTAGATATCGG 1 145 0 GCTCAGTACT 0.652564 -118 AGCGGCGCCTCGGCTGCACCTCGCGCTCGA 2 15 0 CGGCTGCACC 0.961871 -33 AGCCGAGGCGCCGCTGCCACTGGCGCAG 2 30 1 CCGCTGCCAC 0.973961 -18 GGGAAAAGAAGCGCTTTACCTATCACCTGT 3 25 1 GCGCTTTACC 0.962436 -145 ********** Masking position 4 Map Score: 5.58938 Number of sites scoring better than the average of aligned sites = 1564 Number in coding regions = 1452 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 6 ********** No masking Map Score: -1.32571e-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: -1.32571e-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: -1.32571e-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