AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i262_3_5_1_28_hinf_reg_100.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -x5 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 = 0.38 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HI0063 247 poly(A) polymerase (pcnB) #2 HI0065 75 conserved hypothetical protein Motif number 1 TTAATTTTAACCGCACTTTTGTATTTTTCA 1 21 0 CCGCACTTTT 0.999509 -227 TTAAAATTAACCGCACTTTTTTGCATTTAA 1 41 1 CCGCACTTTT 0.999509 -207 GTGGATTTTCCTGCATTTTTAAATGCAAAA 1 59 0 CTGCATTTTT 0.990688 -189 AAATTTCACCGCACTTTTATGAACCTCA 2 9 1 CCGCACTTTT 0.999509 -67 GCTGATTCTACCGCACTTTTGAGGTTCATA 2 28 0 CCGCACTTTT 0.999509 -48 TAGAATCAGCCCACATTTTTCTTCATTCAT 2 48 1 CCACATTTTT 0.990688 -28 ********** Masking position 5 Map Score: 25.2986 Number of sites scoring better than the average of aligned sites = 654 Number in coding regions = 386 Number in noncoding regions = 268 Number of orfs with sites within 600 bp upstream = 208 Fraction of orfs with sites within 600 bp upstream = 0.0334083 Motif number 2 TTAACCGCACTTTTGTATTTTTCAATAGAATGAA 1 8 0 TTTTGTTAAA 0.805823 -240 TTTTCCTGCATTTTTAAATGCAAAAAAGTGCGGTTAA 1 47 0 TTTTTATAAA 0.609435 -201 GACTTGGCTCTTTTCTTGTAAAGAAAAAGGCAAGTGG 1 85 0 TTTTCTTAAA 0.585368 -163 ATTTACTCCGTTTTGTTGTTGGAAATAAATGACTTGG 1 115 0 TTTTGTTAAA 0.991133 -133 CCAAACAAATTTTTGATATAAGTAAGAATAATTTACT 1 145 0 TTTTGATAAA 0.993153 -103 CTTTTGATTTTTTTGTCTTCTTGCCAAACAAATTTTT 1 168 0 TTTTGTTCCA 0.951983 -80 TCTACCGCACTTTTGAGGTTCATAAAAGTGCGGTGAA 2 15 0 TTTTGATAAA 0.790926 -61 ****** * ** * Masking position 17 Map Score: 9.42634 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 47 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 3 TTTAACCGCACTTTTGTATTTTTCAATAGAATGAA 1 10 0 CTTTTGTTAA 0.996643 -238 TAACCGCACTTTTTTGCATTTAAAAATGCAGGAAAA 1 48 1 TTTTTGTTAA 0.982696 -200 TGACTTGGCTCTTTTCTTGTAAAGAAAAAGGCAAGT 1 87 0 CTTTTCTAAA 0.961274 -161 AATTTACTCCGTTTTGTTGTTGGAAATAAATGACTT 1 117 0 GTTTTGTTAA 0.98828 -131 GCCAAACAAATTTTTGATATAAGTAAGAATAATTTA 1 147 0 TTTTTGTAAA 0.977286 -101 TTGGCAACCTCTTTTGATTTTTTTGTCTTCTTGCCA 1 179 0 CTTTTGTTGT 0.949919 -69 TTCTACCGCACTTTTGAGGTTCATAAAAGTGCGGTG 2 17 0 CTTTTGTTAA 0.996628 -59 ****** ** ** Masking position 10 Map Score: 8.30732 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 169 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 4 GCAAAAAAGTGCGGTTAATTTTAACCGCAC 1 35 0 GCGGTTAATT 0.974833 -213 ATTTAAAAATGCAGGAAAATCCACTTGCCT 1 65 1 GCAGGAAAAT 0.985533 -183 ACAACAAAACGGAGTAAATTATTCTTACTT 1 133 1 GGAGTAAATT 0.958365 -115 TCATAAAAGTGCGGTGAAATTT 2 3 0 GCGGTGAAAT 0.990751 -73 CCTCAAAAGTGCGGTAGAATCAGCCCACAT 2 34 1 GCGGTAGAAT 0.988629 -42 GGTCATGAATGAAGAAAAATGTGGGCTGAT 2 52 0 GAAGAAAAAT 0.898035 -24 ********** Masking position 8 Map Score: 4.6718 Number of sites scoring better than the average of aligned sites = 584 Number in coding regions = 439 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 5 TGCAGGAAAATCCACTTGCCTTTTTCTTTA 1 74 1 TCCACTTGCC 0.995586 -174 GATTTTTTTGTCTTCTTGCCAAACAAATTT 1 170 0 TCTTCTTGCC 0.993701 -78 AGTTGAGCGTTCTAATAGCCAA 1 236 1 TCTAATAGCC 0.98296 -12 ********** Masking position 6 Map Score: 1.50206 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 16 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 TAATTTTAACCGCACTTTTGTATTTTTCAA 1 20 0 CGCACTTTTG 0.966983 -228 AAATTAACCGCACTTTTTTGCATTTAAAAA 1 44 1 CACTTTTTTG 0.834508 -204 GAATAATTTACTCCGTTTTGTTGTTGGAAA 1 127 0 CTCCGTTTTG 0.974664 -121 TATATCAAAAATTTGTTTGGCAAGAAGACA 1 162 1 ATTTGTTTGG 0.778697 -86 TGTTTTGGCAACCTCTTTTGATTTTTTTGT 1 189 0 ACCTCTTTTG 0.980463 -59 TAGAATGAGCACTTGTTTTGGCAACCTCTT 1 202 0 ACTTGTTTTG 0.962639 -46 AGAACGCTCAACTCGTTTAGAATGAGCACT 1 219 0 ACTCGTTTAG 0.815995 -29 CTGATTCTACCGCACTTTTGAGGTTCATAA 2 27 0 CGCACTTTTG 0.966983 -49 ********** Masking position 6 Map Score: 4.64213 Number of sites scoring better than the average of aligned sites = 584 Number in coding regions = 455 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 7 ********** No masking Map Score: 7.55607e-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: 7.55607e-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 9 ********** No masking Map Score: 7.55607e-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