AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i101_aful_mthe_300.orf -o101_aful_mthe_300.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RAG50006 125 Archaeoglobus_fulgidus #2 RAG50003 79 Archaeoglobus_fulgidus #3 RAG48052 82 Archaeoglobus_fulgidus #4 RAG35071 300 Archaeoglobus_fulgidus Motif number 1 AGGTTACAAAGAACAGTAAATTTATGAGAAGAA 1 25 0 GAACAAATTT 0.959211 -101 GTAACACCAAAAACCAAAATTTTAATCTTCAGT 1 61 1 AAACAATTTT 0.988583 -65 TGTTTTCGTGAAATATGAATTTTGCCTTGCAGC 2 30 0 AAATAATTTT 0.872905 -50 TATTTCACGAAAACATTAAATATTACACGACTA 2 48 1 AAACAAATAT 0.968163 -32 GTTTGCCATTAAATGGCAATTTTAATTGCAATT 3 25 0 AAATAATTTT 0.949444 -58 ATTTAATGGCAAACATAAAATTTTTATATTTTT 3 44 1 AAACAAATTT 0.940333 -39 GTATGAAAGTAAACTAAAAATATAAAAATTTTA 3 59 0 AAACAAATAT 0.968163 -24 ATCGCCCTTTAAACCACAATATTCATAAATCCT 4 246 0 AAACAATATT 0.940806 -55 **** ****** Masking position 8 Map Score: 11.2137 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 64 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 2 TTTTCTTTCAATTTTTCTTCTCATA 1 5 1 CTTTCAATTT 0.595619 -121 ATTTACTGTTCTTTGTAACCTTTGGTAACAC 1 37 1 CTTTGTACCT 0.888823 -89 ATGAATTTTGCCTTGCAGCTCTATGCGTAGA 2 18 0 CCTTGCACTC 0.939489 -62 TACACGTCCACTTTCAATCCCATTTTGGTCT 4 33 0 CTTTCAACCC 0.990743 -268 CTTCTTGAACCTCCCAAACTCAACGAACAGA 4 106 1 CTCCCAACTC 0.946622 -195 GGGTTCGAGGGTTCGAATCCCTCCCCCCGCA 4 143 0 GTTCGAACCC 0.944094 -158 GGATTCGAACCCTCGAACCCCTACGGGACAG 4 154 1 CCTCGAACCC 0.989345 -147 CGGGACAGGACCCTCAATCCTGCGCCTTTGT 4 177 1 CCCTCAACCT 0.938682 -124 CCTTTGTCCGCTCGGCAACCCCCGCTCAGAT 4 201 1 CTCGGCACCC 0.944232 -100 CTTCATATAACTTTGAAATCCACCTTCTAC 4 281 1 CTTTGAATCC 0.964704 -20 ******* *** Masking position 7 Map Score: 6.68128 Number of sites scoring better than the average of aligned sites = 1856 Number in coding regions = 1621 Number in noncoding regions = 235 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 3 AGTAAATTTATGAGAAGAAAAATTGAAAGAA 1 13 0 TAGAAGAAAA 0.93918 -113 TAACCTTTGGTAACACCAAAAACCAAAATTT 1 52 1 TACACCAAAA 0.95655 -74 ATGGCAGACTGAAGATTAAAATTTTGGTTTT 1 70 0 GAGATTAAAA 0.900185 -56 AAAATTCATATTTCACGAAAACATTAAATAT 2 40 1 TTCACGAAAA 0.939075 -40 AGTATGAAAGTAAACTAAAAATATAAAAAT 3 63 0 GAAACTAAAA 0.836452 -20 TAAGTTGAAATCAGACCAAAATGGGATTGAA 4 21 1 TAGACCAAAA 0.981193 -280 AGATATCTCTGATGACGAAAAGAAGATTTAC 4 61 0 GTGACGAAAA 0.972839 -240 CAACCCCCGCTCAGATGAAAAATTCTGCATA 4 216 1 TAGATGAAAA 0.964576 -85 * ********* Masking position 5 Map Score: 5.58474 Number of sites scoring better than the average of aligned sites = 331 Number in coding regions = 218 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 4 TAACAACTGTGCTAATGGCAGACTGAAGAT 1 85 0 GCTAATGGCA 0.937361 -41 ATACTTACACTTTAATTGCAATTAAAATTG 3 12 1 TTTAATTGCA 0.983142 -71 AAAATTGCCATTTAATGGCAAACATAAAAT 3 35 1 TTTAATGGCA 0.980127 -48 ATATTTTTAGTTTACTTTCATACT 3 69 1 TTTACTTTCA 0.94343 -14 CCCATTTTGGTCTGATTTCAACTTACTGTG 4 16 0 TCTGATTTCA 0.859017 -285 AGAGATATCTTTTACTTGGACATGCTTCTT 4 82 1 TTTACTTGGA 0.91865 -219 ********** Masking position 6 Map Score: 1.74313 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 97 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 TTGTTAGTAACACCACACAAAAAGGTG 1 109 1 CCACACAAAG 0.99183 -17 TTCCAACTCTACGCATAGAGCTGCAAGGCA 2 7 1 CCACGCAAAG 0.738103 -73 CGGAACACAGTAAGTTGAAATCAG 4 1 1 CGACACATAG 0.971423 -300 ACCTCCCAAACTCAACGAACAGAACTAAATGCGG 4 114 1 CCACGAAAAA 0.914004 -187 TCGAATCCCTCCCCCCGCATTTAGTTCTGTTCGT 4 128 0 CCCCGCATAG 0.988518 -173 GCGGGGGTTGCCGAGCGGACAAAGGCGCAGGATT 4 192 0 CGGCGGAAAG 0.960029 -109 * * ***** * ** Masking position 9 Map Score: 0.684285 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 92 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 ********** No masking Map Score: -7.08111e-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: -7.08111e-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: -7.08111e-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