AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i164_NIF1_aful_reg_100.orf -o164_aful_100.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 RAG04733 300 Archaeoglobus_fulgidus #2 RAG12654 142 Archaeoglobus_fulgidus #3 RAG07415 102 Archaeoglobus_fulgidus Motif number 1 GTATCGTCAGCTTATGAAACGTTCTGAACCATC 1 20 0 CTTATGAAAT 0.902455 -281 GTTTCATAAGCTGACGATACGTTTCATCTCCAA 1 33 1 CTGACGATAT 0.938675 -268 CTCGGCAGGCTGGATGAAAATGTTGATAAAGTA 1 142 0 TGGATGAAAT 0.816834 -159 ACTATTTTTTTTCCCGAAACTTTTAAATAGTTA 1 260 1 TTCCCGAAAT 0.962419 -41 GGACAATTCCTGCAGGAAATTGTTGCATAATAA 2 15 1 TGCAGGAAAT 0.962419 -128 GGTATCGACACTCCCGAAAGGCTCTACGCCCCA 2 108 1 CTCCCGAAAT 0.989102 -35 CTTATTAACACTCAGGAAAAATTGCTTCG 3 7 0 CTCAGGAAAT 0.995285 -96 ATAAGGTTGACTGAGGCAATCCTTACACTCCAG 3 35 1 CTGAGGCAAT 0.957781 -68 TCCAGGAAAACTCACGAAACATTAAATAGCTCA 3 63 1 CTCACGAAAT 0.995285 -40 CATTAAATAGCTCAGGAAAGCGTTAACCATT 3 82 1 CTCAGGAAAT 0.995285 -21 ********* * Masking position 9 Map Score: 14.0969 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 235 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 2 ATTTAAAAGTTTCGGGAAAAAAAATAGTTTC 1 257 0 TTCGGGAAAA 0.773032 -44 GGAAGGACAATTCCTGCAGGAAATTGTTGCA 2 11 1 TTCCTGCAGA 0.901347 -132 ACCGCTCGTCTCCCTGCGAGAGTTCGCTTAG 2 80 0 TCCCTGCGGA 0.941492 -63 CGTAGAGCCTTTCGGGAGTGTCGATACCGCT 2 105 0 TTCGGGAGGT 0.989715 -38 GAAGCAATTTTTCCTGAGTGTTAATAAGGTT 3 12 1 TTCCTGAGGT 0.992083 -91 TCGTGAGTTTTCCTGGAGTGTAAGGATTGCC 3 49 0 TCCTGGAGGT 0.931893 -54 TATTTAATGTTTCGTGAGTTTTCCTGGAGTG 3 60 0 TTCGTGAGTT 0.964019 -43 GGTTAACGCTTTCCTGAGCTATTTAATGTTT 3 79 0 TTCCTGAGTA 0.971857 -24 ******** ** Masking position 1 Map Score: 6.52641 Number of sites scoring better than the average of aligned sites = 662 Number in coding regions = 620 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 3 TATTTAAGACAATAGTTGCAGATAAAACGA 1 72 0 AATAGTTGCA 0.978903 -229 CAAAATGAAAAATAATTACCTGCCACGAGA 1 215 0 AATAATTACC 0.967164 -86 CGGGAAAAAAAATAGTTTCCACATAGGGAG 1 246 0 AATAGTTTCC 0.977174 -55 GAAACTTTTAAATAGTTACCTTAACAATGT 1 275 1 AATAGTTACC 0.990837 -26 TCCTGCAGGAAATTGTTGCATAATAAAAGA 2 22 1 AATTGTTGCA 0.933787 -121 CCTGGAGTGTAAGGATTGCCTCAGTCAACC 3 39 0 AAGGATTGCC 0.922095 -64 AATGGTTAACGCTTTCCTGA 3 93 0 AATGGTTAAC 0.920836 -10 ********** Masking position 2 Map Score: 6.84543 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 172 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 4 ATGAAACGTATCGTCAGCTTATGAAACGTT 1 30 0 TCGTCAGCTT 0.974815 -271 GTAGAGCCTTTCGGGAGTGTCGATACCGCT 2 105 0 TCGGGAGTGT 0.983972 -38 AAGCAATTTTTCCTGAGTGTTAATAAGGTT 3 13 1 TCCTGAGTGT 0.989425 -90 ATTTAATGTTTCGTGAGTTTTCCTGGAGTG 3 60 0 TCGTGAGTTT 0.992141 -43 GTTAACGCTTTCCTGAGCTATTTAATGTTT 3 79 0 TCCTGAGCTA 0.966029 -24 ********** Masking position 6 Map Score: 4.31212 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 88 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 5 AAGCTGCCAGATGGTTCAGAA 1 1 1 AAGCTGCAGA 0.956431 -300 TTGATAAAGTAGGATTTCAGATTTTAGGACA 1 122 0 AGGATTCAGA 0.907465 -179 GTAACTCGGCAGGCTGGATGAAAATGTTGAT 1 148 0 AGGCTGATGA 0.952951 -153 AACTATTTAAAAGTTTCGGGAAAAAAAATAG 1 261 0 AAGTTTGGGA 0.871487 -40 AAAGAGACAGAGGTTGAGAGAGTAATCTACA 2 47 1 AGGTTGGAGA 0.988704 -96 AGTAATCTACAGGCTAAGCGAACTCTCGCAG 2 67 1 AGGCTAGCGA 0.922332 -76 AGTGTTAATAAGGTTGACTGAGGCAATCCTT 3 28 1 AGGTTGCTGA 0.985215 -75 GAGCTATTTAATGTTTCGTGAGTTTTCCTGG 3 64 0 ATGTTTGTGA 0.867657 -39 ****** **** Masking position 1 Map Score: 3.44368 Number of sites scoring better than the average of aligned sites = 894 Number in coding regions = 828 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 6 AAGCTGCCAGATGGTTCAGAAC 1 3 1 GCTGCCAGAT 0.922151 -298 ATAATTACCTGCCACGAGAGGATGATCACC 1 204 0 GCCACGAGAG 0.888537 -97 AGAGACAGAGGTTGAGAGAGTAATCTACAG 2 49 1 GTTGAGAGAG 0.975749 -94 CGCTCGTCTCCCTGCGAGAGTTCGCTTAGC 2 79 0 CCTGCGAGAG 0.989804 -64 GGCGTAGAGCCTTTCGGGAGTGTCGATACC 2 108 0 CTTTCGGGAG 0.932035 -35 TGTTAATAAGGTTGACTGAGGCAATCCTTA 3 30 1 GTTGACTGAG 0.950024 -73 GCTATTTAATGTTTCGTGAGTTTTCCTGGA 3 63 0 GTTTCGTGAG 0.981652 -40 ATGGTTAACGCTTTCCTGAGCTATTTAATG 3 82 0 CTTTCCTGAG 0.957401 -21 ********** Masking position 9 Map Score: 7.20924 Number of sites scoring better than the average of aligned sites = 849 Number in coding regions = 796 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 TTAATAAATCCAGGTAACTCGGCAGGCTGG 1 162 0 CAGGTAACTC 0.971732 -139 CCTCTCGTGGCAGGTAATTATTTTTCATTT 1 213 1 CAGGTAATTA 0.986083 -88 TAACATTGTTAAGGTAACTATTTAAAAGTT 1 277 0 AAGGTAACTA 0.964188 -24 ACAATTCCTGCAGGAAATTGTTGCATAATA 2 17 1 CAGGAAATTG 0.960725 -126 ********** Masking position 6 Map Score: 1.67446 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 8 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 8 ********** No masking Map Score: -8.21797e-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: -8.21797e-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 10 ********** No masking Map Score: -8.21797e-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