AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i195_dna_replication1_aful_reg_300.orf -o195_aful_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 RAG45884 251 Archaeoglobus_fulgidus #2 RAG10471 117 Archaeoglobus_fulgidus #3 RAG10470 60 Archaeoglobus_fulgidus #4 RAG10469 81 Archaeoglobus_fulgidus #5 RAG50259 146 Archaeoglobus_fulgidus #6 RAG45831 300 Archaeoglobus_fulgidus Motif number 1 TTGGGGACATTTTCAATGTTGAAACGGGAACGACACCATC 1 77 1 TTAGAAAGAA 0.949246 -175 AGAACACATATTTCCGTTTCAGAAAGAAAAATAACTGAGA 1 193 1 TTGAGAAGAA 0.560651 -59 TTAAGGAGTTTTTGAGTGAGGAAAAGTTAAGTTTTTATTG 2 50 1 TTGGAAAGAA 0.989031 -68 TTTATTGGTTTTAAGATATTAGAATACGAAGAAAAGGTGT 2 83 1 TTAAGAAAAA 0.720052 -35 TATCGGCTACTTCGCCCCACAGAAGGCCAAAGAGGGGGAG 5 60 1 TTCAGAAGAA 0.942755 -87 GCCGAGCCCATTTTTGTTTTGAAATGCTAAATTCTGCTGG 6 61 1 TTGGAAAGAA 0.584948 -240 CCAATGCACTTTTTTGAGTTGGAATCTGAACACTGCTCCT 6 125 0 TTGGGAACAA 0.952374 -176 TGAACTCTGCTTAAAACAGTTGAAGGGAAACAATATTTGA 6 209 0 TTATGAAGAA 0.918866 -92 TTTTGCGAAATTAAAGCTAAAAAATGTGAACTCTGCTTAA 6 235 0 TTGAAAAGAA 0.978401 -66 TAGCTTTAATTTCGCAAAAGGAAAAGATAATATTTGCCTA 6 256 1 TTAGAAAGAA 0.978678 -45 ** * **** * ** Masking position 13 Map Score: 9.08789 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 100 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 2 CAAGCCTAACAACCTCCCAATCCTCAGGAA 1 50 0 AACCTCCCAA 0.975766 -202 CAACATTGAAAATGTCCCCAAGCCTAACAA 1 68 0 AATGTCCCCA 0.853943 -184 TTGAAACGGGAACGACACCATCTACAAAAA 1 95 1 AACGACACCA 0.926042 -157 ATCTGCTTCTGACCACTCCAGCAAACCTTT 3 14 1 GACCACTCCA 0.85168 -47 TAACATCTCAAACCAACCCAAATAC 4 67 1 AACCAACCCA 0.897696 -15 GCTATCACTCGCCCTTCCCAGAT 5 4 0 GCCCTTCCCA 0.954463 -143 GCCACTCGTAAGCGTCACCAAGAATGCTAT 5 29 0 AGCGTCACCA 0.820734 -118 AAGGGGTGAAAACCTCCCCCTCTTTGGCCT 5 83 0 AACCTCCCCC 0.956697 -64 TGAGCTCAACAACCTCCGAAGGGGTGAAAA 5 101 0 AACCTCCGAA 0.887389 -46 TTATGACGTCGCCCTTACAAGGCGGAGATC 6 16 1 GCCCTTACAA 0.570815 -285 TTCGAATCCGGCCGAGCCCATTTTTGTTTT 6 51 1 GCCGAGCCCA 0.832734 -250 GCCAAAGGTGAACGTTCCAATGCACTTTTT 6 151 0 AACGTTCCAA 0.863393 -150 ATTTGCCTAAACCCACCGCAAACA 6 287 1 ACCCACCGCA 0.935111 -14 ********** Masking position 10 Map Score: 7.8698 Number of sites scoring better than the average of aligned sites = 1726 Number in coding regions = 1636 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 3 CCAATCCTCAGGAATCCTCCCGATTGGTGT 1 34 0 GGAATCCTCC 0.949113 -218 CCCCAAGCCTAACAACCTCCCAATCCTCAG 1 53 0 AACAACCTCC 0.988636 -199 ACAATTAATTGGCTAACTCCAACTGATTTA 1 148 1 GGCTAACTCC 0.950899 -104 TTTCCTCACTCAAAAACTCCTTAATCGATT 2 44 0 CAAAAACTCC 0.922856 -74 GATGTTAAATAACTTACTCCTATTTTCATA 4 44 0 AACTTACTCC 0.888536 -38 CCGAAGGGGTGAAAACCTCCCCCTCTTTGG 5 86 0 GAAAACCTCC 0.985122 -61 CGATGAGCTCAACAACCTCCGAAGGGGTGA 5 104 0 AACAACCTCC 0.988636 -43 ********** Masking position 8 Map Score: 6.40035 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 428 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 4 ACATAGCATCCAGATACAAGGAAA 1 2 1 CATAGCCAGA 0.994735 -250 CTCCTATTTTCATAGCTCCCAATCTTCAGGCAG 4 25 0 CATAGCCAAT 0.98155 -57 TGAAATTATTCATAGCCAGCAGAATTTAGCATT 6 83 0 CATAGCCAGA 0.994736 -218 ACGATATGCCCGTAGCTGCCAAAGGTGAACGTT 6 165 0 CGTAGCCAAA 0.98747 -136 CAGCTACGGGCATATCGTTCAAAATCTTGTCAA 6 180 1 CATATCCAAA 0.97105 -121 ****** **** Masking position 4 Map Score: 3.73989 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 15 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 AAATCTGCTTCTGACCACTCCAGCAAACCTT 3 12 1 CTGACCCTCC 0.98648 -49 TTTTGAAATGCTAAATTCTGCTGGCTATGAA 6 77 1 CTAAATCTGC 0.91252 -224 GAGTTGGAATCTGAACACTGCTCCTCCACAC 6 119 0 CTGAACCTGC 0.995014 -182 GCTGCCAAAGGTGAACGTTCCAATGCACTTT 6 153 0 GTGAACTTCC 0.941629 -148 GCTAAAAAATGTGAACTCTGCTTAAAACAGT 6 229 0 GTGAACCTGC 0.990502 -72 TAATATTTGCCTAAACCCACCGCAAACA 6 283 1 CTAAACCACC 0.943294 -18 ****** **** Masking position 4 Map Score: 3.52723 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 174 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 TGAGAAAGCATTAAGAGATTACAACCTTACA 1 228 1 TTAAGAATTA 0.978843 -24 GTTATGAAATTATAGTTCACCC 2 2 1 TTATGAATTA 0.948111 -116 TTTATTGGTTTTAAGATATTAGAATACGAAG 2 83 1 TTAAGAATTA 0.978843 -35 TTGGGTTGGTTTGAGATGTTAAATAACTTAC 4 57 0 TTGAGAGTTA 0.957463 -25 TCTTTTCCTTTTGCGAAATTAAAGCTAAAAA 6 252 0 TTGCGAATTA 0.967004 -49 ****** **** Masking position 6 Map Score: 2.07493 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 4 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 7 ACGGAAATATGTGTTCTCCCATTTAGTTTA 1 180 0 GTGTTCTCCC 0.962569 -72 TATGAAATTATAGTTCACCCAAAAGTCGCA 2 13 1 TAGTTCACCC 0.966268 -105 GCTTATCGGCTACTTCGCCCCACAGAAGGC 5 57 1 TACTTCGCCC 0.977936 -90 AGAGGGGGAGGTTTTCACCCCTTCGGAGGT 5 90 1 GTTTTCACCC 0.919603 -57 AGCGGTTATGACGTCGCCCTTACAAGGCG 6 10 1 GACGTCGCCC 0.983358 -291 TTACAAGGCGGAGATCGCCGGTTCGAATCC 6 30 1 GAGATCGCCG 0.930145 -271 ********** Masking position 5 Map Score: 1.71985 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 149 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 CTAACTCCAACTGATTTAAGTAAACTAAAT 1 160 1 CTGATTTAAG 0.912228 -92 AAGTTTTTATTGGTTTTAAGATATTAGAAT 2 78 1 TGGTTTTAAG 0.950229 -40 GTATTTGGGTTGGTTTGAGATGTTAAATA 4 63 0 TTGGTTTGAG 0.965992 -19 GAGCCCATTTTTGTTTTGAAATGCTAAATT 6 64 1 TTGTTTTGAA 0.816317 -237 TTCCAATGCACTTTTTTGAGTTGGAATCTG 6 137 0 CTTTTTTGAG 0.842914 -164 TTCCCTTCAACTGTTTTAAGCAGAGTTCAC 6 220 1 CTGTTTTAAG 0.971634 -81 TGTTTGCGGTGGGTTTAGGCAAATATTAT 6 282 0 TGGGTTTAGG 0.829651 -19 ********** Masking position 5 Map Score: 1.58307 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 228 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 9 ********** No masking Map Score: -3.50765e-12 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: -3.50765e-12 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 11 ********** No masking Map Score: -3.50765e-12 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