AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i155_Hydrogenase_2_aful_reg_300.orf -o155_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 RAG48483 139 Archaeoglobus_fulgidus #2 RAG50190 144 Archaeoglobus_fulgidus #3 RAG50188 135 Archaeoglobus_fulgidus #4 RAG48480 189 Archaeoglobus_fulgidus Motif number 1 TATTAATTTATTAACTTTTTTCAACTAAAAATTG 1 24 1 TTATTTTTAA 0.974562 -116 ACTAAAAATTGCACAATTTTTCATGCATCTATTA 1 47 1 GCATTTTTAT 0.953869 -93 CTATTAACTTTTACAATTTTTCATGTATGTAATT 1 75 1 TTATTTTTAT 0.977911 -65 TTTTAATTTCTTATTCTTTTTTAAATGCATTTAA 2 13 0 TTATTTTTAA 0.974566 -132 TGCAGAAAAGTTAATATTTTTAATTTCTTATTCT 2 30 0 TTATTTTTAT 0.977968 -115 TAACTTTTCTGCATTTTTTTTAATGGAAATCTTT 2 51 1 GCATTTTTAT 0.953869 -94 TTTTTTAATGGAAATCTTTTTTATTAATTGAAAA 2 66 1 GAATTTTTAT 0.883461 -79 ATTTTTATCCTTAGCATTTTCAATTAATAAAAAA 2 82 0 TTATTTTCAT 0.866226 -63 ATCACAGTTGTTGCTTTTTTGGATTATGGGTTTA 3 25 1 TTGTTTTGAT 0.796499 -111 TTGTCTGCGTCTGAGGTTTTTAAACCCATAATCC 3 45 0 CTGTTTTTAA 0.860171 -91 ACAAATTGGATTGCGATTTTTTAGGAAGTAAAGT 3 75 1 TTGTTTTTAG 0.929078 -61 TTTTTAGGAAGTAAAGTTTTTTAATTGTAGATTT 3 92 1 GTATTTTTAA 0.983982 -44 TTGTAGATTTGTACAATTTTTTCGATGAGG 3 116 1 GTATTTTTCG 0.82531 -20 TAAAGAGATAGTAAAATTTTTAAATGTTGAGGAT 4 23 0 GTATTTTTAA 0.983977 -167 CCTCTACGTAGTGGAATTTCTAAAGAGATAGTAA 4 43 0 GTGTTTCTAA 0.834516 -147 *** ***** ** Masking position 7 Map Score: 20.319 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 124 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 2 AAAAAAGTTAATAAATTAATATGTTAACTAA 1 14 0 AAAATTAATA 0.931818 -126 ATTAACTTTTTTCAACTAAAAATTGCACAAT 1 33 1 TCAACTAAAA 0.907968 -107 GAAAAATTGTAAAAGTTAATAGATGCATGAA 1 66 0 AAAGTTAATA 0.869797 -74 TTTTAAATGCATTTAAAAAAGAATAAGA 2 8 1 TCATTTAAAA 0.943037 -137 AAAAAGAATAAGAAATTAAAAATATTAACTT 2 26 1 AAAATTAAAA 0.958643 -119 AAAAATGCAGAAAAGTTAATATTTTTAATTT 2 38 0 AAAGTTAATA 0.869797 -107 TAAAAAAGATTTCCATTAAAAAAAATGCAGA 2 58 0 TCCATTAAAA 0.907968 -87 CCTTAGCATTTTCAATTAATAAAAAAGATTT 2 77 0 TCAATTAATA 0.96864 -68 TGTACAAATCTACAATTAAAAAACTTTACTT 3 100 0 TCAATTAAAA 0.981269 -36 TTTTATCCTCAACATTTAAAAATTTTACTAT 4 19 1 ACATTTAAAA 0.933028 -171 TTCCCAAAGCTGAAATTAAAGAGGTAAGGAA 4 119 0 TAAATTAAAG 0.838377 -71 * ********* Masking position 8 Map Score: 12.1958 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 56 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 3 ATTGCACAATTTTTCATGCATCTATTAACTTTT 1 54 1 TTTATGCATT 0.991873 -86 CTTTTACAATTTTTCATGTATGTAATTATTTAT 1 82 1 TTTATGTATT 0.958994 -58 AAAGCTGGAATTCAAATGAATTTGG 1 125 1 TTCATGAATT 0.877989 -15 TTTTAAATGCATTTAAAAAAGAAT 2 2 1 TTTATGCATT 0.991873 -143 AAAATATTAACTTTTCTGCATTTTTTTTAATGG 2 44 1 CTTCTGCATT 0.961933 -101 TCTGCATTTTTTTTAATGGAAATCTTTTTTATT 2 58 1 TTTATGGAAT 0.877983 -87 CGCAATCCAATTTGTCTGCGTCTGAGGTTTTTA 3 57 0 TTTCTGCGTT 0.961933 -79 *** ****** * Masking position 7 Map Score: 2.96913 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 35 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 4 AAATGATTTAAAGCTGGAATTCAAATGAATT 1 116 1 AAGCTGAATT 0.984696 -24 TTTAAAAAAGAATAAGAAATTAAAAATATTA 2 22 1 AATAAGAATT 0.785581 -123 GAAAATGCTAAGGATAAAAATGGAGGGTCTG 2 95 1 AGGATAAAAT 0.810752 -50 TAATCCAAAAAAGCAACAACTGTGATATCCC 3 20 0 AAGCAAAACT 0.894491 -116 AAATTGTACAAATCTACAATTAAAAAACTTT 3 104 0 AATCTAAATT 0.935539 -32 TTAAATGTTGAGGATAAAATTAGGTAA 4 7 0 AGGATAAATT 0.94552 -183 CTGATTCCCAAAGCTGAAATTAAAGAGGTAA 4 123 0 AAGCTGAATT 0.984617 -67 ****** **** Masking position 8 Map Score: 1.45592 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 234 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 5 AATTAATATGTTAACTAACTT 1 2 0 TTAACTAACT 0.937666 -138 AACATATTAATTTATTAACTTTTTTCAACT 1 20 1 TTTATTAACT 0.954367 -120 TTTTCATGCATCTATTAACTTTTACAATTT 1 64 1 TCTATTAACT 0.813489 -76 AGTTAATATTTTTAATTTCTTATTCTTTTT 2 26 0 TTTAATTTCT 0.524146 -119 GGAAATCTTTTTTATTAATTGAAAATGCTA 2 75 1 TTTATTAATT 0.783336 -70 ATTAAAAAACTTTACTTCCTAAAAAATCGC 3 87 0 TTTACTTCCT 0.884874 -49 TTACCTAATTTTATCCTCAA 4 1 1 TTACCTAATT 0.559683 -189 ATTTAAAAATTTTACTATCTCTTTAGAAAT 4 32 1 TTTACTATCT 0.962425 -158 CTCCTCTGGATTCTCTATCTTTGCCAGATG 4 82 1 TTCTCTATCT 0.722165 -108 ATGCGCCGCATTCCTTACCTCTTTAATTTC 4 109 1 TTCCTTACCT 0.795728 -81 ********** Masking position 6 Map Score: 2.11689 Number of sites scoring better than the average of aligned sites = 392 Number in coding regions = 323 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 6 ********** No masking Map Score: 9.61665e-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: 9.61665e-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: 9.61665e-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