AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i150_ATP_synthase_1_aquae_reg_300.orf -o150_aquae_300.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RAA00888 49 Aquifex_aeolicus #2 RAA01468 39 Aquifex_aeolicus #3 RAA01493 138 Aquifex_aeolicus #4 RAA01475 82 Aquifex_aeolicus #5 RAA01504 33 Aquifex_aeolicus #6 RAA01472 63 Aquifex_aeolicus #7 RAA01142 70 Aquifex_aeolicus Motif number 1 TTCCCTTACCTCTTTTGCAATTGGCT 1 34 0 TTACCTCTTT 0.974713 -16 GCCGGGTGCTCTACCACCTGAGCTACCGGGC 3 55 1 CTACCACCTA 0.975919 -84 ACCCACCTCCTGTTATTTTTTTA 4 70 0 CCACCTCCTT 0.993942 -13 AAGGTAAAAACTTCCTCATTTTTTTACCTCC 5 11 0 CTTCCTCATT 0.944833 -23 ACTCTACCTCCTAACCTTCTTTAA 6 50 0 CTACCTCCTA 0.995597 -14 CCTTTACCTCCTTTGCGAAGGTTT 7 4 1 TTACCTCCTT 0.992973 -67 TTAAATTATACTACTTCCTTTAGACATTAGT 7 33 1 CTACTTCCTT 0.992973 -38 AACGCTACTTATTATAAACTAATGT 7 56 0 CTACTTATTT 0.811475 -15 ********* * Masking position 9 Map Score: 13.4491 Number of sites scoring better than the average of aligned sites = 318 Number in coding regions = 267 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 2 TTCCCTTACCTCTTTTGCAATTG 1 37 0 CCTTACCTCT 0.987331 -13 CAGCCGGGTGCTCTACCACCTGAGCTACCG 3 53 1 CTCTACCACC 0.990692 -86 ACCCACCTCCTGTTATTTTT 4 73 0 ACCCACCTCC 0.953142 -10 TTCCTCATTTTTTTACCTCC 5 1 0 TTTTACCTCC 0.993077 -33 ATGAGGAAGTTTTTACCTTTT 5 23 1 TTTTACCTTT 0.835416 -11 ACTCTACCTCCTAACCTTCTT 6 53 0 CTCTACCTCC 0.998053 -11 CCTTTACCTCCTTTGCGAAGG 7 2 1 CTTTACCTCC 0.99765 -69 ********** Masking position 5 Map Score: 12.7377 Number of sites scoring better than the average of aligned sites = 392 Number in coding regions = 313 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 3 TTGGCTCAGAAAATTATAACATAAATTTG 1 7 0 AAATTAAATA 0.947009 -43 ATAAATTCTAAAGCTATAAAATTTTGAGT 2 7 0 AAGTTAAATT 0.919515 -33 AATCTGGATAATAAATTCTAAAG 2 27 0 AATTGATATA 0.920819 -13 CCTTACGACAAAAATATATTATATATTCCATTC 3 85 1 AAATTATATA 0.971503 -54 GGAATTTTTATGATTTTAATAAGAA 4 3 1 AATTTATATT 0.877754 -80 ATCATTCACGAAAGTGTATACTAAAAAAATAAC 4 49 1 AAATTATCTA 0.912968 -34 AAGTTAGATTATAGGTATTTTCT 6 1 1 AAGTGATATA 0.971765 -63 ACCTTCTTTAAAGGTTTATTGTAGCACAGAAAA 6 28 0 AAGTTATGTA 0.955875 -36 CTCCTTTGCGAAGGTTTAAATTATACTACTTCC 7 18 1 AAGTTAATTA 0.882477 -53 *** * *** *** Masking position 8 Map Score: 6.61885 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 61 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 4 CAATTGGCTCAGAAAATTATAACATAAATT 1 13 0 AGAAAATTAT 0.879197 -37 TTCTAAAGCTATAAAATTTTGAGT 2 5 0 ATAAAATTTT 0.658552 -35 AATCTGGATAATAAATTCTAAAGCTATAA 2 21 0 AATAAATTCT 0.925537 -19 TTACGACAAAAATATATTATATATTCCATT 3 87 1 AATATATTAT 0.567116 -52 ACAATTAAATTATGACACTTGAA 3 126 0 ATTAAATTAT 0.889649 -13 ATTAAAATCATAAAAATTCC 4 1 0 TAAAAATTCC 0.765101 -82 AAGAAACTTGAATGAATTATCATTCACGAA 4 31 1 AATGAATTAT 0.702007 -52 GTGTATACTAAAAAAATAACAGGAGGTGGG 4 62 1 AAAAAATAAC 0.846636 -21 AAAAGGTAAAAACTTCCTCATTTTTTT 5 17 0 AAAAACTTCC 0.834353 -17 ATTGTAGCACAGAAAATACCTATAATCTAA 6 14 0 AGAAAATACC 0.744776 -50 TTTGCGAAGGTTTAAATTATACTACTTCCT 7 22 1 TTTAAATTAT 0.677082 -49 GCTACTTATTATAAACTAATGTCTAAAGGA 7 48 0 ATAAACTAAT 0.609302 -23 ********** Masking position 7 Map Score: 4.67451 Number of sites scoring better than the average of aligned sites = 678 Number in coding regions = 539 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 5 TGGTGGCCCAGGGCGGAGTCGA 3 3 1 GTGGCCCAGG 0.982601 -136 CCAGGGCGGAGTCGAACCGCCGACACCCCG 3 18 1 GTCGAACCGC 0.891476 -121 TCGAACCGCCGACACCCCGGTTTTCAGCCG 3 29 1 GACACCCCGG 0.976205 -110 TCAGGTGGTAGAGCACCCGGCTGAAAACCG 3 46 0 GAGCACCCGG 0.992826 -93 TCTACCACCTGAGCTACCGGGCCTTACGAC 3 64 1 GAGCTACCGG 0.988695 -75 CTTCGCAAAGGAGGTAAAGG 7 1 0 GAGGTAAAGG 0.870166 -70 ********** Masking position 9 Map Score: 1.74386 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 200 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 ********** No masking Map Score: -5.51791e-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: -5.51791e-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: -5.51791e-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