AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i150_ATP_synthase_1_aquae_reg_100.orf -o150_aquae_100.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 RAA01493 138 Aquifex_aeolicus #3 RAA01475 82 Aquifex_aeolicus #4 RAA01504 33 Aquifex_aeolicus #5 RAA01472 63 Aquifex_aeolicus #6 RAA01142 70 Aquifex_aeolicus Motif number 1 TTCCCTTACCTCTTTTGCAATTGGCT 1 34 0 TTACCTCTTT 0.977733 -16 GCCGGGTGCTCTACCACCTGAGCTACCGGGC 2 55 1 CTACCACCTA 0.978798 -84 ACCCACCTCCTGTTATTTTTTTA 3 70 0 CCACCTCCTT 0.994678 -13 AAGGTAAAAACTTCCTCATTTTTTTACCTCC 4 11 0 CTTCCTCATT 0.951244 -23 ACTCTACCTCCTAACCTTCTTTAA 5 50 0 CTACCTCCTA 0.996132 -14 CCTTTACCTCCTTTGCGAAGGTTT 6 4 1 TTACCTCCTT 0.993826 -67 TTAAATTATACTACTTCCTTTAGACATTAGT 6 33 1 CTACTTCCTT 0.993826 -38 AACGCTACTTATTATAAACTAATGT 6 56 0 CTACTTATTT 0.830603 -15 ********* * Masking position 9 Map Score: 14.059 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 CAATTGCAAAAGAGGTAAGGGAA 1 37 1 AGAGGTAAGG 0.987622 -13 CGGTAGCTCAGGTGGTAGAGCACCCGGCTG 2 53 0 GGTGGTAGAG 0.990906 -86 AAAAATAACAGGAGGTGGGT 3 73 1 GGAGGTGGGT 0.954181 -10 GGAGGTAAAAAAATGAGGAA 4 1 1 GGAGGTAAAA 0.993237 -33 AAAAGGTAAAAACTTCCTCAT 4 23 0 AAAGGTAAAA 0.838624 -11 AAGAAGGTTAGGAGGTAGAGT 5 53 1 GGAGGTAGAG 0.998098 -11 CCTTCGCAAAGGAGGTAAAGG 6 2 0 GGAGGTAAAG 0.997705 -69 ********** Masking position 6 Map Score: 13.2803 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 AAAATTATAACATAAATTTG 1 1 0 CATAAATTTG 0.803924 -49 AAATTTATGTTATAATTTTCTGAGCCAATT 1 12 1 TATAATTTTC 0.919227 -38 GAATATATAATATATTTTTGTCGTAAGGCC 2 83 0 TATATTTTTG 0.899419 -56 GTTCAAGTGTCATAATTTAATTGT 2 125 1 CATAATTTAA 0.954558 -14 GGAATTTTTATGATTTTAATAAGAAACT 3 9 1 TATGATTTTA 0.905642 -74 CACCTCCTGTTATTTTTTTAGTATACACTT 3 60 0 TATTTTTTTA 0.861914 -23 AAAACTTCCTCATTTTTTTACCTCC 4 6 0 CATTTTTTTA 0.8166 -28 AGAAAATACCTATAATCTAACTT 5 4 0 TATAATCTAA 0.927504 -60 AAGGAAGTAGTATAATTTAAACCTTCGCAA 6 23 0 TATAATTTAA 0.966473 -48 CGCTACTTATTATAAACTAATGTCTAAAGG 6 49 0 TATAAACTAA 0.781165 -22 ********** Masking position 3 Map Score: 7.60918 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 104 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 4 TGGTGGCCCAGGGCGGAGTCGA 2 3 1 GTGGCCCAGG 0.985509 -136 CCAGGGCGGAGTCGAACCGCCGACACCCCG 2 18 1 GTCGAACCGC 0.908104 -121 TCGAACCGCCGACACCCCGGTTTTCAGCCG 2 29 1 GACACCCCGG 0.980161 -110 TCAGGTGGTAGAGCACCCGGCTGAAAACCG 2 46 0 GAGCACCCGG 0.994035 -93 TCTACCACCTGAGCTACCGGGCCTTACGAC 2 64 1 GAGCTACCGG 0.990568 -75 CTTCGCAAAGGAGGTAAAGG 6 1 0 GAGGTAAAGG 0.889759 -70 ********** Masking position 9 Map Score: 2.20885 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 5 TAATTTTCTGAGCCAATTGCAAAAGAGGTA 1 24 1 AGCCAATTGC 0.900965 -26 AATTAAATTATGACACTTGAACTCAAAGGG 2 117 0 TGACACTTGA 0.908725 -22 ATTAAAATCATAAAAATTCC 3 1 0 TAAAAATTCC 0.924867 -82 GATTTTAATAAGAAACTTGAATGAATTATC 3 22 1 AGAAACTTGA 0.92306 -61 CTTTCGTGAATGATAATTCATTCAAGTTTC 3 33 0 TGATAATTCA 0.867442 -50 AAAAGGTAAAAACTTCCTCATTTTTTT 4 17 0 AAAAACTTCC 0.951325 -17 ATTGTAGCACAGAAAATACCTATAATCTAA 5 14 0 AGAAAATACC 0.849616 -50 GTTTAAATTATACTACTTCCTTTAGACATT 6 31 1 TACTACTTCC 0.855756 -40 ********** Masking position 5 Map Score: 1.66045 Number of sites scoring better than the average of aligned sites = 1099 Number in coding regions = 1040 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 6 ********** No masking Map Score: 6.84553e-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: 6.84553e-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: 6.84553e-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