AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i117_Oligopeptide_Transport_aquae_reg_300.orf -o117_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 RAA00348 137 Aquifex_aeolicus #2 RAA00349 69 Aquifex_aeolicus #3 RAA00355 36 Aquifex_aeolicus #4 RAA00486 113 Aquifex_aeolicus #5 RAA00837 118 Aquifex_aeolicus Motif number 1 AAGGAAGTATTTTAAAGGTGGACTAA 1 5 1 AAGTTTTAAA 0.986729 -133 AAGGTGGACTAAGAATTTTTAAGAAATAAAAT 1 25 1 AAGTTTTTAA 0.930187 -113 CCTCCCTTGAAAGTTTTTTACACTTTTTATTT 1 53 0 AAGTTTTACA 0.991592 -85 CAGCCTCAACAAAGGTTTTACC 1 126 1 AAATTTTACC 0.986464 -12 AAAAATCAAAAAGTGTTTTAAATTAACTTGAC 4 60 0 AAGTTTTAAA 0.986729 -54 ACTTAAAGATTTTACCTCTAGAGATT 4 98 0 AAATTTTACC 0.986464 -16 AAAAGGGCGTATATATTTTAAAGAC 5 4 0 ATATTTTAAA 0.893619 -115 AGTAAAAATTTTACCGCTCGGAAAC 5 104 0 AAATTTTACC 0.986464 -15 *** ******* Masking position 1 Map Score: 13.826 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 157 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 2 TGAAAGTTTTTTACACTTTTTATTTTATTTCTT 1 45 0 TTCCTTTTAT 0.903749 -93 ATGAGTCAAGTTACTCAATCTTTCAGAAAAAGT 1 91 1 TTCCAATTTT 0.868897 -47 TCTGCTAGGTTGCACCCTTCTTTCTTTTTCCT 2 10 1 TTCCCCTCTT 0.988852 -60 TTCTTTCTTTTTCCTCTTTTCTTTTAACCTTTA 2 28 1 TTCCTTTCTT 0.994528 -42 CTCTTTTCTTTTAACCTTTATTTATATAGGATT 2 41 1 TTACTTTTTT 0.869305 -29 TCGCCTTGATTTTGGCTTTCCTTATT 3 21 1 TTGCTTTCTT 0.967824 -16 ATGAATAAAATTACACTCTACTTTCGGAGGAGA 4 14 0 TTCCTCTCTT 0.996543 -100 TAAATTAACTTGACACACTTCTTCAAAATGAAT 4 41 0 TGCCACTCTT 0.961023 -73 TGGTGGAAATTTTCGCTCTACTTGTCACACTAT 5 63 1 TTCCTCTCTT 0.996543 -56 ** * **** *** Masking position 9 Map Score: 13.5749 Number of sites scoring better than the average of aligned sites = 430 Number in coding regions = 396 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 3 TTAGTCCACCTTTAAAATACTTCCTT 1 6 0 TTTAAAAACT 0.946947 -132 ATTTTATTTCTTAAAAATTCTTAGTCCACCT 1 26 0 TTAAAAATCT 0.913226 -112 AAATAAAAAGTGTAAAAAACTTTCAAGGGAG 1 53 1 TGTAAAAACT 0.971386 -85 TCAATCTTTCAGAAAAAGTCTCAGCCTCAAC 1 105 1 AGAAAAATCT 0.896952 -33 GGTAAAACCTTTGTTGAGGCT 1 127 0 GGTAAAACTT 0.950962 -11 GATAAAAATCCTATATAAATAA 2 58 0 ATAAAAACCT 0.84683 -12 TTCTTCAAAATGAATAAAATTACACTCTACT 4 25 0 TGAATAAATT 0.645983 -89 GTCAAGTTAATTTAAAACACTTTTTGATTTT 4 60 1 TTTAAAAACT 0.946949 -54 TTTGATTTTTGTTATAAATCTCTAGAGGTAA 4 82 1 GTTATAATCT 0.850789 -32 AATCTCTAGAGGTAAAATCTTTAAGT 4 98 1 GGTAAAACTT 0.950962 -16 GTTTCCGAGCGGTAAAATTTTTACT 5 104 1 GGTAAAATTT 0.941377 -15 ******* *** Masking position 6 Map Score: 11.2565 Number of sites scoring better than the average of aligned sites = 823 Number in coding regions = 752 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 4 AGATTGAGTAACTTGACTCATGGCACACCT 1 82 0 ACTTGACTCA 0.994542 -56 TTTTAAATTAACTTGACACACTTCTTCAAA 4 47 0 ACTTGACACA 0.996897 -67 TTTTCGCTCTACTTGTCACACTATAGATAC 5 72 1 ACTTGTCACA 0.994542 -47 ********** Masking position 1 Map Score: 4.07456 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 3 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 TAACTTGACTCATGGCACACCTCCCTTGAA 1 74 0 CATGGCACAC 0.995501 -64 TTTAAATTAACTTGACACACTTCTTCAAAA 4 46 0 CTTGACACAC 0.996217 -68 TTTCGCTCTACTTGTCACACTATAGATACA 5 73 1 CTTGTCACAC 0.996217 -46 ********** Masking position 7 Map Score: 3.46303 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 4 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 ********** No masking Map Score: 5.92755e-14 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: 5.92755e-14 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: 5.92755e-14 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