AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i215_Ribosomal_Operon_2_aquae_reg_300.orf -o215_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 RAA00617 40 Aquifex_aeolicus #2 RAA01771 33 Aquifex_aeolicus #3 RAA00587 196 Aquifex_aeolicus #4 RAA00783 77 Aquifex_aeolicus #5 RAA01636 39 Aquifex_aeolicus #6 RAA01651 73 Aquifex_aeolicus #7 RAA01663 26 Aquifex_aeolicus Motif number 1 TTACCTCCTGAAGCTAAGTATTTTA 2 2 0 AGAAGTATTT 0.923045 -32 TATTGGACACAGGGTAAATTTTTTATTTGCAGAG 3 19 0 AGAAATTTTT 0.984867 -178 GATAATTCTTATTGTTAAGTTATTGGACACAGGG 3 39 0 ATTAAGTTTT 0.89901 -158 GGCTTAAAGAAGTGTTAATTTATTATAGTTTGCG 3 79 1 ATTAATTTTT 0.884856 -118 TATGTTAGAAACGCGAAGGTTTTTACAGCTCACT 3 122 0 AGAAGGTTTT 0.984132 -75 TCGCGTTTCTAACATAAATTTGTTATAATATCAA 3 140 1 ACAAATTTTT 0.942223 -57 CTTTCGTGTCAAGTTTAATTATTTTAAACAATT 4 10 0 AGTAATTATT 0.837369 -68 TCCTTTGCAAAAGAAAAAGTTATTCCTGGACAAC 4 44 0 AGAAAGTTTT 0.986398 -34 GAATATCTTAAAGGAGAGTTTATCATCTTAACCT 5 11 0 AGGAGTTTTC 0.9131 -29 AACTTGAATATCTTAAAGGAGAGT 5 26 0 ACGAATATTT 0.688233 -14 GTTAATAGAAAAGGCTAAGTTCTTCAGGAAGCCC 6 15 1 AGTAAGTTTT 0.980951 -59 CGGGAATTTCACGGAAAGGTTTTC 6 60 1 AGAAGGTTTC 0.955545 -14 * * ****** ** Masking position 7 Map Score: 13.9043 Number of sites scoring better than the average of aligned sites = 444 Number in coding regions = 413 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 2 TACAAACCTCCTTCAAGCCGGCAGTTG 1 24 0 CTCCTTCAAG 0.989163 -17 CCTAACTTTACCTCCTGAAGCTAAGTATTT 2 13 0 CCTCCTGAAG 0.96865 -21 TAAATTAACACTTCTTTAAGCCAGTATTGA 3 71 0 CTTCTTTAAG 0.978686 -126 GGCTTTTCACCCCTTTAATTAGAGTAAGG 3 178 0 CCCCTTTAAT 0.954816 -19 ATGATAAACTCTCCTTTAAGATATTCAAGT 5 19 1 CTCCTTTAAG 0.993369 -21 TAAGGCAGGGCTTCCTGAAGAACTTAGCCT 6 26 0 CTTCCTGAAG 0.770181 -48 ********** Masking position 6 Map Score: 10.2982 Number of sites scoring better than the average of aligned sites = 319 Number in coding regions = 295 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 3 GCAGTTGGGCTTTAAACCCC 1 1 0 TTTAAACCCC 0.980544 -40 TACAAACCTCCTTCAAGCCG 1 31 0 TACAAACCTC 0.941825 -10 CTATAATAAATTAACACTTCTTTAAGCCAG 3 77 0 TTAACACTTC 0.91677 -120 CGCGAAGGTTTTTACAGCTCACTTTAGCCC 3 115 0 TTTACAGCTC 0.976331 -82 GGCTTTTCACCCCTTTAATTAGA 3 184 0 TTTTCACCCC 0.973542 -13 CTTTCACACCTCCTTTGCAAAA 4 66 0 TTCACACCTC 0.994877 -12 ********** Masking position 6 Map Score: 5.75968 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 190 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 4 AAATTTTTTATTTGCAGAGGTCAGGGA 3 8 0 TTTGCAGAGG 0.997101 -189 TTTATTATAGTTTGCGGTGGGCTAAAGTGA 3 97 1 TTTGCGGTGG 0.993938 -100 AACTTTTTCTTTTGCAAAGGAGGTGTGAAA 4 57 1 TTTGCAAAGG 0.992136 -21 ********** Masking position 3 Map Score: 2.51007 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 23 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 5 TCCCTGACCTCTGCAAATAA 3 1 1 TCCCTGACCT 0.980652 -196 TTACCCTGTGTCCAATAACTTAACAATAAG 3 36 1 TCCAATAACT 0.947527 -161 CTTAGCCTTTTCTATTAACTCAT 6 4 0 TCTATTAACT 0.919253 -70 GAAAACCTTTCCGTGAAATTCCCGTATGT 6 55 0 TCCGTGAAAT 0.955673 -19 TCCTTGAACTGAAGCTCATA 7 1 1 TCCTTGAACT 0.986998 -26 ********** Masking position 7 Map Score: 1.19404 Number of sites scoring better than the average of aligned sites = 344 Number in coding regions = 330 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 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