AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i215_Ribosomal_Operon_2_aquae_reg_100.orf -o215_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 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 TAAAATACTTAGCTTCAGGAGGTAA 2 2 1 AAATACTGCT 0.784486 -32 CTCTGCAAATAAAAAATTTACCCTGTGTCCAATA 3 19 1 AAAAATTCCT 0.985933 -178 CCCTGTGTCCAATAACTTAACAATAAGAATTATC 3 39 1 AAAACTTCAT 0.963302 -158 CGCAAACTATAATAAATTAACACTTCTTTAAGCC 3 79 0 AAAAATTCAT 0.932438 -118 AGTGAGCTGTAAAAACCTTCGCGTTTCTAACATA 3 122 1 AAAACCTGCT 0.981978 -75 TTGATATTATAACAAATTTATGTTAGAAACGCGA 3 140 0 AAAAATTTGT 0.807248 -57 GTTATTCCTGGACAACCTTTCGTGTCAAGTTTAA 4 26 0 GAAACCTCGG 0.865354 -52 GTTGTCCAGGAATAACTTTTTCTTTTGCAAAGGA 4 44 1 AAAACTTTCT 0.959803 -34 AGGTTAAGATGATAAACTCTCCTTTAAGATATTC 5 11 1 GAAAACTCCT 0.983308 -29 GGGCTTCCTGAAGAACTTAGCCTTTTCTATTAAC 6 15 0 AAAACTTCCT 0.992553 -59 GAAAACCTTTCCGTGAAATTCCCG 6 60 0 GAAACCTCCT 0.991154 -14 ** ***** ** * Masking position 4 Map Score: 14.4526 Number of sites scoring better than the average of aligned sites = 725 Number in coding regions = 683 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 2 TACAAACCTCCTTCAAGCCGGCAGTTG 1 24 0 CTCCTTCAAG 0.99123 -17 CCTAACTTTACCTCCTGAAGCTAAGTATTT 2 13 0 CCTCCTGAAG 0.966339 -21 TAAATTAACACTTCTTTAAGCCAGTATTGA 3 71 0 CTTCTTTAAG 0.977474 -126 GGCTTTTCACCCCTTTAATTAGAGTAAGG 3 178 0 CCCCTTTAAT 0.964409 -19 ATGATAAACTCTCCTTTAAGATATTCAAGT 5 19 1 CTCCTTTAAG 0.994521 -21 TAAGGCAGGGCTTCCTGAAGAACTTAGCCT 6 26 0 CTTCCTGAAG 0.741268 -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 TTTACCTCCTGAAGCTAAGTATTTTA 2 7 0 GAAGCTAAGT 0.85115 -27 TTAGCTTCAGGAGGTAAAGTTAGGT 2 19 1 GAGGTAAAGT 0.980045 -15 TATTGGACACAGGGTAAATTTTTTATTTGC 3 23 0 AGGGTAAATT 0.940859 -174 GATAATTCTTATTGTTAAGTTATTGGACAC 3 43 0 ATTGTTAAGT 0.730719 -154 GGCTTAAAGAAGTGTTAATTTATTATAGTT 3 79 1 AGTGTTAATT 0.821245 -118 AGTTTGCGGTGGGCTAAAGTGAGCTGTAAA 3 105 1 GGGCTAAAGT 0.925047 -92 TAATTAGAGTAAGGCAAATTGATATTATAA 3 162 0 AAGGCAAATT 0.932149 -35 CTTTCGTGTCAAGTTTAATTATTTTAAACA 4 14 0 AAGTTTAATT 0.759403 -64 GTTAATAGAAAAGGCTAAGTTCTTCAGGAA 6 15 1 AAGGCTAAGT 0.97928 -59 GTCCGCTATGAGCTTCAGTTCAAGGA 7 8 0 GAGCTTCAGT 0.820414 -19 ********** Masking position 8 Map Score: 5.86775 Number of sites scoring better than the average of aligned sites = 1004 Number in coding regions = 924 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 4 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 5 TCCCTGACCTCTGCAAATAAAAAATTT 3 8 1 CCTCTGCAAA 0.997026 -189 TCACTTTAGCCCACCGCAAACTATAATAAA 3 97 0 CCACCGCAAA 0.993782 -100 TTTCACACCTCCTTTGCAAAAGAAAAAGTT 4 57 0 CCTTTGCAAA 0.991934 -21 ********** Masking position 8 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 6 TAGCTTCAGGAGGTAAAGTTAGGT 2 20 1 AGGTAAAGTT 0.936083 -14 TATGTTAGAAACGCGAAGGTTTTTACAGCT 3 126 0 ACGCGAAGGT 0.977016 -71 TAAACTTGACACGAAAGGTTGTCCAGGAAT 4 27 1 ACGAAAGGTT 0.896069 -51 GAATATCTTAAAGGAGAGTTTATCATCTTA 5 15 0 AAGGAGAGTT 0.867801 -25 TTAATAGAAAAGGCTAAGTTCTTCAGGAAG 6 16 1 AGGCTAAGTT 0.923887 -58 TGCCTTACATACGGGAATTTCACGGAAAGG 6 49 1 ACGGGAATTT 0.922909 -25 CGGGAATTTCACGGAAAGGTTTTC 6 60 1 ACGGAAAGGT 0.986817 -14 ********** Masking position 1 Map Score: 2.31327 Number of sites scoring better than the average of aligned sites = 621 Number in coding regions = 585 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 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 Motif number 9 ********** 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