AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i215_Ribosomal_Operon_2_bbur_reg_100.orf -o215_borburg_100.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -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 = 0.28 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RBB00736 178 3615 #2 RBB00735 61 3615 #3 RBB00734 56 3615 #4 RBB00725 54 3615 Motif number 1 AATATAAAATTAAGCAAAAACACAACAGGC 1 25 0 TAAGCAAAAA 0.911088 -154 CTAGACAAAAAAATATAAAATTAAGCAAAA 1 36 0 AAATATAAAA 0.88156 -143 TTTTAATTATTAAGATAAAAACCTAGACAA 1 58 0 TAAGATAAAA 0.95789 -121 TTTATCTTAATAATTAAAATTATAAAATAA 1 69 1 TAATTAAAAT 0.915925 -110 GTAAGGCAGCTAATTTAAAAATTAGCCACA 1 115 0 TAATTTAAAA 0.990029 -64 CTTACATGAGTAATTTAAAAAAAGAGCTAT 1 140 1 TAATTTAAAA 0.990029 -39 TTGGTCTTGATATTTGAAAAATATATAAAC 2 20 1 TATTTGAAAA 0.942023 -42 ATTGTAAATTTAATAAAAAAGAAAAGTCAA 3 19 0 TAATAAAAAA 0.975605 -38 TTTTAATTGAAAAGATTGGAGAT 4 4 1 TAATTGAAAA 0.991767 -51 TTTTTGGTTTTAATTGAAAAATTGGAGAAA 4 33 1 TAATTGAAAA 0.991767 -22 ********** Masking position 7 Map Score: 20.0951 Number of sites scoring better than the average of aligned sites = 754 Number in coding regions = 446 Number in noncoding regions = 308 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 2 TTGTGTTTTTGCTTAATTTTATATTTTTTT 1 30 1 GCTTAATTTT 0.891335 -149 TATTTTTTTGTCTAGGTTTTTATCTTAATA 1 51 1 TCTAGGTTTT 0.961713 -128 AAGAGCTATAATTTGGTTTTAAGGAGGA 1 161 1 ATTTGGTTTT 0.976124 -18 ATTTGGCTTTTGGTCTTGAT 2 1 1 ATTTGGCTTT 0.964925 -61 TGGCTTTTGGTCTTGATATTTGAAAAATAT 2 14 1 TCTTGATATT 0.924023 -48 TTTAATGCTTGACTTTTCTTTTTTAT 3 7 1 GCTTGACTTT 0.97704 -50 GATTGGAGATTTTTGGTTTTAATTGAAAAA 4 24 1 TTTTGGTTTT 0.983216 -31 ********** Masking position 3 Map Score: 6.88314 Number of sites scoring better than the average of aligned sites = 506 Number in coding regions = 360 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 3 ATAAACATATAGATGGGATAAGTAGGTT 2 44 1 AGATGGGATA 0.988419 -18 TTAATTGAAAAGATTGGAGATTTTTGGTTT 4 13 1 AGATTGGAGA 0.996403 -42 TTTAATTGAAAAATTGGAGAAAGT 4 41 1 AAATTGGAGA 0.990248 -14 ********** Masking position 3 Map Score: 2.15463 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 5 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 4 CTAGACAAAAAAATATAAAATTAAGCAAAA 1 36 0 AAATATAAAA 0.967647 -143 TAATAATTAAAATTATAAAATAAGTTGTAT 1 76 1 AATTATAAAA 0.930927 -103 CCACAAACATCATTATACAACTTATTTTAT 1 90 0 CATTATACAA 0.908104 -89 GTAAGGCAGCTAATTTAAAAATTAGCCACA 1 115 0 TAATTTAAAA 0.872667 -64 CTTACATGAGTAATTTAAAAAAAGAGCTAT 1 140 1 TAATTTAAAA 0.872667 -39 TATATTTTTCAAATATCAAGACCAAAAGCC 2 15 0 AAATATCAAG 0.817008 -47 GATATTTGAAAAATATATAAACATATAGAT 2 28 1 AAATATATAA 0.880874 -34 CTTTTTTATTAAATTTACAATGTTTAGTTG 3 28 1 AAATTTACAA 0.960209 -29 TTAAAACCAAAAATCTCCAATCTTTTCAAT 4 16 0 AAATCTCCAA 0.948843 -39 ACTTTCTCCAATTTTTCAATT 4 44 0 CTTTCTCCAA 0.400901 -11 ********** Masking position 6 Map Score: 7.78827 Number of sites scoring better than the average of aligned sites = 1548 Number in coding regions = 968 Number in noncoding regions = 580 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 5 AACAATTAATTGGCCTGTTGTGTTTTTGCTT 1 13 1 TGGCCTGTGT 0.940251 -166 TGTTGTGTTTTTGCTTAATTTTATATTTTTT 1 28 1 TTGCTTAATT 0.833868 -151 ATGATGTTTGTGGCTAATTTTTAAATTAGCT 1 107 1 TGGCTAATTT 0.912745 -72 AGCTATAATTTGGTTTTAAGGAGGA 1 164 1 TGGTTTTAGG 0.879785 -15 ATTTGGCTTTTGGTCTTGATATTT 2 4 1 TGGCTTTTGT 0.991269 -58 TTTAATGCTTGACTTTTCTTTTTTATTAAA 3 10 1 TGACTTTTTT 0.92421 -47 TGGAGATTTTTGGTTTTAATTGAAAAATTGG 4 27 1 TGGTTTTATT 0.951681 -28 ******** ** Masking position 1 Map Score: 1.11089 Number of sites scoring better than the average of aligned sites = 539 Number in coding regions = 370 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 6 ********** No masking Map Score: -2.46258e-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: -2.46258e-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: -2.46258e-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