AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i215_Ribosomal_Operon_2_bbur_reg_300.orf -o215_borburg_300.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 GCCTGTTGTGTTTTTGCTTAATTTTATATT 1 25 1 TTTTTGCTTA 0.908918 -154 TTTTGCTTAATTTTATATTTTTTTGTCTAG 1 36 1 TTTTATATTT 0.878766 -143 TTGTCTAGGTTTTTATCTTAATAATTAAAA 1 58 1 TTTTATCTTA 0.956808 -121 TTATTTTATAATTTTAATTATTAAGATAAA 1 69 0 ATTTTAATTA 0.913864 -110 TGTGGCTAATTTTTAAATTAGCTGCCTTAC 1 115 1 TTTTAAATTA 0.989772 -64 ATAGCTCTTTTTTTAAATTACTCATGTAAG 1 140 0 TTTTAAATTA 0.989772 -39 GTTTATATATTTTTCAAATATCAAGACCAA 2 20 0 TTTTCAAATA 0.940704 -42 TTGACTTTTCTTTTTTATTAAATTTACAAT 3 19 1 TTTTTTATTA 0.974986 -38 ATCTCCAATCTTTTCAATTAAAA 4 4 0 TTTTCAATTA 0.991552 -51 TTTCTCCAATTTTTCAATTAAAACCAAAAA 4 33 0 TTTTCAATTA 0.991552 -22 ********** Masking position 4 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 AAAAAAATATAAAATTAAGCAAAAACACAA 1 30 0 AAAATTAAGC 0.871814 -149 TATTAAGATAAAAACCTAGACAAAAAAATA 1 51 0 AAAACCTAGA 0.954185 -128 TCCTCCTTAAAACCAAATTATAGCTCTT 1 161 0 AAAACCAAAT 0.971345 -18 ATCAAGACCAAAAGCCAAAT 2 1 0 AAAGCCAAAT 0.958001 -61 ATATTTTTCAAATATCAAGACCAAAAGCCA 2 14 0 AATATCAAGA 0.909779 -48 ATAAAAAAGAAAAGTCAAGCATTAAA 3 7 0 AAAGTCAAGC 0.972439 -50 TTTTTCAATTAAAACCAAAAATCTCCAATC 4 24 0 AAAACCAAAA 0.979827 -31 ********** Masking position 8 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 0.989017 -18 TTAATTGAAAAGATTGGAGATTTTTGGTTT 4 13 1 AGATTGGAGA 0.99659 -42 TTTAATTGAAAAATTGGAGAAAGT 4 41 1 AAATTGGAGA 0.990752 -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 TTTTGCTTAATTTTATATTTTTTTGTCTAG 1 36 1 TTTTATATTT 0.968444 -143 ATACAACTTATTTTATAATTTTAATTATTA 1 76 0 TTTTATAATT 0.932552 -103 ATAAAATAAGTTGTATAATGATGTTTGTGG 1 90 1 TTGTATAATG 0.910238 -89 TGTGGCTAATTTTTAAATTAGCTGCCTTAC 1 115 1 TTTTAAATTA 0.87553 -64 ATAGCTCTTTTTTTAAATTACTCATGTAAG 1 140 0 TTTTAAATTA 0.87553 -39 GGCTTTTGGTCTTGATATTTGAAAAATATA 2 15 1 CTTGATATTT 0.820874 -47 ATCTATATGTTTATATATTTTTCAAATATC 2 28 0 TTATATATTT 0.883567 -34 CAACTAAACATTGTAAATTTAATAAAAAAG 3 28 0 TTGTAAATTT 0.961194 -29 ATTGAAAAGATTGGAGATTTTTGGTTTTAA 4 16 1 TTGGAGATTT 0.950094 -39 AATTGAAAAATTGGAGAAAGT 4 44 1 TTGGAGAAAG 0.40718 -11 ********** Masking position 5 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 AAGCAAAAACACAACAGGCCAATTAATTGTT 1 13 0 ACACAGGCCA 0.94225 -166 AAAAAATATAAAATTAAGCAAAAACACAACA 1 28 0 AATTAAGCAA 0.838818 -151 AGCTAATTTAAAAATTAGCCACAAACATCAT 1 107 0 AAATTAGCCA 0.915583 -72 TCCTCCTTAAAACCAAATTATAGCT 1 164 0 CCTAAAACCA 0.883558 -15 AAATATCAAGACCAAAAGCCAAAT 2 4 0 ACAAAAGCCA 0.991576 -58 TTTAATAAAAAAGAAAAGTCAAGCATTAAA 3 10 0 AAAAAAGTCA 0.926705 -47 CCAATTTTTCAATTAAAACCAAAAATCTCCA 4 27 0 AATAAAACCA 0.953317 -28 ** ******** Masking position 11 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