AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i216_Ribosomal_Operon_3_pyro_reg_100.orf -o216_pyro_100.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -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 = 0.42 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RPH01519 185 Pyrococcus_OT3 #2 RPH01554 37 Pyrococcus_OT3 #3 RPH01557 59 Pyrococcus_OT3 #4 RPH01559 70 Pyrococcus_OT3 #5 RPH01560 55 Pyrococcus_OT3 #6 RPH01561 233 Pyrococcus_OT3 Motif number 1 CACCATGCTAATATTTGCTTAACTTAAATTTAAACC 1 18 1 AATTTAATTA 0.965052 -168 ATAAAACTCCACAATTTCTTGAATTATTGTCGAATG 1 103 1 AAATTGATTA 0.988922 -83 TCCCTCGCCAAAATTTGGTTGCCTTAATACTTCCTT 1 159 0 AATTTGCTTA 0.940086 -27 CCTTTTTACAAAAATTTAATATCTTATAAAGGTAAT 3 15 1 AAATTATTTA 0.822099 -45 AAAGGTAATAAAAACTCTGGGAGTTACT 3 42 1 AAACTGATTA 0.943937 -18 GTTGAAATTTCTTCAAGCTATTTCTCCGCA 4 5 1 AATTTAACTA 0.945159 -66 CAAAAGATTTATAATTCCTGGAACTATCAACTCCAC 4 39 1 AAATTGACTA 0.982453 -32 ATTTTTAAGTAGATTTCCATGAGCTATTCTTCG 5 33 1 AATTTGACTA 0.97922 -23 GAGAAATGGAAGAATTTGCCAATTTATGGTC 6 6 0 AAATTAATTA 0.969738 -228 TGGCCAAATAAGGATTCAATGAATTATAAATAATTG 6 119 0 AGATTGATTA 0.943928 -115 AAAACTATATAAATTTTTCGGATTTCTCATGCCTGC 6 165 0 AATTTGATTC 0.933384 -69 * **** ** *** Masking position 1 Map Score: 12.3932 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 109 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 2 CAATCCTTTTAGACGTTTTGAAAACTCACAGAGG 1 69 1 AGACTTAAAA 0.777009 -117 ACATTCGACAATAATTCAAGAAATTGTGGAGTTT 1 106 0 ATAATCAAAT 0.964842 -80 GGTTGCCTTAATACTTCCTTAAAAAGGTTATGTA 1 145 0 ATACTCAAAA 0.968917 -41 ATCCCTCGCCAAAATTTGGTTGCC 1 172 0 ATCCTCAAAA 0.842549 -14 TATTACCTTTATAAGATATTAAATTTTTGTAAAA 3 18 0 ATAAATAAAT 0.66486 -42 TTGCGGAGAAATAGCTTGAAGAAATTTCAAC 4 8 0 ATAGTTGAAA 0.892126 -63 CGTGGAGTTGATAGTTCCAGGAATTATAAATCTT 4 42 0 ATAGTCGAAT 0.949039 -29 CTACTTAAAAATAATACTAAAAAAGAAAGAAACA 5 11 0 ATAAACAAAA 0.894373 -45 CGAAGAATAGCTCATGGAAATCTACTTAAA 5 36 0 ATAGTCGAAA 0.962467 -20 GACCATAAATTGGCAAATTCTTCCATTT 6 5 1 ATAATTAAAT 0.89852 -229 CCAATTATTTATAATTCATTGAATCCTTATTTGG 6 118 1 ATAATCGAAT 0.957557 -116 TGCAGGCATGAGAAATCCGAAAAATTTATATAGT 6 164 1 AGAATCAAAA 0.929065 -70 **** ** **** Masking position 12 Map Score: 11.251 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 203 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 3 TTTTTGGGCAATCCTTTTAGACGTTTTGAAAA 1 61 1 ATCTTTAGAC 0.803422 -125 AACTCCACAATTTCTTGAATTATTGTCGAATG 1 107 1 TTCTTGATTA 0.663328 -79 TTCAGTTACATAACCTTTTTAAGGAAGTATTA 1 139 1 TACCTTTTAA 0.757088 -47 CAAAATTTGGTTGCCTTAATACTTCCTTAAAA 1 155 0 TTCCTTATAC 0.9804 -31 CAAGTTAATCTTACTTTAAGACCC 2 3 0 TTCTTTAGAC 0.942765 -35 TTTTCCTTTTTACAAAAATTTAA 3 2 1 TTCCTTTTAC 0.952208 -58 AGAGTTTTTATTACCTTTATAAGATATTAAAT 3 28 0 TTCCTTATAA 0.969264 -32 TGCGGAGAAATAGCTTGAAGAAATTTCAAC 4 9 0 TACTTGAGAA 0.706722 -62 TGTTTCTTTCTTTTTTAGTATTATTTTT 5 7 1 TTCTTTTTAG 0.888584 -49 ATTTCTCTTCTTACCTGGATAGCATCTTTACT 6 35 1 TTCCTGATAG 0.972688 -199 CGGATTTCTCATGCCTGCATAGAGATTATGGC 6 151 0 ATCCTGATAG 0.898341 -83 ** **** **** Masking position 6 Map Score: 7.28678 Number of sites scoring better than the average of aligned sites = 470 Number in coding regions = 429 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 4 AACCTTGTGCATTTTTGGGCAATCCTTTTA 1 50 1 ATTTTTGGGC 0.965432 -136 AATTGTGGAGTTTTATCCTCTGTGAGTTTT 1 89 0 TTTTATCCTC 0.846565 -97 TCTTCAAGCTATTTCTCCGCAAAAGATTTA 4 20 1 ATTTCTCCGC 0.986197 -51 GAATTTGCCAATTTATGGTC 6 1 0 ATTTATGGTC 0.904187 -233 AAATTCTTCCATTTCTCTTCTTACCTGGAT 6 25 1 ATTTCTCTTC 0.896982 -209 AACTATATAAATTTTTCGGATTTCTCATGC 6 169 0 ATTTTTCGGA 0.89567 -65 AATTTATATAGTTTTTCCGCCCATTTTGAA 6 186 1 GTTTTTCCGC 0.960319 -48 ********** Masking position 6 Map Score: 2.33682 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 179 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 5 ********** No masking Map Score: 1.63668e-12 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 6 ********** No masking Map Score: 1.63668e-12 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: 1.63668e-12 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