AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i221_Ribosomal_Operon_8_pyro_reg_300.orf -o221_pyro_300.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 RPH01502 121 Pyrococcus_OT3 #2 RPH01503 58 Pyrococcus_OT3 #3 RPH01506 155 Pyrococcus_OT3 #4 RPH01507 26 Pyrococcus_OT3 #5 RPH01510 101 Pyrococcus_OT3 #6 RPH01511 63 Pyrococcus_OT3 Motif number 1 GCCAAGCTACCCCACGGCCCCACTTAAACA 1 25 0 CCCACGGCCC 0.997476 -97 CTTGGCTATCCTCCCGGCCTGGGGCGCCGG 1 49 1 CTCCCGGCCT 0.985623 -73 ACCCGGGTCTCCGGCGCCCCAGGCCGGGAG 1 59 0 CCGGCGCCCC 0.996668 -63 GGTTCAAATCCCGGCGGCCCCACCAAAATA 1 86 1 CCGGCGGCCC 0.995989 -36 GGGACCCACCCCACTTGTCTTCGA 2 45 0 CCCACCCCAC 0.883457 -14 GGCTCGGCAACCCCCGCTCAAT 3 3 0 CCCCCGCTCA 0.983659 -153 GACCCTAAATCCCGCGCCTTTGACCAGGCT 3 29 0 CCCGCGCCTT 0.971046 -127 GGGATTTAGGGTCCCGTCCCGTAGGGGTTC 3 46 1 GTCCCGTCCC 0.898347 -110 GGGGTTCAAATCCCCGCCCCCGCACCAAAA 3 77 1 TCCCCGCCCC 0.997362 -79 GAAAGCATTCCCCCTTCTTGCAGTTAAA 3 138 0 TCCCCCTTCT 0.736593 -18 GCTCTCAAGGCCCGCGCCCTACCAGG 5 7 0 CCCGCGCCCT 0.998182 -95 CGGGCAAACGCCCACGGGCTCTCAAGGCCC 5 24 0 CCCACGGGCT 0.972473 -78 GATTTGAACCCCGGCGGGCAAACGCCCACG 5 38 0 CCGGCGGGCA 0.934277 -64 GGGGTTCAAATCCCCGTCCCGGCGCCAGAA 5 56 1 TCCCCGTCCC 0.99453 -46 TTTATCCCCCTCCAGATTGAGTGA 5 88 0 TCCCCCTCCA 0.932324 -14 ********** Masking position 5 Map Score: 33.8233 Number of sites scoring better than the average of aligned sites = 383 Number in coding regions = 294 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 2 GGCTATCCTCCCGGCCTGGGGCGCCGGAGACCCGGG 1 52 1 CCGCTGCCCG 0.966139 -70 GCGCCGGAGACCCGGGTTCAAATCCCGGCGGCCCCA 1 72 1 CCGGTAACCC 0.999297 -50 GCGCCTTTGACCAGGCTCGGCAACCCCCGCTCAAT 3 10 0 CCGGTGACCC 0.998956 -146 CCCTACGGGACGGGACCCTAAATCCCGCGCCTTTGA 3 36 0 CGGACAACCC 0.972403 -120 CGTAGGGGTTCCGGGGTTCAAATCCCCGCCCCCGCA 3 65 1 CCGGTAACCC 0.999268 -91 TGGTAGGGCGCGGGCCTTGAGAGCCCGTGGGCGTTT 5 13 1 CGGCTAACCC 0.996644 -89 CGTTTGCCCGCCGGGGTTCAAATCCCCGTCCCGGCG 5 44 1 CCGGTAACCC 0.999268 -58 ** ** * * * *** Masking position 4 Map Score: 14.6962 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 47 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 3 CCGGGTTCAAATCCCGGCGGCCCCACCAAA 1 83 1 ATCCCGGCGG 0.95225 -39 CACCTCAAGTATTTTGGTGGGGCCGCCGGG 1 95 0 ATTTTGGTGG 0.99121 -27 ATTAATGTAAATTTTGGTGCGGGGGCGGGG 3 88 0 ATTTTGGTGC 0.988486 -68 TCATTTTCCCATTTTGGAGGAA 4 15 1 ATTTTGGAGG 0.993849 -12 ATTGAGTGAAATTCTGGCGCCGGGACGGGG 5 67 0 ATTCTGGCGC 0.993803 -35 AATTTCACTCAATCTGGAGGGGGATAAA 5 84 1 AATCTGGAGG 0.975905 -18 CTTTTTAACTATTTTGGAGCTTGATGTTTT 6 42 1 ATTTTGGAGC 0.991936 -22 ********** Masking position 1 Map Score: 14.1982 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 53 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 4 CCTTTCTCTGTTTAAGTGGGGCCGTGGGGTA 1 17 1 TTTAAGTGGG 0.911931 -105 ACCTCAAGTATTTTGGTGGGGCCGCCGGGAT 1 93 0 TTTTGGTGGG 0.996068 -29 ACCAAAATACTTGAGGTGGTGCTGA 1 107 1 TTGAGGTGGG 0.971351 -15 TTAATGTAAATTTTGGTGCGGGGGCGGGGAT 3 86 0 TTTTGGTGCG 0.993618 -70 CATTTTCCCATTTTGGAGGAA 4 16 1 TTTTGGAGGA 0.961878 -11 TTGAGTGAAATTCTGGCGCCGGGACGGGGAT 5 65 0 TTCTGGCGCG 0.97925 -37 ATTTCACTCAATCTGGAGGGGGATAAA 5 85 1 ATCTGGAGGG 0.959113 -17 TTTTTAACTATTTTGGAGCTTGATGTTTTTG 6 43 1 TTTTGGAGCT 0.939425 -21 ********* * Masking position 2 Map Score: 10.3349 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 120 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 5 TTTCTCTGTTTAAGTGGGGCCGTGGGGTAG 1 19 1 TAAGTGGGGC 0.925969 -103 AAGTGGGGCCGTGGGGTAGCTTGGCTATCC 1 30 1 GTGGGGTAGC 0.854272 -92 CTATCCTCCCGGCCTGGGGCGCCGGAGACC 1 54 1 GGCCTGGGGC 0.957204 -68 CTCAAGTATTTTGGTGGGGCCGCCGGGATT 1 92 0 TTGGTGGGGC 0.992802 -30 CAAAATACTTGAGGTGGTGCTGA 1 109 1 GAGGTGGTGC 0.9845 -13 GAAGACAAGTGGGGTGGGTCCC 2 47 1 GGGGTGGGTC 0.983898 -12 ATTGAGCGGGGGTTGCCGAGCCT 3 4 1 GAGCGGGGGT 0.931256 -152 GTCCCGTCCCGTAGGGGTTCCGGGGTTCAA 3 56 1 GTAGGGGTTC 0.777476 -100 GTAAATTTTGGTGCGGGGGCGGGGATTTGA 3 82 0 GTGCGGGGGC 0.996627 -74 CCTGGTAGGGCGCGGGCCTTG 5 2 1 CTGGTAGGGC 0.943855 -100 TTCACTCAATCTGGAGGGGGATAAA 5 87 1 CTGGAGGGGG 0.851535 -15 ********** Masking position 6 Map Score: 12.6244 Number of sites scoring better than the average of aligned sites = 489 Number in coding regions = 421 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 6 GGGGCCGCCGGGATTTGAACCCGGGTCTCC 1 77 0 GGATTTGAAC 0.990347 -45 TAAATCCCGCGCCTTTGACCAGGCTCGGCA 3 24 0 GCCTTTGACC 0.986543 -132 GCGGGGGCGGGGATTTGAACCCCGGAACCC 3 70 0 GGATTTGAAC 0.990347 -86 CTCTTCATTTTCCCATTTTGGAGG 4 5 1 TCATTTTCCC 0.794872 -22 GAGCCCGTGGGCGTTTGCCCGCCGGGGTTC 5 33 1 GCGTTTGCCC 0.980126 -69 GCCGGGACGGGGATTTGAACCCCGGCGGGC 5 49 0 GGATTTGAAC 0.990347 -53 TTTACGTCAAGCTTTTTAACTATTTTGGAG 6 31 1 GCTTTTTAAC 0.917858 -33 ********** Masking position 5 Map Score: 9.47741 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 81 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 7 ********** No masking Map Score: 4.64285e-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: 4.64285e-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 9 ********** No masking Map Score: 4.64285e-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