AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i117_Oligopeptide_Transport_pyro_reg_300.orf -o117_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 Purged sequences: RPH01295 16 Pyrococcus_OT3 Input sequences: #1 RPH00320 85 Pyrococcus_OT3 #2 RPH00319 174 Pyrococcus_OT3 #3 RPH00318 41 Pyrococcus_OT3 #4 RPH01291 61 Pyrococcus_OT3 #5 RPH01292 23 Pyrococcus_OT3 #6 RPH01294 90 Pyrococcus_OT3 #7 RPH01298 250 Pyrococcus_OT3 #8 RPH01299 117 Pyrococcus_OT3 #9 RPH01808 198 Pyrococcus_OT3 #10 RPH01071 300 Pyrococcus_OT3 Motif number 1 TAAATTTGTCGAATTGAAAGTCCAAAACT 2 1 0 GAAAAGAAAT 0.929671 -174 AAATTTATTCAAAAATATAGGGTTAAATTTTAACATATC 2 33 1 AAATAGAAAT 0.618223 -142 TGGCATTGAAGATCATAGATTCTCAAGATTGCATTAGTG 2 71 0 GATGATAAGT 0.804269 -104 CTTCAATGCCAAATTCCGATCCATAAAAATTAAATATAC 2 99 1 AAAGATAAAA 0.857765 -76 GATTACCCCCAATTTTAAATCTTAAAACTATGTACGTCG 2 142 0 AATAATAAAT 0.635058 -33 TCCCAGAACAGAAGAAAAATTCTCAAGGGGAAGTGGAGG 6 37 0 GAAAATAAGG 0.800861 -54 ATAACAATTAGTAATAAAATTATGAAGTTCATTTACACT 7 120 0 GTAAATAAGT 0.658662 -131 CACTTTGTGGAAAATAGAAGATCCAAATTATAACAATTA 7 149 0 AAAAAGAAAT 0.927243 -102 TCCACAAAGTGAACCAAGATCGAAAAGCTTATTAGCGAG 7 177 1 GAAGATAAGT 0.96668 -74 GGGCAATAAAGAAAAGAGAGAAGAAAGATTA 8 3 0 GAAGAGAAGT 0.967838 -115 CGATGTTATAGAACAAGAATGTACAAGGAGGGGCAAAT 8 90 1 GAAAATAAGA 0.916658 -28 TCTAAAATTTAAAAATCAAGGAGAAAACTAAAGGGGAGG 9 16 0 AAAAAGAAAT 0.927244 -183 AAAGTCATCTAAACGATAAGCCGAAAGAACTAACGAGAA 9 76 0 AAAAAGAAGA 0.916658 -123 ATGACTTTCGAAAGTAAGATATATAAGGTAGTTTTACAA 9 107 1 AAAGATAAGT 0.965483 -92 ACAAGCTTGAAAAAGATAATGTTCAAACTTGTTCCTTCA 9 142 1 AAAAATAAAT 0.924739 -57 CGTAGAACCAAAAAAGAAAGGTAGAAAAAACTTAAGAAC 10 29 0 AAAAAGAAAA 0.846093 -272 CTTTATACACAAACTCTGATATTTAAGGATTGCGACTAT 10 201 0 AAAGATAAGA 0.923463 -100 TCCAAATTTGAAACAGAGATGCCTAAGGTAGTGCTTACA 10 248 0 AAAGATAAGT 0.965483 -53 *** *** *** * Masking position 9 Map Score: 17.2683 Number of sites scoring better than the average of aligned sites = 536 Number in coding regions = 455 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 2 GTTATCTCTAGAGAATTTAAGCTTATGGTAA 1 56 0 GAGAATTAAG 0.962932 -30 AGTGATATGTTAAAATTTAACCCTATATTTT 2 44 0 TAAAATTAAC 0.926411 -131 TTCCGATCCATAAAAATTAAATATACGCTTC 2 112 1 TAAAATTAAA 0.888972 -63 AAAAGGGGAATAAAAATAAAAA 3 2 0 TAAAATAAAA 0.740042 -40 AAGCTTTCTTGAGAAGTTAAGGCT 4 4 0 GAGAATTAAG 0.962932 -58 CAAGAAAGCTTAAAAGTTAACTCCCCAAACG 4 24 1 TAAAATTAAC 0.926411 -38 TCTGTTCTGGGAAAACTAAACCATCGGGGTG 6 64 1 GAAAATAAAC 0.89489 -27 AAATCAAGGAGAAAACTAAAGGGGAGGAGAA 9 12 0 GAAAATAAAG 0.942925 -187 GAAGGGTTTCTAAAATTTAAAAATCAAGGAG 9 32 0 TAAAATTAAA 0.888972 -167 TAACGAGAAAGAGAGCTTAAGAGAAGGGTTT 9 54 0 GAGAGTTAAG 0.816835 -145 GAAAGGTAGAAAAAACTTAAGAACCTTTTAA 10 22 0 AAAAATTAAG 0.857698 -279 CGACTATTCCGCAAATTTAAGCTATAAATGG 10 177 0 GCAAATTAAG 0.888604 -124 ***** ***** Masking position 4 Map Score: 11.782 Number of sites scoring better than the average of aligned sites = 257 Number in coding regions = 212 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 3 TTCAATTCGACAAATTTATTCAAAAATATAGG 2 22 1 CAAATTATCA 0.964915 -153 TAAGCATCTTCAAGGTGAAACAATAAGC 7 7 0 CAAGTGAACA 0.949366 -244 GTTTTATGATCAAAATGATACACCACTGATTT 7 40 0 CAAATGATCA 0.932812 -211 TTCATTTACACTAGGTTAAACATCTCAAAAAA 7 100 0 CTAGTTAACA 0.798079 -151 CTATTTTCCACAAAGTGAACCAAGATCGAAAA 7 171 1 CAAATGAACA 0.909789 -80 CATCACCAGGGAAGGTTATCCAAAGAGATATA 7 225 0 GAAGTTATCA 0.909146 -26 TGTTATAGAACAAGAATGTACAAGGAGGGGCA 8 93 1 CAAGATGTCA 0.733105 -25 TTATCTTTTTCAAGCTTGTAAAACTACCTTAT 9 129 0 CAAGTTGTAA 0.837101 -70 TTTGAAGGAACAAGTTTGAACATTATCTTTTT 9 151 0 CAAGTTGACA 0.949366 -48 TTAGAAAGTTATTAAAAGGTTCTTA 10 4 1 GAAATTATAA 0.517277 -297 GGCTATAGCTCAAATTTATTAACAATTACGCT 10 124 0 CAAATTATAA 0.845568 -177 GGTATTCGGCCAAGATTAGACAGGCTATAGCT 10 146 0 CAAGTTAGCA 0.931414 -155 GACTATTCCGCAAATTTAAGCTATAAATGGGT 10 175 0 CAAATTAACT 0.680099 -126 **** **** ** Masking position 3 Map Score: 9.49007 Number of sites scoring better than the average of aligned sites = 273 Number in coding regions = 243 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 AACAAAGCTATTAAACAGGGGGTGAAACTAG 1 11 0 TTAAAAGGGG 0.811647 -75 AATTTATTCAAAAATATAGGGTTAAATTTTA 2 34 1 AAAATTAGGG 0.683453 -141 TTTTAAGATTTAAAATTGGGGGTAATCTTAG 2 154 1 TAAAATGGGG 0.845873 -21 CACCTCCAACAAAGAAAAGGGGAATAAAAAT 3 16 0 AAAGAAAGGG 0.971164 -26 GTTAAATACTAAAAAGGAGAGAC 5 3 0 AAAAAGAGAG 0.801955 -21 AAACATCTCAAAAAATAAGGGAATTAGAGAG 7 84 0 AAAAAAAGGG 0.981743 -167 TAAGGGCAATAAAGAAAAGAGAGAAGAAAGA 8 14 0 AAAGAAAGAG 0.838412 -104 ATTTTGGTGTTTAAATAAGGGCAATAAAGAA 8 29 0 TTAAAAAGGG 0.918219 -89 AACAAGAATGTACAAGGAGGGGCAAAT 8 101 1 TACAAGAGGG 0.806405 -17 AAAGAGAGCTTAAGAGAAGGGTTTCTAAAAT 9 47 0 TAAGAAAGGG 0.965919 -152 CGTAGAACCAAAAAAGAAAGGTAGAAAAAAC 10 37 0 AAAAAAAAGG 0.809049 -264 ***** ***** Masking position 11 Map Score: 7.14418 Number of sites scoring better than the average of aligned sites = 654 Number in coding regions = 580 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 5 GAACAAAGCTATTAAACAGGGGGTGAAACT 1 13 0 ATTAAACAGG 0.950077 -73 GTTAAATACTAAAAAGGAGAGAC 5 7 0 ACTAAAAAGG 0.893905 -17 AAATAAGGGAATTAGAGAGATGTTTTTGAA 7 73 0 ATTAGAGAGA 0.923045 -178 CGAAAAGCTTATTAGCGAGGTGCCTGGTTA 7 197 1 ATTAGCGAGG 0.967304 -54 CAAGGAGAAAACTAAAGGGGAGGAGAAA 9 9 0 ACTAAAGGGG 0.931174 -190 AGCCGAAAGAACTAACGAGAAAGAGAGCTT 9 67 0 ACTAACGAGA 0.889755 -132 TTCGGCCAAGATTAGACAGGCTATAGCTCA 10 144 0 ATTAGACAGG 0.958301 -157 ********** Masking position 4 Map Score: 2.17742 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 125 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 TTTAACCCTATATTTTTGAATAAATTTGTC 2 30 0 TATTTTTGAA 0.66873 -145 GATACACCACTGATTTTTAAGCATCTTCAA 7 26 0 TGATTTTTAA 0.960023 -225 ATTAGAGAGATGTTTTTGAATGTTTTATGA 7 63 0 TGTTTTTGAA 0.947582 -188 TTATTTTTTGAGATGTTTAACCTAGTGTAA 7 97 1 AGATGTTTAA 0.855405 -154 ATAAAAATTTTGGTGTTTAAATAAGGGCAA 8 36 0 TGGTGTTTAA 0.879223 -82 GTTTTCTCCTTGATTTTTAAATTTTAGAAA 9 27 1 TGATTTTTAA 0.960023 -172 TGAACATTCCAGTTTTTGAAGGAACAAGTT 9 167 0 AGTTTTTGAA 0.86873 -32 ACACAAACTCTGATATTTAAGGATTGCGAC 10 204 0 TGATATTTAA 0.85558 -97 ********** Masking position 9 Map Score: 3.58562 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 62 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 CTCTCACCTCCAACAAAGAAAAGGGGAATA 3 21 0 CAACAAAGAA 0.967944 -21 TTAGTTTTCCCAGAACAGAAGAAAAATTCT 6 53 0 CAGAACAGAA 0.912636 -38 TTAAACATCTCAAAAAATAAGGGAATTAGA 7 87 0 CAAAAAATAA 0.907954 -164 TAAATAAGGGCAATAAAGAAAAGAGAGAAG 8 19 0 CAATAAAGAA 0.953212 -99 AACGTAGAACCAAAAAAGAAAGGTAGAAAA 10 40 0 CAAAAAAGAA 0.980944 -261 ********** Masking position 5 Map Score: 1.77568 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 59 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 ********** No masking Map Score: 1.97774e-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 9 ********** No masking Map Score: 1.97774e-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 10 ********** No masking Map Score: 1.97774e-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