AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i286_hypothetical_lipid_degradation_pyro_reg_300.orf -o286_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 RPH01314 224 Pyrococcus_OT3 #2 RPH01343 200 Pyrococcus_OT3 Motif number 1 AAACCAAAGATATTAAACCAAAGGTTGAACACTTT 1 81 1 TTTACAAGGT 0.99477 -144 TATTTTTTCTTCTTCAGAGAGAAGATAGCGTAGAA 1 154 0 TTTAAAAAGA 0.843101 -71 TAAAATAGCGTTTTAAACCAATGGTTGAGGAGGTT 1 195 1 TTTACATGGT 0.967732 -30 TTCCTAATCTTGCTTATAAAAAGGTTTTCCTATAT 2 28 1 TCTAAAAGGT 0.992057 -173 TGTAGAAAACTCTTCACATATAGGAAAACCTTTTT 2 45 0 TTTAAAAGGA 0.978368 -156 TGAATAAAAATATTCATATATATGTAGAAAACTCT 2 67 0 TTTAAAATGT 0.971893 -134 AATATTTTTATTCATATCTATAGGTTTCAAACTTT 2 88 1 TCAACAAGGT 0.950148 -113 GGTTTCAAACTTTTGTGACAAAGGTAAACATTTAT 2 110 1 TTTTAAAGGT 0.979896 -91 GTTAAGGACTTATTCTTATAAATGTTTACCTTTGT 2 127 0 TTTTAAATGT 0.905765 -74 TAAGAATAAGTCCTTAACCATGGGTGAAATTTATT 2 144 1 TCTACAGGGT 0.969357 -57 * ** * * * **** Masking position 10 Map Score: 12.0536 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 121 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 2 TTTGGGGCACAATTGTGTATCACCAAAACCAAAG 1 56 1 AATGTTCACC 0.938023 -169 CACCAAAACCAAAGATATTAAACCAAAGGTTGAA 1 76 1 AAAATTAACC 0.977006 -149 AATTGAAAATAAAAGTGTTCAACCTTTGGTTTAA 1 93 0 AAAGTTAACC 0.996372 -132 GGAAGTAAAATAGCGTTTTAAACCAATGGTTGAG 1 190 1 TAGGTTAACC 0.938061 -35 CTCCAAACCTCCTCAACCATTGGTTTAA 1 207 0 AAACTCAACC 0.991274 -18 CACCACCAACAAATCTTCCTAATCTTGCTTATAA 2 13 1 AAACTCAATC 0.926929 -188 CCTTTGTCACAAAAGTTTGAAACCTATAGATATG 2 100 0 AAAGTTAACC 0.996372 -101 ATTTATAAGAATAAGTCCTTAACCATGGGTGAAA 2 139 1 ATAGTCAACC 0.979693 -62 *** ** * **** Masking position 12 Map Score: 8.82572 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 83 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 3 TGTGCCCCAAAATGCTTTTAAATATTCACTA 1 36 0 AATGCTTTAA 0.853843 -189 CACCAAAACCAAAGATATTAAACCAAAGGTT 1 76 1 AAAGATTTAA 0.95708 -149 AATTGAAAATAAAAGTGTTCAACCTTTGGTT 1 96 0 AAAAGTTTCA 0.984576 -129 AAGATAGCGTAGAAATCTTAAAAGGGTTTTT 1 137 0 AGAAATTTAA 0.862918 -88 TTGCTTATAAAAAGGTTTTCCTATATGTGAA 2 37 1 AAAGGTTTCC 0.925154 -164 ATATATGTAGAAAACTCTTCACATATAGGAA 2 54 0 AAAACTTTCA 0.97769 -147 AGATATGAATAAAAATATTCATATATATGTA 2 76 0 AAAAATTTCA 0.981515 -125 CCTTTGTCACAAAAGTTTGAAACCTATAGAT 2 103 0 AAAAGTTGAA 0.884094 -98 TTTTCCTTTTAATAAATTTCACCCATGGTTA 2 158 0 AATAAATTCA 0.725709 -43 ****** **** Masking position 8 Map Score: 6.15375 Number of sites scoring better than the average of aligned sites = 311 Number in coding regions = 235 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 4 GTGTATCACCAAAACCAAAGATATTAAACCAAA 1 70 1 AAAAAAGATA 0.97276 -155 TTTAAAGCTTAGAATTGAAAATAAAAGTGTTCA 1 106 0 AAAGAAAATA 0.977776 -119 TTTTCTTCTTCAGAGAGAAGATAGCGTAGAAAT 1 152 0 CGAGAAGATA 0.916673 -73 TTCTCTCTGAAGAAGAAAAAATAAGGAAGTAAA 1 166 1 AAAAAAAATA 0.981505 -59 AGAAAAAATAAGGAAGTAAAATAGCGTTTTAAA 1 179 1 AGATAAAATA 0.951169 -46 ACCTATAGATATGAATAAAAATATTCATATATA 2 80 0 AGAAAAAATA 0.984636 -121 GAAATTTATTAAAAGGAAAAATCCATGCGGGGA 2 169 1 AAAAAAAATC 0.942295 -32 * ** ******* Masking position 8 Map Score: 5.04805 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 94 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 5 TTCCTTCACCTCCACGTAGCTCTTT 1 6 1 TCACCTCCAC 0.995635 -219 CTCCAAACCTCCTCAACCATTGGT 1 211 0 AAACCTCCTC 0.970199 -14 GTCACCACCAACAAATCTTCC 2 2 1 TCACCACCAA 0.957842 -199 TTTTACCCCTCCCCGCATGGATTT 2 187 0 ACCCCTCCCC 0.991186 -14 ********** Masking position 5 Map Score: 0.924076 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 158 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 6 ********** No masking Map Score: -4.02005e-14 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: -4.02005e-14 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: -4.02005e-14 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