AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i286_hypothetical_lipid_degradation_pyro_reg_100.orf -o286_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 RPH01314 224 Pyrococcus_OT3 #2 RPH01343 200 Pyrococcus_OT3 Motif number 1 TTGTGCCCCAAAATGCTTTTAAATATTCACTAA 1 35 0 AAACTTTAAA 0.821993 -190 CACCAAAACCAAAGATATTAAACCAAAGGTTGA 1 76 1 AAATTTAAAC 0.9773 -149 AATTGAAAATAAAAGTGTTCAACCTTTGGTTTA 1 94 0 AAATTTCAAC 0.985568 -131 AAGATAGCGTAGAAATCTTAAAAGGGTTTTTTA 1 135 0 AGATTTAAAA 0.848709 -90 CTCCAAACCTCCTCAACCATTGGTTTA 1 208 0 AAATCTCAAC 0.95946 -17 ACATATAGGAAAACCTTTTTATAAGCAAGATTA 2 32 0 AAATTTTATA 0.882039 -169 ATATATGTAGAAAACTCTTCACATATAGGAAAA 2 52 0 AAATTTCACA 0.948309 -149 AGATATGAATAAAAATATTCATATATATGTAGA 2 74 0 AAATTTCATA 0.922241 -127 CCTTTGTCACAAAAGTTTGAAACCTATAGATAT 2 101 0 AAATTGAAAC 0.880824 -100 ACTTATTCTTATAAATGTTTACCTTTGTCACAA 2 122 0 ATATTTTACC 0.821214 -79 ATTTATAAGAATAAGTCCTTAACCATGGGTGAA 2 139 1 ATATCTTAAC 0.787335 -62 ACCATGGGTGAAATTTATTAAAAGGAAAAATCC 2 160 1 AAATTTAAAA 0.964157 -41 *** * ****** Masking position 3 Map Score: 11.4118 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 271 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 2 AGCTACGTGGAGGTGAAGGAA 1 2 0 AGGTGAAGGA 0.869489 -223 TGCCCCAAAATGCTTTTAAATATTCACTAA 1 35 0 TGCTTTTAAA 0.878075 -190 TCTTTGGTTTTGGTGATACACAATTGTGCC 1 61 0 TGGTGATACA 0.817707 -164 GTTCAACCTTTGGTTTAATATCTTTGGTTT 1 81 0 TGGTTTAATA 0.915348 -144 ATTAAACCAAAGGTTGAACACTTTTATTTT 1 92 1 AGGTTGAACA 0.923845 -133 TTCAATTCTAAGCTTTAAAAAACCCTTTTA 1 120 1 AGCTTTAAAA 0.929246 -105 CCTCAACCATTGGTTTAAAACGCTATTTTA 1 195 0 TGGTTTAAAA 0.981157 -30 TTTAAACCAATGGTTGAGGAGGTTTGGAG 1 206 1 TGGTTGAGGA 0.931401 -19 TTCCTAATCTTGCTTATAAAAAGGTTTTCC 2 28 1 TGCTTATAAA 0.830976 -173 TCATATCTATAGGTTTCAAACTTTTGTGAC 2 99 1 AGGTTTCAAA 0.898379 -102 ATTTCACCCATGGTTAAGGACTTATTCTTA 2 144 0 TGGTTAAGGA 0.939154 -57 CCATGCGGGGAGGGGTAAAA 2 191 1 AGGGGTAAAA 0.784079 -10 ********** Masking position 10 Map Score: 8.77033 Number of sites scoring better than the average of aligned sites = 905 Number in coding regions = 800 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 3 TTCCTTCACCTCCACGTAGCTCTTTT 1 3 1 CCTTCATCAG 0.975062 -222 TGCTTTTAAATATTCACTAAAAGAGCTACGTGGA 1 21 0 TATTCAAAAA 0.848745 -204 AACACTTTTATTTTCAATTCTAAGCTTTAAAAAA 1 108 1 TTTTCATCAG 0.97373 -117 TATTTTTTCTTCTTCAGAGAGAAGATAGCGTAGA 1 155 0 TCTTCAGAAG 0.978914 -70 TGTAGAAAACTCTTCACATATAGGAAAACCTTTT 2 46 0 TCTTCATAAG 0.992958 -155 TGAATAAAAATATTCATATATATGTAGAAAACTC 2 68 0 TATTCATAAG 0.991681 -133 TGAATATTTTTATTCATATCTATAGGTTTCAAAC 2 86 1 TATTCATCAA 0.964147 -115 GTTAAGGACTTATTCTTATAAATGTTTACCTTTG 2 128 0 TATTCTTAAG 0.955222 -73 ****** ** * * Masking position 12 Map Score: 8.01259 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 130 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 4 ATAAAAGTGTTCAACCTTTGGTTTAATATC 1 89 0 TCAACCTTTG 0.993893 -136 CCAAACCTCCTCAACCATTGGTTTAAAACG 1 203 0 TCAACCATTG 0.98868 -22 TCTATAGGTTTCAAACTTTTGTGACAAAGG 2 104 1 TCAAACTTTT 0.894951 -97 CTTATAAATGTTTACCTTTGTCACAAAAGT 2 118 0 TTTACCTTTG 0.982318 -83 GAATAAGTCCTTAACCATGGGTGAAATTTA 2 147 1 TTAACCATGG 0.953076 -54 CCGCATGGATTTTTCCTTTTAATAAATTTC 2 169 0 TTTTCCTTTT 0.822417 -32 ********** Masking position 8 Map Score: 5.09868 Number of sites scoring better than the average of aligned sites = 339 Number in coding regions = 318 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 5 AACACTTTTATTTTCAATTCTAAGCTTTAAA 1 108 1 TTTTCATTCT 0.893956 -117 TGTAGAAAACTCTTCACATATAGGAAAACCT 2 49 0 TCTTCAATAT 0.97441 -152 TGAATAAAAATATTCATATATATGTAGAAAA 2 71 0 TATTCAATAT 0.984828 -130 TGAATATTTTTATTCATATCTATAGGTTTCA 2 86 1 TATTCAATCT 0.985931 -115 GTTAAGGACTTATTCTTATAAATGTTTACCT 2 131 0 TATTCTATAA 0.85701 -70 ****** **** Masking position 4 Map Score: 0.847044 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 66 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 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