AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i203_dna_repair_pyro_reg_300.orf -o203_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 RPH00084 300 Pyrococcus_OT3 #2 RPH00083 95 Pyrococcus_OT3 #3 RPH00082 57 Pyrococcus_OT3 #4 RPH00081 261 Pyrococcus_OT3 Motif number 1 TAAATAAAAACTCTCAAACCTTTTCCAAAAA 1 43 1 CTCTCAAACT 0.928772 -258 TCAAACCTTTTCCAAAAATATATCCTCCTCA 1 56 1 TCCAAAAAAT 0.859864 -245 ATTTAAAAATTTCAAAAATTTTCGTAACAAT 1 94 1 TTCAAAAATT 0.948628 -207 ACTCTAATCCCTCTAAAACCTCTATTCTAAA 1 179 1 CTCTAAAACT 0.982397 -122 AAAACCTCTATTCTAAAAATTAAGCCTAGAC 1 193 1 TTCTAAAATT 0.930621 -108 CAAAAATAATCCCAAATATCTTGCACCGAAA 1 237 1 CCCAAATACT 0.934397 -64 ATAGTAATTATTCAAAAATTTTTCGGTGCAA 1 257 0 TTCAAAAATT 0.948628 -44 TCTTCAAATCCCCATAAATTTAAATCTTCGA 4 30 1 CCCATAAATT 0.973332 -232 ACTTTTCAAGCTCTAAAACTTTCATACATCT 4 118 0 CTCTAAAATT 0.976519 -144 TCTAATTCATCCCATAAATTTACAGTCAAAT 4 180 1 CCCATAAATT 0.973332 -82 CCCTCTTATTCCCATAAACCTTTTTAACCCT 4 216 1 CCCATAAACT 0.979992 -46 ACCTTTTTAACCCTAAAATCTCTTAGATACA 4 233 1 CCCTAAAACT 0.988929 -29 ******** ** Masking position 6 Map Score: 20.5484 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 215 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 2 AGGTTTTAGAGGGATTAGAGTTTGACTTAGT 1 169 0 GGGTTAGAGT 0.979197 -132 AAAAAGATGTGGGAGAAAAGTT 2 2 0 GGGGAAAAGT 0.946897 -94 AAGTGGCTCGGGGAGATGAGGGAGGAGAGAA 2 74 1 GGGGATGAGG 0.982478 -22 GAATAGAAAAGGGGTTGGAGG 4 1 0 GGGTTGGAGG 0.987853 -261 TAAATTTATGGGGATTTGAAGAATAGAAAAG 4 21 0 GGGTTTGAAG 0.928693 -241 GAACACTCCTGGGGTAAAATTGAGGTTGATA 4 65 0 GGGTAAAATT 0.736219 -197 TATAATCCTCGGGCTTACAGGAGAACACTCC 4 87 0 GGGTTACAGG 0.983767 -175 GTAAGCCCGAGGATTATAAGATGTATGAAAG 4 100 1 GGATATAAGA 0.616221 -162 ATTAGAGAGCGGGTGTGCAGATTTTTACTAC 4 155 0 GGGGTGCAGA 0.830972 -107 AAGGTTTATGGGAATAAGAGGGTGGTAATTT 4 207 0 GGATAAGAGG 0.963361 -55 AGAGATTTTAGGGTTAAAAAGGTTTATGGGA 4 225 0 GGGTAAAAAG 0.937565 -37 *** ******* Masking position 9 Map Score: 9.76833 Number of sites scoring better than the average of aligned sites = 986 Number in coding regions = 930 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 3 AGAGTTTTTATTTAATTTTTGTAAAAAGTTA 1 26 0 TTAATTTTTG 0.984052 -275 ATATATCCTCCTCAATATTTTATTTAAAAAT 1 73 1 CTAATATTTT 0.708774 -228 ACGAAAATTTTTGAAATTTTTAAATAAAATA 1 88 0 TTAAATTTTT 0.763512 -213 AGTTTTGTTATTAAATTGTTACGAAAATTTT 1 108 0 TTAATTGTTA 0.845772 -193 TTTCCTTATGTTAAAGTTTTGTTATTAAATT 1 122 0 TTAAGTTTTG 0.963759 -179 TTTGTCTAGGCTTAATTTTTAGAATAGAGGT 1 196 0 CTAATTTTTA 0.929525 -105 GGGATTATTTTTGGATTTTTGGCTTTGTCTA 1 219 0 TTGATTTTTG 0.959974 -82 TGAATTGTTGTTTGAGTTTTGATTTAAAAAG 2 27 0 TTGAGTTTTG 0.911605 -69 CGGGGAAGAACTGAATTGTTGTTTGAGTTTT 2 38 0 CTAATTGTTG 0.957314 -58 TCATAAGGGGCTTAATTTTTTCTTTTCCTGG 3 23 1 CTAATTTTTT 0.950345 -35 AATCGAAGATTTAAATTTATGGGGATTTGAA 4 32 0 TTAATTTATG 0.886747 -230 ** ******** Masking position 5 Map Score: 11.0041 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 147 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 4 AAAGTTAGTACTTTTCTTGGCT 1 2 0 CTTTTCTGGC 0.989149 -299 GATTTTTGGCTTTGTCTAGGCTTAATTTTTA 1 206 0 TTTGTCTGGC 0.974385 -95 TATTCAAAAATTTTTCGGTGCAAGATATTTG 1 249 0 TTTTTCGTGC 0.972405 -52 GGGGCTTAATTTTTTCTTTTCCTGGTTGGAG 3 29 1 TTTTTCTTTC 0.972002 -29 CCTCCAACCCCTTTTCTATTCTTCAAATCCC 4 11 1 CTTTTCTTTC 0.974011 -251 ******* *** Masking position 5 Map Score: 1.73316 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 26 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 5 GAGCCACTTGGGCACGGGGAAGAACTGAAT 2 53 0 GGCACGGGGA 0.99604 -43 GTGCCCAAGTGGCTCGGGGAGATGAGGGAG 2 68 1 GGCTCGGGGA 0.991305 -28 TTCTCCTGTAAGCCCGAGGATTATAAGATG 4 93 1 AGCCCGAGGA 0.976487 -169 ********** Masking position 10 Map Score: 1.67357 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 6 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 6 TTTTATTTAATTTTTGTAAAAAGTTAGTACTT 1 20 0 TTTTTGTAAA 0.588772 -281 ATTTTTGAAATTTTTAAATAAAATATTGAGGA 1 81 0 TTTTTAAAAA 0.701361 -220 ATTTCAAAAATTTTCGTAACAATTTAATAACA 1 102 1 TTTTCGTAAA 0.939428 -199 TATGTTAAAGTTTTGTTATTAAATTGTTACGA 1 115 0 TTTTGTTAAA 0.917258 -186 ACTTATTAGCTTTTGATAGTAATTATTCAAAA 1 271 0 TTTTGATAAA 0.96319 -30 CTCCCACATCTTTTTAAATCAAAACTCAAACA 2 18 1 TTTTTAAAAA 0.91173 -78 ******** ** Masking position 8 Map Score: 1.14251 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 20 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 ATTTTTGTAAAAAGTTAGTACTTTTCTTGG 1 13 0 AAAGTTAGTA 0.861256 -288 TTTTATTTAAAAATTTCAAAAATTTTCGTA 1 90 1 AAATTTCAAA 0.770893 -211 TTAGTTACTTAAAATTAGTATTTTCCTTAT 1 144 0 AAAATTAGTA 0.586746 -157 AAGCCTAGACAAAGCCAAAAATCCAAAAAT 1 214 1 AAAGCCAAAA 0.818448 -87 ATTACTATCAAAAGCTAATAAGTGGTTAGA 1 280 1 AAAGCTAATA 0.955784 -21 TTTTTAAATCAAAACTCAAACAACAATTCA 2 28 1 AAAACTCAAA 0.887445 -68 AAAGGGTAAAGCTCATAAGGGGCTTAA 3 8 1 AAAGCTCATA 0.971808 -50 TATAACTTTTCAAGCTCTAAAACTTTCATA 4 123 0 CAAGCTCTAA 0.817561 -139 TAGAGCTTGAAAAGTTATAAAGTAGTAAAA 4 134 1 AAAGTTATAA 0.85186 -128 TTTAACCCTAAAATCTCTTAGATACACGAT 4 238 1 AAATCTCTTA 0.830923 -24 ********** Masking position 3 Map Score: 4.70571 Number of sites scoring better than the average of aligned sites = 801 Number in coding regions = 712 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 8 TAAAAACTCTCAAACCTTTTCCAAAAATAT 1 47 1 CAAACCTTTT 0.865321 -254 TTCTAACCACTTATTAGCTTTT 1 289 0 CTAACCACTT 0.959275 -12 CTCATCTCCCCGAGCCACTTGGGCACGGGG 2 64 0 CGAGCCACTT 0.974151 -32 AAGAAAAAATTAAGCCCCTTATGAGCTTTA 3 17 0 TAAGCCCCTT 0.914744 -41 CCTCCAACCCCTTTTCTATTCTT 4 4 1 CCAACCCCTT 0.990038 -258 AGTCAAATTACCACCCTCTTATTCCCATAA 4 203 1 CCACCCTCTT 0.974151 -59 ********** Masking position 3 Map Score: 2.55287 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 257 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 9 TTGTAAAAAGTTAGTACTTTTCTTGGCT 1 9 0 TTAGTACTTT 0.967538 -292 TATATCCTCCTCAATATTTTATTTAAAAAT 1 74 1 TCAATATTTT 0.854384 -227 TTACTTAAAATTAGTATTTTCCTTATGTTA 1 140 0 TTAGTATTTT 0.973016 -161 TGGGATTATTTTTGGATTTTTGGCTTTGTC 1 221 0 TTTGGATTTT 0.765473 -80 CATAAGGGGCTTAATTTTTTCTTTTCCTGG 3 24 1 TTAATTTTTT 0.798454 -34 GTGCAGATTTTTACTACTTTATAACTTTTC 4 142 0 TTACTACTTT 0.917949 -120 ********** Masking position 8 Map Score: 0.349836 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 75 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 10 ********** No masking Map Score: -2.32047e-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 11 ********** No masking Map Score: -2.32047e-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 12 ********** No masking Map Score: -2.32047e-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