AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i146_NADH-formate_Dehydrogenase_pyro_reg_100.orf -o146_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 AAACCAAAGATATTAAACCAAAGGTTGAACACTTT 1 81 1 TTTACAAGGT 0.992263 -144 TAAAATAGCGTTTTAAACCAATGGTTGAGGAGGTT 1 195 1 TTTACAAGGT 0.992264 -30 TTCCTAATCTTGCTTATAAAAAGGTTTTCCTATAT 2 28 1 TCTAAAAGGT 0.987971 -173 TGTAGAAAACTCTTCACATATAGGAAAACCTTTTT 2 45 0 TTTAAATGGA 0.927246 -156 TGAATAAAAATATTCATATATATGTAGAAAACTCT 2 67 0 TTTAAATTGT 0.940908 -134 AATATTTTTATTCATATCTATAGGTTTCAAACTTT 2 88 1 TCAACATGGT 0.931203 -113 GGTTTCAAACTTTTGTGACAAAGGTAAACATTTAT 2 110 1 TTTTAAAGGT 0.969213 -91 GTTAAGGACTTATTCTTATAAATGTTTACCTTTGT 2 127 0 TTTTAAATGT 0.861094 -74 TAAGAATAAGTCCTTAACCATGGGTGAAATTTATT 2 144 1 TCTACATGGT 0.988479 -57 * ** * * ** *** Masking position 10 Map Score: 11.1283 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 67 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 2 CTTTGGTTTTGGTGATACACAATTGTGCCCCAAA 1 56 0 GGTGAACATT 0.928191 -169 TTCAACCTTTGGTTTAATATCTTTGGTTTTGGTG 1 76 0 GGTTAATTTT 0.973177 -149 TTAAACCAAAGGTTGAACACTTTTATTTTCAATT 1 93 1 GGTTAACTTT 0.995754 -132 CTCAACCATTGGTTTAAAACGCTATTTTACTTCC 1 190 0 GGTTAACCTA 0.928223 -35 TTAAACCAATGGTTGAGGAGGTTTGGAG 1 207 1 GGTTGAGTTT 0.989796 -18 TTATAAGCAAGATTAGGAAGATTTGTTGGTGGTG 2 13 0 GATTGAGTTT 0.915482 -188 CATATCTATAGGTTTCAAACTTTTGTGACAAAGG 2 100 1 GGTTAACTTT 0.995754 -101 TTTCACCCATGGTTAAGGACTTATTCTTATAAAT 2 139 0 GGTTGACTAT 0.976301 -62 **** * ** *** Masking position 9 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 TTCTCTCTGAAGAAGAAAAAATAAGGAAGT 1 166 1 AGAAGAAAAA 0.945151 -59 AGAAGAAAAAATAAGGAAGTAAAATAGCGT 1 176 1 ATAAGGAAGT 0.919589 -49 AAACCTTTTTATAAGCAAGATTAGGAAGAT 2 25 0 ATAAGCAAGA 0.934568 -176 TTCTACATATATATGAATATTTTTATTCAT 2 73 1 ATATGAATAT 0.812049 -128 AAACCTATAGATATGAATAAAAATATTCAT 2 85 0 ATATGAATAA 0.937052 -116 GTAAACATTTATAAGAATAAGTCCTTAACC 2 133 1 ATAAGAATAA 0.972971 -68 GAAATTTATTAAAAGGAAAAATCCATGCGG 2 169 1 AAAAGGAAAA 0.906005 -32 ********** Masking position 7 Map Score: 3.2452 Number of sites scoring better than the average of aligned sites = 394 Number in coding regions = 330 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 4 AAAAGAGCTACGTGGAGGTGAAGGAA 1 7 0 CGTGGAGGTG 0.994222 -218 TATTTAAAAGCATTTTGGGGCACAATTGTG 1 43 1 CATTTTGGGG 0.88439 -182 TAATATCTTTGGTTTTGGTGATACACAATT 1 66 0 GGTTTTGGTG 0.973671 -159 TTAAACCAATGGTTGAGGAGGTTTGGAG 1 207 1 GGTTGAGGAG 0.977434 -18 AGGAAGATTTGTTGGTGGTGAC 2 3 0 GTTGGTGGTG 0.970568 -198 AAAATCCATGCGGGGAGGGGTAAAA 2 186 1 CGGGGAGGGG 0.985492 -15 ********** Masking position 7 Map Score: 4.20023 Number of sites scoring better than the average of aligned sites = 352 Number in coding regions = 312 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 5 CCCCAAAATGCTTTTAAATATTCACTAAAA 1 33 0 CTTTTAAATA 0.960359 -192 AGGTTGAACACTTTTATTTTCAATTCTAAG 1 102 1 CTTTTATTTT 0.722732 -123 CAATTCTAAGCTTTAAAAAACCCTTTTAAG 1 122 1 CTTTAAAAAA 0.923353 -103 TTAAAAAACCCTTTTAAGATTTCTACGCTA 1 134 1 CTTTTAAGAT 0.937767 -91 CCTAATCTTGCTTATAAAAAGGTTTTCCTA 2 30 1 CTTATAAAAA 0.903438 -171 TGGATTTTTCCTTTTAATAAATTTCACCCA 2 164 0 CTTTTAATAA 0.968036 -37 ********** Masking position 6 Map Score: 3.26635 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 85 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 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