AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i224_Holliday_Junction_enzyme_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -x5 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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 tgt 26 tRNA-guanine transglycosylase #2 queA 222 S-adenosylmethionine tRNA ribosyltransferase #3 ruvB 250 Holliday junction DNA helicase #4 ruvA 138 Holliday junction DNA helicase Motif number 1 TTTGAGAACAGGAGGCCTCATC 1 3 1 TGAGAACAGG 0.874243 -24 CCGATAATAAGCAAAACAGCACCAAGAATC 2 29 0 GCAAAACAGC 0.981069 -194 CCGACAAAATGCAAAACTGCTCCGATAATA 2 50 0 GCAAAACTGC 0.87927 -173 GATATTTTTGTAAAAAAAGGAAATGTTACG 2 93 1 TAAAAAAAGG 0.872065 -130 TGACAACCGGGAAGAAAAACGTAACATTTC 2 112 0 GAAGAAAAAC 0.913981 -111 GGCCCGTACAGAAGAACATGATCCAGCGTC 3 173 0 GAAGAACATG 0.923265 -78 CCCGGACTCGGAAAAACAACGCTTGCTTCG 3 204 1 GAAAAACAAC 0.972034 -47 ATTCTTTCACGAAAAAAAAGACATGAATAC 4 31 0 GAAAAAAAAG 0.887863 -108 CATTGTACCATAAAAACAGCCAAAGTCTTA 4 93 0 TAAAAACAGC 0.967663 -46 ATGGTACAATGAAGAACAGTCAAAGAGGTG 4 112 1 GAAGAACAGT 0.946738 -27 ********** Masking position 5 Map Score: 9.84018 Number of sites scoring better than the average of aligned sites = 2713 Number in coding regions = 2431 Number in noncoding regions = 282 Number of orfs with sites within 600 bp upstream = 246 Fraction of orfs with sites within 600 bp upstream = 0.0395117 Motif number 2 CGGAGCAGTTTTGCATTTTGTCGGCAAGATGCCGGGA 2 56 1 TGCATTTCAA 0.9804 -167 AAACGTAACATTTCCTTTTTTTACAAAAATATCTCCC 2 89 0 TTCCTTTTAA 0.8667 -134 AGTGTGGTATTATCAATTTTGCTTAATCTTTTTGGCA 2 156 1 TTCAATTCAT 0.936359 -67 TCTTTTGTTATTTCATTCTGCCAAAAAGATTAAGCAA 2 174 0 TTCATTTCAA 0.993899 -49 GCGTCTCCTGTCTCATTTTCGCCGCATCTATAAACAC 3 141 0 TTCATTTCAT 0.986086 -110 TTCGCTTCTCTCTCATTCTTTCACGAAAAAAAAGACA 4 38 0 TTCATTTCAA 0.993899 -101 TTTGACTGTTCTTCATTGTACCATAAAAACAGCCAAA 4 99 0 CTCATTTCAA 0.980441 -40 * ***** * * ** Masking position 16 Map Score: 5.14952 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 115 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 3 TTTGTAAAAAAAGGAAATGTTACGTTTTTCTT 2 99 1 AAGGAAAGTA 0.930177 -124 TTTTTGGCAGAATGAAATAACAAAAGACTAGA 2 184 1 AATGAAAAAA 0.902885 -39 GACTAGAATAAAGGTGAAATCATC 2 209 1 AAGGTGAATA 0.912283 -14 CGGGCAGCATAAGGTAAAAGAAAATTTGCGCG 3 110 1 AAGGTAAAGA 0.962247 -141 ATGCGGCGAAAATGAGACAGGAGACGCTGGAT 3 151 1 AATGAGAAGA 0.983218 -100 GATTGTTGCTAATGAAATGGGAGTGGAA 3 233 1 AATGAAAGGA 0.97028 -18 TTCGTGAAAGAATGAGAGAGAAGCGAACATAT 4 48 1 AATGAGAAGA 0.983218 -91 ******* ** * Masking position 7 Map Score: 4.52848 Number of sites scoring better than the average of aligned sites = 350 Number in coding regions = 283 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 4 TTTGAGAACAGGAGGCCTCATCAAAA 1 8 1 AAGGCTCTCA 0.927236 -19 TTTTACAAAAATATCTCCCGGCATCTTGCCGACAAA 2 72 0 AATCCGCTCT 0.981985 -151 TCACTGATTCATGGTTGTCTGCTTCACTTGAGACGA 3 34 0 AGGGCGCTCA 0.981224 -217 ATACTGTGCCAGATTTTGCGGCCTCAGGCTTTGCTC 3 72 0 AATTCGCTCA 0.987154 -179 CTGGCACAGTATATCGGGCAGCATAAGGTAAAAGAA 3 96 1 AATGCGCTAA 0.970077 -155 GTACAGAAGAACATGATCCAGCGTCTCCTGTCTCAT 3 162 0 AATTCGCTCT 0.984502 -89 AGAAAAGTTAACATATGTTCGCTTCTCTCTCATTCT 4 56 0 AATGTGCTCT 0.96174 -83 * ** * * ** *** Masking position 1 Map Score: 2.89023 Number of sites scoring better than the average of aligned sites = 529 Number in coding regions = 492 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 5 TTTTGATGAGGCCTCCTGTTCTCAAA 1 11 0 TGAGGCCTCC 0.551709 -16 GAGCAAAGCCTGAGGCCGCAAAATCTGGCA 3 72 1 TGAGGCCGCA 0.539416 -179 GCACAGTATATCGGGCAGCATAAGGTAAAA 3 99 1 TCGGGCAGCA 0.981929 -152 GTTCTTCTGTACGGGCCGCCCGGACTCGGA 3 186 1 ACGGGCCGCC 0.992856 -65 ********** Masking position 5 Map Score: 1.7821 Number of sites scoring better than the average of aligned sites = 145 Number in coding regions = 134 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 TTCACCTTTATTCTAGTCTTTTGTTATTTC 2 197 0 TTCTAGTCTT 0.952813 -26 AAGACATGAATACATGTCTTCAATCAGCGG 4 14 0 TACATGTCTT 0.972664 -125 AAGACATGTATTCATGTCTTTTTTTTCGTG 4 24 1 TTCATGTCTT 0.989006 -115 GCAAATTCACCTCTTTGACTGTTCT 4 124 0 TTCACCTCTT 0.96576 -15 ********** Masking position 7 Map Score: 1.24342 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 104 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 TTCATTAGCAACAATCGAAGCAAGCGTTGT 3 219 0 ACAATCGAAG 0.977203 -32 TACCATAAAAACAGCCAAAGTCTTATAGAA 4 88 0 ACAGCCAAAG 0.99152 -51 ACAATGAAGAACAGTCAAAGAGGTGAATTT 4 117 1 ACAGTCAAAG 0.992863 -22 ********** Masking position 3 Map Score: 0.59934 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 50 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 8 GCATCTTGCCGACAAAATGCAAAACTGCTCC 2 57 0 GAAAAATGCA 0.933096 -166 TAATCTTTTTGGCAGAATGAAATAACAAAAG 2 179 1 GGAGAATGAA 0.986678 -44 TATAGATGCGGCGAAAATGAGACAGGAGACG 3 146 1 GCAAAATGAG 0.965628 -105 TTTTTTTCGTGAAAGAATGAGAGAGAAGCGA 4 43 1 GAAGAATGAG 0.981025 -96 CTGTTTTTATGGTACAATGAAGAACAGTCAA 4 104 1 GGACAATGAA 0.97576 -35 ** ******** Masking position 6 Map Score: 0.528109 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 130 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 9 ********** No masking Map Score: 1.5372e-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: 1.5372e-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 11 ********** No masking Map Score: 1.5372e-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