AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i207_holliday_junction_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 GATGAGGCCTCCTGTTCTCAAA 1 3 0 CCTGTTCTCA 0.872753 -24 GATTCTTGGTGCTGTTTTGCTTATTATCGG 2 29 1 GCTGTTTTGC 0.980818 -194 TATTATCGGAGCAGTTTTGCATTTTGTCGG 2 50 1 GCAGTTTTGC 0.877836 -173 CGTAACATTTCCTTTTTTTACAAAAATATC 2 93 0 CCTTTTTTTA 0.870554 -130 GAAATGTTACGTTTTTCTTCCCGGTTGTCA 2 112 1 GTTTTTCTTC 0.912916 -111 GACGCTGGATCATGTTCTTCTGTACGGGCC 3 173 1 CATGTTCTTC 0.922305 -78 CGAAGCAAGCGTTGTTTTTCCGAGTCCGGG 3 204 0 GTTGTTTTTC 0.971666 -47 GTATTCATGTCTTTTTTTTCGTGAAAGAAT 4 31 1 CTTTTTTTTC 0.886514 -108 TAAGACTTTGGCTGTTTTTATGGTACAATG 4 93 1 GCTGTTTTTA 0.967238 -46 CACCTCTTTGACTGTTCTTCATTGTACCAT 4 112 0 ACTGTTCTTC 0.946054 -27 ********** Masking position 5 Map Score: 9.84018 Number of sites scoring better than the average of aligned sites = 2701 Number in coding regions = 2421 Number in noncoding regions = 280 Number of orfs with sites within 600 bp upstream = 244 Fraction of orfs with sites within 600 bp upstream = 0.0391905 Motif number 2 CGGAGCAGTTTTGCATTTTGTCGGCAAGATGCCGGGA 2 56 1 TGCATTTCAA 0.981364 -167 AAACGTAACATTTCCTTTTTTTACAAAAATATCTCCC 2 89 0 TTCCTTTTAA 0.872556 -134 AGTGTGGTATTATCAATTTTGCTTAATCTTTTTGGCA 2 156 1 TTCAATTCAT 0.939369 -67 TCTTTTGTTATTTCATTCTGCCAAAAAGATTAAGCAA 2 174 0 TTCATTTCAA 0.994204 -49 GCGTCTCCTGTCTCATTTTCGCCGCATCTATAAACAC 3 141 0 TTCATTTCAT 0.986777 -110 TTCGCTTCTCTCTCATTCTTTCACGAAAAAAAAGACA 4 38 0 TTCATTTCAA 0.994204 -101 TTTGACTGTTCTTCATTGTACCATAAAAACAGCCAAA 4 99 0 CTCATTTCAA 0.981407 -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 0.926012 -124 TTTTTGGCAGAATGAAATAACAAAAGACTAGA 2 184 1 AATGAAAAAA 0.897272 -39 GACTAGAATAAAGGTGAAATCATC 2 209 1 AAGGTGAATA 0.907157 -14 CGGGCAGCATAAGGTAAAAGAAAATTTGCGCG 3 110 1 AAGGTAAAGA 0.959913 -141 ATGCGGCGAAAATGAGACAGGAGACGCTGGAT 3 151 1 AATGAGAAGA 0.982157 -100 GATTGTTGCTAATGAAATGGGAGTGGAA 3 233 1 AATGAAAGGA 0.968426 -18 TTCGTGAAAGAATGAGAGAGAAGCGAACATAT 4 48 1 AATGAGAAGA 0.982157 -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 TTGAGAACAGGAGGCCTCATCAAAA 1 12 1 GAGGCCTCAT 0.917395 -15 TTGTCGGCAAGATGCCGGGAGATATTTTTG 2 73 1 GATGCCGGGA 0.991062 -150 AGCAAAGCCTGAGGCCGCAAAATCTGGCAC 3 73 1 GAGGCCGCAA 0.986922 -178 TTTACCTTATGCTGCCCGATATACTGTGCC 3 98 0 GCTGCCCGAT 0.961242 -153 CGTGTTTATAGATGCGGCGAAAATGAGACA 3 140 1 GATGCGGCGA 0.950875 -111 TGAGACAGGAGACGCTGGATCATGTTCTTC 3 163 1 GACGCTGGAT 0.921732 -88 TTCTGTACGGGCCGCCCGGACTCGGAAAAA 3 190 1 GCCGCCCGGA 0.976325 -61 ********** Masking position 5 Map Score: 3.35768 Number of sites scoring better than the average of aligned sites = 1133 Number in coding regions = 1052 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 5 TTATTATAAGTGTGGTATTATCAATTTTGCTTAA 2 148 1 TTGGATATAA 0.966515 -75 GCTTAATCTTTTTGGCAGAATGAAATAACAAAAG 2 176 1 TTGGAAATAA 0.991527 -47 GGCCGCAAAATCTGGCACAGTATATCGGGCAGCA 3 85 1 TTGGAAGTTA 0.959896 -166 TCGGGCAGCATAAGGTAAAAGAAAATTTGCGCGT 3 109 1 TAGGAAAGAA 0.913463 -142 GCCAAAGTCTTATAGAAAAGTTAACATATGTTCG 4 71 0 TTAGAAGTAA 0.937508 -68 TGGCTGTTTTTATGGTACAATGAAGAACAGTCAA 4 101 1 TTGGAAATAA 0.991526 -38 * *** * *** ** Masking position 7 Map Score: 1.72762 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 58 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 6 TTCACCTTTATTCTAGTCTTTTGTTATTTC 2 197 0 TTCTAGTCTT 0.956373 -26 AAGACATGAATACATGTCTTCAATCAGCGG 4 14 0 TACATGTCTT 0.974763 -125 AAGACATGTATTCATGTCTTTTTTTTCGTG 4 24 1 TTCATGTCTT 0.989864 -115 GCAAATTCACCTCTTTGACTGTTCT 4 124 0 TTCACCTCTT 0.968375 -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 ATACAAGTGACAACCGGGAAGAAAAACGTA 2 119 0 CAACCGGGAA 0.977122 -104 ACGAGCCGTTCATCCATGAACATCACC 3 8 0 CATCCATGAA 0.99201 -243 GTGAAGCAGACAACCATGAATCAGTGATAG 3 43 1 CAACCATGAA 0.99201 -208 ATTTTCGCCGCATCTATAAACACGCGCAAA 3 134 0 CATCTATAAA 0.887201 -117 ********** Masking position 2 Map Score: 1.14618 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 61 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 GCAAAACAGCACCAAGAATCATAATGATCT 2 19 0 ACCAAGAATC 0.992401 -204 GAAGCAGACAACCATGAATCAGTGATAGAG 3 45 1 ACCATGAATC 0.986678 -206 CCATTTCATTAGCAACAATCGAAGCAAGCG 3 223 0 AGCAACAATC 0.974723 -28 ********** Masking position 4 Map Score: 0.163137 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 11 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 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