AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i224_Holliday_Junction_enzyme_bsub_reg_300.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 #5 bofC 47 bofC #6 csbX 70 alpha-ketoglutarate permease #7 yrbE 237 similar to opine catabolism Motif number 1 TTTGAGAACAGGAGGCCTCATC 1 3 1 TGAGAACAGG 0.777367 -24 CCGATAATAAGCAAAACAGCACCAAGAATC 2 29 0 GCAAAACAGC 0.968141 -194 CCGACAAAATGCAAAACTGCTCCGATAATA 2 50 0 GCAAAACTGC 0.763801 -173 GATATTTTTGTAAAAAAAGGAAATGTTACG 2 93 1 TAAAAAAAGG 0.818417 -130 TGACAACCGGGAAGAAAAACGTAACATTTC 2 112 0 GAAGAAAAAC 0.877142 -111 GGCCCGTACAGAAGAACATGATCCAGCGTC 3 173 0 GAAGAACATG 0.863454 -78 CCCGGACTCGGAAAAACAACGCTTGCTTCG 3 204 1 GAAAAACAAC 0.965853 -47 ATTCTTTCACGAAAAAAAAGACATGAATAC 4 31 0 GAAAAAAAAG 0.834914 -108 CATTGTACCATAAAAACAGCCAAAGTCTTA 4 93 0 TAAAAACAGC 0.961843 -46 ATGGTACAATGAAGAACAGTCAAAGAGGTG 4 112 1 GAAGAACAGT 0.908916 -27 ATGATTTTCCTATAAACAGCTGCATAAAAT 7 32 0 TATAAACAGC 0.728445 -206 AACTGTTCAGGAAAAAGAGCCTAATTCTAG 7 63 1 GAAAAAGAGC 0.959099 -175 ATCTGGTCTTGAAGAAGAAGGCTACTTATA 7 96 1 GAAGAAGAAG 0.847637 -142 ********** Masking position 5 Map Score: 10.3548 Number of sites scoring better than the average of aligned sites = 3177 Number in coding regions = 2825 Number in noncoding regions = 352 Number of orfs with sites within 600 bp upstream = 310 Fraction of orfs with sites within 600 bp upstream = 0.0497912 Motif number 2 GATGATTTCACCTTTATTCTAGTC 2 209 0 TATTCACCTT 0.919777 -14 CGCGCAAATTTTCTTTTACCTTATGCTGCCCG 3 110 0 TCTTTACCTT 0.919777 -141 ATCCAGCGTCTCCTGTCTCATTTTCGCCGCAT 3 151 0 TCTTCTCATT 0.969289 -100 TTCCACTCCCATTTCATTAGCAA 3 238 0 TCATCCCATT 0.979999 -13 ATATGTTCGCTTCTCTCTCATTCTTTCACGAA 4 48 0 TCTTCTCATT 0.969289 -91 TTCATTCACCTTCTTTGCTCTA 7 1 1 TCATCACCTT 0.968297 -237 CATAGAACGTTTAATTTCCATTCTTGAAAAGC 7 149 1 TAATTCCATT 0.655158 -89 TTAAAATTAATACTATCCCATTTGTAAGCGCT 7 178 0 TCTTCCCATT 0.989407 -60 GGCTTCTTCCCCCTTGATCATTCAC 7 223 0 TCTCCCCCTT 0.965632 -15 * ** ******* Masking position 11 Map Score: 9.70898 Number of sites scoring better than the average of aligned sites = 326 Number in coding regions = 234 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 3 TTTGAGAACAGGAGGCCTCAT 1 2 1 TTGAGAACAG 0.911818 -25 GAATCAGTGATAGAGCAAAGCCTGAGGCCG 3 60 1 TAGAGCAAAG 0.984067 -191 GTGAAAGAATGAGAGAGAAGCGAACATATG 4 51 1 GAGAGAGAAG 0.910215 -88 GCCAAAGTCTTATAGAAAAGTTAACATATG 4 75 0 TATAGAAAAG 0.813029 -64 TATGATTAGTTTGACCAAAGAGG 5 4 0 TTGACCAAAG 0.922324 -44 AATCATAAACGTGTGCAAAGAGGTGTAGAG 5 27 1 GTGTGCAAAG 0.9152 -21 CTGCATAAAATAGAGCAAAGAAGGTGAATG 7 13 0 TAGAGCAAAG 0.984067 -225 AGCATGAATTGTGATAAAAGAGACATAGAA 7 126 1 GTGATAAAAG 0.831954 -112 ********** Masking position 9 Map Score: 5.4336 Number of sites scoring better than the average of aligned sites = 391 Number in coding regions = 324 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 4 TAAGCAAAACAGCACCAAGAATCATAATGATC 2 20 0 ACACAAGAAT 0.938834 -203 TGAAATAACAAAAGACTAGAATAAAGGTGAAA 2 196 1 AAGCTAGAAT 0.960454 -27 AGTGAAGCAGACAACCATGAATCAGTGATAGA 3 42 1 AAACATGAAT 0.976732 -209 TCACGAAAAAAAAGACATGAATACATGTCTTC 4 23 0 AAGCATGAAT 0.978409 -116 TCAAGACCAGATACACTAGAATTAGGCTCTTT 7 76 0 AACCTAGAAT 0.929419 -162 AAGGCTACTTATAAGCATGAATTGTGATAAAA 7 113 1 AAACATGAAT 0.976732 -125 * ** ******* Masking position 10 Map Score: 2.45049 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 110 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 AAATGAGACAGGAGACGCTGGATCATGTTCT 3 160 1 GAGACGCTGG 0.976152 -91 AACAATCGAAGCAAGCGTTGTTTTTCCGAGT 3 209 0 GAAGCGTTGT 0.978778 -42 GATACTTTAAGTAGGCGGTGGAGAAA 6 55 1 GAGGCGGTGG 0.987607 -16 TATCCCATTTGTAAGCGCTTTTCAAGAATGG 7 166 0 GAAGCGCTTT 0.987858 -72 GATCATTCACGAAAGCGCTTTATTTAAAATT 7 202 0 GAAGCGCTTT 0.987854 -36 * ********* Masking position 3 Map Score: 1.64012 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 263 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 6 ATTATCAATTTTGCTTAATCTTTTTGGCAG 2 164 1 TTGCTTAATC 0.960588 -59 GCCTCAGGCTTTGCTCTATCACTGATTCAT 3 58 0 TTGCTCTATC 0.985181 -193 GTACCCAAGCTTGCTGAATTGTAATCCTGT 6 15 0 TTGCTGAATT 0.958938 -56 TTCACCTTCTTTGCTCTATTTTATGCAGCT 7 15 1 TTGCTCTATT 0.977261 -223 ********** Masking position 5 Map Score: 0.674061 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 46 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 7 TTGAGAACAGGAGGCCTCATCAAAA 1 12 1 GAGCCTCATA 0.955771 -15 TTGTCGGCAAGATGCCGGGAGATATTTTTGTA 2 73 1 GAGCCGGGAA 0.991672 -150 AGCAAAGCCTGAGGCCGCAAAATCTGGCACAG 3 73 1 GAGCCGCAAA 0.993849 -178 CGTGTTTATAGATGCGGCGAAAATGAGACAGG 3 140 1 GAGCGGCGAA 0.984865 -111 TGAGACAGGAGACGCTGGATCATGTTCTTCTG 3 163 1 GAGCTGGATA 0.951186 -88 ** ******* * Masking position 2 Map Score: 0.0692366 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 205 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 ********** No masking Map Score: -1.97998e-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 9 ********** No masking Map Score: -1.97998e-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: -1.97998e-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