AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i224_Holliday_Junction_enzyme_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 queA 92 synthesis of queuine in tRNA; probably S-adenosylmethionine:tRNA ribosyltransferase-isomerase #2 tgt 55 tRNA-guanine transglycosylase #3 ruvA 175 Holliday junction helicase subunit B; branch migration; repair #4 ruvC 34 Holliday junction nuclease; resolution of structures; repair #5 yebC 28 orf, hypothetical protein #6 ntpA 117 dATP pyrophosphohydrolase #7 HI0244 300 tRNA-guanine transglycosylase (tgt) #8 HI0245 123 queuosine biosynthesis protein (queA) #9 HI0313 62 Holliday junction DNA helicase (ruvA) #10 HI0314 46 crossover junction endodeoxyribonuclease (ruvC) #11 HI0315 159 conserved hypothetical protein Motif number 1 TGGAAGCAAATATTTTAATATTACATATTCA 3 8 0 TATTTATATC 0.804266 -168 CCTCGCAAGTTTTCTTCATCCTTCGCTGGATATC 3 94 1 TTTTTATCTC 0.990464 -82 CTATCCAGCATTTTTTTATCATACAGCATTATCT 3 127 1 TTTTTATCTC 0.990464 -49 TAATGATGACCAACTTAATCATAAATTTAGTCAT 7 88 1 CAATTATCTA 0.705794 -213 AATTTAGTCATATTTTTATCCTTAGTATGATTAA 7 111 1 TATTTATCTA 0.952539 -190 AGATCCTGAGTTTGTTAATCATACTAAGGATAAA 7 125 0 TTTTTATCTC 0.990464 -176 TAATTGCTGGTTATTTTATCTTCCCCGAGGGGAG 8 31 1 TTATTATCTC 0.966524 -93 TACCGCCTATTTTATTTAACCTAAATTTTGTT 8 102 1 TTTTTAACTA 0.861703 -22 TATGCGTTAATTTTTTTATCATTCGGAAGAATT 9 40 1 TTTTTATCTC 0.990464 -23 CTGTTTTGATCTTATTGATCTTGATTTAATTAAA 11 125 0 CTTTTATCTA 0.950148 -35 *** ** *** * * Masking position 8 Map Score: 12.1649 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 111 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 2 TATATTCTATCCAAAAGGGGGTAAAGGTTGCAGG 1 15 1 CAAAGGGGAA 0.908226 -78 TCAGACTAAAATAAGAGGCGGGTAGTCTAGTGCC 1 60 0 AAAAGGGGTA 0.986271 -33 TGTATGATAAAAAAATGCTGGATAGATATCCAGC 3 118 0 AAATGCGGTA 0.959037 -58 GTTGATGCCGACAAGAGATGGTTACCGCCATCTC 7 11 0 AAAAGAGGTA 0.983468 -290 GTGCTACTTTTCAATAACAGGCAAAGTAGAATAA 7 57 1 TAAAACGGAA 0.684785 -244 TTTTTTAAACAAAAAAGCCTGTTAAAAAATACAG 7 247 0 AAAAGCTGTA 0.881444 -54 AATGACCAGCATAATTGCTGGTTATTTTATCTTC 8 20 1 AAATGCGGTA 0.959035 -104 TAGGTTAAATAAAATAGGCGGTAAGTCTAGTTTG 8 91 0 AAAAGGGGAA 0.976935 -33 TGATGCAATAAATGGGTAATTTAATTAC 10 5 1 GAAAAAGGTA 0.774923 -42 AATTTCTATAAAAAATGGGTAATTAAATTAC 10 26 0 AAAAAAGGTA 0.936451 -21 CAATAAGATCAAAACAGAAGGAAATAAA 11 142 1 AAAAGAGGAA 0.97228 -18 * ** *** ** ** Masking position 4 Map Score: 11.0379 Number of sites scoring better than the average of aligned sites = 431 Number in coding regions = 361 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 3 CCTGCAACCTTTACCCCCTTTTGGATAGAA 1 19 0 TTACCCCCTT 0.991645 -74 GTTCACTCAGTTGCCGCCTCGATGCAACGC 6 37 0 TTGCCGCCTC 0.953873 -81 CAAGAGATGGTTACCGCCATCTC 7 4 0 TTACCGCCAT 0.960964 -297 AGTCCGCCAGTTGCCGCTGTCGGGCTATTT 7 162 0 TTGCCGCTGT 0.909194 -139 CAAACTAGACTTACCGCCTATTTTATTTAA 8 91 1 TTACCGCCTA 0.960964 -33 GGTAATTAAATTACCCATTTATTGCATCA 10 10 0 TTACCCATTT 0.929299 -37 GGTAATTTAATTACCCATTTTTTATAGAAA 10 25 1 TTACCCATTT 0.929299 -22 AGTAAAAGTGTTACCCCGTTGGGAGTGGAT 11 63 0 TTACCCCGTT 0.971189 -97 ********** Masking position 2 Map Score: 6.91242 Number of sites scoring better than the average of aligned sites = 501 Number in coding regions = 434 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 4 CACTGACTCAGACTAAAATAAGAGGCGGGT 1 71 0 GACTAAAATA 0.957245 -22 GGTTATATTGGAAGCAAATATTTTAATATT 3 20 0 GAAGCAAATA 0.964333 -156 ATAACCTGTAGAATAAATTATACTGTGCCA 3 44 1 GAATAAATTA 0.876305 -132 CCTGCGTAATGAATCAAAGATAATGCTGTA 3 148 0 GAATCAAAGA 0.926909 -28 TATGACTCAAATACACGAAATCA 6 4 1 GACTCAAATA 0.964333 -114 AATTTAGGTTAAATAAAATAGGCGGTAAGT 8 99 0 AAATAAAATA 0.815333 -25 TTAACGCATAGAATAAAATAAAACTGGACG 9 20 0 GAATAAAATA 0.975331 -43 GATCAAAACAGAAGGAAATAAA 11 148 1 GAAGGAAATA 0.909795 -12 ********** Masking position 6 Map Score: 7.14682 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 75 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 5 AAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTA 1 38 1 GGAAGCGCCG 0.981201 -55 CAACGTTTTAAACCAGCGCCGCGGAA 2 3 0 AACAGCGCCG 0.982217 -53 TACGTCAGAAAAACAGTCCAACGTTTTAAACCAG 2 21 0 AAAAGTCCCT 0.961964 -35 AAATATCTCCAGATAGCCCTGCCTGT 5 3 0 AGAAGCCCCT 0.985188 -26 AACTACTAATAGCCAGTGCTACTTTTCAATAACA 7 42 1 AGCAGTGCCT 0.960481 -259 AGGATCTACGAAATAGCCCGACAGCGGCAACTGG 7 152 1 AAAAGCCCCG 0.990815 -149 GGATCTACTAAGATAGTCCGCCAGTTGCCGCTGT 7 172 0 AGAAGTCCCG 0.990816 -129 *** ***** * * Masking position 5 Map Score: 4.83678 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 236 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 6 TCTTCATCCTTCGCTGGATATCTATCCAGC 3 106 1 TCGCTGGATA 0.928096 -70 TGATAAAAAAATGCTGGATAGATATCCAGC 3 118 0 ATGCTGGATA 0.982021 -58 ATCAAAGATAATGCTGTATGATAAAAAAAT 3 136 0 ATGCTGTATG 0.946798 -40 CGTCTCCGTTTTGCTGTTTAGCAGGCCTCA 4 11 0 TTGCTGTTTA 0.963566 -24 CATATTTTCAATGCTCTTTGAGCAGAGGCG 7 205 0 ATGCTCTTTG 0.816678 -96 ACCAGCAATTATGCTGGTCATTTGGGATTA 8 12 0 ATGCTGGTCA 0.956303 -112 ACCAGCATAATTGCTGGTTATTTTATCTTC 8 24 1 TTGCTGGTTA 0.982021 -100 ********** Masking position 5 Map Score: 4.61408 Number of sites scoring better than the average of aligned sites = 752 Number in coding regions = 704 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 7 CGATTATATTCTATCCAAAAGGGGGT 1 7 1 TATTCTATCC 0.878742 -86 TAGAATAAATTATACTGTGCCATTTTTCAG 3 52 1 TATACTGTGC 0.901536 -124 ACTGTGCCATTTTTCAGTTCATCGAGACAC 3 65 1 TTTTCAGTTC 0.92372 -111 ATTCACATAGTTATCTATGCTCATGGGAGT 6 65 0 TTATCTATGC 0.903299 -53 TGATATCATATTTTCAATGCTCTTTGAGCA 7 211 0 TTTTCAATGC 0.962287 -90 CTCCAACGAATAAACAGTTCGAAGATTTTT 7 276 0 TAAACAGTTC 0.618744 -25 CTTGAGATCATTTTCAATTCAAACTAGACT 8 72 1 TTTTCAATTC 0.925119 -52 AGTTTTATTTTATTCTATGCGTTAATTTTT 9 25 1 TATTCTATGC 0.962287 -38 ********** Masking position 8 Map Score: 3.52747 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 185 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 8 GCAGGGAGAGCGCCCCGGCACTAGACTACCC 1 44 1 CGCCCCGCAC 0.947974 -49 CTAGACTACCCGCCTCTTATTTTAGTCTGAG 1 64 1 CGCCTCTATT 0.917752 -29 TTTTTCTCCACTACGTCAGAAAAACA 2 40 0 CTCCACTCGT 0.896776 -16 ATGACGCTCCTGCGTAATGAATCAA 3 161 0 CGCTCCTCGT 0.964943 -15 CACGCGTCTCCGTTTTGCTGTTT 4 22 0 CGCGTCTCGT 0.983773 -13 ACTCAGTTGCCGCCTCGATGCAACGCGAATG 6 32 0 CGCCTCGTGC 0.957812 -86 GCTGCCTCTTCGTTGACTGCCTT 6 105 0 TGCCTCTCGT 0.972387 -13 TTAGTAGATCCGCCTCTGCTCAAAGAGCATT 7 195 1 CGCCTCTCTC 0.98828 -106 ******* *** Masking position 6 Map Score: 3.21437 Number of sites scoring better than the average of aligned sites = 1292 Number in coding regions = 1211 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 9 GAGCGCCCCGGCACTAGACTACCCGCCTCT 1 51 1 GCACTAGACT 0.957843 -42 TTTTCAATTCAAACTAGACTTACCGCCTAT 8 82 1 AAACTAGACT 0.959879 -42 CACTTTTACTAACCTAGGCTATACCTAGCC 11 83 1 AACCTAGGCT 0.817867 -77 TAAACGTTTTGACCTAGGCTAGGTATAGCC 11 99 0 GACCTAGGCT 0.97184 -61 ********** Masking position 5 Map Score: 0.762072 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 ATGTAATATTAAAATATTTGCTTCCAATATA 3 16 1 AAAAATTTGC 0.874745 -160 AAAAATATCTCCAGATAGCCCT 5 17 0 AAAAATCTCC 0.989868 -12 TTTTTTGTTTAAAAAATCTTCGAACTGTTTA 7 265 1 AAAAATCTTC 0.960872 -36 TGATCTCAAGAAAAAATCTCCCCTCGGGGAA 8 51 0 AAAAATCTCC 0.989865 -73 TTTGAATTGAAAATGATCTCAAGAAAAAATC 8 64 0 AAATATCTCA 0.850529 -60 **** ****** Masking position 6 Map Score: 0.674491 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 79 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 11 ********** No masking Map Score: -8.71535e-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: -8.71535e-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 13 ********** No masking Map Score: -8.71535e-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