AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i207_holliday_junction_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 0.795332 -168 CCTCGCAAGTTTTCTTCATCCTTCGCTGGATATC 3 94 1 TTTTTATCTC 0.989922 -82 CTATCCAGCATTTTTTTATCATACAGCATTATCT 3 127 1 TTTTTATCTC 0.989922 -49 TAATGATGACCAACTTAATCATAAATTTAGTCAT 7 88 1 CAATTATCTA 0.694075 -213 AATTTAGTCATATTTTTATCCTTAGTATGATTAA 7 111 1 TATTTATCTA 0.949952 -190 AGATCCTGAGTTTGTTAATCATACTAAGGATAAA 7 125 0 TTTTTATCTC 0.989922 -176 TAATTGCTGGTTATTTTATCTTCCCCGAGGGGAG 8 31 1 TTATTATCTC 0.964671 -93 TACCGCCTATTTTATTTAACCTAAATTTTGTT 8 102 1 TTTTTAACTA 0.85493 -22 TATGCGTTAATTTTTTTATCATTCGGAAGAATT 9 40 1 TTTTTATCTC 0.989922 -23 CTGTTTTGATCTTATTGATCTTGATTTAATTAAA 11 125 0 CTTTTATCTA 0.947437 -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 0.930022 -78 TCAGACTAAAATAAGAGGCGGGTAGTCTAGTGCC 1 60 0 AAAAGGGGTA 0.989741 -33 TGTATGATAAAAAAATGCTGGATAGATATCCAGC 3 118 0 AAATGCGGTA 0.969175 -58 GTTGATGCCGACAAGAGATGGTTACCGCCATCTC 7 11 0 AAAAGAGGTA 0.987638 -290 GTGCTACTTTTCAATAACAGGCAAAGTAGAATAA 7 57 1 TAAAACGGAA 0.744734 -244 TTTTTTAAACAAAAAAGCCTGTTAAAAAATACAG 7 247 0 AAAAGCTGTA 0.908963 -54 AATGACCAGCATAATTGCTGGTTATTTTATCTTC 8 20 1 AAATGCGGTA 0.969173 -104 TAGGTTAAATAAAATAGGCGGTAAGTCTAGTTTG 8 91 0 AAAAGGGGAA 0.982724 -33 TGATGCAATAAATGGGTAATTTAATTAC 10 5 1 GAAAAAGGTA 0.82218 -42 AATTTCTATAAAAAATGGGTAATTAAATTAC 10 26 0 AAAAAAGGTA 0.951899 -21 CAATAAGATCAAAACAGAAGGAAATAAA 11 142 1 AAAAGAGGAA 0.979212 -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 0.990603 -74 GTTCACTCAGTTGCCGCCTCGATGCAACGC 6 37 0 TTGCCGCCTC 0.948365 -81 CAAGAGATGGTTACCGCCATCTC 7 4 0 TTACCGCCAT 0.956272 -297 AGTCCGCCAGTTGCCGCTGTCGGGCTATTT 7 162 0 TTGCCGCTGT 0.898917 -139 CAAACTAGACTTACCGCCTATTTTATTTAA 8 91 1 TTACCGCCTA 0.956272 -33 GGTAATTAAATTACCCATTTATTGCATCA 10 10 0 TTACCCATTT 0.921099 -37 GGTAATTTAATTACCCATTTTTTATAGAAA 10 25 1 TTACCCATTT 0.921099 -22 AGTAAAAGTGTTACCCCGTTGGGAGTGGAT 11 63 0 TTACCCCGTT 0.967679 -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 0.958888 -22 GGTTATATTGGAAGCAAATATTTTAATATT 3 20 0 GAAGCAAATA 0.965714 -156 ATAACCTGTAGAATAAATTATACTGTGCCA 3 44 1 GAATAAATTA 0.88067 -132 CCTGCGTAATGAATCAAAGATAATGCTGTA 3 148 0 GAATCAAAGA 0.929633 -28 TATGACTCAAATACACGAAATCA 6 4 1 GACTCAAATA 0.965713 -114 AATTTAGGTTAAATAAAATAGGCGGTAAGT 8 99 0 AAATAAAATA 0.821414 -25 TTAACGCATAGAATAAAATAAAACTGGACG 9 20 0 GAATAAAATA 0.976296 -43 GATCAAAACAGAAGGAAATAAA 11 148 1 GAAGGAAATA 0.913097 -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 0.982169 -55 CAACGTTTTAAACCAGCGCCGCGGAA 2 3 0 AACAGCGCCG 0.983132 -53 TACGTCAGAAAAACAGTCCAACGTTTTAAACCAG 2 21 0 AAAAGTCCCT 0.963886 -35 AAATATCTCCAGATAGCCCTGCCTGT 5 3 0 AGAAGCCCCT 0.985354 -26 AACTACTAATAGCCAGTGCTACTTTTCAATAACA 7 42 1 AGCAGTGCCT 0.962106 -259 AGGATCTACGAAATAGCCCGACAGCGGCAACTGG 7 152 1 AAAAGCCCCG 0.991293 -149 GGATCTACTAAGATAGTCCGCCAGTTGCCGCTGT 7 172 0 AGAAGTCCCG 0.991293 -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 ACCCCCTTTTGGATAGAATATAATCG 1 7 0 GGATAGAATA 0.863747 -86 CTGAAAAATGGCACAGTATAATTTATTCTA 3 52 0 GCACAGTATA 0.889003 -124 GTGTCTCGATGAACTGAAAAATGGCACAGT 3 65 0 GAACTGAAAA 0.913741 -111 ACTCCCATGAGCATAGATAACTATGTGAAT 6 65 1 GCATAGATAA 0.890964 -53 TGCTCAAAGAGCATTGAAAATATGATATCA 7 211 1 GCATTGAAAA 0.95712 -90 AAAAATCTTCGAACTGTTTATTCGTTGGAG 7 276 1 GAACTGTTTA 0.586717 -25 AGTCTAGTTTGAATTGAAAATGATCTCAAG 8 72 0 GAATTGAAAA 0.915306 -52 AAAAATTAACGCATAGAATAAAATAAAACT 9 25 0 GCATAGAATA 0.95712 -38 ********** Masking position 3 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 GGGTAGTCTAGTGCCGGGGCGCTCTCCCTGC 1 44 0 GTGCCGGGCG 0.981663 -49 TTTTAAACCAGCGCCGCGGAA 2 1 0 GCGCCGGGAA 0.955737 -55 TGTTTTTCTGACGTAGTGGAGAAAAA 2 40 1 ACGTAGGGAG 0.953526 -16 TTGATTCATTACGCAGGAGCGTCAT 3 161 1 ACGCAGAGCG 0.971779 -15 AAACAGCAAAACGGAGACGCGTG 4 22 1 ACGGAGCGCG 0.935462 -13 CATTCGCGTTGCATCGAGGCGGCAACTGAGT 6 32 1 GCATCGGGCG 0.939663 -86 AAGGCAGTCAACGAAGAGGCAGC 6 105 1 ACGAAGGGCA 0.920857 -13 AATGCTCTTTGAGCAGAGGCGGATCTACTAA 7 195 0 GAGCAGGGCG 0.98202 -106 ****** **** Masking position 6 Map Score: 2.52857 Number of sites scoring better than the average of aligned sites = 2918 Number in coding regions = 2802 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 9 AGAGGCGGGTAGTCTAGTGCCGGGGCGCTC 1 51 0 AGTCTAGTGC 0.95626 -42 ATAGGCGGTAAGTCTAGTTTGAATTGAAAA 8 82 0 AGTCTAGTTT 0.9585 -42 GGCTAGGTATAGCCTAGGTTAGTAAAAGTG 11 83 0 AGCCTAGGTT 0.821566 -77 GGCTATACCTAGCCTAGGTCAAAACGTTTA 11 99 1 AGCCTAGGTC 0.972075 -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 0.877367 -160 AAAAATATCTCCAGATAGCCCT 5 17 0 AAAAATCTCC 0.990107 -12 TTTTTTGTTTAAAAAATCTTCGAACTGTTTA 7 265 1 AAAAATCTTC 0.961768 -36 TGATCTCAAGAAAAAATCTCCCCTCGGGGAA 8 51 0 AAAAATCTCC 0.990104 -73 TTTGAATTGAAAATGATCTCAAGAAAAAATC 8 64 0 AAATATCTCA 0.853574 -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