AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i207_holliday_junction_ecoli_hinf_reg_300.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 aspS 276 aspartate tRNA synthetase #8 HI0244 300 tRNA-guanine transglycosylase (tgt) #9 HI0245 123 queuosine biosynthesis protein (queA) #10 HI0246 300 H. influenzae predicted coding region HI0246 #11 HI0313 62 Holliday junction DNA helicase (ruvA) #12 HI0314 46 crossover junction endodeoxyribonuclease (ruvC) #13 HI0315 159 conserved hypothetical protein #14 HI0316 21 datP pyrophosphohydrolase (ntpA) #15 HI0317 218 aspartyl-tRNA synthetase (aspS) Motif number 1 TATATTCTATCCAAAAGGGGGTAAAGGTTGCAGG 1 15 1 CAAAGGGGAA 0.865698 -78 TCAGACTAAAATAAGAGGCGGGTAGTCTAGTGCC 1 60 0 AAAAGGGGTA 0.983317 -33 TGTATGATAAAAAAATGCTGGATAGATATCCAGC 3 118 0 AAATGCGGTA 0.889811 -58 TTCAGGCCCGATATAAAGTGGTAACGAGGCGTTC 7 106 1 AATAAGGGAA 0.770807 -171 CAACTGAATGAAAAAAGGCGGCTATTATACTGGA 7 175 0 AAAAGGGGTA 0.983317 -102 GTTGATGCCGACAAGAGATGGTTACCGCCATCTC 8 11 0 AAAAGAGGTA 0.959054 -290 GTGCTACTTTTCAATAACAGGCAAAGTAGAATAA 8 57 1 TAAAACGGAA 0.708376 -244 AAGCCTGTTAAAAAATACAGGCTTTGTGATATCA 8 233 0 AAATACGGTT 0.54867 -68 TTTTTTAAACAAAAAAGCCTGTTAAAAAATACAG 8 247 0 AAAAGCTGTA 0.635648 -54 AATGACCAGCATAATTGCTGGTTATTTTATCTTC 9 20 1 AAATGCGGTA 0.889808 -104 TAGGTTAAATAAAATAGGCGGTAAGTCTAGTTTG 9 91 0 AAAAGGGGAA 0.979385 -33 GTTATTGGCAAAAAGAAGTGGGATTAAAGGCAGA 10 39 1 AAAAAGGGAT 0.87733 -262 TTATTGAAATAAAAAAGGTGGGATCTGCCCCACC 10 208 0 AAAAGGGGAT 0.934678 -93 TGATGCAATAAATGGGTAATTTAATTAC 12 5 1 GAAAAAGGTA 0.613662 -42 AATTTCTATAAAAAATGGGTAATTAAATTAC 12 26 0 AAAAAAGGTA 0.921303 -21 CAATAAGATCAAAACAGAAGGAAATAAA 13 142 1 AAAAGAGGAA 0.949695 -18 TAATTTAATCTCAACAAGCGGCATAATATAACAA 15 27 1 TAAAAGGGAT 0.535856 -192 AAACCAAGAGAGATAAAAAGGTTATTTATGCTGA 15 137 0 AATAAAGGTA 0.623788 -82 * ** *** ** ** Masking position 3 Map Score: 15.4551 Number of sites scoring better than the average of aligned sites = 703 Number in coding regions = 566 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 2 ATTCTATCCAAAAGGGGGTAAAGGTTGCAGG 1 18 1 AAAGGGGGAA 0.890428 -75 GACTAAAATAAGAGGCGGGTAGTCTAGTGCC 1 60 0 AGAGGCGGTA 0.95465 -33 CGCGTTGCATCGAGGCGGCAACTGAGTGAAC 6 36 1 CGAGGCGGAA 0.923532 -82 TGGGATGAGCGAAGGCAGTCAACGAAGAGGC 6 94 1 GAAGGCAGCA 0.797777 -24 GCGATTAGCCGATGGCGGAACGACAAATTTT 7 19 1 GATGGCGGAC 0.95695 -258 CTGAATGAAAAAAGGCGGCTATTATACTGGA 7 175 0 AAAGGCGGTA 0.97658 -102 GAGATGGCGGTAACCATCTCTTG 8 3 1 GATGGCGGAA 0.979718 -298 GAAATAGCCCGACAGCGGCAACTGGCGGACT 8 161 1 GACAGCGGAA 0.84942 -140 CTCTTTGAGCAGAGGCGGATCTACTAAGATA 8 191 0 AGAGGCGGTC 0.906431 -110 GTTAAATAAAATAGGCGGTAAGTCTAGTTTG 9 91 0 ATAGGCGGAA 0.919645 -33 AAGTGGGATTAAAGGCAGAAATTTTACATTT 10 54 1 AAAGGCAGAA 0.942297 -247 ATTTAGAAATAAAAGCAGAAAGTTGGAAATG 10 80 0 AAAAGCAGAA 0.808917 -221 TAATTATGGTGATAGCGGTTCTCTTTTGGGA 13 24 1 GATAGCGGTC 0.727352 -136 CTGTCGCAATTATAGCGGAAAACCAAGAGAG 15 159 0 TATAGCGGAA 0.659539 -60 ******** ** Masking position 5 Map Score: 9.46625 Number of sites scoring better than the average of aligned sites = 2505 Number in coding regions = 2337 Number in noncoding regions = 168 Number of orfs with sites within 600 bp upstream = 172 Fraction of orfs with sites within 600 bp upstream = 0.0276261 Motif number 3 GGCGGGTAGTCTAGTGCCGGGGCGCTCTCCCTGC 1 44 0 CTGTGGGGCG 0.952537 -49 ACGTTTTAAACCAGCGCCGCGGAA 2 1 0 CCGCGGGGAA 0.915776 -55 GACTGTTTTTCTGACGTAGTGGAGAAAAA 2 37 1 CTACGGGGAG 0.913694 -19 ATGAAGAAAACTTGCGAGGTGTCTCGATGAACTG 3 79 0 CTGCGGGTCT 0.937256 -97 GGATAGATATCCAGCGAAGGATGAAGAAAACTTG 3 99 0 CCGCGGATGA 0.725628 -77 TCTTTGATTCATTACGCAGGAGCGTCAT 3 158 1 ATACGGAGCG 0.745348 -18 CACGAAATCATTCGCGTTGCATCGAGGCGGCAAC 6 24 1 TTGCGGATCG 0.830302 -94 GCGAAGGCAGTCAACGAAGAGGCAGC 6 102 1 TCACGGGGCA 0.883662 -16 ATGCGATTAGCCGATGGCGGAACGACAAATTTTG 7 17 1 CCATGGAACG 0.6597 -260 TTATAGCAAACTGGCGTAGAGTCTGATTTCAGGC 7 79 1 CTGCGGGTCT 0.937256 -198 AAGAGCCTGGCCCGCGCTGGAACGCCTCGTTACC 7 125 0 CCGCGGAACG 0.973715 -152 GGGCCAGGCTCTTACGGTGCGGCAGAATTTCCAG 7 146 1 CTACGGGGCA 0.973133 -131 TGACATACAGCTAACGCTGCGACTTGGTCACCTG 7 209 1 CTACGGGACT 0.879263 -68 GACTTGGTCACCTGCGCAGCAGGGGGCATCCGCC 7 229 1 CCGCGGAGGG 0.953777 -48 TTCAATGCTCTTTGAGCAGAGGCGGATCTACTAA 8 195 0 TTGAGGGGCG 0.654468 -106 ACATCCACTCCCAACGGGGTAACACTTTTACTAA 13 61 1 CCACGGAACA 0.877702 -99 ** *** * **** Masking position 6 Map Score: 11.0742 Number of sites scoring better than the average of aligned sites = 5066 Number in coding regions = 4856 Number in noncoding regions = 210 Number of orfs with sites within 600 bp upstream = 193 Fraction of orfs with sites within 600 bp upstream = 0.030999 Motif number 4 ATTAAGTTGGTCATCATTATTCTACTTTGCC 8 76 0 TCACATTATT 0.895833 -225 TCCCAAATGACCAGCATAATTGCTGGTTATT 9 15 1 CCACATAATT 0.918116 -109 TTGGTAAAAATCAACATAATTGTATCGTTTA 10 166 1 TCACATAATT 0.979587 -135 GCTACTTAGATGCTCTTAATTAAATAAAGTT 10 245 0 TGCCTTAATT 0.863784 -56 TATTAAATCCTCTTAATTAATCCCCTAT 10 283 0 TCCCTTAATT 0.924839 -18 AGAACCGCTATCACCATAATTAGCTGTGATT 13 15 0 TCACATAATT 0.979587 -145 TTGATCTTATTGATCTTGATTTAATTAAACG 13 123 0 TGACTTGATT 0.775064 -37 GATTGATTTGTCAGCATAAATAACCTTTTTA 15 127 1 TCACATAAAT 0.883247 -92 GACAGATTTTTGAGCATAATTAAAAGAGTAC 15 185 1 TGACATAATT 0.961136 -34 *** ******* Masking position 7 Map Score: 6.1828 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 83 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 TATATTGGAAGCAAATATTTTAATATTACAT 3 16 0 GAAATATTTT 0.853511 -160 AGGGCTATCTGGAGATATTTTT 5 17 1 GAGATATTTT 0.946746 -12 GACAAATTTTGTTAATTTTTATGAGTTCGGG 7 40 1 GTAATTTTTA 0.648033 -237 TAAACAGTTCGAAGATTTTTTAAACAAAAAA 8 265 0 GAGATTTTTT 0.971283 -36 TTCCCCGAGGGGAGATTTTTTCTTGAGATCA 9 51 1 GAGATTTTTT 0.971337 -73 GGGATTAAAGGCAGAAATTTTACATTTCCAA 10 58 1 GAGAAATTTT 0.737017 -243 ATACAATTATGTTGATTTTTACCAACGATAC 10 160 0 GTGATTTTTA 0.848895 -141 TATTCTATGCGTTAATTTTTTTATCATTCGG 11 35 1 GTAATTTTTT 0.853511 -28 TGCCATATCATCAGATTTTTTGTTATATTAT 15 49 0 TAGATTTTTT 0.76864 -170 * ********* Masking position 5 Map Score: 4.92097 Number of sites scoring better than the average of aligned sites = 396 Number in coding regions = 320 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 6 GCTGGATAGATATCCAGCGAAGGATGAAGA 3 106 0 TATCCAGCGA 0.853302 -70 GCTGGATATCTATCCAGCATTTTTTTATCA 3 118 1 TATCCAGCAT 0.946739 -58 ATTTTTTTATCATACAGCATTATCTTTGAT 3 136 1 CATACAGCAT 0.946739 -40 TGAGGCCTGCTAAACAGCAAAACGGAGACG 4 11 1 TAAACAGCAA 0.954456 -24 TCAGTTGTGACATACAGCTAACGCTGCGAC 7 202 1 CATACAGCTA 0.796937 -75 CGCCTCTGCTCAAAGAGCATTGAAAATATG 8 205 1 CAAAGAGCAT 0.760881 -96 TAATCCCAAATGACCAGCATAATTGCTGGT 9 12 1 TGACCAGCAT 0.836514 -112 GAAGATAAAATAACCAGCAATTATGCTGGT 9 24 0 TAACCAGCAA 0.964261 -100 CGCAACTCGGCAAACAGCAAAATGTGGGCG 10 120 1 CAAACAGCAA 0.964261 -181 ********** Masking position 6 Map Score: 5.31245 Number of sites scoring better than the average of aligned sites = 604 Number in coding regions = 566 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 7 TGGCACAGTATAATTTATTCTACAGGTTAT 3 44 0 TAATTTATTC 0.620149 -132 CTATCCAGCATTTTTTTATCATACAGCATT 3 127 1 TTTTTTTATC 0.831235 -49 AATTTAGTCATATTTTTATCCTTAGTATGA 8 111 1 TATTTTTATC 0.809581 -190 TAATTGCTGGTTATTTTATCTTCCCCGAGG 9 31 1 TTATTTTATC 0.938807 -93 ACCGCCTATTTTATTTAACCTAAATTTTGT 9 103 1 TTATTTAACC 0.737065 -21 AAAATCAACATAATTGTATCGTTTATTGAT 10 172 1 TAATTGTATC 0.694507 -129 TAATGGAACTTTATTTAATTAAGAGCATCT 10 239 1 TTATTTAATT 0.779657 -62 TTAAATCCTCTTAATTAATCCCCTATATGG 10 279 0 TTAATTAATC 0.654141 -22 TCGTCCAGTTTTATTTTATTCTATGCGTTA 11 19 1 TTATTTTATT 0.753351 -44 TATGCGTTAATTTTTTTATCATTCGGAAGA 11 40 1 TTTTTTTATC 0.831235 -23 AATAAATGGGTAATTTAATTACCCATTTTT 12 17 1 TAATTTAATT 0.75335 -30 TCAAAACGTTTAATTAAATCAAGATCAATA 13 117 1 TAATTAAATC 0.639878 -43 ATCCTTAACGTAATTTAATCTCAACAAGCG 15 17 1 TAATTTAATC 0.938806 -202 ********** Masking position 5 Map Score: 7.215 Number of sites scoring better than the average of aligned sites = 356 Number in coding regions = 242 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 8 CGATTATATTCTATCCAAAAGGGGGT 1 7 1 TATTCTATCC 0.701899 -86 TAGAATAAATTATACTGTGCCATTTTTCAG 3 52 1 TATACTGTGC 0.801944 -124 ACTGTGCCATTTTTCAGTTCATCGAGACAC 3 65 1 TTTTCAGTTC 0.546018 -111 ATTCACATAGTTATCTATGCTCATGGGAGT 6 65 0 TTATCTATGC 0.925732 -53 TGATATCATATTTTCAATGCTCTTTGAGCA 8 211 0 TTTTCAATGC 0.925732 -90 CTTGAGATCATTTTCAATTCAAACTAGACT 9 72 1 TTTTCAATTC 0.65757 -52 AGTTTTATTTTATTCTATGCGTTAATTTTT 11 25 1 TATTCTATGC 0.947872 -38 GATTTTTTGTTATATTATGCCGCTTGTTGA 15 37 0 TATATTATGC 0.67587 -182 AAATAAAGGCTTTTTTGTGCCATATCATCA 15 67 0 TTTTTTGTGC 0.876276 -152 TATTTATTACTTTTCTTTGCTTTTTTGATT 15 101 1 TTTTCTTTGC 0.846786 -118 GATAAAAAGGTTATTTATGCTGACAAATCA 15 130 0 TTATTTATGC 0.800812 -89 TTGTACTCTTTTAATTATGCTCAAAAATCT 15 188 0 TTAATTATGC 0.588371 -31 ********** Masking position 8 Map Score: 4.96565 Number of sites scoring better than the average of aligned sites = 734 Number in coding regions = 583 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 190 Fraction of orfs with sites within 600 bp upstream = 0.0305172 Motif number 9 TAATTTATTCTACAGGTTATATTGGAAGCA 3 34 0 TACAGGTTAT 0.908484 -142 CAGTTTGCTATAAAGGTGTTGCCCGAACTC 7 62 0 TAAAGGTGTT 0.851468 -215 TGTTAAAAAATACAGGCTTTGTGATATCAT 8 232 0 TACAGGCTTT 0.964968 -69 TGTATTTTTTAACAGGCTTTTTTGTTTAAA 8 248 1 AACAGGCTTT 0.922521 -53 TTGATTTAATTAAACGTTTTGACCTAGGCT 13 109 0 TAAACGTTTT 0.738577 -51 ATATTCAAAATAAAGGCTTTTTTGTGCCAT 15 74 0 TAAAGGCTTT 0.957956 -145 AAGAGAGATAAAAAGGTTATTTATGCTGAC 15 136 0 AAAAGGTTAT 0.780141 -83 ********** Masking position 4 Map Score: 1.76115 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 179 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 10 TTCCGCGGCGCTGGTTTAAAACGT 2 5 1 GCGGCGCTGG 0.845047 -51 TTTTATGAGTTCGGGCAACACCTTTATAGC 7 56 1 TCGGGCAACA 0.427121 -221 CCACTTTATATCGGGCCTGAAATCAGACTC 7 97 0 TCGGGCCTGA 0.929119 -180 GCGTTCCAGCGCGGGCCAGGCTCTTACGGT 7 134 1 GCGGGCCAGG 0.982899 -143 GGCTCTTACGGTGCGGCAGAATTTCCAGTA 7 152 1 GTGCGGCAGA 0.939913 -125 TTGGTCACCTGCGCAGCAGGGGGCATCCGC 7 232 1 GCGCAGCAGG 0.708533 -45 AAATCTCCCCTCGGGGAAGATAAAATAACC 9 39 0 TCGGGGAAGA 0.887683 -85 ACAGCAAAATGTGGGCGTGAAATTGGGGTA 10 133 1 GTGGGCGTGA 0.853426 -168 GATAAACAAGGTGGGGCAGATCCCACCTTT 10 199 1 GTGGGGCAGA 0.975703 -102 TGTTACCCCGTTGGGAGTGGATGTAGCTTT 13 55 0 TTGGGAGTGG 0.491722 -105 TCCGCTATAATTGCGACAGATTTTTGAGCA 15 171 1 TTGCGACAGA 0.691699 -48 ********** Masking position 3 Map Score: 0.501966 Number of sites scoring better than the average of aligned sites = 3046 Number in coding regions = 2866 Number in noncoding regions = 180 Number of orfs with sites within 600 bp upstream = 166 Fraction of orfs with sites within 600 bp upstream = 0.0266624 Motif number 11 TCATCCTTCGCTGGATATCTATCCAGCATT 3 109 1 CTGGATATCT 0.924849 -67 ACAGGCAGGGCTATCTGGAGATATTT 5 7 1 AGGGCTATCT 0.984659 -22 AGCTAAGTTAAGGGATATCTC 7 266 1 AGGGATATCT 0.96595 -11 TTGCCGCTGTCGGGCTATTTCGTAGATCCT 8 152 0 CGGGCTATTT 0.965191 -149 CGGCAACTGGCGGACTATCTTAGTAGATCC 8 176 1 CGGACTATCT 0.965191 -125 ********** Masking position 6 Map Score: 1.84963 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 210 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 12 ********** No masking Map Score: -7.17405e-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 13 TCGATGAACTGAAAAATGGCACAGTATAAT 3 60 0 GAAAAATGGC 0.944661 -116 GAAGGATGAAGAAAACTTGCGAGGTGTCTC 3 88 0 GAAAACTTGC 0.844896 -88 CTGCTAAACAGCAAAACGGAGACGCGTG 4 17 1 GCAAAACGGA 0.748202 -18 CACCTTTATAGCAAACTGGCGTAGAGTCTG 7 74 1 GCAAACTGGC 0.978102 -203 ACAACTGAATGAAAAAAGGCGGCTATTATA 7 180 0 GAAAAAAGGC 0.753667 -97 GCCTGTTATTGAAAAGTAGCACTGGCTATT 8 49 0 GAAAAGTAGC 0.878104 -252 TCAATAACAGGCAAAGTAGAATAATGATGA 8 67 1 GCAAAGTAGA 0.82514 -234 CATTTTCAATTCAAACTAGACTTACCGCCT 9 80 1 TCAAACTAGA 0.640072 -44 TAGAATAAAATAAAACTGGACGAACATCCA 11 12 0 TAAAACTGGA 0.779447 -51 ********** Masking position 5 Map Score: 0.733755 Number of sites scoring better than the average of aligned sites = 1471 Number in coding regions = 1361 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 14 ********** No masking Map Score: -7.17405e-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 15 ********** No masking Map Score: -7.17405e-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