AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i224_Holliday_Junction_enzyme_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 0.854427 -78 TCAGACTAAAATAAGAGGCGGGTAGTCTAGTGCC 1 60 0 AAAAGGGGTA 0.981709 -33 TGTATGATAAAAAAATGCTGGATAGATATCCAGC 3 118 0 AAATGCGGTA 0.880284 -58 TTCAGGCCCGATATAAAGTGGTAACGAGGCGTTC 7 106 1 AATAAGGGAA 0.753838 -171 CAACTGAATGAAAAAAGGCGGCTATTATACTGGA 7 175 0 AAAAGGGGTA 0.981709 -102 GTTGATGCCGACAAGAGATGGTTACCGCCATCTC 8 11 0 AAAAGAGGTA 0.955212 -290 GTGCTACTTTTCAATAACAGGCAAAGTAGAATAA 8 57 1 TAAAACGGAA 0.688652 -244 AAGCCTGTTAAAAAATACAGGCTTTGTGATATCA 8 233 0 AAATACGGTT 0.525381 -68 TTTTTTAAACAAAAAAGCCTGTTAAAAAATACAG 8 247 0 AAAAGCTGTA 0.613687 -54 AATGACCAGCATAATTGCTGGTTATTTTATCTTC 9 20 1 AAATGCGGTA 0.880282 -104 TAGGTTAAATAAAATAGGCGGTAAGTCTAGTTTG 9 91 0 AAAAGGGGAA 0.977406 -33 GTTATTGGCAAAAAGAAGTGGGATTAAAGGCAGA 10 39 1 AAAAAGGGAT 0.866885 -262 TTATTGAAATAAAAAAGGTGGGATCTGCCCCACC 10 208 0 AAAAGGGGAT 0.92872 -93 TGATGCAATAAATGGGTAATTTAATTAC 12 5 1 GAAAAAGGTA 0.591228 -42 AATTTCTATAAAAAATGGGTAATTAAATTAC 12 26 0 AAAAAAGGTA 0.914237 -21 CAATAAGATCAAAACAGAAGGAAATAAA 13 142 1 AAAAGAGGAA 0.945025 -18 TAATTTAATCTCAACAAGCGGCATAATATAACAA 15 27 1 TAAAAGGGAT 0.512494 -192 AAACCAAGAGAGATAAAAAGGTTATTTATGCTGA 15 137 0 AATAAAGGTA 0.60156 -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 GCAGGGAGAGCGCCCCGGCACTAGACTACCCGCC 1 44 1 CGCCCCACAG 0.948779 -49 TTCCGCGGCGCTGGTTTAAAACGT 2 1 1 TTCCCCGCGG 0.909385 -55 TTTTTCTCCACTACGTCAGAAAAACAGTC 2 37 0 CTCCCCGTAG 0.90716 -19 CAGTTCATCGAGACACCTCGCAAGTTTTCTTCAT 3 79 1 AGACCCGCAG 0.932374 -97 CAAGTTTTCTTCATCCTTCGCTGGATATCTATCC 3 99 1 TCATCCGCGG 0.709386 -77 ATGACGCTCCTGCGTAATGAATCAAAGA 3 158 0 CGCTCCGTAT 0.729838 -18 GTTGCCGCCTCGATGCAACGCGAATGATTTCGTG 6 24 0 CGATCCGCAA 0.818708 -94 GCTGCCTCTTCGTTGACTGCCTTCGC 6 102 0 TGCCCCGTGA 0.875166 -16 CAAAATTTGTCGTTCCGCCATCGGCTAATCGCAT 7 17 0 CGTTCCATGG 0.641483 -260 GCCTGAAATCAGACTCTACGCCAGTTTGCTATAA 7 79 0 AGACCCGCAG 0.932374 -198 GGTAACGAGGCGTTCCAGCGCGGGCCAGGCTCTT 7 125 1 CGTTCCGCGG 0.971584 -152 CTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCC 7 146 0 TGCCCCGTAG 0.970957 -131 CAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCA 7 209 0 AGTCCCGTAG 0.870493 -68 GGCGGATGCCCCCTGCTGCGCAGGTGACCAAGTC 7 229 0 CCCTCCGCGG 0.950112 -48 TTAGTAGATCCGCCTCTGCTCAAAGAGCATTGAA 8 195 1 CGCCCCTCAA 0.636125 -106 TTAGTAAAAGTGTTACCCCGTTGGGAGTGGATGT 13 61 0 TGTTCCGTGG 0.868835 -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 3 CCGGCACTAGACTACCCGCCTCTTATTTTAGT 1 58 1 ATACCGCCTC 0.948442 -35 GAGTTCACTCAGTTGCCGCCTCGATGCAACGC 6 37 0 ATTCCGCCTC 0.983112 -81 CTGCCTCTTCGTTGACTGCCTTCGCTCATCCC 6 95 0 GTGCTGCCTT 0.864032 -23 TTTCCAGTATAATAGCCGCCTTTTTTCATTCA 7 173 1 ATACCGCCTT 0.974116 -104 GACAAGAGATGGTTACCGCCATCTC 8 4 0 GTTCCGCCAT 0.964023 -297 ATAGTCCGCCAGTTGCCGCTGTCGGGCTATTT 8 162 0 ATTCCGCTGT 0.899245 -139 TTCAAACTAGACTTACCGCCTATTTTATTTAA 9 89 1 ATTCCGCCTA 0.955241 -35 GGAAATGTAAAATTTCTGCCTTTAATCCCACT 10 55 0 ATTCTGCCTT 0.9711 -246 TACATTTCCAACTTTCTGCTTTTATTTCTAAA 10 78 1 ATTCTGCTTT 0.904591 -223 ATCTCTCTTGGTTTTCCGCTATAATTGCGACA 15 157 1 GTTCCGCTAT 0.883184 -62 * ** ******* Masking position 3 Map Score: 7.87561 Number of sites scoring better than the average of aligned sites = 669 Number in coding regions = 606 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 4 GCTGGATAGATATCCAGCGAAGGATGAAGA 3 106 0 TATCCAGCGA 0.84338 -70 GCTGGATATCTATCCAGCATTTTTTTATCA 3 118 1 TATCCAGCAT 0.942713 -58 ATTTTTTTATCATACAGCATTATCTTTGAT 3 136 1 CATACAGCAT 0.942713 -40 TGAGGCCTGCTAAACAGCAAAACGGAGACG 4 11 1 TAAACAGCAA 0.950983 -24 TCAGTTGTGACATACAGCTAACGCTGCGAC 7 202 1 CATACAGCTA 0.784168 -75 CGCCTCTGCTCAAAGAGCATTGAAAATATG 8 205 1 CAAAGAGCAT 0.746565 -96 TAATCCCAAATGACCAGCATAATTGCTGGT 9 12 1 TGACCAGCAT 0.825689 -112 GAAGATAAAATAACCAGCAATTATGCTGGT 9 24 0 TAACCAGCAA 0.961506 -100 CGCAACTCGGCAAACAGCAAAATGTGGGCG 10 120 1 CAAACAGCAA 0.961506 -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 5 ACCCCCTTTTGGATAGAATATAATCG 1 7 0 GGATAGAATA 0.758727 -86 CTGAAAAATGGCACAGTATAATTTATTCTA 3 52 0 GCACAGTATA 0.843141 -124 ACTCCCATGAGCATAGATAACTATGTGAAT 6 65 1 GCATAGATAA 0.941518 -53 TGCTCAAAGAGCATTGAAAATATGATATCA 8 211 1 GCATTGAAAA 0.833413 -90 AAAAATTAACGCATAGAATAAAATAAAACT 11 25 0 GCATAGAATA 0.960452 -38 TCAACAAGCGGCATAATATAACAAAAAATC 15 37 1 GCATAATATA 0.82434 -182 TGATGATATGGCACAAAAAAGCCTTTATTT 15 67 1 GCACAAAAAA 0.881189 -152 AATCAAAAAAGCAAAGAAAAGTAATAAATA 15 101 0 GCAAAGAAAA 0.864345 -118 TGATTTGTCAGCATAAATAACCTTTTTATC 15 130 1 GCATAAATAA 0.872943 -89 AGATTTTTGAGCATAATTAAAAGAGTACAA 15 188 1 GCATAATTAA 0.756749 -31 ********** Masking position 3 Map Score: 5.28101 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 186 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 6 TATATTGGAAGCAAATATTTTAATATTACAT 3 16 0 GAAATATTTT 0.873129 -160 AGGGCTATCTGGAGATATTTTT 5 17 1 GAGATATTTT 0.954543 -12 GACAAATTTTGTTAATTTTTATGAGTTCGGG 7 40 1 GTAATTTTTA 0.685013 -237 TAAACAGTTCGAAGATTTTTTAAACAAAAAA 8 265 0 GAGATTTTTT 0.975562 -36 TTCCCCGAGGGGAGATTTTTTCTTGAGATCA 9 51 1 GAGATTTTTT 0.975626 -73 GGGATTAAAGGCAGAAATTTTACATTTCCAA 10 58 1 GAGAAATTTT 0.767996 -243 ATACAATTATGTTGATTTTTACCAACGATAC 10 160 0 GTGATTTTTA 0.869037 -141 TATTCTATGCGTTAATTTTTTTATCATTCGG 11 35 1 GTAATTTTTT 0.873129 -28 TGCCATATCATCAGATTTTTTGTTATATTAT 15 49 0 TAGATTTTTT 0.796917 -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 7 ATAACCTGTAGAATAAATTATACTGTGCCA 3 44 1 GAATAAATTA 0.609611 -132 AATGCTGTATGATAAAAAAATGCTGGATAG 3 127 0 GATAAAAAAA 0.824899 -49 TCATACTAAGGATAAAAATATGACTAAATT 8 111 0 GATAAAAATA 0.802626 -190 CCTCGGGGAAGATAAAATAACCAGCAATTA 9 31 0 GATAAAATAA 0.936199 -93 ACAAAATTTAGGTTAAATAAAATAGGCGGT 9 103 0 GGTTAAATAA 0.728349 -21 ATCAATAAACGATACAATTATGTTGATTTT 10 172 0 GATACAATTA 0.684984 -129 AGATGCTCTTAATTAAATAAAGTTCCATTA 10 239 0 AATTAAATAA 0.771917 -62 CCATATAGGGGATTAATTAAGAGGATTTAA 10 279 1 GATTAATTAA 0.644004 -22 TAACGCATAGAATAAAATAAAACTGGACGA 11 19 0 AATAAAATAA 0.744988 -44 TCTTCCGAATGATAAAAAAATTAACGCATA 11 40 0 GATAAAAAAA 0.824899 -23 AAAAATGGGTAATTAAATTACCCATTTATT 12 17 0 AATTAAATTA 0.744988 -30 TATTGATCTTGATTTAATTAAACGTTTTGA 13 117 0 GATTTAATTA 0.629562 -43 CGCTTGTTGAGATTAAATTACGTTAAGGAT 15 17 0 GATTAAATTA 0.936199 -202 ********** Masking position 6 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 GCCAGTTTGCTATAAAGGTGTTGCCCGAACTC 7 62 0 TAAAGGTGTT 0.866925 -215 TATAAAGTGGTAACGAGGCGTTCCAGCGCGGG 7 117 1 TACAGGCGTT 0.92451 -160 CCTGTTAAAAAATACAGGCTTTGTGATATCAT 8 232 0 AAAAGGCTTT 0.964689 -69 CCTGTATTTTTTAACAGGCTTTTTTGTTTAAA 8 246 1 TTAAGGCTTT 0.91749 -55 TAGGTTAAATAAAATAGGCGGTAAGTCTAGTT 9 93 0 AAAAGGCGGT 0.837853 -31 AGGGGATTAATTAAGAGGATTTAATA 10 285 1 TTAAGGATTT 0.717786 -16 CACTTTTACTAACCTAGGCTATACCTAGCCTA 13 83 1 AACAGGCTAT 0.787805 -77 AAATATTCAAAATAAAGGCTTTTTTGTGCCAT 15 74 0 AAAAGGCTTT 0.964694 -145 CCAAGAGAGATAAAAAGGTTATTTATGCTGAC 15 136 0 TAAAGGTTAT 0.743019 -83 ATTAAAAGAGTACAAAGGATTTTGAA 15 203 1 TAAAGGATTT 0.901474 -16 ** * ******* Masking position 6 Map Score: 2.71452 Number of sites scoring better than the average of aligned sites = 341 Number in coding regions = 296 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 9 AAAAGGGGGTAAAGGTTGCAGGGAGAGCGC 1 27 1 AAAGGTTGCA 0.597789 -66 GACTAAAATAAGAGGCGGGTAGTCTAGTGC 1 61 0 AGAGGCGGGT 0.97022 -32 AGAAAACTTGCGAGGTGTCTCGATGAACTG 3 79 0 CGAGGTGTCT 0.689883 -97 CGCGTTGCATCGAGGCGGCAACTGAGTGAA 6 36 1 CGAGGCGGCA 0.985056 -82 AGGCAGTCAACGAAGAGGCAGC 6 106 1 CGAAGAGGCA 0.716397 -12 CTGAATGAAAAAAGGCGGCTATTATACTGG 7 176 0 AAAGGCGGCT 0.953587 -101 CTCTTTGAGCAGAGGCGGATCTACTAAGAT 8 192 0 AGAGGCGGAT 0.861971 -109 ATTGGCAAAAAGAAGTGGGATTAAAGGCAG 10 42 1 AGAAGTGGGA 0.88111 -259 TATTGATAAACAAGGTGGGGCAGATCCCAC 10 195 1 CAAGGTGGGG 0.786058 -106 TTGAAATAAAAAAGGTGGGATCTGCCCCAC 10 209 0 AAAGGTGGGA 0.927369 -92 TTTAATCTCAACAAGCGGCATAATATAACA 15 30 1 ACAAGCGGCA 0.770459 -189 ********** Masking position 3 Map Score: 3.86358 Number of sites scoring better than the average of aligned sites = 1500 Number in coding regions = 1338 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 10 TTCTATCCAAAAGGGGGTAAAGGTTGCAGG 1 19 1 AAGGGGGTAA 0.986081 -74 GGCCCGATATAAAGTGGTAACGAGGCGTTC 7 110 1 AAAGTGGTAA 0.930596 -167 GAGATGGCGGTAACCATCTCTTG 8 4 1 ATGGCGGTAA 0.853745 -297 ATTTATGATTAAGTTGGTCATCATTATTCT 8 84 0 AAGTTGGTCA 0.80312 -217 TTAAATAAAATAGGCGGTAAGTCTAGTTTG 9 91 0 TAGGCGGTAA 0.853745 -33 TAAAAGCAGAAAGTTGGAAATGTAAAATTT 10 72 0 AAGTTGGAAA 0.733496 -229 TGATGCAATAAATGGGTAATTTAATTACC 12 10 1 AAATGGGTAA 0.933754 -37 TTTCTATAAAAAATGGGTAATTAAATTACC 12 25 0 AAATGGGTAA 0.933754 -22 ATCCACTCCCAACGGGGTAACACTTTTACT 13 63 1 AACGGGGTAA 0.942009 -97 ********** Masking position 10 Map Score: 5.1872 Number of sites scoring better than the average of aligned sites = 274 Number in coding regions = 237 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 11 TCATCCTTCGCTGGATATCTATCCAGCATT 3 109 1 CTGGATATCT 0.919475 -67 ACAGGCAGGGCTATCTGGAGATATTT 5 7 1 AGGGCTATCT 0.983487 -22 AGCTAAGTTAAGGGATATCTC 7 266 1 AGGGATATCT 0.963422 -11 TTGCCGCTGTCGGGCTATTTCGTAGATCCT 8 152 0 CGGGCTATTT 0.962585 -149 CGGCAACTGGCGGACTATCTTAGTAGATCC 8 176 1 CGGACTATCT 0.962585 -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 TCTATCCAAAAGGGGGTAAAGGTTGCAGGGAGAGC 1 20 1 AGGGTAGTTG 0.767238 -73 CATCCTTCGCTGGATATCTATCCAGCATTTTTTTA 3 110 1 TGGATACCAG 0.744538 -66 TCTATGCTCATGGGAGTTCACTCAGTTGCCGCCTC 6 47 0 TGGGTATCAG 0.98785 -71 CACTTTATATCGGGCCTGAAATCAGACTCTACGCC 7 91 0 CGGGTATCAG 0.961539 -186 CAAAAAGAAGTGGGATTAAAGGCAGAAATTTTACA 10 47 1 TGGGTAGCAG 0.987604 -254 CAGCAAAATGTGGGCGTGAAATTGGGGTATCGTTG 10 134 1 TGGGTATTGG 0.931577 -167 ATCCCCTATATGGGGTGCTACTTAGATGCTCTTAA 10 257 0 TGGGGATTAG 0.922938 -44 CACCCCATATAGGGGATTAATTAAGAGGATTTAAT 10 275 1 AGGGTATAAG 0.850828 -26 GTTACCCCGTTGGGAGTGGATGTAGCTTTTCCCAA 13 49 0 TGGGTAGTAG 0.980485 -111 **** * * **** Masking position 10 Map Score: 1.64777 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 114 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 13 TCGATGAACTGAAAAATGGCACAGTATAAT 3 60 0 GAAAAATGGC 0.947159 -116 GAAGGATGAAGAAAACTTGCGAGGTGTCTC 3 88 0 GAAAACTTGC 0.851173 -88 CTGCTAAACAGCAAAACGGAGACGCGTG 4 17 1 GCAAAACGGA 0.757292 -18 CACCTTTATAGCAAACTGGCGTAGAGTCTG 7 74 1 GCAAACTGGC 0.97909 -203 ACAACTGAATGAAAAAAGGCGGCTATTATA 7 180 0 GAAAAAAGGC 0.762623 -97 GCCTGTTATTGAAAAGTAGCACTGGCTATT 8 49 0 GAAAAGTAGC 0.883235 -252 TCAATAACAGGCAAAGTAGAATAATGATGA 8 67 1 GCAAAGTAGA 0.832071 -234 CATTTTCAATTCAAACTAGACTTACCGCCT 9 80 1 TCAAACTAGA 0.651244 -44 TAGAATAAAATAAAACTGGACGAACATCCA 11 12 0 TAAAACTGGA 0.787729 -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 AACCTTTACCCCCTTTTGGATAGAATATAA 1 14 0 CCCTTTTGGA 0.869804 -79 CTTTTTTCATTCAGTTGTGACATACAGCTA 7 192 1 TCAGTTGTGA 0.917362 -85 ATTATGCTGGTCATTTGGGATTAA 9 5 0 TCATTTGGGA 0.971149 -119 GTTGCAACAATCATTTGGGCGTTATTGGCA 10 19 1 TCATTTGGGC 0.91208 -282 ATAGCGGTTCTCTTTTGGGAAAAGCTACAT 13 35 1 TCTTTTGGGA 0.959227 -125 AAAGTGTTACCCCGTTGGGAGTGGATGTAG 13 59 0 CCCGTTGGGA 0.967286 -101 TTTATTTCCTTCTGTTTTGATCTTATTGAT 13 140 0 TCTGTTTTGA 0.678919 -20 ********** Masking position 5 Map Score: 1.34107 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 117 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 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