AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i207_holliday_junction_hinf_reg_300.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HI0244 300 tRNA-guanine transglycosylase (tgt) #2 HI0245 123 queuosine biosynthesis protein (queA) #3 HI0246 300 H. influenzae predicted coding region HI0246 #4 HI0313 62 Holliday junction DNA helicase (ruvA) #5 HI0314 46 crossover junction endodeoxyribonuclease (ruvC) #6 HI0315 159 conserved hypothetical protein #7 HI0316 21 datP pyrophosphohydrolase (ntpA) #8 HI0317 218 aspartyl-tRNA synthetase (aspS) Motif number 1 CCGCTGTCGGGCTATTTCGTAGATCCTGAG 1 149 0 GCTATTTCGT 0.81597 -152 TTTTTAACAGGCTTTTTTGTTTAAAAAATC 1 253 1 GCTTTTTTGT 0.986422 -48 ACAGTTCGAAGATTTTTTAAACAAAAAAGC 1 263 0 GATTTTTTAA 0.816722 -38 ATAATTGCTGGTTATTTTATCTTCCCCGAG 2 30 1 GTTATTTTAT 0.682461 -94 CCCGAGGGGAGATTTTTTCTTGAGATCATT 2 54 1 GATTTTTTCT 0.859546 -70 AGACTTACCGCCTATTTTATTTAACCTAAA 2 97 1 CCTATTTTAT 0.907803 -27 ATCTGCCCCACCTTGTTTATCAATAAACGA 3 190 0 CCTTGTTTAT 0.826219 -111 GCAGATCCCACCTTTTTTATTTCAATAATG 3 214 1 CCTTTTTTAT 0.965151 -87 TTTAATTACCCATTTTTTATAGAAATT 5 30 1 CATTTTTTAT 0.910515 -17 CATATCATCAGATTTTTTGTTATATTATGC 8 47 0 GATTTTTTGT 0.963886 -172 CAAAATAAAGGCTTTTTTGTGCCATATCAT 8 69 0 GCTTTTTTGT 0.986422 -150 ACTTTTCTTTGCTTTTTTGATTGATTTGTC 8 109 1 GCTTTTTTGA 0.942119 -110 ********** Masking position 6 Map Score: 12.9389 Number of sites scoring better than the average of aligned sites = 436 Number in coding regions = 304 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 2 GGCAAAGTAGAATAATGATGACCAACTTAAT 1 76 1 AATAATGTGA 0.929127 -225 ATATGACTAAATTTATGATTAAGTTGGTCAT 1 93 0 ATTTATGTTA 0.749907 -208 AATAACCAGCAATTATGCTGGTCATTTGGGA 2 15 0 AATTATGTGG 0.945484 -109 TAAACGATACAATTATGTTGATTTTTACCAA 3 166 0 AATTATGTGA 0.988118 -135 AACTTTATTTAATTAAGAGCATCTAAGTAGC 3 245 1 AATTAAGGCA 0.892982 -56 ATAGGGGATTAATTAAGAGGATTTAATA 3 283 1 AATTAAGGGA 0.941831 -18 AATCACAGCTAATTATGGTGATAGCGGTTCT 6 15 1 AATTATGTGA 0.988118 -145 CGTTTAATTAAATCAAGATCAATAAGATCAA 6 123 1 AATCAAGTCA 0.819301 -37 TAAAAAGGTTATTTATGCTGACAAATCAATC 8 127 0 ATTTATGTGA 0.958536 -92 GTACTCTTTTAATTATGCTCAAAAATCTGTC 8 185 0 AATTATGTCA 0.977199 -34 ******* *** Masking position 5 Map Score: 10.8939 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 109 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 3 ATTCTACTTTGCCTGTTATTGAAAAGTAGC 1 59 0 GCCTGTTATT 0.813027 -242 ATATCACAAAGCCTGTATTTTTTAACAGGC 1 235 1 GCCTGTATTT 0.954768 -66 TAAAATTTCTGCCTTTAATCCCACTTCTTT 3 50 0 GCCTTTAATC 0.900513 -251 CCAACTTTCTGCTTTTATTTCTAAATCTCA 3 85 1 GCTTTTATTT 0.934871 -216 CAAAATGTGGGCGTGAAATTGGGGTATCGT 3 137 1 GCGTGAAATT 0.867378 -164 CTACTTAGATGCTCTTAATTAAATAAAGTT 3 245 0 GCTCTTAATT 0.814217 -56 TTTATTCTATGCGTTAATTTTTTTATCATT 4 33 1 GCGTTAATTT 0.862528 -30 CTAGGTCAAAACGTTTAATTAAATCAAGAT 6 112 1 ACGTTTAATT 0.764123 -48 GCACAAAAAAGCCTTTATTTTGAATATTTA 8 77 1 GCCTTTATTT 0.96737 -142 TCCTTTGTACTCTTTTAATTATGCTCAAAA 8 192 0 TCTTTTAATT 0.673224 -27 ********** Masking position 9 Map Score: 5.05807 Number of sites scoring better than the average of aligned sites = 373 Number in coding regions = 310 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 4 CAAGAGATGGTTACCGCCATCTC 1 4 0 TTACCGCCAT 0.94969 -297 AGTCCGCCAGTTGCCGCTGTCGGGCTATTT 1 162 0 TTGCCGCTGT 0.915952 -139 CAAACTAGACTTACCGCCTATTTTATTTAA 2 91 1 TTACCGCCTA 0.893703 -33 AAATGTAAAATTTCTGCCTTTAATCCCACT 3 55 0 TTTCTGCCTT 0.865599 -246 CATTTCCAACTTTCTGCTTTTATTTCTAAA 3 80 1 TTTCTGCTTT 0.867912 -221 ATTTTGCTGTTTGCCGAGTTGCGAACCTTG 3 113 0 TTGCCGAGTT 0.88624 -188 GGTAATTAAATTACCCATTTATTGCATCA 5 10 0 TTACCCATTT 0.884169 -37 GGTAATTTAATTACCCATTTTTTATAGAAA 5 25 1 TTACCCATTT 0.884169 -22 AGTAAAAGTGTTACCCCGTTGGGAGTGGAT 6 63 0 TTACCCCGTT 0.947929 -97 CTCTCTTGGTTTTCCGCTATAATTGCGACA 8 159 1 TTTCCGCTAT 0.923141 -60 ********** Masking position 2 Map Score: 5.46364 Number of sites scoring better than the average of aligned sites = 540 Number in coding regions = 464 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 5 TTAATCCCAAATGACCAGCATAAT 2 5 1 TCCCAAATGA 0.991575 -119 TGCCAATAACGCCCAAATGATTGTTGCAAC 3 19 0 GCCCAAATGA 0.985739 -282 AATTCTTCCGAATGATAAAAAAATT 4 48 0 TTCCGAATGA 0.945648 -15 ATGTAGCTTTTCCCAAAAGAGAACCGCTAT 6 35 0 TCCCAAAAGA 0.978998 -125 ********** Masking position 6 Map Score: 1.87995 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 16 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 CTCTGCTCAAAGAGCATTGAAAATATGATA 1 208 1 AGAGCATTGA 0.891439 -93 ATGATATCACAAAGCCTGTATTTTTTAACA 1 232 1 AAAGCCTGTA 0.935326 -69 TTTAAACAAAAAAGCCTGTTAAAAAATACA 1 248 0 AAAGCCTGTT 0.883531 -53 TTTTTTCTTGAGATCATTTTCAATTCAAAC 2 66 1 AGATCATTTT 0.643791 -58 TATTTAATTAAGAGCATCTAAGTAGCACCC 3 250 1 AGAGCATCTA 0.927801 -51 GGATTAATTAAGAGGATTTAATA 3 288 1 AGAGGATTTA 0.947676 -13 CCCCGTTGGGAGTGGATGTAGCTTTTCCCA 6 50 0 AGTGGATGTA 0.736743 -110 ATGGCACAAAAAAGCCTTTATTTTGAATAT 8 74 1 AAAGCCTTTA 0.936522 -145 AAAAGAGTACAAAGGATTTTGAA 8 206 1 AAAGGATTTT 0.82849 -13 ********** Masking position 7 Map Score: 2.01101 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 220 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 7 GTCATATTTTTATCCTTAGTATGATTAACA 1 117 1 TATCCTTAGT 0.933178 -184 GAAATTGGGGTATCGTTGGTAAAAATCAAC 3 151 1 TATCGTTGGT 0.953913 -150 AGGCTAGGTATAGCCTAGGTTAGTAAAAGT 6 84 0 TAGCCTAGGT 0.988483 -76 AGGCTATACCTAGCCTAGGTCAAAACGTTT 6 98 1 TAGCCTAGGT 0.988483 -62 ********** Masking position 6 Map Score: 0.686359 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 5 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 8 ********** No masking Map Score: 1.97064e-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: 1.97064e-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 TAGATCCTGAGTTTGTTAATCATACTAAGGA 1 129 0 GTTTTTAATC 0.715625 -172 TATTTTCAATGCTCTTTGAGCAGAGGCGGAT 1 202 0 GCTCTTGAGC 0.923734 -99 AAAAATACAGGCTTTGTGATATCATATTTTC 1 226 0 GCTTGTGATA 0.886189 -75 AGGGGAGATTTTTTCTTGAGATCATTTTCAA 2 58 1 TTTTTTGAGA 0.837549 -66 TAATTGTATCGTTTATTGATAAACAAGGTGG 3 182 1 GTTTTTGATA 0.934095 -119 TCTGTTTTGATCTTATTGATCTTGATTTAAT 6 129 0 TCTTTTGATC 0.904138 -31 ATATTATGCCGCTTGTTGAGATTAAATTACG 8 25 0 GCTTTTGAGA 0.9782 -194 AATTGCGACAGATTTTTGAGCATAATTAAAA 8 179 1 GATTTTGAGC 0.931971 -40 **** ****** Masking position 9 Map Score: 2.05465 Number of sites scoring better than the average of aligned sites = 315 Number in coding regions = 266 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 11 ********** No masking Map Score: 1.97064e-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 12 ********** No masking Map Score: 1.97064e-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 ********** No masking Map Score: 1.97064e-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