AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i224_Holliday_Junction_enzyme_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 0.809314 -152 TTTTTAACAGGCTTTTTTGTTTAAAAAATC 1 253 1 GCTTTTTTGT 0.985823 -48 ACAGTTCGAAGATTTTTTAAACAAAAAAGC 1 263 0 GATTTTTTAA 0.810087 -38 ATAATTGCTGGTTATTTTATCTTCCCCGAG 2 30 1 GTTATTTTAT 0.672913 -94 CCCGAGGGGAGATTTTTTCTTGAGATCATT 2 54 1 GATTTTTTCT 0.854185 -70 AGACTTACCGCCTATTTTATTTAACCTAAA 2 97 1 CCTATTTTAT 0.904079 -27 ATCTGCCCCACCTTGTTTATCAATAAACGA 3 190 0 CCTTGTTTAT 0.819852 -111 GCAGATCCCACCTTTTTTATTTCAATAATG 3 214 1 CCTTTTTTAT 0.96365 -87 TTTAATTACCCATTTTTTATAGAAATT 5 30 1 CATTTTTTAT 0.906889 -17 CATATCATCAGATTTTTTGTTATATTATGC 8 47 0 GATTTTTTGT 0.962333 -172 CAAAATAAAGGCTTTTTTGTGCCATATCAT 8 69 0 GCTTTTTTGT 0.985823 -150 ACTTTTCTTTGCTTTTTTGATTGATTTGTC 8 109 1 GCTTTTTTGA 0.939688 -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 ATTAAGTTGGTCATCATTATTCTACTTTGCC 1 76 0 TCACATTATT 0.923584 -225 ATGACCAACTTAATCATAAATTTAGTCATAT 1 93 1 TAACATAAAT 0.734355 -208 TCCCAAATGACCAGCATAATTGCTGGTTATT 2 15 1 CCACATAATT 0.941139 -109 TTGGTAAAAATCAACATAATTGTATCGTTTA 3 166 1 TCACATAATT 0.987125 -135 GCTACTTAGATGCTCTTAATTAAATAAAGTT 3 245 0 TGCCTTAATT 0.884962 -56 TATTAAATCCTCTTAATTAATCCCCTAT 3 283 0 TCCCTTAATT 0.937215 -18 AGAACCGCTATCACCATAATTAGCTGTGATT 6 15 0 TCACATAATT 0.987125 -145 TTGATCTTATTGATCTTGATTTAATTAAACG 6 123 0 TGACTTGATT 0.806953 -37 GATTGATTTGTCAGCATAAATAACCTTTTTA 8 127 1 TCACATAAAT 0.955182 -92 GACAGATTTTTGAGCATAATTAAAAGAGTAC 8 185 1 TGACATAATT 0.975315 -34 *** ******* Masking position 7 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 GAGATGGCGGTAACCATCTCTTG 1 4 1 ATGGCGGTAA 0.953341 -297 AAATAGCCCGACAGCGGCAACTGGCGGACT 1 162 1 ACAGCGGCAA 0.921857 -139 TTAAATAAAATAGGCGGTAAGTCTAGTTTG 2 91 0 TAGGCGGTAA 0.900999 -33 AGTGGGATTAAAGGCAGAAATTTTACATTT 3 55 1 AAGGCAGAAA 0.874558 -246 TTTAGAAATAAAAGCAGAAAGTTGGAAATG 3 80 0 AAAGCAGAAA 0.876738 -221 CAAGGTTCGCAACTCGGCAAACAGCAAAAT 3 113 1 AACTCGGCAA 0.893992 -188 TGATGCAATAAATGGGTAATTTAATTACC 5 10 1 AAATGGGTAA 0.892044 -37 TTTCTATAAAAAATGGGTAATTAAATTACC 5 25 0 AAATGGGTAA 0.892044 -22 ATCCACTCCCAACGGGGTAACACTTTTACT 6 63 1 AACGGGGTAA 0.951706 -97 TGTCGCAATTATAGCGGAAAACCAAGAGAG 8 159 0 ATAGCGGAAA 0.92858 -60 ********** Masking position 9 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 4 ATTCTACTTTGCCTGTTATTGAAAAGTAGC 1 59 0 GCCTGTTATT 0.819704 -242 ATATCACAAAGCCTGTATTTTTTAACAGGC 1 235 1 GCCTGTATTT 0.956653 -66 TAAAATTTCTGCCTTTAATCCCACTTCTTT 3 50 0 GCCTTTAATC 0.904432 -251 CCAACTTTCTGCTTTTATTTCTAAATCTCA 3 85 1 GCTTTTATTT 0.937531 -216 CAAAATGTGGGCGTGAAATTGGGGTATCGT 3 137 1 GCGTGAAATT 0.872418 -164 CTACTTAGATGCTCTTAATTAAATAAAGTT 3 245 0 GCTCTTAATT 0.82086 -56 TTTATTCTATGCGTTAATTTTTTTATCATT 4 33 1 GCGTTAATTT 0.867724 -30 CTAGGTCAAAACGTTTAATTAAATCAAGAT 6 112 1 ACGTTTAATT 0.772056 -48 GCACAAAAAAGCCTTTATTTTGAATATTTA 8 77 1 GCCTTTATTT 0.968747 -142 TCCTTTGTACTCTTTTAATTATGCTCAAAA 8 192 0 TCTTTTAATT 0.682945 -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 5 TTAATCCCAAATGACCAGCATAAT 2 5 1 TCCCAAATGA 0.990702 -119 TGCCAATAACGCCCAAATGATTGTTGCAAC 3 19 0 GCCCAAATGA 0.984268 -282 AATTCTTCCGAATGATAAAAAAATT 4 48 0 TTCCGAATGA 0.940292 -15 ATGTAGCTTTTCCCAAAAGAGAACCGCTAT 6 35 0 TCCCAAAAGA 0.976851 -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 TCATCATTATTCTACTTTGCCTGTTATTGA 1 67 0 TCTACTTTGC 0.846938 -234 TGATATCATATTTTCAATGCTCTTTGAGCA 1 211 0 TTTTCAATGC 0.960438 -90 CTTGAGATCATTTTCAATTCAAACTAGACT 2 72 1 TTTTCAATTC 0.904666 -52 AGGCAGAAATTTTACATTTCCAACTTTCTG 3 66 1 TTTACATTTC 0.855393 -235 GATCCCACCTTTTTTATTTCAATAATGGAA 3 217 1 TTTTTATTTC 0.68459 -84 AGTTTTATTTTATTCTATGCGTTAATTTTT 4 25 1 TATTCTATGC 0.913503 -38 GATTTTTTGTTATATTATGCCGCTTGTTGA 8 37 0 TATATTATGC 0.600918 -182 TATTTATTACTTTTCTTTGCTTTTTTGATT 8 101 1 TTTTCTTTGC 0.960438 -118 ********** Masking position 3 Map Score: 1.54085 Number of sites scoring better than the average of aligned sites = 523 Number in coding regions = 445 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 7 TCAACTACTAATAGCCAGTGCTACTTTTCA 1 40 1 ATAGCCAGTG 0.802732 -261 ATGATATCACAAAGCCTGTATTTTTTAACA 1 232 1 AAAGCCTGTA 0.966808 -69 TTTAAACAAAAAAGCCTGTTAAAAAATACA 1 248 0 AAAGCCTGTT 0.976594 -53 TATTAAATCCTCTTAATTAATCCC 3 287 0 AAATCCTCTT 0.840257 -14 ATGGCACAAAAAAGCCTTTATTTTGAATAT 8 74 1 AAAGCCTTTA 0.948775 -145 GTCAGCATAAATAACCTTTTTATCTCTCTT 8 136 1 ATAACCTTTT 0.688633 -83 TTCAAAATCCTTTGTACTCTTTTA 8 205 0 AAATCCTTTG 0.906358 -14 ********** Masking position 3 Map Score: 1.54025 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 229 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 8 TGTTAATCATACTAAGGATAAAAATATGAC 1 117 0 ACTAAGGATA 0.930213 -184 GTTGATTTTTACCAACGATACCCCAATTTC 3 151 0 ACCAACGATA 0.95182 -150 ACTTTTACTAACCTAGGCTATACCTAGCCT 6 84 1 ACCTAGGCTA 0.98794 -76 AAACGTTTTGACCTAGGCTAGGTATAGCCT 6 98 0 ACCTAGGCTA 0.98794 -62 ********** Masking position 5 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 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 ********** 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 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