AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i262_3_5_1_28_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 HI0062 258 dnaK suppressor protein (dksA) #2 HI0063 247 poly(A) polymerase (pcnB) #3 HI0065 75 conserved hypothetical protein Motif number 1 ATATCGTAAAAATAAATTTTTCAGGAAAATT 1 96 1 AATAAATTTT 0.629114 -163 TATTTTAGGAACCCAATTTTTGCGGGCGGTA 1 159 0 ACCCAATTTT 0.953349 -100 TTTGTTCCTGACTGCTATTTTAGGAACCCAA 1 174 0 ACTGCTTTTT 0.937333 -85 GTTAATTTTAACCGCACTTTTGTATTTTTCA 2 21 0 ACCGCATTTT 0.997353 -227 GTTAAAATTAACCGCACTTTTTTGCATTTAA 2 40 1 ACCGCATTTT 0.997353 -208 AGTGGATTTTCCTGCATTTTTAAATGCAAAA 2 59 0 CCTGCATTTT 0.97859 -189 CTTCTTGCCAAACAAATTTTTGATATAAGTA 2 158 0 AACAAATTTT 0.857026 -90 AAATTTCACCGCACTTTTATGAACCTCA 3 8 1 ACCGCATTTT 0.997353 -68 GGCTGATTCTACCGCACTTTTGAGGTTCATA 3 28 0 ACCGCATTTT 0.997353 -48 GTAGAATCAGCCCACATTTTTCTTCATTCAT 3 47 1 CCCACATTTT 0.981512 -29 ****** **** Masking position 8 Map Score: 22.2178 Number of sites scoring better than the average of aligned sites = 1658 Number in coding regions = 1136 Number in noncoding regions = 522 Number of orfs with sites within 600 bp upstream = 339 Fraction of orfs with sites within 600 bp upstream = 0.0544491 Motif number 2 CAATTTTTGCGGGCGGTATAAATATCAGAAG 1 146 0 GGGCGGTTAA 0.994199 -113 AAATACAAAAGTGCGGTTAAAATTAACCGCA 2 25 1 GTGCGGTAAA 0.998169 -223 ATGCAAAAAAGTGCGGTTAATTTTAACCGCA 2 36 0 GTGCGGTAAT 0.992619 -212 TAAACGAGTTGAGCGTTCTAATAGCCAA 2 230 1 GAGCGTTTAA 0.947058 -18 GTTCATAAAAGTGCGGTGAAATTT 3 4 0 GTGCGGTAAA 0.998169 -72 AACCTCAAAAGTGCGGTAGAATCAGCCCACA 3 32 1 GTGCGGTGAA 0.996882 -44 ******* *** Masking position 7 Map Score: 13.0192 Number of sites scoring better than the average of aligned sites = 596 Number in coding regions = 382 Number in noncoding regions = 214 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 3 ATAAAAGATTAATTCCAGCCTCTCTAAGCCT 1 15 1 ATTCCAGCCT 0.930951 -244 AGCAAGTAAATTTTCCTGAAAAATTTATTTT 1 104 0 TTTCCTGAAA 0.960992 -155 TATTTTAGTTTGTTCCTGACTGCTATTTTAG 1 182 0 TTTCCTGACT 0.98513 -77 GGATTTCACGACTTCCTGTCTTGTTATTTTA 1 206 0 ATTCCTGTCT 0.966469 -53 GGCAAGTGGATTTTCCTGCATTTTTAAATGC 2 63 0 TTTCCTGCAT 0.986354 -185 GACTTGGCTCTTTTCTTGTAAAGAAAAAGGC 2 91 0 TTTCTTGTAA 0.870478 -157 GATTTTTTTGTCTTCTTGCCAAACAAATTTT 2 169 0 TTTCTTGCCA 0.969016 -79 * ********* Masking position 4 Map Score: 5.92197 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 141 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 4 GAAGCAACCGTTTGCATATTTAAATAAAACT 1 51 0 TTTGATATTT 0.866723 -208 CAAACGGTTGCTTCAAATTTTGCGATCCATA 1 68 1 CTTCAATTTT 0.829219 -191 GACTTCCTGTCTTGTTATTTTAGTTTGTTCC 1 197 0 CTTGTATTTT 0.940204 -62 TAACCGCACTTTTGTATTTTTCAATAGAATG 2 13 0 TTTGATTTTT 0.969064 -235 AGTGGATTTTCCTGCATTTTTAAATGCAAAA 2 59 0 CCTGATTTTT 0.955126 -189 GGAAAATCCACTTGCCTTTTTCTTTACAAGA 2 78 1 CTTGCTTTTT 0.985171 -170 AAATAAATGACTTGGCTCTTTTCTTGTAAAG 2 99 0 CTTGCTCTTT 0.953363 -149 GGCAACCTCTTTTGATTTTTTTGTCTTCTTG 2 182 0 TTTGTTTTTT 0.943785 -66 **** ****** Masking position 3 Map Score: 6.609 Number of sites scoring better than the average of aligned sites = 341 Number in coding regions = 285 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 5 CCTAGGCTAGTTTTATTTAAATATGCAAACGG 1 43 1 TTTTTTAAAT 0.762955 -216 CCTGAAAAATTTATTTTTACGATATGGATCGC 1 89 0 TTTTTTACGA 0.884107 -170 AGCAAGTAAATTTTCCTGAAAAATTTATTTTT 1 103 0 TTTCTGAAAA 0.866597 -156 CAGAAGTTGTTTGTTTTAGCAAGTAAATTTTC 1 120 0 TTTTTAGCAA 0.920965 -139 TTCATTCTATTGAAAAATACAAAAGT 2 5 1 TTTTTGAAAA 0.976987 -243 CCGCACTTTTTTGCATTTAAAAATGCAGGAAA 2 51 1 TTCTTTAAAA 0.811995 -197 CCACTTGCCTTTTTCTTTACAAGAAAAGAGCC 2 85 1 TTTTTTACAA 0.93315 -163 TACTCCGTTTTGTTGTTGGAAATAAATGACTT 2 117 0 TGTTTGGAAA 0.910573 -131 ATATCAAAAATTTGTTTGGCAAGAAGACAAAA 2 163 1 TTGTTGGCAA 0.947826 -85 GAATGAGCACTTGTTTTGGCAACCTCTTTTGA 2 198 0 TTTTTGGCAA 0.984767 -50 ** * ******* Masking position 7 Map Score: 5.94479 Number of sites scoring better than the average of aligned sites = 544 Number in coding regions = 426 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 6 AAATAAATTTTTCAGGAAAATTTACTTGCT 1 105 1 TTCAGGAAAA 0.894963 -154 TGACTGCTATTTTAGGAACCCAATTTTTGC 1 167 0 TTTAGGAACC 0.990443 -92 TAAAATAGCAGTCAGGAACAAACTAAAATA 1 183 1 GTCAGGAACA 0.952696 -76 GAGCACTTGTTTTGGCAACCTCTTTTGATT 2 196 0 TTTGGCAACC 0.896758 -52 TCACCGCACTTTTATGAACCTCAAAAGTGC 3 16 1 TTTATGAACC 0.972245 -60 TTTTTCTTCATTCATGACCCGTT 3 63 1 TTCATGACCC 0.952697 -13 ********** Masking position 7 Map Score: 2.37556 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 64 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 ********** No masking Map Score: 1.24588e-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 8 ********** No masking Map Score: 1.24588e-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: 1.24588e-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