AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -icoldbox_hinf_opreg_300.orf -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 HI0229 298 polynucleotide phosphorylase (pnp) #2 HI0230 81 conserved hypothetical protein #3 HI0231 120 ATP-dependent RNA helicase (deaD) Motif number 1 TAGGTTCTTTTATATGAAATATAATGTAATGATG 1 15 0 TATTAAAAAA 0.952898 -284 AAAAGAACCTAATTTCAGAGAGAACAATCAATTT 1 38 1 AATTAGAAAA 0.969034 -261 TTAAGTTGGTAATGTGAAATAAAGTTAGCCATTA 1 104 1 AATTAAAAAG 0.937335 -195 GCCGCACGCTAATGTAGAAAATAAAGCCCGTGCA 1 158 0 AATTGAAAAA 0.988013 -141 TGCTAGTCGCAATCTGGGAAATAAGGCATTGTTT 1 249 1 AATTGGAAAA 0.97578 -50 CCTTAAAATTTATATTAAAAACAATGCCTTATTT 1 267 0 TATTAAAAAA 0.952898 -32 TTTTAATATAAATTTTAAGGAAAACATT 1 281 1 AATTAAGAAA 0.937334 -18 TCTTGGAATATAGAATCAAAACTTGGTAGC 2 7 1 AATTGAACAA 0.950635 -75 TTATGCCTAAAAGTTGGAAAACAACAAAACTTGG 2 49 0 AAGTGAAAAA 0.950635 -33 *** * *** * ** Masking position 5 Map Score: 9.88183 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 111 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 2 TGGTAATGTGAAATAAAGTTAGCCATTAAA 1 110 1 AAATAAAGTT 0.925803 -189 CTAATGTAGAAAATAAAGCCCGTGCATTAT 1 154 0 AAATAAAGCC 0.961018 -145 GCGGCTATCAAAAGAAATTTTTAAACGCCC 1 187 1 AAAGAAATTT 0.897102 -112 GCGACTAGCAAAAGAAATCTTTCGAAAAAA 1 229 0 AAAGAAATCT 0.974477 -70 GCAATCTGGGAAATAAGGCATTGTTTTTAA 1 257 1 AAATAAGGCA 0.917783 -42 TATAAATTTTAAGGAAAACATT 1 287 1 AAGGAAAACA 0.904022 -12 TTTTAGGCATAAAGAAAGCAA 2 71 1 AAAGAAAGCA 0.990785 -11 GAATATAAATAAGGAAAGCTCAAAGAGGCC 3 91 0 AAGGAAAGCT 0.987543 -30 ********** Masking position 5 Map Score: 8.92032 Number of sites scoring better than the average of aligned sites = 459 Number in coding regions = 358 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 3 AGAGAGAACAATCAATTTTTAGGAGGAAAA 1 54 1 ATCAATTTTT 0.964708 -245 CAACTTAATTATCATTGTTTCGACAGTATT 1 82 0 ATCATTGTTT 0.876023 -217 GGCTATCAAAAGAAATTTTTAAACGCCCAA 1 189 1 AGAAATTTTT 0.805088 -110 CCAAAGTGCGGTCATTTTTTCGAAAGATTT 1 215 1 GTCATTTTTT 0.949008 -84 TGGGAAATAAGGCATTGTTTTTAATATAAA 1 263 1 GGCATTGTTT 0.916567 -36 AGCGAATGCTACCAAGTTTTGATTCTATAT 2 18 0 ACCAAGTTTT 0.949595 -64 AGCATTCGCTGCCAAGTTTTGTTGTTTTCC 2 38 1 GCCAAGTTTT 0.960413 -44 TGCAAAGAGCGGTAAGTTTTGGATTGATTT 3 11 0 GGTAAGTTTT 0.820913 -110 AGCAGAGCGAATGAATTTTTCTATTCGTTC 3 44 0 ATGAATTTTT 0.840976 -77 ********** Masking position 4 Map Score: 6.74329 Number of sites scoring better than the average of aligned sites = 912 Number in coding regions = 757 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 4 AAAATTTCTTTTGATAGCCGCACGCTAATG 1 178 0 TTGATAGCCG 0.979527 -121 AAGATTTCTTTTGCTAGTCGCAATCTGGGA 1 238 1 TTGCTAGTCG 0.992266 -61 CGAATGAATTTTTCTATTCGTTCTACTGCA 3 37 0 TTTCTATTCG 0.981847 -84 GCTTTCCTTATTTATATTCGAGTATTTTA 3 102 1 TTTATATTCG 0.972203 -19 ********** Masking position 5 Map Score: 2.87636 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 10 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 5 TATTTCATATAAAAGAACCTAATTTCAGAGAG 1 28 1 AAAAAACCAA 0.987674 -271 AAGAAATTTTTAAACGCCCAAAGTGCGGTCAT 1 198 1 TAAAGCCCAA 0.941235 -101 ATCTTTCGAAAAAATGACCGCACTTTGGGCGT 1 211 0 AAAAGACCCA 0.923384 -88 TCTTGGAATATAGAATCAAAACTTGGTAGC 2 9 1 TATAAATCAA 0.777727 -73 TAAAAGTTGGAAAACAACAAAACTTGGCAGCG 2 44 0 AAAAAACAAA 0.899479 -38 AAATCAATCCAAAACTTACCGC 3 1 1 AAATAATCAA 0.919786 -120 CTGCTCAACTTAATAAACCGAAGGCCTCTTTG 3 69 1 TAATAACCAA 0.948149 -52 TAAAATACTCGAATATAAATAAG 3 108 0 AAAAACTCAA 0.946629 -13 **** **** ** Masking position 2 Map Score: 3.49024 Number of sites scoring better than the average of aligned sites = 566 Number in coding regions = 428 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 6 TTTTCTACATTAGCGTGCGGCTATCAAAAG 1 171 1 TAGCGTGCGG 0.983171 -128 TTTAAACGCCCAAAGTGCGGTCATTTTTTC 1 206 1 CAAAGTGCGG 0.996359 -93 CCTTATTTCCCAGATTGCGACTAGCAAAAG 1 245 0 CAGATTGCGA 0.963926 -54 CGTTCTACTGCAAAGAGCGGTAAGTTTTGG 3 19 0 CAAAGAGCGG 0.990835 -102 ********** Masking position 2 Map Score: 2.25891 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 173 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 ********** No masking Map Score: -8.78641e-13 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: -8.78641e-13 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: -8.78641e-13 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