AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -ioxyR_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 HI0161 215 glutathione reductase (gor) #2 HI0162 93 lipoprotein, putative #3 HI0571 122 hydrogen peroxide-inducible genes activator (oxyR) #4 HI1349 273 conserved hypothetical protein Motif number 1 AACAGATGATTAGTTTGAAATGATTTTATGTGAAGCC 1 83 0 TTTTAGATTT 0.973709 -133 TATTTTTTACTCTTTTGAACAGATGATTAGTTTGAAA 1 100 0 TTTTAGATAT 0.772447 -116 TTGATGTAATTGGTTTTATGAATATTTTTTACTCTTT 1 122 0 TTTTAATATT 0.872376 -94 AGTTTGAACCTTTTTTAAACTAAAATTTTTTTGTATT 1 189 0 TTTTAAAATT 0.974987 -27 TTTCATTTTAGTTTTTGTGGAGAACTTATA 2 4 0 GTTTTGAATT 0.934049 -90 GAAACGCTATACATTAATAAGGAAGTTTGTAAGAATA 2 37 1 ATTATGAATT 0.664259 -57 CAATTCTAATTGATTTATGGGGAAATT 2 77 1 TTTTTGAATT 0.979917 -17 CTCCTATTGGTTGTTAATTTAAATTTTACGTGCTGTA 3 19 1 TTTATAATTT 0.83972 -104 TTTACGTGCTGTATTATAGGGAAAATTATGATATAGT 3 43 1 GTTAAAAATT 0.813307 -80 ATTAATTCTATTCTTTTAATTGAATTTTTCTATAGGG 3 88 1 TTTTAGAATT 0.986091 -35 AGTACAGTTATAATTTTTAATATTTTTCCTAAGGATA 4 15 0 TTTTTATTTT 0.70466 -259 ATAACTGTACTTATTAAATCAAAATTTATTGTTAGCC 4 41 1 TTTAAAAATT 0.937526 -233 TTAGCCGCGATAGTTTGATTAAATATTCATTAAAACT 4 72 1 TTTTAAATTT 0.951387 -202 AGTCTTAGCCTTGTTTGTTAAGAAATTGTAATAAATA 4 138 0 TTTTTGAATT 0.979777 -136 TACGTTTCTATAATTTGAAGTGAAATTGTTCTATTCA 4 186 0 TTTTAGAATT 0.986225 -88 * *** * *** ** Masking position 5 Map Score: 17.9195 Number of sites scoring better than the average of aligned sites = 716 Number in coding regions = 536 Number in noncoding regions = 180 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 2 ATATCTACAGTGAGGAAGATTGAACAATCT 1 15 1 TGAGGAAGAT 0.967046 -201 TGATAGAAAAAGAGGAAGATTGTTCAATCT 1 31 0 AGAGGAAGAT 0.939 -185 TATACATTAATAAGGAAGTTTGTAAGAATA 2 44 1 TAAGGAAGTT 0.966529 -50 AATTGATTTATGGGGAAATT 2 84 1 TGGGGAAATT 0.982679 -10 TGCTGTATTATAGGGAAAATTATGATATAG 3 49 1 TAGGGAAAAT 0.988337 -74 AATTTTTCTATAGGGAAAATCTC 3 110 1 TAGGGAAAAT 0.988337 -13 AACATATCCTTAGGAAAAATATTAAAAATT 4 11 1 TAGGAAAAAT 0.892561 -263 CTATAATTTGAAGTGAAATTGTTCTATTCA 4 186 0 AAGTGAAATT 0.779595 -88 TCAACTAGAAAAAGGAAATTATT 4 261 1 AAAGGAAATT 0.948359 -13 ********** Masking position 6 Map Score: 12.7906 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 211 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 3 AAGAGTAAAAAATATTCATAAAACCAATTAC 1 123 1 AATATTATAA 0.755678 -93 GAATGCTATAAATTGATGTAATTGGTTTTAT 1 140 0 AATTGAGTAA 0.780171 -76 TATTCTGCCTAATTTTTATAAAGAATGCTAT 1 162 0 AATTTTATAA 0.946869 -54 AATACAAAAAAATTTTAGTTTAAAAAAGGTT 1 189 1 AATTTTGTTT 0.811594 -27 AATCAATTAGAATTGTGCTATTCTTACAAAC 2 61 0 AATTGTCTAT 0.963356 -33 GCACAATTCTAATTGATTTATGGGGAAATT 2 74 1 AATTGATTAT 0.657498 -20 ATTGGTTGTTAATTTAAATTTTACGTGCTGT 3 24 1 AATTTAATTT 0.789241 -99 TTATAGGGAAAATTATGATATAGTCATAATC 3 56 1 AATTATATAT 0.805635 -67 CTTTTAATTGAATTTTTCTATAGGGAAAATC 3 100 1 AATTTTCTAT 0.955813 -23 TACAGTTATAATTTTTAATATTTTTCCTAAG 4 19 0 ATTTTTATAT 0.70623 -255 GCTAACAATAAATTTTGATTTAATAAGTACA 4 46 0 AATTTTATTT 0.909205 -228 AGTTTGATTAAATATTCATTAAAACTGTGAT 4 83 1 AATATTATTA 0.541 -191 TTTGTTAAGAAATTGTAATAAATAGAAGCTA 4 131 0 AATTGTATAA 0.955865 -143 TTTGAAGTGAAATTGTTCTATTCAATATAAT 4 179 0 AATTGTCTAT 0.963355 -95 CTAGTTGAATAATTGAGCTAATGCCCTCCCT 4 238 0 AATTGACTAA 0.871632 -36 ****** **** Masking position 1 Map Score: 14.154 Number of sites scoring better than the average of aligned sites = 648 Number in coding regions = 504 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 4 AGTGAGGAAGATTGAACAATCTTCCTCTTT 1 23 1 ATTGAACAAT 0.902473 -193 AAATAGCGTGATAGAAAAAGAGGAAGATTG 1 39 0 ATAGAAAAAG 0.980268 -177 GTTTGTAAGAATAGCACAATTCTAATTGAT 2 61 1 ATAGCACAAT 0.968677 -33 GATTTTCCCTATAGAAAAATTCAATTAAAA 3 101 0 ATAGAAAAAT 0.983517 -22 ATTATATTGAATAGAACAATTTCACTTCAA 4 179 1 ATAGAACAAT 0.986292 -95 AATTATTCAACTAGAAAAAGGAAATTATT 4 255 1 CTAGAAAAAG 0.947884 -19 ********** Masking position 6 Map Score: 7.4998 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 53 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 AACTAATCATCTGTTCAAAAGAGTAAAAAA 1 105 1 CTGTTCAAAA 0.819297 -111 AGAGTAAAAAATATTCATAAAACCAATTAC 1 124 1 ATATTCATAA 0.886405 -92 AAATGAAACGCTATACATTAATAAGGAAGT 2 33 1 CTATACATTA 0.904411 -61 CTTAGGAAAAATATTAAAAATTATAACTGT 4 19 1 ATATTAAAAA 0.712886 -255 GTTTGATTAAATATTCATTAAAACTGTGAT 4 84 1 ATATTCATTA 0.937239 -190 TAAATAGAAGCTATCAAATAAGTGATCAAG 4 114 0 CTATCAAATA 0.891166 -160 TTGATAGCTTCTATTTATTACAATTTCTTA 4 127 1 CTATTTATTA 0.875731 -147 AAGGCTAAGACTATCAATTATATTGAATAG 4 163 1 CTATCAATTA 0.909788 -111 TGAAATTGTTCTATTCAATATAATTGATAG 4 173 0 CTATTCAATA 0.973679 -101 ********** Masking position 4 Map Score: 6.33981 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 189 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 6 AACCTTTTTTAAACTAAAATTTTTTTGTAT 1 190 0 AAACTAAAAT 0.975935 -26 TTCTCCACAAAAACTAAAATGAAACGCTAT 2 17 1 AAACTAAAAT 0.975935 -77 ACAGCACGTAAAATTTAAATTAACAACCAA 3 25 0 AAATTTAAAT 0.912204 -98 TGTACTTATTAAATCAAAATTTATTGTTAG 4 46 1 AAATCAAAAT 0.939003 -228 ********** Masking position 7 Map Score: 1.62275 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 82 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 7 ********** No masking Map Score: 1.19614e-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: 1.19614e-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: 1.19614e-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