AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i015_Glycolysis_2_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 HI0982 95 6-phosphofructokinase (pfkA) #2 HI0985 300 DNA processing chain A (dprA) Motif number 1 CTCTAGCAAAATTTGACGGGATTTTGATCTACA 1 10 0 ATTTGACTTT 0.939305 -86 AATTTACCTACTTTTAACCATAAT 1 82 0 AATTTACTTT 0.941306 -14 CTGTCAAACTATTTTTTGGCATTTTATATTAAAA 2 25 1 ATTTTTTTTT 0.990875 -276 TTAAATGTATATTTGATGAAGTGTAAGTAGGTTT 2 61 0 ATTTGATTGT 0.837482 -240 AAATATGCTAATTTTATTAAGTTTATTAGTTAAA 2 90 0 ATTTTATTTT 0.984701 -211 CTAATCAACAAATTTTTCTTATTGGATTTTTTAC 2 137 1 AATTTTTTTG 0.891198 -164 TTCTTATTGGATTTTTTACATTTTCAAAATAAGA 2 152 1 ATTTTTTTTT 0.99092 -149 AAATTGCAAAATTTTTCTTATTTTGAAAATGTAA 2 167 0 ATTTTTCTTT 0.985587 -134 AAATTTTGCAATTTTTTATTCATTAAAAAGAATT 2 187 1 ATTTTTTATT 0.932682 -114 CATTAAAAAGAATTTTTGCGATCTGCATCGCAAA 2 207 1 AATTTTTTCT 0.900694 -94 ATTTTTTCCTTTTTATTTGAAAAT 2 287 0 ATTTTTTTTT 0.990926 -14 ******* *** Masking position 1 Map Score: 15.5834 Number of sites scoring better than the average of aligned sites = 750 Number in coding regions = 516 Number in noncoding regions = 234 Number of orfs with sites within 600 bp upstream = 203 Fraction of orfs with sites within 600 bp upstream = 0.0326052 Motif number 2 CATTTTCAATTATGGTTAAAAGTAGGTAAAT 1 74 1 TATGGTAAAA 0.952639 -22 TTTAATATAAAATGCCAAAAAATAGTTTGAC 2 27 0 AATGCAAAAA 0.978387 -274 TTTGGCATTTTATATTAAAAATAAACCTACT 2 39 1 TATATAAAAA 0.902497 -262 TAAAAAATCCAATAAGAAAAATTTGTTGATT 2 139 0 AATAAAAAAA 0.961966 -162 TTATTTTGAAAATGTAAAAAATCCAATAAGA 2 153 0 AATGTAAAAA 0.98177 -148 ACATTTTCAAAATAAGAAAAATTTTGCAATT 2 169 1 AATAAAAAAA 0.961966 -132 AATTCTTTTTAATGAATAAAAAATTGCAAAA 2 190 0 AATGATAAAA 0.960609 -111 GAAAATCTAGTATGGAAAAAACGAGGGAGAG 2 262 0 TATGGAAAAA 0.984532 -39 TTTCAAATAAAAAGGAAAAAAT 2 289 1 AAAGGAAAAA 0.950321 -12 ***** ***** Masking position 8 Map Score: 14.054 Number of sites scoring better than the average of aligned sites = 427 Number in coding regions = 333 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 3 CTTATGCCCATTTTCAATTATGGTTAAAAG 1 66 1 TTTTCAATTA 0.981274 -30 TGACAGCCAGTTTTTTATTC 2 1 0 TTTTTTATTC 0.819862 -300 TTTTTTGGCATTTTATATTAAAAATAAACC 2 36 1 TTTTATATTA 0.954186 -265 TTTTTTACATTTTCAAAATAAGAAAAATTT 2 163 1 TTTCAAAATA 0.866607 -138 GCAAAAATTCTTTTTAATGAATAAAAAATT 2 196 0 TTTTTAATGA 0.911601 -105 CGCAAAATGCTTTTAAATTAATCGTTTCTC 2 235 1 TTTTAAATTA 0.979339 -66 CCATACTAGATTTTCAAATAAAAAGGAAAA 2 278 1 TTTTCAAATA 0.956423 -23 ********** Masking position 7 Map Score: 6.03844 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 196 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 4 AATTTACCTACTTTTAACCATA 1 84 0 ATTTACCTAT 0.990899 -12 TATATTAAAAATAAACCTACTTACACTTCAT 2 49 1 ATAAACCTAT 0.945028 -252 TCAAATATACATTTAACTAATAAACTTAATA 2 79 1 ATTTAACTAT 0.984984 -222 AAATTAGCATATTTAACCAATACAACCCTAA 2 110 1 ATTTAACCAT 0.976297 -191 ********* * Masking position 5 Map Score: 0.683558 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 49 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 TAATCTTATGCCCATTTTCAATTATGGTTA 1 62 1 CCCATTTTCA 0.984363 -34 TTGGATTTTTTACATTTTCAAAATAAGAAA 2 158 1 TACATTTTCA 0.988855 -143 TTTTCCATACTAGATTTTCAAATAAAAAGG 2 274 1 TAGATTTTCA 0.979721 -27 ********** Masking position 4 Map Score: 0.359343 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 52 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 ********** No masking Map Score: -5.80213e-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 7 ********** No masking Map Score: -5.80213e-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: -5.80213e-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