AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i015_Glycolysis_2_hinf_reg_100.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 0.93826 -86 AATTTACCTACTTTTAACCATAAT 1 82 0 AATTTACTTT 0.940296 -14 CTGTCAAACTATTTTTTGGCATTTTATATTAAAA 2 25 1 ATTTTTTTTT 0.990711 -276 TTAAATGTATATTTGATGAAGTGTAAGTAGGTTT 2 61 0 ATTTGATTGT 0.83499 -240 AAATATGCTAATTTTATTAAGTTTATTAGTTAAA 2 90 0 ATTTTATTTT 0.984425 -211 CTAATCAACAAATTTTTCTTATTGGATTTTTTAC 2 137 1 AATTTTTTTG 0.889422 -164 TTCTTATTGGATTTTTTACATTTTCAAAATAAGA 2 152 1 ATTTTTTTTT 0.990755 -149 AAATTGCAAAATTTTTCTTATTTTGAAAATGTAA 2 167 0 ATTTTTCTTT 0.985326 -134 AAATTTTGCAATTTTTTATTCATTAAAAAGAATT 2 187 1 ATTTTTTATT 0.931534 -114 CATTAAAAAGAATTTTTGCGATCTGCATCGCAAA 2 207 1 AATTTTTTCT 0.899056 -94 ATTTTTTCCTTTTTATTTGAAAAT 2 287 0 ATTTTTTTTT 0.990761 -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 ATTTACCTACTTTTAACCATAATTGAAAATG 1 74 0 TTTTACCATA 0.951905 -22 GTCAAACTATTTTTTGGCATTTTATATTAAA 2 27 1 TTTTTGCATT 0.978042 -274 AGTAGGTTTATTTTTAATATAAAATGCCAAA 2 39 0 TTTTTATATA 0.901067 -262 AATCAACAAATTTTTCTTATTGGATTTTTTA 2 139 1 TTTTTTTATT 0.96137 -162 TCTTATTGGATTTTTTACATTTTCAAAATAA 2 153 1 TTTTTACATT 0.981478 -148 AATTGCAAAATTTTTCTTATTTTGAAAATGT 2 169 0 TTTTTTTATT 0.96137 -132 TTTTGCAATTTTTTATTCATTAAAAAGAATT 2 190 1 TTTTATCATT 0.959993 -111 CTCTCCCTCGTTTTTTCCATACTAGATTTTC 2 262 1 TTTTTCCATA 0.984284 -39 ATTTTTTCCTTTTTATTTGAAA 2 289 0 TTTTTCCTTT 0.949553 -12 ***** ***** Masking position 4 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 CTTTTAACCATAATTGAAAATGGGCATAAG 1 66 0 TAATTGAAAA 0.979609 -30 GAATAAAAAACTGGCTGTCA 2 1 1 GAATAAAAAA 0.806579 -300 GGTTTATTTTTAATATAAAATGCCAAAAAA 2 36 0 TAATATAAAA 0.950335 -265 AAATTTTTCTTATTTTGAAAATGTAAAAAA 2 163 0 TATTTTGAAA 0.856238 -138 AATTTTTTATTCATTAAAAAGAATTTTTGC 2 196 1 TCATTAAAAA 0.904484 -105 GAGAAACGATTAATTTAAAAGCATTTTGCG 2 235 0 TAATTTAAAA 0.977588 -66 TTTTCCTTTTTATTTGAAAATCTAGTATGG 2 278 0 TATTTGAAAA 0.952917 -23 ********** Masking position 8 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 TATGGTTAAAAGTAGGTAAATT 1 84 1 ATAGGTAAAT 0.989684 -12 ATGAAGTGTAAGTAGGTTTATTTTTAATATA 2 49 0 ATAGGTTTAT 0.937964 -252 TATTAAGTTTATTAGTTAAATGTATATTTGA 2 79 0 ATAGTTAAAT 0.983247 -222 TTAGGGTTGTATTGGTTAAATATGCTAATTT 2 110 0 ATGGTTAAAT 0.973198 -191 * ********* Masking position 7 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 ********** 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 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