AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -inagC_aquae_opreg_100.orf -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 glmS 29 glucosamine-fructose-6-phosphate aminotransferase #2 aq_603 211 putative protein #3 lpxA 33 acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine acyltransferase #4 aq_966 300 putative protein Motif number 1 TCAATTATAATTCTTGTTTAA 1 1 0 TTCTTGTTAA 0.892893 -29 TTTTAATCTCTTCCTCTTTAAAGAGTTCCTT 2 57 0 TTCCTCTTAA 0.992616 -155 TCGTCTTCCTTTCCTTTTTAATCTCTTCCTC 2 72 0 TTCCTTTTAA 0.929482 -140 AGGAAGACGATACCCCTTGAGAAGTTTGAAA 2 93 1 TACCCCTTAG 0.972498 -119 TTCTTAAAAATTCCCCTTTTGTATTCCCTGC 2 139 0 TTCCCCTTTG 0.969291 -73 CAGGTAAAAGTTCTTCTTAAAAATTCCCCTT 2 152 0 TTCTTCTTAA 0.982869 -60 TCCCTGCTCCTTTAAATAGGTGTTT 3 19 0 TGCTCCTTAA 0.969148 -15 GGATGTTGTTTTCCCCTTAAAAAATCTATAA 4 110 0 TTCCCCTTAA 0.996835 -191 GGAAAACAACATCCCCTTCAGAGTAGTTTCC 4 127 1 ATCCCCTTAG 0.969291 -174 TTCTATTCCCTTCTCCTTTAATTTTTCAATT 4 187 0 TTCTCCTTAA 0.992616 -114 ******** ** Masking position 7 Map Score: 19.3658 Number of sites scoring better than the average of aligned sites = 424 Number in coding regions = 396 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 2 ACTCTTTAAAGAGGAAGAGATTAAAAAGGA 2 62 1 GAGGAAGAGA 0.968157 -150 AAAAGGAAAGGAAGACGATACCCCTTGAGA 2 85 1 GAAGACGATA 0.892406 -127 ATAAGGACTGTAAGCAGGGAATACAAAAGG 2 126 1 TAAGCAGGGA 0.945183 -86 GCGTTTTGACCAAGCAGGTAAAAGTTCTTC 2 167 0 CAAGCAGGTA 0.874551 -45 CCTATTTAAAGGAGCAGGGA 3 24 1 GGAGCAGGGA 0.992209 -10 ATTAATTGCGGGGGACGGGTTGAGTTGTTG 4 157 0 GGGGACGGGT 0.970757 -144 AAAAATTAAAGGAGAAGGGAATAGAACTGA 4 192 1 GGAGAAGGGA 0.993565 -109 CAGAGTACCTGAGGAAGGAAGGTATAAAAT 4 258 1 GAGGAAGGAA 0.976809 -43 TTCCTATTACGAAGACGGATTTTATACCTT 4 276 0 GAAGACGGAT 0.930121 -25 ********** Masking position 4 Map Score: 10.392 Number of sites scoring better than the average of aligned sites = 1066 Number in coding regions = 972 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 3 AAAAGTTAAATTTGAAAACCTCGGAGAATTT 2 23 1 TTGAAAACCT 0.914071 -189 AAGAGTTCCTTGAAAAATTCTCCGAGGTTTT 2 37 0 TGAAAATTCT 0.923364 -175 TCCTTATGGTTTCAAACTTCTCAAGGGGTAT 2 102 0 TTAAACTTCT 0.958985 -110 AAAGTTCTTCTTAAAAATTCCCCTTTTGTAT 2 146 0 TTAAAATTCC 0.741749 -66 CGCCATCACATTAATAAATCTCTCTTCC 2 194 1 TTATAAATCT 0.642652 -18 AATACTTTAAACACCTATTTAAAGGA 3 6 1 TTAAACACCT 0.969973 -28 TTGTCTTTGGTGAGTACTCCGTCCATGTCTA 4 47 0 TGGTACTCCG 0.78206 -254 TTAAAAAATCTATAAACTCCTTTGCATCGGG 4 94 0 TAAAACTCCT 0.971552 -207 GTTGAGTTGTTGGAAACTACTCTGAAGGGGA 4 138 0 TGAAACTACT 0.87446 -163 GGAAGGAAGGTATAAAATCCGTCTTCGTAAT 4 270 1 TAAAAATCCG 0.885333 -31 GTCTTCGTAATAGGAACACCT 4 290 1 TAGAACACCT 0.926535 -11 ** ******** Masking position 6 Map Score: 6.41892 Number of sites scoring better than the average of aligned sites = 1203 Number in coding regions = 1128 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 4 TTCAAATTTAACTTTTTCCTCAAAATCT 2 9 0 ACTTTTTCCT 0.912588 -203 TCCTTTTTAATCTCTTCCTCTTTAAAGAGT 2 62 0 TCTCTTCCTC 0.91348 -150 GGTATCGTCTTCCTTTCCTTTTTAATCTCT 2 77 0 TCCTTTCCTT 0.931225 -135 ATTCCCCTTTTGTATTCCCTGCTTACAGTC 2 131 0 TGTATTCCCT 0.965992 -81 TTTAAGAAGAACTTTTACCTGCTTGGTCAA 2 162 1 ACTTTTACCT 0.855504 -50 AGGAGTTAAATCCATTTCCCGATGCAAAGG 4 77 1 TCCATTTCCC 0.923991 -224 AAGGGGATGTTGTTTTCCCCTTAAAAAATC 4 115 0 TGTTTTCCCC 0.973157 -186 AACCTTCAGTTCTATTCCCTTCTCCTTTAA 4 197 0 TCTATTCCCT 0.987698 -104 ********** Masking position 5 Map Score: 6.40842 Number of sites scoring better than the average of aligned sites = 1552 Number in coding regions = 1460 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 5 ********** No masking Map Score: 1.06114e-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 6 ********** No masking Map Score: 1.06114e-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 7 ********** No masking Map Score: 1.06114e-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