AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -ifruR_mgen_opreg_300.orf -g0.317 -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 = 0.317 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MG040 158 lipoprotein, putative #2 MG062 300 PTS system, fructose-specific IIABC component (fruA) Motif number 1 CTTCTAGTATTTAGTTAGTTATTTTGCAAAAAAGG 1 19 1 TTAGTTTTTT 0.985526 -140 GTTTTATAGTTGTGATTTACTTTTTGGTATCTCTA 1 58 1 TGTGTATTTT 0.964263 -101 TAAAAAAATGTTTGATACTACTTTTTATAGAGATA 1 85 0 TTTGTTTTTT 0.991415 -74 TTTTTTATCTTTTGATTTCTTTTTACTAAAAATAA 1 113 1 TTTGTCTTTA 0.943881 -46 TGACGGTATTTTAGCTAATTATTTTTAGTAAAAAG 1 131 0 TTAGTTTTTT 0.985526 -28 TAAAAAACAATTAGCTACAGCTTTTAAAATTAGTC 2 30 0 TTAGTATTTT 0.985526 -271 TTTCAAATTCTTTGATTCAGTTTGTTCTAAAAAAC 2 57 0 TTTGTATTGT 0.95604 -244 ACCATCAGGGTCTGTTTTTTATTTTTATTCAATTT 2 124 0 TCTGTTTTTT 0.980259 -177 ACCCTGATGGTCTGTTGGATATTTAATGGCGGAAG 2 148 1 TCTGTATTTA 0.951874 -153 ACGCTCCCAGTTTGTTGTTAAATTTATTATAAATA 2 255 1 TTTGTTATTT 0.936198 -46 AAAGCGCTAATTAGTTGCATATTTATAATAAATTT 2 274 0 TTAGTATTTA 0.96444 -27 **** * * **** Masking position 6 Map Score: 16.2622 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 316 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 2 AAAGGATTAGTTTTATAGTTGTGATTTACT 1 49 1 TTTTATAGTT 0.740209 -110 TATAGTTGTGATTTACTTTTTGGTATCTCT 1 62 1 ATTTACTTTT 0.851574 -97 TCAAACATTTTTTTATCTTTTGATTTCTTT 1 105 1 TTTTATCTTT 0.916074 -54 TTATCTTTTGATTTCTTTTTACTAAAAATA 1 117 1 ATTTCTTTTT 0.90958 -42 TATTTTAGCTAATTATTTTTAGTAAAAAGA 1 130 0 AATTATTTTT 0.925612 -29 AGCTGTAGCTAATTGTTTTTTAGAACAAAC 2 43 1 AATTGTTTTT 0.941292 -258 AAGAATTTGAAATTGTCTTTCATTGTTAAC 2 80 1 AATTGTCTTT 0.886856 -221 TTTTATTCAATTTTGTTGTTAAATGCTGTT 2 107 0 TTTTGTTGTT 0.953422 -194 AGGGTCTGTTTTTTATTTTTATTCAATTTT 2 123 0 TTTTATTTTT 0.957138 -178 TACGCTCCCAGTTTGTTGTTAAATTTATTA 2 254 1 GTTTGTTGTT 0.902164 -47 ********** Masking position 4 Map Score: 9.80432 Number of sites scoring better than the average of aligned sites = 627 Number in coding regions = 542 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 3 TAGTCTAATGTAAATTCTGTCTTA 2 5 0 TAAATTCTGT 0.989696 -296 AGACTAATTTTAAAAGCTGTAGCTAATTGT 2 29 1 TAAAAGCTGT 0.969251 -272 AAGACAATTTCAAATTCTTTGATTCAGTTT 2 69 0 CAAATTCTTT 0.892458 -232 ATTTTGTTGTTAAATGCTGTTAACAATGAA 2 98 0 TAAATGCTGT 0.990456 -203 TTATTTTTATTCAATTTTGTTGTTAAATGC 2 111 0 TCAATTTTGT 0.891596 -190 ********** Masking position 4 Map Score: 3.16558 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 36 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 4 AAACTAATCCTTTTTTGCAAAATAACTAACTA 1 30 0 TTTTTTGAAA 0.964087 -129 CTTTTTGGTATCTCTATAAAAAGTAGTATCAA 1 77 1 TCTCTATAAA 0.577587 -82 TAGCTAATTATTTTTAGTAAAAAGAAATCAAA 1 123 0 TTTTTAGAAA 0.957274 -36 TTACTAAAAATAATTAGCTAAAATACCGTCAT 1 135 1 TAATTAGTAA 0.696285 -24 AGCTAATTGTTTTTTAGAACAAACTGAATCAA 2 49 1 TTTTTAGAAA 0.954422 -252 TTTATTCAATTTTGTTGTTAAATGCTGTTAAC 2 104 0 TTTGTTGTAA 0.925011 -197 ACGCTCCCAGTTTGTTGTTAAATTTATTATAA 2 255 1 TTTGTTGTAA 0.925011 -46 ATTAGTTGCATATTTATAATAAATTTAACAAC 2 268 0 TATTTATAAA 0.773113 -33 ******* * ** Masking position 11 Map Score: 2.06519 Number of sites scoring better than the average of aligned sites = 368 Number in coding regions = 338 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 5 ********** No masking Map Score: -2.24942e-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: -2.24942e-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: -2.24942e-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