AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -igalR_pyro_opreg_100.orf -g0.419 -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 = 0.419 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 PH0365 54 327aa long hypothetical galactose-1-phosphate uridyltransferase #2 PH0369 92 350aa long hypothetical galactokinase #3 PH0378 56 318aa long hypothetical UDP-glucose 4-epimerase #4 PH1713 45 498aa long hypothetical sugar transport ATP-binding protein #5 PH1714 300 405aa long hypothetical protein #6 PH1742 55 306aa long hypothetical UDP-glucose 4-epimerase Motif number 1 AATTTTATTAAGTTTTTGACTATTATAGTCAAAAC 2 8 0 ATTTGAATAG 0.995044 -85 AACTTAATAAAATTTTCGACAATGTGAGTGAGCTTGAA 2 32 1 ATTTGAATAG 0.995044 -61 GAGCTTGAAGATTTTTAGACTCTACAACATTACTGATC 2 61 1 ATTTGACTAC 0.960275 -32 TTTAGGGCACTTAACGAGAATCAAAGACTTATATTG 5 9 1 ATTAGAATAG 0.96937 -292 CTTTAAACGTTTTTCTTGAGGATCTCAGTAGGAGGACA 5 72 1 TTTTGAATAG 0.96937 -229 ATGAGTCCTAACTCTTTAAGTATTCTAGCGTTGAGTTT 5 131 0 ATCTAAATAG 0.981908 -170 AAGAGTTAGGACTCATAGATTATGGTACCAGAGATAGG 5 153 1 ATCTGAATAC 0.988418 -148 TTGAGGAGGTAATCGTTAAATATCCCACGATTCTTTTT 5 256 1 ATCTAAATAC 0.96548 -45 TGGGGCCCCTAATTATTAAAAATTTGAGGCATTTAAAC 6 27 0 ATTTAAATAG 0.985029 -29 * ** * ** ** ** Masking position 9 Map Score: 12.0146 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 61 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 2 AGTTCAAAGTATATTAAAGGTGGTCGTAA 1 4 0 ATTAGGTGTG 0.986139 -51 TGAACTAAACAATTTTAAGGTTGGTGAGAGT 1 34 1 ATTAGGTGGG 0.94974 -21 AATGTGAGTGAGCTTGAAGATTTTTAGACTCTACAA 2 52 1 ATTAGATTTA 0.967977 -41 AGACTCTACAACATTACTGATCTTTA 2 77 1 ATTTGATTTA 0.809642 -16 AACCCACTAGACCTTACAGTTATATAATTATGCCCA 3 20 0 ATTAGTTTAA 0.790813 -37 TTAAAACACACCTTAAAGGTAGAAAAGGAAAAAGG 4 21 0 ATTAGGTGAA 0.969303 -25 ATATAAACGGAAATTACAGATCTTTAAACGTTTTTC 5 51 1 ATTAGATTTA 0.967977 -250 TCTTCAGTTAACTTTACAGGCTTTGGCCTATCTCTG 5 181 0 ATTAGGCTTG 0.969787 -120 GAGGGGGATGAAATTTGAGGAGGTAATCGTTAAATA 5 242 1 ATTAGGAGTA 0.947109 -59 TAATTATTAAAAATTTGAGGCATTTAAACGATTTCG 6 20 0 ATTAGGCTTA 0.9783 -36 * ** **** ** * Masking position 5 Map Score: 7.8723 Number of sites scoring better than the average of aligned sites = 337 Number in coding regions = 290 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 3 TTACGACCACCTTTAATATACTTTGAACTAAA 1 10 1 CCTTTATACT 0.82469 -45 AATGTTGTAGAGTCTAAAAATCTTCAAGCTCAC 2 59 0 AGTCTAATCT 0.605187 -34 AGTTTTTATTCCTTTTTCCTTTT 4 1 1 AGTTTTACCT 0.932172 -45 CTTTGATTCTCGTTAAGTGCCCTAAA 5 4 0 CGTTAATCCT 0.974042 -297 CTGTAATTTCCGTTTATATTCCTCAATATAAGT 5 37 0 CGTTTAACCT 0.995571 -264 TCAAGAAAAACGTTTAAAGATCTGTAATTTCCG 5 58 0 CGTTTAATCT 0.983578 -243 ACAAGCAAACCGATTTCAACACTAAAACTCAAC 5 107 1 CGATTTAACT 0.750782 -194 AGGAGGTAATCGTTAAATATCCCACGATTCTTT 5 259 1 CGTTAATCCC 0.897625 -42 TCCCCGAAATCGTTTAAATGCCTCAAATTTTTA 6 16 1 CGTTTAACCT 0.995398 -40 ****** * *** Masking position 12 Map Score: 5.25671 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 224 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 4 TTTATTCCTTTTTCCTTTTCTACCTTTAAG 4 15 1 TTTCCTTTTC 0.859252 -31 TCGGTTTGCTTGTCCTCCTACTGAGATCCT 5 90 0 TGTCCTCCTA 0.95496 -211 AGAATGACCTTTCCCTCTTCAGTTAACTTT 5 202 0 TTCCCTCTTC 0.975012 -99 CCTCCTCAAATTTCATCCCCCTCCAGGAGC 5 235 0 TTTCATCCCC 0.93773 -66 TATTTAACGATTACCTCCTCAAATTTCATC 5 248 0 TTACCTCCTC 0.981287 -53 TAGTATCCACCTAATTTAAAAAG 5 288 0 TATCCACCTA 0.839667 -13 TACCCTCCCCGAAATCGTTT 6 1 1 TACCCTCCCC 0.980984 -55 ********** Masking position 1 Map Score: 3.81919 Number of sites scoring better than the average of aligned sites = 1186 Number in coding regions = 1098 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 5 ACTCTCACCAACCTTAAAAT 1 45 0 ACTCTCACCA 0.925088 -10 GAATGACCTTTCCCTCTTCAGTTAACTTTA 5 201 0 TCCCTCTTCA 0.986352 -100 TCAAATTTCATCCCCCTCCAGGAGCATGAG 5 230 0 TCCCCCTCCA 0.986551 -71 ATTTAACGATTACCTCCTCAAATTTCATCC 5 247 0 TACCTCCTCA 0.955399 -54 TACCCTCCCCGAAATCGTTTA 6 2 1 ACCCTCCCCG 0.987529 -54 ********** Masking position 6 Map Score: 1.61458 Number of sites scoring better than the average of aligned sites = 389 Number in coding regions = 358 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 6 CACCAACCTTAAAATTGTTTAGTTCAAAGT 1 30 0 AAAATTGTTT 0.915186 -25 GATCCTCAAGAAAAACGTTTAAAGATCTGT 5 66 0 AAAAACGTTT 0.944241 -235 TTTTAGTGTTGAAATCGGTTTGCTTGTCCT 5 104 0 GAAATCGGTT 0.983139 -197 ATTTGAGGAGGTAATCGTTAAATATCCCAC 5 254 1 GTAATCGTTA 0.922833 -47 TACCCTCCCCGAAATCGTTTAAATGCCTCA 6 11 1 GAAATCGTTT 0.992306 -45 ********** Masking position 4 Map Score: 2.94598 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 47 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 ********** No masking Map Score: 1.55852e-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: 1.55852e-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: 1.55852e-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