AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -ifruR_tpal_opreg_100.orf -g0.528 -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 = 0.528 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 TP0108 101 pyrophosphate--fructose 6-phosphate 1-phosphotransferase (pfk) #2 TP0568 121 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxyphosphogluconate aldolase (eda) #3 TP0747 88 T. pallidum predicted coding region TP0747 #4 TP0844 92 glyceraldehyde 3-phosphate dehydrogenase (gap) Motif number 1 GTTAGCCTGAGGGAGTCTCTACGCACGCGG 1 67 1 GGGAGTCTCT 0.926544 -35 GGGGTCCTCCGCGTACCGCGT 1 91 0 GGGTCCTCCG 0.977101 -11 TAGCTTAGGCGGGTGCACTGCATGTGGTGT 2 68 1 GGGTGCACTG 0.982404 -54 AAAAGTTCCAGGGAGCTTCGGATCACGACA 3 30 0 GGGAGCTTCG 0.97933 -59 TTCTGTTTCGGGGAGCTTTTTAATCATCAA 3 58 1 GGGAGCTTTT 0.989333 -31 GGGAGCCCTACAGCAAAGAG 4 1 1 GGGAGCCCTA 0.983741 -92 TGCGCGGGATGTGTGCTCTTTTTAGAGGAG 4 64 1 GTGTGCTCTT 0.95205 -29 ********** Masking position 3 Map Score: 8.42286 Number of sites scoring better than the average of aligned sites = 334 Number in coding regions = 300 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 2 CCCAGGGCATCTTCGCATCTTTAATTCATAT 1 16 1 CTTCGCATCT 0.939896 -86 GGGGTCCTCCGCGTACCGCGTGCGTAGAG 1 83 0 CCGCGTACCC 0.996963 -19 AAATCAAGATCTGCGTATAACACCAATCAAC 2 20 0 CTGCGTATAC 0.984928 -102 CTCCTCTTGCCCGCGGACATCTTTTCAGACA 2 95 0 CCGCGGACAC 0.994206 -27 TTCCAGGGAGCTTCGGATCACGACAAAGTCT 3 24 0 CTTCGGATCC 0.990204 -65 AGCACACATCCCGCGCAACGCTATCTGAAAA 4 50 0 CCGCGCAACC 0.994655 -43 ********* * Masking position 7 Map Score: 6.8354 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 251 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 3 TAAGCTAATGTCCTTTATGATCAAAAATCA 2 45 0 TCCTTTATGA 0.94013 -77 CCCGCGGACATCTTTTCAGACACCACATGC 2 87 0 TCTTTTCAGA 0.987439 -35 GCTCCCTGGAACTTTTCTGTTTCGGGGAGC 3 44 1 ACTTTTCTGT 0.942281 -45 GTAACACTCCTTTGATGATTAAAAAGCT 3 71 0 CCTTTGATGA 0.926488 -18 CGTCAATCCCTCTTTGCTGTAGGGCTCCC 4 10 0 TCTTTGCTGT 0.977995 -83 CGTGCCGATCTTTTTTCAGATAGCGTTGCG 4 38 1 TTTTTTCAGA 0.938011 -55 GGATGTGTGCTCTTTTTAGAGGAGGTTGGG 4 70 1 TCTTTTTAGA 0.953319 -23 ********** Masking position 5 Map Score: 5.47357 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 209 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 4 AAACACCCAGGGCATCTTCGCATCT 1 6 1 CCCAGGGCAT 0.989719 -96 ATCTTTAATTCATATTGCATCTTTCACCCC 1 32 1 CATATTGCAT 0.78597 -70 CATCTTTCACCCCATTGCGTTAGCCTGAGG 1 49 1 CCCATTGCGT 0.983926 -53 TTGCGTTAGCCTGAGGGAGTCTCTACGCAC 1 63 1 CTGAGGGAGT 0.904352 -39 CCTCCGCGTACCGCGTGCGTAGAGACTCCC 1 77 0 CCGCGTGCGT 0.993004 -25 GAAAAGATGTCCGCGGGCAAGAGGAGGGAA 2 100 1 CCGCGGGCAA 0.962425 -22 GATCTTTTTTCAGATAGCGTTGCGCGGGAT 4 44 1 CAGATAGCGT 0.939947 -49 ********** Masking position 7 Map Score: 4.00496 Number of sites scoring better than the average of aligned sites = 667 Number in coding regions = 610 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 5 AAGATGCAATATGAATTAAAGATGCGAAGA 1 25 0 ATGAATTAAA 0.953241 -77 AATGTCCTTTATGATCAAAAATCAAGATCT 2 39 0 ATGATCAAAA 0.981968 -83 CACTCCTTTGATGATTAAAAAGCTCCCCGA 3 65 0 ATGATTAAAA 0.98479 -24 ********** Masking position 4 Map Score: 0.0567593 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 2 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 ********** No masking Map Score: -1.32571e-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: -1.32571e-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: -1.32571e-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