AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -imalT_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 TP0075 118 sugar ABC transporter, permease protein (y4oQ) #2 TP0076 39 sugar ABC transporter, permease protein (y4oR) #3 TP0652 175 spermidine/putrescine ABC transporter, ATP-binding protein (potA) #4 TP0802 45 T. pallidum predicted coding region TP0802 #5 TP0804 77 sugar ABC transporter, ATP-binding protein (ugpC) Motif number 1 CTTCTTCTTGGGGGAAGAGAGGGCAGAAAAGA 1 18 1 GGGGAAGAGG 0.996392 -101 CTGGATATGAGCGGAAACAGAATGACGTGTTC 1 52 1 GCGGAAAGAA 0.795232 -67 ACGTTGGGTAGCGTAAGAGGGGGAGTGC 1 101 1 GCGTAAGGGG 0.998796 -18 GGTTGCGTACGGGTTAGATAAGAGCAGGAGCA 2 12 1 GGGTTAGAAG 0.964185 -28 AATGCGTAAGACGGGGTGGTCCTTT 3 4 1 GCGTAAGGGG 0.998795 -172 AAGTGCGCATGAGGAAGAAAGGACCACCCCGT 3 21 0 GAGGAAGAGG 0.981455 -155 CTCGCGGTTGGGGTACGCAAGGCGTCCGTGTG 3 101 0 GGGTACGAGG 0.992186 -75 GGCCGATGGTGCGGTATTTGGGTATGTTCTGT 3 138 0 GCGGTATGGG 0.949689 -38 TCCCCCACGAGGGTATGGAGAGGAA 4 4 0 GGGTATGGAG 0.970178 -42 GAAGCGTACACAGGGGGGCATCCCC 4 31 0 GCGTACAGGG 0.984045 -15 CCTCCCGTTTGCGTAAGGAAAGTAGTGTGTTG 5 24 1 GCGTAAGAAG 0.9938 -54 ******* *** Masking position 3 Map Score: 22.7474 Number of sites scoring better than the average of aligned sites = 368 Number in coding regions = 314 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 2 CCCCTCTTACGCTACCCAACGTAACGCGCTCC 1 91 0 GCACCCACGT 0.930452 -28 GCACTCCCCCTCTTACGCTACCCA 1 105 0 ACCCCCTCTT 0.964806 -14 GCTATCTGCTCCTGCTCTTATCTAACCCG 2 21 0 GCCCTGTCTT 0.887642 -19 GAAGAAAGGACCACCCCGTCTTACGCATT 3 8 0 CCCCCCTCTT 0.987113 -168 CACTTCTCGCGCCAGCGAGCGTAACACGCCAG 3 48 1 GCAGCGGCGT 0.957924 -128 AGCGAGCGTAACACGCCAGCGGTAATCTGTCC 3 61 1 ACCGCCGCGG 0.924224 -115 GGTACGCAAGGCGTCCGTGTGTCCTTGCTGGA 3 90 0 GCTCCGGTGT 0.720384 -86 TTCTGTCAAGGCTCGCGGTTGGGGTACGCAAG 3 112 0 GCCGCGTTGG 0.829748 -64 TACCCAAATACCGCACCATCGGCCTCCGCAAT 3 146 1 CCCACCTCGG 0.956349 -30 TTCCTCTCCATACCCTCGTGGGGGATGCC 4 8 1 CCTACCTCGT 0.879989 -38 CGTGGGGGATGCCCCCCTGTGTACGCTTC 4 27 1 GCCCCCGTGT 0.994306 -19 GACAACACCACCTCCCGTTTGCGTAAGGAAAG 5 14 1 CCCCCGTTGC 0.834207 -64 AGTGTGTTGCGCACCCGTGTTTCAAAAGGAAT 5 47 1 GCCCCGGTTT 0.963653 -31 ** **** **** Masking position 2 Map Score: 17.1413 Number of sites scoring better than the average of aligned sites = 2005 Number in coding regions = 1824 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 3 CTTCCCCCAAGAAGAAGAGACTTT 1 5 0 GAAGAAGAGA 0.872514 -114 CTTCTTGGGGGAAGAGAGGGCAGAAAAGAT 1 21 1 GAAGAGAGGG 0.982016 -98 AGATGCTGGATATGAGCGGAAACAGAATGA 1 47 1 TATGAGCGGA 0.865293 -72 TTGGGTAGCGTAAGAGGGGGAGTGC 1 104 1 TAAGAGGGGG 0.988241 -15 ACGGGTTAGATAAGAGCAGGAGCAGATAGC 2 20 1 TAAGAGCAGG 0.928301 -20 AATGCGTAAGACGGGGTGGTCCTTTC 3 7 1 TAAGACGGGG 0.959788 -169 TGCGCATGAGGAAGAAAGGACCACCCCGTC 3 20 0 GAAGAAAGGA 0.955574 -156 GTCCAGCAAGGACACACGGACGCCTTGCGT 3 89 1 GACACACGGA 0.879904 -87 GCGGTTGGGGTACGCAAGGCGTCCGTGTGT 3 100 0 TACGCAAGGC 0.827805 -76 GAAGCGTACACAGGGGGGCATCCCCC 4 30 0 TACACAGGGG 0.927507 -16 CATTCCTTTTGAAACACGGGTGCGCAACAC 5 50 0 GAAACACGGG 0.960183 -28 ********** Masking position 2 Map Score: 9.84221 Number of sites scoring better than the average of aligned sites = 1077 Number in coding regions = 962 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 4 TCTTACGCTACCCAACGTAACGCGCTCCAC 1 89 0 CCCAACGTAA 0.899123 -30 CTTATCTAACCCGTACGCAACCC 2 4 0 CCGTACGCAA 0.960285 -36 CGAGAAGTGCGCATGAGGAAGAAAGGACCA 3 27 0 GCATGAGGAA 0.783783 -149 TCTCGCGCCAGCGAGCGTAACACGCCAGCG 3 52 1 GCGAGCGTAA 0.98198 -124 AGCGTAACACGCCAGCGGTAATCTGTCCAG 3 65 1 GCCAGCGGTA 0.931246 -111 GGTACGCAAGGCGTCCGTGTGTCCTTGCTG 3 92 0 GCGTCCGTGT 0.828047 -84 CTTGCGTACCCCAACCGCGAGCCTTGACAG 3 112 1 CCAACCGCGA 0.93821 -64 CGCACCATCGGCCTCCGCAATGAGAAGGA 3 157 1 GCCTCCGCAA 0.984904 -19 CTTTCCTTACGCAAACGGGAGGTGGTGTTG 5 16 0 GCAAACGGGA 0.943085 -62 TTTGAAACACGGGTGCGCAACACACTACTT 5 43 0 GGGTGCGCAA 0.935794 -35 ********** Masking position 7 Map Score: 6.88115 Number of sites scoring better than the average of aligned sites = 1664 Number in coding regions = 1561 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 5 ACGTGTTCTATCTGTGGAGCGCGTTACGTT 1 76 1 TCTGTGGAGC 0.991614 -43 CCAGCGGTAATCTGTCCAGCAAGGACACAC 3 76 1 TCTGTCCAGC 0.980289 -100 TTGGGTATGTTCTGTCAAGGCTCGCGGTTG 3 123 0 TCTGTCAAGG 0.988076 -53 ********** Masking position 8 Map Score: 0.721206 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 5 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 ********** No masking Map Score: 5.42445e-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: 5.42445e-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: 5.42445e-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