AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00740_tpal_reg_300.orf -o00740_tpal_300.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -g0.53 -x5 -e 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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 TP0891 175 translation initiation factor 2 (infB) #2 TP0892 49 N utilization substance protein A (nusA) #3 TP0893 174 conserved hypothetical protein #4 TP0895 21 T. pallidum predicted coding region TP0895 #5 TP0900 38 T. pallidum predicted coding region TP0900 #6 TP0901 40 conserved hypothetical integral membrane protein Motif number 1 GCAGGCTGTGCGTTCACCGGTGACGTCTGGTC 1 68 1 CGTCACCGGG 0.998103 -108 AACTACCTCTCGTACACGGGCGGATGTTGACG 1 101 1 CGTCACGGGG 0.99652 -75 CAGTCTGTAACGTGCACCGGCGTGGTGCGGAG 3 19 1 CGTCACCGGG 0.99809 -156 AGGGTGCTAACGCACTCGGGCGGCACCTCCGC 3 45 0 CGCCTCGGGG 0.911204 -130 ACGCCCGCTACACACTACGCGGGCCTCGGTTA 3 82 0 CACCTACGCG 0.975046 -93 TTAAAACTCTCACACAAGGGCCCACAAAAATG 3 119 0 CACCAAGGGC 0.978479 -56 GAGTTTTAAACATGCTAGAGTGAGCCCCGCGA 3 142 1 CATCTAGAGG 0.673475 -33 GCACGCACCCCTCGCGGGGCTCA 3 162 0 CACCACCCCC 0.946656 -13 CACGCAGCGGAGGTAGGCGGG 4 1 1 CACCAGCGGG 0.988693 -21 TCCATGCTCCGTGCCTTACCCGAA 5 25 0 CATCTCCGTC 0.938101 -14 CCGTGCACCGCACTCCCTTTTGG 6 28 0 CGTCACCGCC 0.992756 -13 *** ****** * Masking position 5 Map Score: 20.6474 Number of sites scoring better than the average of aligned sites = 821 Number in coding regions = 740 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 2 ATACGCCTAAAGACACTTCCCGTGTTGCTAGTG 1 34 1 AGACTCCCGT 0.961067 -142 TCACCGGTGAACGCACAGCCTGCTCACTAGCAA 1 58 0 ACGCGCCTGC 0.971671 -118 CGTCTGGTCAAACTACCTCTCGTACACGGGCGG 1 91 1 AACCTCTCGT 0.898707 -85 CCTTTACGTCAACATCCGCCCGTGTACGAGAGG 1 106 0 AACCGCCCGT 0.991995 -70 GAAGGTGCAGACCAAAAGCCCTT 2 1 0 ACCAGCCCTT 0.965134 -49 GGTGCACGTTACAGACTGCCCGTCTG 3 4 0 ACACGCCCGT 0.730148 -171 CGTGGTGCGGAGGTGCCGCCCGAGTGCGTTAGC 3 39 1 AGGCGCCCGA 0.976968 -136 CCCTCACAGTAACCGAGGCCCGCGTAGTGTGTA 3 73 1 AACAGCCCGC 0.987668 -102 CACAAAAATGAGGATACGCCCGCTACACACTAC 3 96 0 AGGAGCCCGC 0.990237 -79 GCACGCACCCCTCGCGGGGCTCACT 3 160 0 ACGCCCTCGC 0.920933 -15 CCGTGCACCGCACTCCCTTTTGGGTAGAC 6 22 0 ACCATCCCTT 0.88829 -19 *** * ****** Masking position 1 Map Score: 15.7743 Number of sites scoring better than the average of aligned sites = 529 Number in coding regions = 468 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 3 TGCGTTCACCGGTGACGTCTGGTCAAACTAC 1 76 1 GGGACGTCTG 0.949733 -100 CTTTACGTCAACATCCGCCCGTGTACGAGAG 1 107 0 ACTCCGCCCG 0.983937 -69 GTGGTGCGGAGGTGCCGCCCGAGTGCGTTAG 3 40 1 GGGCCGCCCG 0.965643 -135 CTGTGAGGGTGCTAACGCACTCGGGCGGCAC 3 51 0 GCAACGCACT 0.8375 -124 CCTCACAGTAACCGAGGCCCGCGTAGTGTGT 3 74 1 ACGAGGCCCG 0.992541 -101 ACAAAAATGAGGATACGCCCGCTACACACTA 3 97 0 GGTACGCCCG 0.997891 -78 AACATGCTAGAGTGAGCCCCGCGAGGGGTGC 3 150 1 AGGAGCCCCG 0.979894 -25 CCCGCCTACCTCCGCTGCGTG 4 8 0 GCTACCTCCG 0.958248 -14 ACGTCCTTCGGGTAAGGCACGGAGCATGGA 5 19 1 GGAAGGCACG 0.970733 -20 ** ******** Masking position 10 Map Score: 11.8708 Number of sites scoring better than the average of aligned sites = 547 Number in coding regions = 494 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 4 TGACCCTACGAGACAATACGCCTAAAGACA 1 19 1 AGACAATACG 0.812483 -157 ACGCCTAAAGACACTTCCCGTGTTGCTAGT 1 36 1 ACACTTCCCG 0.956425 -140 GCTAGTGAGCAGGCTGTGCGTTCACCGGTG 1 60 1 AGGCTGTGCG 0.970812 -116 GAAGACAATCAAAGTGCGCGCAAAGAAA 1 158 1 AAAGTGCGCG 0.942362 -18 TGCACGTTACAGACTGCCCGTCTG 3 5 0 AGACTGCCCG 0.989682 -170 CCGCACCACGCCGGTGCACGTTACAGACTG 3 19 0 CCGGTGCACG 0.921321 -156 TAGCACCCTCACAGTAACCGAGGCCCGCGT 3 68 1 ACAGTAACCG 0.746499 -107 CGCCCGCTACACACTACGCGGGCCTCGGTT 3 83 0 ACACTACGCG 0.976365 -92 CGGGTAAGGCACGGAGCATGGA 5 27 1 ACGGAGCATG 0.743249 -12 CCTTTTGGGTAGACATCACGTAACA 6 6 0 AGACATCACG 0.914651 -35 TCTACCCAAAAGGGAGTGCGGTGCACGG 6 23 1 AGGGAGTGCG 0.942665 -18 ********** Masking position 10 Map Score: 8.6098 Number of sites scoring better than the average of aligned sites = 2126 Number in coding regions = 1942 Number in noncoding regions = 184 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 5 CGCACAGCCTGCTCACTAGCAACACGGGAA 1 50 0 GCTCACTAGC 0.973162 -126 CTTTTGGTCTGCACCTTCGCCCAAAATCGC 2 16 1 GCACCTTCGC 0.996401 -34 AGGCGGCTCCTTAGGCGATTTTGGG 2 35 0 GCTCCTTAGG 0.964227 -15 CACTCGGGCGGCACCTCCGCACCACGCCGG 3 35 0 GCACCTCCGC 0.990334 -140 GAGTGCGTTAGCACCCTCACAGTAACCGAG 3 60 1 GCACCCTCAC 0.988375 -115 CCCTCGCGGGGCTCACTCTAGCATGTTTAA 3 147 0 GCTCACTCTA 0.846278 -28 ********** Masking position 4 Map Score: 5.46435 Number of sites scoring better than the average of aligned sites = 394 Number in coding regions = 354 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 6 ********** No masking Map Score: 7.55607e-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: 7.55607e-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: 7.55607e-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