AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00790_tpal_reg_300.orf -o00790_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 TP0060 105 ribosomal protein L9 (rplI) #2 TP0061 116 ribosomal protein S18 (rpsR) #3 TP0063 141 ribosomal protein S6 (rpsF) #4 TP0102_TP0103 64 TP0102: rep helicase, single-stranded DNA-dependent ATPase (rep), TP0103: ATP-dependent DNA helicase, putative #5 TP0900 38 T. pallidum predicted coding region TP0900 #6 TP0901 40 conserved hypothetical integral membrane protein #7 TP1028 82 DNA helicase II (uvrD) #8 TP1030 27 T. pallidum predicted coding region TP1030 #9 TP1036 152 cation-transporting ATPase, P-type Motif number 1 GCTGTGCATAGGCAGAGTGGCTCTGCGTGGAC 1 53 1 GGCGGTGGCT 0.993261 -53 GCGGCGAGACGCCAGCGTAGCGTAAATCTGTG 3 42 0 GCCGGTAGCG 0.986171 -100 AGCGTGCGCAGAACGCGCGGCGAGACGCCAGC 3 58 0 GAAGGCGGCG 0.988218 -84 CACCCGACAAGGAGGAGTAGCGTGCGCAGAAC 3 76 0 GGAGGTAGCG 0.985623 -66 CTACCCAAAAGGGAGTGCGGTGCACGG 6 24 1 GGGGGCGGTG 0.980488 -17 GGAACATGCCGTCAGTGCAGGGCGCCGCCCGG 7 11 1 GTCGGCAGGG 0.934118 -72 GTGCCACCGCGCCCGGGCGGCGCCCTGCACTG 7 23 0 GCCGGCGGCG 0.99498 -60 TGGCACTCGGTGCGGTGCGGCAGTTTTCGGTT 7 49 1 TGCGGCGGCA 0.953509 -34 AGTTTTCGGTTGCAGGGCTGCGC 7 70 1 TGCGGCTGCG 0.975305 -13 CTGCGTCGCGGCGGGGCGCGCTC 8 15 0 TGCTGCGGCG 0.980745 -13 AAAGCTCTGGGGAGGAGCGGCTGGCAGTGACG 9 89 0 GGAGGCGGCT 0.994123 -64 *** * ****** Masking position 7 Map Score: 20.9614 Number of sites scoring better than the average of aligned sites = 580 Number in coding regions = 533 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 2 GCCACTCTGCCTATGCACAGCAACTTCTAC 1 44 0 CTATGCACAG 0.766852 -62 GAATAAAAGTCCACGCAGAGCCACTCTGCC 1 63 0 CCACGCAGAG 0.790408 -43 TATTCATTATGCATGCTCCTTGTGGGGAAA 2 16 0 GCATGCTCCT 0.71994 -101 CAGGCGAACGCCAGGTTCGGTCATACTTTT 2 45 0 CCAGGTTCGG 0.875728 -72 TAGCGTAAATCTGTGTGCCGCATCAAGTCT 3 27 0 CTGTGTGCCG 0.898641 -115 AGGAGGAGTAGCGTGCGCAGAACGCGCGGC 3 69 0 GCGTGCGCAG 0.847424 -73 AATAACTCCTATGGACGGCTCACCTTAT 3 124 0 CTATGGACGG 0.561293 -18 TCCATGCTCCGTGCCTTACCC 5 28 0 CCATGCTCCG 0.990835 -11 CCGTGCACCGCACTCCCTTT 6 31 0 CCGTGCACCG 0.603846 -10 GCCGTCAGTGCAGGGCGCCGCCCGGGCGCG 7 18 1 CAGGGCGCCG 0.975188 -65 AGGGCGCCGCCCGGGCGCGGTGGCACTCGG 7 29 1 CCGGGCGCGG 0.571487 -54 AAAACTGCCGCACCGCACCGAGTGCCACCG 7 46 0 CACCGCACCG 0.825052 -37 TTTTCGGTTGCAGGGCTGCGC 7 72 1 CAGGGCTGCG 0.854436 -11 TCGCGGCGGGGCGCGCTCAGGC 8 3 0 GCGCGCTCAG 0.92656 -25 CAAGAAACTTGCATGTACCGGATAAAAAAC 9 58 0 GCATGTACCG 0.907299 -95 ********** Masking position 5 Map Score: 16.9187 Number of sites scoring better than the average of aligned sites = 2687 Number in coding regions = 2442 Number in noncoding regions = 245 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 3 GACTTTTATTCCTGCGTAGGAGGGGACAAAAC 1 82 1 CCTCTAGGAG 0.992637 -24 GTCTCTTTCCCCACAAGGAGCATGCATAAT 2 9 1 CCCAAAGGAG 0.996553 -108 CTAATTTTTCCACTTCTAGGAGCATATC 2 99 1 CACTTAGGAG 0.909823 -18 ACTAGACTCACCCGACAAGGAGGAGTAGCGTG 3 84 0 CCCAAAGGAG 0.996856 -58 TCTAGTGCAGCCTGATAAGGTGAGCCGTCCAT 3 110 1 CCTAAAGGTG 0.972896 -32 TAAGGTGAGCCGTCCATAGGAGTTATT 3 125 1 CGTCTAGGAG 0.96225 -17 GTGATGTCTACCCAAAAGGGAGTGCGGTGCAC 6 17 1 CCCAAGGGAG 0.988022 -24 AAAAACCCGTCCTGAATAGGAGGTAGTCTTTC 9 131 1 CCTATAGGAG 0.995032 -22 *** * ****** Masking position 9 Map Score: 14.9592 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 28 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 4 TACTGAACTAGGAAAAACAACCGCTGTATAC 1 16 0 GGAAAACAAC 0.960087 -90 CTGCGTAGGAGGGGACAAAACGT 1 93 1 GGGACAAAAC 0.970531 -13 GCTCCTTGTGGGGAAAGAGAC 2 1 0 GGGAAGAGAC 0.993233 -116 CGGATAAAAGGACAAAAGACTTGATGCGGC 3 10 1 GGAAAAAGAC 0.989518 -132 AAAATAGGGCGGAAAAAAGAATATCCGTATG 4 27 0 GGAAAAAGAA 0.91336 -38 TACGTCCTTCGGGTAAGGCACGGAGCATGGA 5 18 1 GGGAAGGCAC 0.943964 -21 TGCATGTACCGGATAAAAAACCGTACACTTT 9 48 0 GGAAAAAAAC 0.98737 -105 CTGGCAGTGACGGCAAGAAACTTGCATGTAC 9 70 0 CGGAAGAAAC 0.952642 -83 *** ******* Masking position 5 Map Score: 7.89563 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 126 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 TCCTTTCTGAGGTCCAGGCGAACGCCAGGT 2 59 0 GGTCCAGGCG 0.935499 -58 GCTACGCTGGCGTCTCGCCGCGCGTTCTGC 3 53 1 CGTCTCGCCG 0.903277 -89 GGGTGAGTCTAGTGCAGCCTGATAAGGTGA 3 103 1 AGTGCAGCCT 0.799384 -39 CTCCTATGGACGGCTCACCTTATCAGGCTG 3 117 0 CGGCTCACCT 0.700736 -25 AGACGCACAAGCGTAGCAAAATA 4 52 0 CGCACAAGCG 0.840644 -13 TGCAGGGCGCCGCCCGGGCGCGGTGGCACT 7 26 1 CGCCCGGGCG 0.499638 -57 CACCGCACCGAGTGCCACCGCGCCCGGGCG 7 36 0 AGTGCCACCG 0.926901 -47 GCGCAGCCCTGCAACCGAAAACTGCCG 7 66 0 CCTGCAACCG 0.879048 -17 GCCTGAGCGCGCCCCGCCGCGACGCAG 8 10 1 CGCCCCGCCG 0.730048 -18 CTTGCCGTCACTGCCAGCCGCTCCTCCCCA 9 84 1 CTGCCAGCCG 0.814328 -69 ********** Masking position 9 Map Score: 5.54964 Number of sites scoring better than the average of aligned sites = 1092 Number in coding regions = 985 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 6 TCCTACGCAGGAATAAAAGTCCACGCAGAG 1 73 0 GAATAAAAGT 0.978151 -33 CATGCATAATGAATAAAAGTATGACCGAAC 2 31 1 GAATAAAAGT 0.978151 -86 CGGATAAAAGGACAAAAGACT 3 2 1 GGATAAAAGG 0.983154 -140 AAAATAGGGCGGAAAAAAGAATATCCGTAT 4 28 0 GGAAAAAAGA 0.902989 -37 CAGCAGATAGGATGAAAAGTGTACGGTTTT 9 33 1 GATGAAAAGT 0.772647 -120 TGCATGTACCGGATAAAAAACCGTACACTT 9 49 0 GGATAAAAAA 0.830333 -104 AACCCGTCCTGAATAGGAGGTAGTCTTTC 9 134 1 GAATAGGAGG 0.820649 -19 ********** Masking position 5 Map Score: 2.43616 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 120 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 ********** No masking Map Score: -5.94424e-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: -5.94424e-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 9 ********** No masking Map Score: -5.94424e-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