AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00790_tpal_reg_100.orf -o00790_tpal_100.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 TP0102_TP0103 64 TP0102: rep helicase, single-stranded DNA-dependent ATPase (rep), TP0103: ATP-dependent DNA helicase, putative #3 TP0900 38 T. pallidum predicted coding region TP0900 #4 TP0901 40 conserved hypothetical integral membrane protein #5 TP1028 82 DNA helicase II (uvrD) #6 TP1030 27 T. pallidum predicted coding region TP1030 #7 TP1036 152 cation-transporting ATPase, P-type Motif number 1 ACTCTGCCTATGCACAGCAACTTCTACTGAA 1 40 0 TGCACGCAAC 0.991134 -66 TAAAAGTCCACGCAGAGCCACTCTGCCTATG 1 59 0 CGCAGGCCAC 0.986001 -47 AGTCTATGCCCTTCCACATACGGATAT 2 7 1 TGCCCTCCAC 0.983753 -58 CCGTGCACCGCACTCCCTTTTGGG 4 27 0 TGCACGCACT 0.968405 -14 GCCCGGGCGGCGCCCTGCACTGACGGCATGT 5 14 0 CGCCCGCACT 0.994571 -69 TGCAGGGCGCCGCCCGGGCGCGGTGGCACTC 5 26 1 CGCCCGGCGC 0.991357 -57 CGAAAACTGCCGCACCGCACCGAGTGCCACC 5 47 0 CGCACGCACC 0.998154 -36 GCGCAGCCCTGCAACCGAAAACTGC 5 68 0 AGCCCGCAAC 0.988626 -15 GCCTGAGCGCGCCCCGCCGCGACGCAG 6 10 1 CGCCCGCCGC 0.998873 -18 CACTGCCAGCCGCTCCTCCCCAGAGCTTTTG 7 92 1 CGCTCTCCCC 0.978417 -61 ***** ***** Masking position 3 Map Score: 23.7468 Number of sites scoring better than the average of aligned sites = 498 Number in coding regions = 448 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 2 GACTTTTATTCCTGCGTAGGAGGGGACAAAACG 1 82 1 CCTGCGGAGG 0.521899 -24 AAAAGAATATCCGTATGTGGAAGGGCATAGACT 2 11 0 CCGTAGGAAG 0.99204 -54 ATGCTCCGTGCCTTACCCGAAGGACGTAACACG 3 13 0 CCTTAGAAGG 0.667392 -26 GGAACATGCCGTCAGTGCAGGGCGCCGCCCG 5 9 1 CCGTCGCAGG 0.523402 -74 AGGGCGCCGCCCGGGCGCGGTGGCACTCGGTGC 5 29 1 CCGGGGGTGG 0.962436 -54 CTGCGTCGCGGCGGGGCGCGCTCAG 6 13 0 GCGTCGCGGG 0.947543 -15 GTTTTTTATCCGGTACATGCAAGTTTCTTGCCG 7 58 1 CGGTAGCAAG 0.949305 -95 AAGTTTCTTGCCGTCACTGCCAGCCGCTCCTCC 7 78 1 CCGTCGCCAG 0.697628 -75 AAAAACCCGTCCTGAATAGGAGGTAGTCTTTC 7 131 1 CCTGAGGAGG 0.845265 -22 ***** ***** Masking position 9 Map Score: 10.0579 Number of sites scoring better than the average of aligned sites = 449 Number in coding regions = 399 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 3 TACTGAACTAGGAAAAACAACCGCTGTATA 1 17 0 GGAAAAACAA 0.940982 -89 CTCCTACGCAGGAATAAAAGTCCACGCAGA 1 74 0 GGAATAAAAG 0.950047 -32 GCGTAGGAGGGGACAAAACGT 1 95 1 GGACAAAACG 0.982456 -11 AAAATAGGGCGGAAAAAAGAATATCCGTAT 2 28 0 GGAAAAAAGA 0.958919 -37 CTTACCCGAAGGACGTAACACGTA 3 5 0 GGACGTAACA 0.88866 -34 ACAGCAGATAGGATGAAAAGTGTACGGTTT 7 32 1 GGATGAAAAG 0.973121 -121 TGCATGTACCGGATAAAAAACCGTACACTT 7 49 0 GGATAAAAAA 0.973091 -104 ********** Masking position 7 Map Score: 4.54254 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 179 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 4 TGCTGTGCATAGGCAGAGTGGCTCTGCGTGG 1 52 1 AGGCAGGTGG 0.982628 -54 CGGGTAAGGCACGGAGCATGGA 3 27 1 ACGGAGATGG 0.834428 -12 TCTACCCAAAAGGGAGTGCGGTGCACGG 4 23 1 AGGGAGGCGG 0.993255 -18 GGAACATGCCGTCAGTGCAGGGCGCCGCCC 5 10 1 CGTCAGGCAG 0.860685 -73 CAGGGCGCCGCCCGGGCGCGGTGGCACTCGG 5 28 1 CCCGGGGCGG 0.940144 -55 GCGCGGTGGCACTCGGTGCGGTGCGGCAGTT 5 43 1 ACTCGGGCGG 0.988539 -40 CAGTTTTCGGTTGCAGGGCTGCGC 5 69 1 TTGCAGGCTG 0.805435 -14 CTGCGTCGCGGCGGGGCGCGCTCAGG 6 12 0 TCGCGGGGGG 0.944255 -16 AAAAGCTCTGGGGAGGAGCGGCTGGCAGTGA 7 91 0 GGGAGGGCGG 0.936554 -62 ACTACCTCCTATTCAGGACGGGTTTTTTATG 7 127 0 ATTCAGACGG 0.84615 -26 ****** **** Masking position 6 Map Score: 6.09905 Number of sites scoring better than the average of aligned sites = 1409 Number in coding regions = 1265 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 5 CGCCCTGCACTGACGGCATGTTCC 5 5 0 TGACGGCATG 0.997155 -78 CGGCTGGCAGTGACGGCAAGAAACTTGCAT 7 74 0 TGACGGCAAG 0.997155 -79 ********** Masking position 3 Map Score: 0.425348 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 4 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 ********** No masking Map Score: -4.16788e-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: -4.16788e-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: -4.16788e-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