AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00620_tpal_reg_300.orf -o00620_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 TP0037 96 D-specific D-2-hydroxyacid dehydrogenase #2 TP0038 48 regulatory protein (pfoS/R) #3 TP0054 170 conserved hypothetical protein #4 TP0055 206 T. pallidum predicted coding region TP0055 #5 TP0091 181 cysteinyl-tRNA synthetase (cysS) #6 TP0092 70 RNA polymerase sigma-24 factor (rpoE) #7 TP0094 137 phosphate acetyltransferase (pta) #8 TP0476 66 acetate kinase (ack) #9 TP0477 60 glucose-6-phosphate 1-dehydrogenase, putative #10 TP0478 72 glucose-6-phosphate 1-dehydrogenase (zwf) #11 TP0479 111 T. pallidum predicted coding region TP0479 Motif number 1 CTCACGCAGGACCTGGGCGGAAACACATAAC 1 22 0 ACTGGGCGGA 0.953712 -75 AGAGACTTAAAATGGCGCGGACTGCAGCCAG 2 12 0 AAGGCGCGGA 0.993248 -37 ACCTCCTCCTGAGTGCGGGCACAGGGTAGTA 3 17 1 GATGCGGGCA 0.910813 -154 GTTCTCAGAGGCACACGCGGACGCACGTCAA 4 75 0 GCCACGCGGA 0.888907 -132 CTTATGCTACAATGGCGCGGTCTTGGCCTTC 5 39 1 AAGGCGCGGT 0.965028 -143 AGACTGAAGCGCAGGCGGGCAAAGGCGTTTG 5 90 1 GCGGCGGGCA 0.983685 -92 GCCCAGCCCCATTGTCGCGCAAACGCCTTTG 5 109 0 ATGTCGCGCA 0.847829 -73 CGGGCGCAGAACACGTGCGGACCACGCCCAG 5 134 0 ACCGTGCGGA 0.871998 -48 AGTTTCTCCCAACCGGGCGCAGAACACGTGC 5 147 0 AACGGGCGCA 0.990057 -35 GAGAAACTTCGAAGGGGCGCAC 5 170 1 GAGGGGCGCA 0.997502 -12 AAACACGTCCGCGCGGGCGCATTATTTTTAC 7 27 0 GCCGGGCGCA 0.993996 -111 GAAAGTGGCGCATTTTGCGTGT 8 2 1 AAGTGGCGCA 0.975367 -65 ACCTACACCGGATGTGCCGCAGGCAGACTCT 10 26 0 GAGTGCCGCA 0.858558 -47 ACCGTTGAAAGAAGGGGCGGTTT 10 60 1 GAGGGGCGGT 0.980566 -13 AGAAAAACTTGACGGCGCGCGCTAAACGCCT 11 49 0 GAGGCGCGCG 0.984367 -63 ** ******** Masking position 9 Map Score: 22.4476 Number of sites scoring better than the average of aligned sites = 1455 Number in coding regions = 1328 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 2 GAGACGCTCCTTACGGAGAGACTT 2 35 0 GACCTCTTAC 0.79545 -14 TACCTCACACCCGTCTACTTTCCCTACTC 4 8 0 CCGCTCTTTC 0.98087 -199 GACAACAGAGCAGGCTGCGTTCTCAGAGGCAC 4 92 0 CAGCTCGTTC 0.971902 -115 CTTGCACAAAGCGTCTTTTTTTTTTACCCTCG 4 146 1 GCGCTTTTTT 0.602391 -61 GCCTGCGCTTCAGTCTACCCTCCCTCGAAACG 5 74 0 CAGCTCCCTC 0.893377 -108 ACGCCTTTGCCCGCCTGCGCTTCAGTCTACCC 5 86 0 CCGCTCGCTT 0.971565 -96 GCTCTTAAAAGCTCCTGCTCATGCAACAATGT 6 24 0 GCTCTCTCAT 0.804211 -47 AAATCTGCATCATCCTGTGCTCTTAAAAGCTC 6 42 0 CATCTTGCTC 0.789653 -29 AGACATTCTCCTTATGGCTACCTGA 7 123 0 CATCTCTTAT 0.769438 -15 AATACACCTCCACCGTTTTGGTAATTTC 8 49 0 CCTCACGTTT 0.666995 -18 CCTCCTCTCTCCCGCTACGTTCTAGTGTCGTT 9 29 0 CCCCTCGTTC 0.978215 -32 GGGCGAACATCCTCCTCTCTCCCGCTACG 9 42 0 CATCTCTCTC 0.971976 -19 GCCGCAGGCAGACTCTCCGCTCCCTAAGGCA 10 10 0 GACCTCGCTC 0.955307 -63 AAACCGCCCCTTCTTTCAACGGTGCGA 10 56 0 GCCCTCTTTC 0.961752 -17 GAGCTCCTCCTTTTTCTAAAGGCT 11 3 1 GCTCTCTTTT 0.929119 -109 CACCGTTTGGCATACTCCTCTTCGCAAGGAAG 11 80 1 CATCTCTCTT 0.944163 -32 *** ** ***** Masking position 5 Map Score: 16.1833 Number of sites scoring better than the average of aligned sites = 828 Number in coding regions = 723 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 3 TCTGCACGTATCTCACGCAGGACCTGGGCGG 1 33 0 TCTCACCAGG 0.981632 -64 AAACAACATTCCTTACCCACGTTCTGCACGT 1 55 0 CCTTACCACG 0.942588 -42 ATGTTGTTTGCCTTACCAAGGAGGTGCGAA 1 77 1 CCTTACAAGG 0.597035 -20 ATTTTAAGTCTCTCCGTAAGGAGCGTCTC 2 30 1 TCTCCGAAGG 0.916232 -19 TACCCTGTGCCCGCACTCAGGAGGAGGTTTC 3 14 0 CCGCACCAGG 0.951581 -157 AGGTTCCATACCTCACACCCGTCTACTTTCC 4 17 0 CCTCACCCCG 0.977352 -190 AGCCCCATTGTCGCGCAAACGCCTTTGCCCG 5 105 0 TCGCGCAACG 0.810668 -77 CTTCGAAGTTTCTCCCAACCGGGCGCAGAAC 5 153 0 TCTCCCACCG 0.972811 -29 CGAACATCCTCCTCTCTCCCGCTACGTTCTA 9 37 0 CCTCTCCCCG 0.949425 -24 CAGACTCTCCGCTCCCTAAGGCA 10 3 0 GCTCCCAAGG 0.94612 -70 AACCGCCCCTTCTTTCAACGGTGCGACCTAC 10 51 0 TCTTTCACGG 0.835392 -22 GGCATACTCCTCTTCGCAAGGAAGGGGGGAG 11 88 1 TCTTCGAAGG 0.732835 -24 ****** **** Masking position 2 Map Score: 10.2569 Number of sites scoring better than the average of aligned sites = 469 Number in coding regions = 405 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 4 ATCTCACGCAGGACCTGGGCGGAAACACAT 1 25 0 GGACCTGGGC 0.817474 -72 GATACGTGCAGAACGTGGGTAAGGAATGTT 1 52 1 GAACGTGGGT 0.470781 -45 CCCGCACTCAGGAGGAGGTTTCATC 3 6 0 GGAGGAGGTT 0.977818 -165 AAAATGTCTGTCTGCAGGGCTCTGTGTCTT 3 87 1 TCTGCAGGGC 0.659748 -84 CTGTGTCTTGTGTGGTGGTCCCTGTTTTGT 3 108 1 TGTGGTGGTC 0.873431 -63 CCCTGTTTTGTGGGTAGGTTTGGGGAAACC 3 127 1 TGGGTAGGTT 0.682329 -44 AACCAATTGCGCTGTAGGTTCCATACCTCA 4 33 0 GCTGTAGGTT 0.67652 -174 AGGCGAACGGGGTCGAGGGTAAAAAAAAAA 4 161 0 GGTCGAGGGT 0.952604 -46 TATGCTACAATGGCGCGGTCTTGGCCTTCT 5 41 1 TGGCGCGGTC 0.709207 -141 TTTGCGTTTCGAGGGAGGGTAGACTGAAGC 5 70 1 GAGGGAGGGT 0.907932 -112 AGACTGAAGCGCAGGCGGGCAAAGGCGTTT 5 90 1 GCAGGCGGGC 0.914724 -92 GCGCGACAATGGGGCTGGGCGTGGTCCGCA 5 120 1 GGGGCTGGGC 0.9498 -62 TTACCAAAACGGTGGAGGTGTATT 8 53 1 GGTGGAGGTG 0.921311 -14 GCGGGAGAGAGGAGGATGTTCGCCC 9 46 1 GGAGGATGTT 0.686138 -15 CGGCACATCCGGTGTAGGTCGCACCGTTGA 10 38 1 GGTGTAGGTC 0.942505 -35 TTTAGAAAAAGGAGGAGCTC 11 1 0 GGAGGAGCTC 0.869212 -111 CGCAAGGAAGGGGGGAGGGC 11 102 1 GGGGGAGGGC 0.99429 -10 ********** Masking position 7 Map Score: 14.9924 Number of sites scoring better than the average of aligned sites = 1615 Number in coding regions = 1394 Number in noncoding regions = 221 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 5 TTCCGCCCAGGTCCTGCGTGAGATACGTGC 1 31 1 GTCCTGCGTG 0.980636 -66 TTCGCACCTCCTTGGTAAGGCAAA 1 83 0 CACCTCCTTG 0.939578 -14 ATGAAACCTCCTCCTGAGTGCGGGCACAGG 3 12 1 CTCCTGAGTG 0.835506 -159 AACGGATTTCCTACGTCTCTGTTAGGT 3 154 0 TTCCTACGTC 0.762953 -17 AGTGCGTGTTGACGTGCGTCCGCGTGTGCC 4 67 1 GACGTGCGTC 0.753509 -140 TTTACAAGTTTTCCTACGCGACAACAGAGC 4 113 0 TTCCTACGCG 0.890908 -94 GCGGGCAACTCCTACGTGATGAATTCAG 4 189 0 CTCCTACGTG 0.968905 -18 CGCCTTTGCCCGCCTGCGCTTCAGTCTACC 5 87 0 CGCCTGCGCT 0.838808 -95 GTCCGCACGTGTTCTGCGCCCGGTTGGGAG 5 143 1 GTTCTGCGCC 0.731946 -39 CTCTTAAAAGCTCCTGCTCATGCAACAATG 6 25 0 CTCCTGCTCA 0.833652 -46 GAACAGGAAACACGTCCGCGCGGGCGCATT 7 35 0 CACGTCCGCG 0.898229 -103 AAACTTGATTGACCTGCTTGTCAGGTAGCC 7 103 1 GACCTGCTTG 0.924054 -35 AATACACCTCCACCGTTTTGGTAA 8 53 0 CACCTCCACC 0.873324 -14 TCAACGGTGCGACCTACACCGGATGTGCCG 10 38 0 GACCTACACC 0.664454 -35 GAGCTCCTCCTTTTTCTAAAGGC 11 4 1 CTCCTCCTTT 0.798669 -108 GTTTGGCATACTCCTCTTCGCAAGGAAGGG 11 84 1 CTCCTCTTCG 0.676154 -28 ********** Masking position 5 Map Score: 9.45833 Number of sites scoring better than the average of aligned sites = 2561 Number in coding regions = 2332 Number in noncoding regions = 229 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 6 GCTGCAGTCCGCGCCATTTTAAGTCTCTCC 2 15 1 GCGCCATTTT 0.905429 -34 TTTACGCCCGCCGCAATTGAGAATTCAAAG 3 59 0 CCGCAATTGA 0.558024 -112 GGAACCTACAGCGCAATTGGTTTTGCAGTG 4 41 1 GCGCAATTGG 0.953519 -166 GGCCAAGACCGCGCCATTGTAGCATAAGCG 5 37 0 GCGCCATTGT 0.977462 -145 GTAGACTGAAGCGCAGGCGGGCAAAGGCGT 5 88 1 GCGCAGGCGG 0.829579 -94 ACCACGCCCAGCCCCATTGTCGCGCAAACG 5 115 0 GCCCCATTGT 0.956875 -67 CGTGTTCTGCGCCCGGTTGGGAGAAACTTC 5 150 1 GCCCGGTTGG 0.932775 -32 GTGCGCCCCTTCGAAGTTTCTCCC 5 168 0 GCCCCTTCGA 0.91961 -14 TAATGCGCCCGCGCGGACGTGTTTCCTGTT 7 34 1 GCGCGGACGT 0.713167 -104 GAAAGTGGCGCATTTTGCGTGTATGCT 8 8 1 GCGCATTTTG 0.738419 -59 GGTGTAGGTCGCACCGTTGAAAGAAGGGGC 10 48 1 GCACCGTTGA 0.846222 -25 AAACCGCCCCTTCTTTCAACGGTGC 10 58 0 GCCCCTTCTT 0.756764 -15 CGTTTAGCGCGCGCCGTCAAGTTTTTCTCA 11 52 1 GCGCCGTCAA 0.83327 -60 ********** Masking position 4 Map Score: 8.38652 Number of sites scoring better than the average of aligned sites = 987 Number in coding regions = 903 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 7 ATATCCTATATGTTATGTGTTTCCGCCCAG 1 11 1 TGTTATGTGT 0.964991 -86 CAGGGCTCTGTGTCTTGTGTGGTGGTCCCT 3 101 1 TGTCTTGTGT 0.976107 -70 TGGTGGTCCCTGTTTTGTGGGTAGGTTTGG 3 120 1 TGTTTTGTGG 0.976107 -51 AAATCGTATATGTTTTCTGTCC 5 3 0 TGTTTTCTGT 0.984192 -179 CGCGCGGACGTGTTTCCTGTTCTTTTCAAA 7 43 1 TGTTTCCTGT 0.965573 -95 ********** Masking position 3 Map Score: 2.8273 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 15 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 GTGAGATACGTGCAGAACGTGGGTAAGGAA 1 48 1 TGCAGAACGT 0.966116 -49 TGGCGCGGACTGCAGCCAGT 2 1 0 TGCAGCCAGT 0.984014 -48 CACAGAGCCCTGCAGACAGACATTTTTACG 3 83 0 TGCAGACAGA 0.976488 -88 CAATTGGTTTTGCAGTGCGTGTTGACGTGC 4 54 1 TGCAGTGCGT 0.943582 -153 CAATCAAGTTTGCAGACAGGAACACCCAAC 7 84 0 TGCAGACAGG 0.984014 -54 ********** Masking position 4 Map Score: 1.84225 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 28 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 GTCCATCAAGTATACTACCCTGTGCCCGCACT 3 28 0 TATACTACTG 0.972269 -143 TTCACGCGCTTATGCTACAATGGCGCGGTCTT 5 31 1 TATGCTACTG 0.992555 -151 AGCTCCTGCTCATGCAACAATGTATCTCCCAA 6 15 0 CATGCAACTG 0.969879 -56 ATTTTGCGTGTATGCTACGGTGTCCGAGAAAT 8 22 1 TATGCTACTG 0.992982 -45 ******** ** Masking position 7 Map Score: 0.659716 Number of sites scoring better than the average of aligned sites = 3 Number in coding regions = 1 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 10 ********** No masking Map Score: 3.38462e-12 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 11 ********** No masking Map Score: 3.38462e-12 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 12 ********** No masking Map Score: 3.38462e-12 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