AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00630_tpal_reg_300.orf -o00630_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 TP0406 190 glutamate racemase (murI) #2 TP0407 127 phosphoglycolate phosphatase (gph-1) #3 TP0553 243 conserved hypothetical integral membrane protein #4 TP0554 34 phosphoglycolate phosphatase (gph-2) #5 TP0568 121 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxyphosphogluconate aldolase (eda) #6 TP0569 24 aminopeptidase P #7 TP0570 26 T. pallidum predicted coding region TP0570 #8 TP0732 95 methylenetetrahydrofolate dehydrogenase (folD) #9 TP0757 40 polypeptide deformylase (def) #10 TP0758 118 ribosomal protein S21 (rpsU) Motif number 1 GCCGTGTATGTGTGTTGACGTATGC 1 6 1 GTATGTGTGT 0.687954 -185 AGCCCGTATAAGCTTTGCGCGCATGTTCGA 1 78 0 AGCTTTGCGC 0.881335 -113 TATACGGGCTGGACGGGTGTGGTGTCAATG 1 98 1 GGACGGGTGT 0.874167 -93 TGTCAATGTATGCGGTGTGCAGGACCTGGG 1 120 1 TGCGGTGTGC 0.713325 -71 ACTGGATATCGGGTGCGTGCACTGTGTGTG 2 18 1 GGGTGCGTGC 0.912649 -110 TGCACTGTGTGTGTTTGTGTGGAGGCGGTA 2 35 1 GTGTTTGTGT 0.658177 -93 GACAGCGCGGTGCTGCGTGCGTACAATGGG 2 82 1 TGCTGCGTGC 0.856228 -46 TATTGTCACGGAGTTTGCGTTAC 3 4 0 GAGTTTGCGT 0.74416 -240 GCGCGTGTCTTGGCGGGTGCTTCTCTCTTT 3 45 0 TGGCGGGTGC 0.944243 -199 CGCCTTCGTTCGGCCTGCGCGTGTCTTGGC 3 61 0 CGGCCTGCGC 0.877468 -183 AGTTCGATTCTGATCGGCGCCTTCGTTCGG 3 78 0 TGATCGGCGC 0.940805 -166 TTACCACTTGGGCACGGCGCCGAGGACCCC 3 137 1 GGCACGGCGC 0.88144 -107 GGCACGCTGTGACCTTGCGCAAAGGGGATT 3 221 1 GACCTTGCGC 0.840246 -23 GATATCTTGCTGCTCGGCGCCCTTTTTATT 4 12 1 TGCTCGGCGC 0.978717 -23 GTTTTCCTGTTGATTGGTGTTATACGCAGA 5 12 1 TGATTGGTGT 0.638203 -110 TCAAAAATCAAGATCTGCGTATAACACCAA 5 25 0 AGATCTGCGT 0.652762 -97 ACATTAGCTTAGGCGGGTGCACTGCATGTG 5 64 1 AGGCGGGTGC 0.85742 -58 AATTGAATCGGTGTTCTGCGTAGT 6 5 1 GAATCGGTGT 0.512596 -20 GTGTGTGCGTTGCCGCGCCA 7 1 1 GTGTGTGCGT 0.930664 -26 CGCTCTTGGCGCGGCAACGCAC 7 15 0 CTCTTGGCGC 0.764363 -12 AAACACCGTATGCTCGGCGTCGT 8 4 0 TGCTCGGCGT 0.954515 -92 TCCGTCTAGTGTCCGTGCGTGTTCGGTCTT 8 42 1 GTCCGTGCGT 0.917192 -54 TGCGTGTTCGGTCTTTGCGCTGTTGCGTGC 8 57 1 GTCTTTGCGC 0.929394 -39 CTTTGCGCTGTTGCGTGCGCGTGTCTATAC 8 69 1 TTGCGTGCGC 0.903201 -27 CGCGTGTCTATACTGGGCGC 8 86 1 TACTGGGCGC 0.931311 -10 GACACGTAGGGTGTGCGTGCAGGGGAGG 10 9 1 GGGTGTGCGT 0.978498 -110 ********** Masking position 7 Map Score: 29.0203 Number of sites scoring better than the average of aligned sites = 5476 Number in coding regions = 5034 Number in noncoding regions = 442 Number of orfs with sites within 600 bp upstream = 254 Fraction of orfs with sites within 600 bp upstream = 0.0407967 Motif number 2 TTGACGTATGCATGAGCTTAGCAAAGTCCGACG 1 25 1 CGGCTTAGCA 0.749056 -166 CGTGTTATCCCCAGGTCCTGCACACCGCATACA 1 126 0 CGTCCTGCAC 0.842481 -65 AGACATCATCCTAGCCTGTTCTTTGA 1 175 0 CCTCCTAGCC 0.94837 -16 CCTCTCTTATCTACCGCCTCCACACAAACACAC 2 43 0 CCGCCTCCAC 0.975679 -85 TGCACGAAACCTCGGCTTCCCCATGGCCCATT 2 106 0 CCGCTTCCCC 0.99101 -22 AAGAGAGAAGCACCCGCCAAGACACGCGCAGGC 3 46 1 CCGCCAAGAC 0.554413 -198 CGGCGCCTTCGTTCGGCCTGCGCGTGTCTTGGC 3 61 0 GCGCCTGCGC 0.889374 -183 TTTTGCAGACCTCTCCCTTACCACTTGGGCACG 3 120 1 CTCCTTACCA 0.53691 -124 GAGGGGTCCTCGGCGCCGTGCCCAAGTGGTAAG 3 136 0 CCCCGTGCCC 0.928885 -108 TCATAAAGGACATTAGCTTAGGCGGGTGCACTG 5 55 1 CTGCTTAGGC 0.834191 -67 AATTCCCTCCTCTTGCCCGCGGACATCT 5 104 0 CCTCTTGCCC 0.96991 -18 TACGGTGTTTCTTGGGCTTCCGTCTAGTGTCCG 8 24 1 CGGCTTCCGT 0.557125 -72 GGTCTTTGCGCTGTTGCGTGCGCGTGTCTATAC 8 66 1 CTGCGTGCGC 0.887487 -30 CGCCTCTTCCCGCTCTTACCCAAGAGAAACT 9 20 0 CGTCTTACCC 0.935158 -21 TCCGAAAGCACTCCTGCCTCCCCTGCACGCACA 10 22 0 CCGCCTCCCC 0.995055 -97 ACGTCTTTTGCGCTAGCCTACCCCTGGTAGGCT 10 73 1 CTGCCTACCC 0.985721 -46 CCTGAAAAAAACACAGCCTACCAGGGGTAGGCT 10 87 0 ACGCCTACCA 0.665701 -32 * * ******** Masking position 7 Map Score: 15.1391 Number of sites scoring better than the average of aligned sites = 1794 Number in coding regions = 1638 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 3 GTTCGAACCCACACCGTATTGCTCTACGTC 1 54 0 ACACCGTATT 0.938982 -137 CAGGTCCTGCACACCGCATACATTGACACC 1 118 0 ACACCGCATA 0.882162 -73 AATTTCACAGGAACCGTGTTATCCCCAGGT 1 143 0 GAACCGTGTT 0.845614 -48 ACACGGCACTGGATATCGGG 2 1 1 ACACGGCACT 0.912604 -127 TCGGGTGCGTGCACTGTGTGTGTTTGTGTG 2 26 1 GCACTGTGTG 0.968026 -102 TACGCACGCAGCACCGCGCTGTCTATCAGC 2 75 0 GCACCGCGCT 0.981099 -53 GTAACGCAAACTCCGTGACAATACAAA 3 8 1 AAACTCCGTG 0.593519 -236 TACCACTTGGGCACGGCGCCGAGGACCCCT 3 138 1 GCACGGCGCC 0.923375 -106 GATACTCCAGGCACGCTGTGACCTTGCGCA 3 212 1 GCACGCTGTG 0.942938 -32 TTAGGCGGGTGCACTGCATGTGGTGTCTGA 5 72 1 GCACTGCATG 0.968026 -50 AGCCCAAGAAACACCGTATGCTCGGCGTCG 8 12 0 ACACCGTATG 0.973016 -84 CCCTGCACGCACACCCTACGTGTC 10 5 0 ACACCCTACG 0.911482 -114 ********** Masking position 3 Map Score: 10.1427 Number of sites scoring better than the average of aligned sites = 1931 Number in coding regions = 1766 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 4 CGGTTGGTTTACCCTTGAACGATTGCGTCTT 3 182 0 ACCCTTGACG 0.955121 -62 GGTAATCCCCTTTGCGCAAGGTCACA 3 228 0 TCCCCTTGCG 0.958833 -16 CACTCCTGCCTCCCCTGCACGCACACCCTAC 10 16 0 TCCCCTGACG 0.996119 -103 GCAAAAGACGTCCCCTGTCAATCGTTTCTTC 10 53 0 TCCCCTGCAA 0.970014 -66 GCGCTAGCCTACCCCTGGTAGGCTGTGTTTT 10 82 1 ACCCCTGTAG 0.971928 -37 CGACCCTCCCCTGAAAAAAACACAGCC 10 102 0 TCCCCTGAAA 0.982188 -17 ******* *** Masking position 6 Map Score: 3.12919 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 153 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 GTGGTAAGGGAGAGGTCTGCAAAACCTTTA 3 114 0 AGAGGTCTGC 0.985694 -130 TGTTAGCCTGAGGGGTCCTCGGCGCCGTGC 3 148 0 AGGGGTCCTC 0.98672 -96 GTGTCTGAAAAGATGTCCGCGGGCAAGAGG 5 94 1 AGATGTCCGC 0.985698 -28 CTAGCGCAAAAGACGTCCCCTGTCAATCGT 10 59 0 AGACGTCCCC 0.974423 -60 ACAGCCTACCAGGGGTAGGCTAGCGCAAAA 10 78 0 AGGGGTAGGC 0.954814 -41 ********** Masking position 6 Map Score: 1.34743 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 51 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 CCGCATACATTGACACCACACCCGTCCAGC 1 105 0 TGACACCACA 0.988683 -86 CCCAGGTCCTGCACACCGCATACATTGACA 1 120 0 GCACACCGCA 0.953135 -71 GCAAACTCCGTGACAATACAAAACTGGGAA 3 16 1 TGACAATACA 0.820407 -228 ACGGCGCCGAGGACCCCTCAGGCTAACAAA 3 150 1 GGACCCCTCA 0.956296 -94 ACATCTTTTCAGACACCACATGCAGTGCAC 5 80 0 AGACACCACA 0.980221 -42 GAACACGCACGGACACTAGACGGAAGCCCA 8 36 0 GGACACTAGA 0.938481 -60 ********** Masking position 3 Map Score: 1.29364 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 96 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 7 ACATCATCCTAGCCTGTTCTTTGAAAAATT 1 169 0 AGCCTGTTCT 0.850638 -22 GCTGTCTATCAGCCTCTCTTATCTACCGCC 2 58 0 AGCCTCTCTT 0.965233 -70 TCTTGGCGGGTGCTTCTCTCTTTTCCCAGT 3 38 0 TGCTTCTCTC 0.917272 -206 GTTCGGCCTGCGCGTGTCTTGGCGGGTGCT 3 54 0 CGCGTGTCTT 0.950905 -190 CTTGAACGATTGCGTCTTTTTTTGTTAGCC 3 170 0 TGCGTCTTTT 0.900204 -74 CTGTTGCGTGCGCGTGTCTATACTGGGCGC 8 76 1 CGCGTGTCTA 0.800841 -20 GCGGGTATGAGTTTCTCTTGGGTAAGAGC 9 10 1 AGTTTCTCTT 0.699139 -31 CGCCTCTTCCCGCTCTTACC 9 31 0 CGCCTCTTCC 0.95627 -10 AAAGCACTCCTGCCTCCCCTGCACGCACAC 10 21 0 TGCCTCCCCT 0.862503 -98 CCCTGTCAATCGTTTCTTCCGAAAGCACTC 10 42 0 CGTTTCTTCC 0.646686 -77 ********** Masking position 5 Map Score: 1.16369 Number of sites scoring better than the average of aligned sites = 904 Number in coding regions = 814 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 8 ********** No masking Map Score: 2.54618e-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 9 ********** No masking Map Score: 2.54618e-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 10 ********** No masking Map Score: 2.54618e-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