AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00252_tpal_reg_100.orf -o00252_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 TP0223 267 aspartate aminotransferase (tpaaT) #2 TP0556 104 asparagine synthetase (asnA) #3 TP0609 300 asparaginyl-tRNA synthetase (asnS) #4 TP0681 88 alanine racemase (alr) #5 TP0682 92 cell division protein (ftsJ) #6 TP0985 143 aspartyl-tRNA synthetase (aspS) #7 TP1017 171 alanyl-tRNA synthetase (alaS) Motif number 1 GCACACAAGCCCGCGCAGCCACACGGATGA 1 43 0 CCGCGCAGCC 0.962126 -225 CACAGTGTAGACACGCCCCCTGACCCTGTC 1 112 0 ACACGCCCCC 0.968228 -156 TTTAACGCACGCGCGCCTTCAGAGAGGTCC 1 148 0 GCGCGCCTTC 0.986616 -120 CGTGCGTTAAACGCTGCTCTTGAAGGAACG 1 167 1 ACGCTGCTCT 0.547089 -101 ACGGTGGTGCACGCGCTGTTATCTCCTCTT 1 194 1 ACGCGCTGTT 0.818925 -74 TGGGGAAAATACGCGCGCAAACCAAGAGGA 1 217 0 ACGCGCGCAA 0.607492 -51 CCGCGCCTCTGCATTCTGTG 1 258 0 CCGCGCCTCT 0.987016 -10 AGTAAACTGTGCACGCATTATTTAATAGGG 2 58 0 GCACGCATTA 0.573587 -47 TGAACGATTACCGCGCCTATAAGACTCC 3 9 0 CCGCGCCTAT 0.913515 -292 AATCGTTCACCCGCGCGTCCTTTCTGCGGG 3 30 1 CCGCGCGTCC 0.969282 -271 GTGACCGGGACCACGCCGTACGACATAGAA 3 91 0 CCACGCCGTA 0.976307 -210 TCACAGAAGACCGCGCCTCGGCCGCTCCTC 3 117 1 CCGCGCCTCG 0.959002 -184 CGCGCCTCGGCCGCTCCTCATCTAGAGAGT 3 128 1 CCGCTCCTCA 0.909585 -173 CCCCAGTCCTGCGCGGCGTTCCATGCAGAT 3 203 1 GCGCGGCGTT 0.947183 -98 CGCACGCCCTGCGCGGCATCTGCATGGAAC 3 220 0 GCGCGGCATC 0.76841 -81 AGCTGTGACGCCACGGCGCACGCCCTGCGC 3 236 0 CCACGGCGCA 0.945304 -65 GCTTGCCGGTCCACGCCCTTCCACAAAGAG 3 266 1 CCACGCCCTT 0.946435 -35 ACAGGCGCCTACGCTCCCTATTCTTACCCA 4 11 0 ACGCTCCCTA 0.794445 -78 CAAAAGGCAAACACGCCGTATAACGGTACT 5 11 0 ACACGCCGTA 0.958048 -82 ACCTTCCTACACGCCCCCCATGCTATGT 5 75 0 ACACGCCCCC 0.968228 -18 CGCGGTCTGTGCGCGGCGTAATGGAATCTT 6 32 0 GCGCGGCGTA 0.959378 -112 GCTACACTTCGCGCGCGGTCTGTGCGCGGC 6 45 0 GCGCGCGGTC 0.96323 -99 AACAGGTGGTACACGCTGCCCGATGAACAC 6 105 1 ACACGCTGCC 0.825195 -39 ********** Masking position 4 Map Score: 36.3652 Number of sites scoring better than the average of aligned sites = 2683 Number in coding regions = 2449 Number in noncoding regions = 234 Number of orfs with sites within 600 bp upstream = 180 Fraction of orfs with sites within 600 bp upstream = 0.028911 Motif number 2 CCACACGGATGAGCTTCCTGCGGCAAATGGTT 1 23 0 GGTTCCTGCG 0.959848 -245 GCGCGGGCTTGTGTGCTCTGAAGTCGGGCTGT 1 57 1 GGGCTCTGAA 0.809006 -211 GTGAGACATGGACCTCTCTGAAGGCGCGCGTG 1 139 1 GCTCTCTGAA 0.911091 -129 CCTCTCTGAAGGCGCGCGTGCGTTAAACGCTG 1 151 1 GCCGCGTGCG 0.843384 -117 CCGCGCCTCTGCATTCTGTGCAACAATCCCGT 1 246 0 GATCTGTGCA 0.966923 -22 ACCTTGTTGAGTAAACTGTGCACGCATTATTT 2 65 0 GAACTGTGCA 0.867545 -40 TCACCCGCGCGTCCTTTCTGCGGGAGTGTTTC 3 36 1 GCTTTCTGCG 0.960635 -265 CCGAGGCGCGGTCTTCTGTGACCGGGACCACG 3 106 0 GCTCTGTGAC 0.832145 -195 ACTGGGGAGAGCGAACCGTGCGAAAAAGCGTC 3 178 0 GGACCGTGCG 0.972674 -123 GTCCTGCGCGGCGTTCCATGCAGATGCCGCGC 3 208 1 GGTCCATGCA 0.846521 -93 ACGCCACGGCGCACGCCCTGCGCGGCATCTGC 3 227 0 GAGCCCTGCG 0.946692 -74 CGGCGTGTTTGCCTTTTGTGCGAGCACGATGT 5 23 1 GCTTTGTGCG 0.969959 -70 CACTTCGCGCGCGGTCTGTGCGCGGCGTAATG 6 39 0 GGTCTGTGCG 0.994857 -105 CGAGAGGCTAGAGGTGTGTGCGAATTCTGTCA 7 53 1 GGTGTGTGCG 0.97651 -119 AAAGAAACGGGGACTCTCTGAGCAACCTTGCG 7 95 0 GATCTCTGAG 0.936419 -77 * * ******** Masking position 9 Map Score: 16.4436 Number of sites scoring better than the average of aligned sites = 1080 Number in coding regions = 1004 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 3 TGTCAATTTATGCACCCCAGTGAATCGACA 1 86 0 TGCACCCCAG 0.980993 -182 CAGCGTTTAACGCACGCGCGCCTTCAGAGA 1 153 0 CGCACGCGCG 0.780467 -115 TAACAGCGCGTGCACCACCGTTCCTTCAAG 1 185 0 TGCACCACCG 0.982994 -83 CCCACGGGATTGTTGCACAGAATGCAGAGG 1 243 1 TGTTGCACAG 0.653411 -25 GGGACCACGCCGTACGACATAGAAAACCAG 3 85 0 CGTACGACAT 0.906693 -216 TGGAACGCCGCGCAGGACTGGGGAGAGCGA 3 196 0 CGCAGGACTG 0.849689 -105 GACGCCACGGCGCACGCCCTGCGCGGCATC 3 230 0 CGCACGCCCT 0.936593 -71 GAGCTGTCAGTGTAACACATAGCATGGGGG 5 59 1 TGTAACACAT 0.68608 -34 CCTTCCTACACGCCCCCCATGCTATGTGTT 5 72 0 CGCCCCCCAT 0.829478 -21 GCGCGCGAAGTGTAGCACAGACTATGCAGC 6 59 1 TGTAGCACAG 0.942118 -85 GCACAGACTATGCAGCACAGTAAACCAACC 6 73 1 TGCAGCACAG 0.976168 -71 TCGGGCAGCGTGTACCACCTGTTCCGGTTG 6 98 0 TGTACCACCT 0.90129 -46 TCTAGCCTCTCGCAAGACAGTTTCGCACCC 7 35 0 CGCAAGACAG 0.923766 -137 ********** Masking position 2 Map Score: 11.4864 Number of sites scoring better than the average of aligned sites = 1232 Number in coding regions = 1140 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 4 GAGCTTCCTGCGGCAAATGGTTACACAAAC 1 15 0 CGGCAAATGG 0.926419 -253 ATCTGACAGCAGGGAGGTGGT 2 2 0 AGGGAGGTGG 0.945645 -103 ATTATTTAATAGGGTGGCGGTGTAGTGCAA 2 42 0 AGGGTGGCGG 0.948401 -63 TTACTCAACAAGGTAAAAGGTTGGCGTTAA 2 83 1 AGGTAAAAGG 0.888778 -22 AAAGGACGCGCGGGTGAACGATTACCGCGC 3 23 0 CGGGTGAACG 0.861848 -278 GGGCGTGGACCGGCAAGCAGCTGTGACGCC 3 254 0 CGGCAAGCAG 0.871771 -47 TTCCACAAAGAGGGTAAAAGCGTTAGA 3 284 1 AGGGTAAAAG 0.932393 -17 GTCTTGCGAGAGGCTAGAGGTGTGTGCGAA 7 47 1 AGGCTAGAGG 0.959158 -125 TGACCCTAAACGGGAAAAAGAAACGGGGAC 7 113 0 CGGGAAAAAG 0.956284 -59 TGACCGCAGCAGGGAAAAGGCGATAATACC 7 148 1 AGGGAAAAGG 0.984027 -24 ********** Masking position 3 Map Score: 7.38189 Number of sites scoring better than the average of aligned sites = 358 Number in coding regions = 305 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 5 AAATTGACAGGGTCAGGGGGCGTGTCTACA 1 107 1 GGTCAGGGGG 0.920921 -161 TGCTCTTGAAGGAACGGTGGTGCACGCGCT 1 181 1 GGAACGGTGG 0.969512 -87 CCCGCAGAAAGGACGCGCGGGTGAACGATT 3 30 0 GGACGCGCGG 0.929571 -271 ACGCCGCGCAGGACTGGGGAGAGCGAACCG 3 192 0 GGACTGGGGA 0.957823 -109 GGAAGGGCGTGGACCGGCAAGCAGCTGTGA 3 258 0 GGACCGGCAA 0.920747 -43 AAACCAACCGGAACAGGTGGTACACGCTGC 6 94 1 GAACAGGTGG 0.959857 -50 CCAGACAAAAGAACCCGTGA 6 134 1 GAACCCGTGA 0.921143 -10 ACGGGAAAAAGAAACGGGGACTCTCTGAGC 7 104 0 GAAACGGGGA 0.951852 -68 CCGCAGCAGGGAAAAGGCGATAATACCCTC 7 151 1 GAAAAGGCGA 0.905409 -21 ********** Masking position 7 Map Score: 5.30383 Number of sites scoring better than the average of aligned sites = 382 Number in coding regions = 336 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 6 ACAAGCCCGCGCAGCCACACGGATGAGCTT 1 39 0 GCAGCCACAC 0.957535 -229 CAGTGAATCGACAGCCCGACTTCAGAGCAC 1 69 0 ACAGCCCGAC 0.955229 -199 GCGTGTCTACACTGTGAGACATGGACCTCT 1 126 1 ACTGTGAGAC 0.85707 -142 CCACCTCCCTGCTGTCAGATTACTTGAGTA 2 12 1 GCTGTCAGAT 0.730066 -93 GTATTGCACTACACCGCCACCCTATTAAAT 2 39 1 ACACCGCCAC 0.812393 -66 AGTATCAGAAACACTCCCGCAGAAAGGACG 3 45 0 ACACTCCCGC 0.758781 -256 TCTCCCCAGTCCTGCGCGGCGTTCCATGCA 3 200 1 CCTGCGCGGC 0.952046 -101 CGGCGCACGCCCTGCGCGGCATCTGCATGG 3 223 0 CCTGCGCGGC 0.952046 -78 CCGGCAAGCAGCTGTGACGCCACGGCGCAC 3 245 0 GCTGTGACGC 0.921514 -56 CCTGTGGCATGCAATCAGGCATTGATCCAT 4 36 1 GCAATCAGGC 0.61624 -53 TACACTGACAGCTCCCACACATCGTGCTCG 5 43 0 GCTCCCACAC 0.923612 -50 GGTGGTACACGCTGCCCGATGAACACCAGA 6 109 1 GCTGCCCGAT 0.905324 -35 ********** Masking position 2 Map Score: 6.54033 Number of sites scoring better than the average of aligned sites = 1474 Number in coding regions = 1357 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 7 AGGAAGCTCATCCGTGTGGCTGCGCGGGCTT 1 36 1 TCCGGTGGCT 0.988057 -232 ACGCGCGCCTTCAGAGAGGTCCATGTCTCAC 1 139 0 TCAGGAGGTC 0.930744 -129 CGCTGTTATCTCCTCTTGGTTTGCGCGCGTA 1 207 1 TCCTTTGGTT 0.865367 -61 AATTTCACCGAGGTTATGACGCAAG 4 74 0 TCACGAGGTT 0.958034 -15 GTATCCTCCCAGAGGTTAAAAAAGATT 6 7 1 TCCCGAGGTT 0.988183 -137 TACCACCTGTTCCGGTTGGTTTACTGTGCTG 6 85 0 TCCGTTGGTT 0.97105 -59 GAAACTGTCTTGCGAGAGGCTAGAGGTGTGT 7 41 1 TGCGGAGGCT 0.953927 -131 **** ****** Masking position 1 Map Score: 3.49388 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 58 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 ********** No masking Map Score: 1.06825e-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: 1.06825e-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: 1.06825e-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