AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00260_tpal_reg_100.orf -o00260_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 TP0329 117 serine hydroxymethyltransferase (glyA) #2 TP0647 49 seryl-tRNA synthetase (serS) #3 TP0651 175 conserved hypothetical integral membrane protein #4 TP0672 134 glycyl-tRNA synthetase (glyS) #5 TP0837 147 threonyl-tRNA synthetase (thrS) Motif number 1 TGGTATGTTCCCCTGTTACGCACGACGGGTATC 1 8 1 TTCCCCGCAC 0.974293 -110 CGACGGGTATCGGGCATGCGGCGCGCGGCGTTTTGT 1 33 1 CGGCACGCGC 0.998242 -85 CGCGGCGTTTTGTCCATTCTTTGCGCTAGAAACAGA 1 56 1 TGTCATGCGC 0.842111 -62 TGACAGAACATACCCAAATACCGCACCATCGGCCTC 3 25 0 TACCACGCAC 0.95145 -151 TGGGTATGTTCTGTCAAGGCTCGCGGTTGGGGTACG 3 45 1 CTGCACGCGG 0.995702 -131 CAAGGACACACGGACGCCTTGCGTACCCCAACCGCG 3 66 0 CGGCGCGTAC 0.814941 -110 CAGATTACCGCTGGCGTGTTACGCTCGCTGGCGCGA 3 107 1 CTGCGCGCTC 0.940881 -69 TTCTTCCTCATGCGCACTTCTCGCGCCAGCGAGCGT 3 127 0 TGCCACGCGC 0.997574 -49 TATTCTCAGTTAACGCGGGCTATAGGGA 4 3 1 TTCCACGCGG 0.994086 -132 CCGCGGCGACCTCACAGAGATCGCGCCCGCCTTTGA 4 62 0 CTCCACGCGC 0.997911 -73 GTCTAGCATACTGTCAGCACCCGCGGCGACCTCACA 4 82 0 CTGCACGCGG 0.995709 -53 GGTGACGCGCCGCTCACCTTCCCCCCTGTCTAGCAT 4 109 0 CGCCACCCCC 0.94774 -26 CCAGTGCGCCTGCGCCGTCACTGCAGTCTGTAGGAA 5 66 0 TGCCCTGCAG 0.774497 -82 TATGGGTGGTTTGTCAATGGGCGCCGTTTTGGAGGA 5 111 0 TTGCACGCCG 0.977812 -37 *** ** ***** Masking position 5 Map Score: 23.286 Number of sites scoring better than the average of aligned sites = 1613 Number in coding regions = 1492 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 2 CCTGTTACGCACGACGGGTATCGGGCATGCGGCGC 1 22 1 AGACGGAGGG 0.929769 -96 GGTATCGGGCATGCGGCGCGCGGCGTTTTGTCCAT 1 38 1 AGCGGGGGCG 0.996595 -80 CAGAATAAGTAAGGGGAGAAAGGCGC 2 34 1 AGGGGGAGCG 0.982315 -16 TGTTCTGTCAAGGCTCGCGGTTGGGGTACGCAAGG 3 51 1 AGCTCCGGGG 0.980029 -125 CTGGCGTGTTACGCTCGCTGGCGCGAGAAGTGCGC 3 117 1 AGCTCCGGCG 0.965173 -59 AGAAGTGCGCATGAGGAAGAAAGGACCACCCCGTC 3 142 1 AGAGGAAGGA 0.836582 -34 AATGCGTAAGACGGGGTGGTCCTTTC 3 160 0 AGCGTAAGGG 0.978686 -16 TTCTCAGTTAACGCGGGCTATAGGGAAAAGAGGTA 4 13 1 AGCGGCAGGG 0.996913 -122 CTATAGGGAAAAGAGGTATGCAGGGGATGTGTTCA 4 30 1 AGAGGAGGGG 0.992645 -105 TATGCAGGGGATGTGTTCAAAGGCGGGCGCGATCT 4 46 1 AGTGTCAGCG 0.846915 -89 TGCTGACAGTATGCTAGACAGGGGGGAAGGTGAGC 4 99 1 AGCTAAAGGG 0.911877 -36 GACAGGGGGGAAGGTGAGCGGCGCGTCACC 4 115 1 AGGTGGGGCG 0.972544 -20 GTAGGAAGGGACGTGGTATGTAGGGTATAGTAGAG 5 38 0 AGTGGAGGGG 0.989494 -110 CCGTCACTGCAGTCTGTAGGAAGGGACGTGGTATG 5 53 0 ATCTGAGGGG 0.920446 -95 * **** * * *** Masking position 1 Map Score: 20.116 Number of sites scoring better than the average of aligned sites = 781 Number in coding regions = 680 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 3 TCCCCTGTTACGCACGACGGGTATCGGGCA 1 19 1 CGCACGACGG 0.899609 -99 GACAAAACGCCGCGCGCCGCATGCCCGATA 1 40 0 CGCGCGCCGC 0.989225 -78 ACCGCACCATCGGCCTCCGCAATGAGAAGG 3 12 0 CGGCCTCCGC 0.936421 -164 GTTCTGTCAAGGCTCGCGGTTGGGGTACGC 3 52 1 GGCTCGCGGT 0.973402 -124 CAAGGACACACGGACGCCTTGCGTACCCCA 3 72 0 CGGACGCCTT 0.911032 -104 GAGCGTAACACGCCAGCGGTAATCTGTCCA 3 103 0 CGCCAGCGGT 0.958732 -73 TGGCGTGTTACGCTCGCTGGCGCGAGAAGT 3 118 1 CGCTCGCTGG 0.96397 -58 TTTTCCCTATAGCCCGCGTTAACTGAGAAT 4 12 0 AGCCCGCGTT 0.872291 -123 ACAGAGATCGCGCCCGCCTTTGAACACATC 4 55 0 CGCCCGCCTT 0.991508 -80 ATACTGTCAGCACCCGCGGCGACCTCACAG 4 81 0 CACCCGCGGC 0.975062 -54 GGTGACGCGCCGCTCACCTTCCC 4 122 0 GACGCGCCGC 0.865817 -13 TGACGGCGCAGGCGCACTGGCTCAGTGCTT 5 82 1 GGCGCACTGG 0.689275 -66 GGTTTGTCAATGGGCGCCGTTTTGGAGGAA 5 110 0 TGGGCGCCGT 0.937278 -38 ********** Masking position 5 Map Score: 16.9292 Number of sites scoring better than the average of aligned sites = 2335 Number in coding regions = 2136 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 4 CGAACAATATTCTGCCTACCTGAGGAGAGA 1 93 1 TCTGCCTACC 0.984326 -25 GCGCCTTTCTCCCCTTACTTATT 2 37 0 CCTTTCTCCC 0.985032 -13 ACACGGACGCCTTGCGTACCCCAACCGCGA 3 65 0 CTTGCGTACC 0.913794 -111 ACGGGGTGGTCCTTTCTTCCTCATGCGCAC 3 146 0 CCTTTCTTCC 0.960203 -30 GAACACATCCCCTGCATACCTCTTTTCCCT 4 34 0 CCTGCATACC 0.992283 -101 CACCTTCCCCCCTGTCTAGCATACTGTCAG 4 101 0 CCTGTCTAGC 0.963993 -34 TCTACTATACCCTACATACCACGTCCCTTC 5 39 1 CCTACATACC 0.96092 -109 ATACCACGTCCCTTCCTACAGACTGCAGTG 5 54 1 CCTTCCTACA 0.985881 -94 CTGGCTCAGTGCTTCCTCCAAAACGGCGCC 5 98 1 GCTTCCTCCA 0.867447 -50 ********** Masking position 7 Map Score: 10.5485 Number of sites scoring better than the average of aligned sites = 332 Number in coding regions = 271 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 5 CATGCGGCGCGCGGCGTTTTGTCCATTCTTTG 1 47 1 GCGCGTTTGT 0.972377 -71 GGCAGAATATTGTTCGCTCTGTTTCTAGCGCA 1 77 0 TGTCGTCTGT 0.830296 -41 GGAGGCCGATGGTGCGGTATTTGGGTATGTTC 3 24 1 GGGCGTATTT 0.946005 -152 GCGGTATTTGGGTATGTTCTGTCAAGGCTCGC 3 37 1 GGATGTCTGT 0.95202 -139 TAACACGCCAGCGGTAATCTGTCCAGCAAGGA 3 96 0 GCGTATCTGT 0.945034 -80 GATTACCGCTGGCGTGTTACGCTCGCTGGCGC 3 109 1 GGGTGTACGC 0.808699 -67 TGCGTAAGACGGGGTGGTCCTTTCTTCCTCAT 3 152 0 GGGTGTCCTT 0.930774 -24 TTCAAAGGCGGGCGCGATCTCTGTGAGGTCGC 4 61 1 GGGCGTCTCT 0.981198 -74 TATAGTAGAGGATGCTTTCTGTTTTGGATGTG 5 16 0 GAGCTTCTGT 0.87396 -132 TGTAGGAAGGGACGTGGTATGTAGGGTATAGT 5 42 0 GAGTGTATGT 0.933295 -106 CTGCGCCGTCACTGCAGTCTGTAGGAAGGGAC 5 61 0 ACGCATCTGT 0.706475 -87 TGAGACCTTATGGGTGGTTTGTCAATGGGCGC 5 123 0 TGGTGTTTGT 0.884251 -25 ** *** ***** Masking position 8 Map Score: 6.90761 Number of sites scoring better than the average of aligned sites = 1125 Number in coding regions = 1029 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 6 ********** No masking Map Score: -2.67574e-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: -2.67574e-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: -2.67574e-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