AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00473_tpal_reg_100.orf -o00473_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 TP0671 30 sn-1,2-diacylglycerol cholinephosphotransferase, putative #2 TP0672 134 glycyl-tRNA synthetase (glyS) #3 TP0681 88 alanine racemase (alr) #4 TP0682 92 cell division protein (ftsJ) Motif number 1 TTTCCCCGCGCGCAGAGAGCGGACAACAAC 1 6 0 CGCCAGCACA 0.997164 -25 TATTCTCAGTTAACGCGGGCTATAGGGAAAA 2 5 1 CTCGTGCGCT 0.88854 -130 CGCCTTTGAACACATCCCCTGCATACCTCTTTTCCCT 2 34 0 CACTCGCACC 0.934666 -101 CCGCGGCGACCTCACAGAGATCGCGCCCGCCTTTGAA 2 61 0 CTCCATCGCC 0.982804 -74 TCTGTGAGGTCGCCGCGGGTGCTGACAGTATGCTAGA 2 80 1 CGCGCGCACA 0.995481 -55 GGTGACGCGCCGCTCACCTTCCCCCCTGTCTA 2 113 0 CGCCCACTCC 0.984492 -22 CAGGCGCCTACGCTCCCTATTCTTACCCA 3 3 0 CGCCCTCACC 0.997293 -86 AGGGAGCGTAGGCGCCTGTGGCATGCAATCAGGCATT 3 22 1 GGCCCGCGCA 0.991814 -67 ACATCGTGCTCGCACAAAAGGCAAACACGCCGTATAA 4 18 0 CGCCAGCACA 0.997164 -75 ACACTGACAGCTCCCACACATCGTGCTCGCACAAAAG 4 35 0 CTCCATCGCT 0.965114 -58 CCTTCCTACACGCCCCCCATGCTATGTGTTACACTGA 4 65 0 CGCCCGCTGT 0.969829 -28 *** ** ** *** Masking position 12 Map Score: 15.7396 Number of sites scoring better than the average of aligned sites = 1353 Number in coding regions = 1237 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 2 TTTCCCCGCGCGCAGAGAGCGGA 1 18 0 CCCCGCGCGC 0.92872 -13 CTTTTCCCTATAGCCCGCGTTAACTGAGAA 2 13 0 TAGCCCGCGT 0.93904 -122 AAGAGGTATGCAGGGGATGTGTTCAAAGGC 2 40 1 CAGGGGATGT 0.788636 -95 ATGTGTTCAAAGGCGGGCGCGATCTCTGTG 2 56 1 AGGCGGGCGC 0.970268 -79 TCTGTGAGGTCGCCGCGGGTGCTGACAGTA 2 80 1 CGCCGCGGGT 0.977262 -55 GGGGAAGGTGAGCGGCGCGTCACC 2 121 1 AGCGGCGCGT 0.963445 -14 TGGGTAAGAATAGGGAGCGTAGGCGCCTGT 3 11 1 TAGGGAGCGT 0.960195 -78 TAGGGAGCGTAGGCGCCTGTGGCATGCAAT 3 21 1 AGGCGCCTGT 0.898658 -68 AGTACCGTTATACGGCGTGTTTGCCTTTTG 4 11 1 TACGGCGTGT 0.976376 -82 ACACATAGCATGGGGGGCGTGTAGGAAGGT 4 73 1 TGGGGGGCGT 0.993896 -20 ********** Masking position 9 Map Score: 11.6307 Number of sites scoring better than the average of aligned sites = 2986 Number in coding regions = 2773 Number in noncoding regions = 213 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 3 TTTCCCCGCGCGCAGAGAGCG 1 20 0 TTCCCCGCGC 0.994689 -11 TCTCTGTGAGGTCGCCGCGGGTGCTGACAG 2 78 1 GTCGCCGCGG 0.996249 -57 GCCGCTCACCTTCCCCCCTGTCTAGCATAC 2 107 0 TTCCCCCCTG 0.99505 -28 AATTTCACCGAGGTTATGACGCA 3 76 0 TTCACCGAGG 0.986612 -13 CTTCCTACACGCCCCCCATGCTATGTGTTA 4 71 0 GCCCCCCATG 0.977468 -22 ********** Masking position 5 Map Score: 4.87155 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 161 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 4 GTTAACGCGGGCTATAGGGAAAAGAGGTAT 2 19 1 GCTATAGGGA 0.979267 -116 CAGGGGATGTGTTCAAAGGCGGGCGCGATC 2 50 1 GTTCAAAGGC 0.955714 -85 CCTGTGGCATGCAATCAGGCATTGATCCAT 3 36 1 GCAATCAGGC 0.953487 -53 ACGCAAGTTTGCTAAATGGATCAATGCCTG 3 51 0 GCTAAATGGA 0.963961 -38 AGTACCGTTATACGGCGTGTTTGCCT 4 7 1 GTTATACGGC 0.982389 -86 ********** Masking position 8 Map Score: 0.0614388 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 105 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 5 ********** No masking Map Score: -5.58897e-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 6 ********** No masking Map Score: -5.58897e-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: -5.58897e-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