AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00473_tpal_reg_300.orf -o00473_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 TP0671 30 sn-1,2-diacylglycerol cholinephosphotransferase, putative #2 TP0672 134 glycyl-tRNA synthetase (glyS) #3 TP0673 177 glutamyl-tRNA synthetase (gltX) #4 TP0681 88 alanine racemase (alr) #5 TP0682 92 cell division protein (ftsJ) Motif number 1 TTTCCCCGCGCGCAGAGAGCGGACAACAA 1 12 0 TCCCGCGCAG 0.942325 -19 TATTCTCAGTTAACGCGGGCTATAGGGAAAAGAG 2 8 1 AGTCGCGGTA 0.738855 -127 AGGGAAAAGAGGTATGCAGGGGATGTGTTCAAAGGCG 2 34 1 GGTCAGGGTG 0.991156 -101 TGTGTTCAAAGGCGGGCGCGATCTCTGTGAGGTCGCC 2 57 1 GGCCGCGATG 0.990819 -78 ATCTCTGTGAGGTCGCCGCGGGTGCTGACAGTATGCT 2 77 1 GGTCGCGGTG 0.995387 -58 CTGACAGTATGCTAGACAGGGGGGAAGGTGAGCGGCG 2 101 1 GCTCAGGGAG 0.939087 -34 GCAGGATGCCGCTTCACGCGGTTGATTGCACAGACAG 3 26 0 GCTCGCGGTT 0.968692 -152 GTCTTCCCCTTCCTACCACGCAGGATGCCGCTTCACG 3 45 0 TCCCACGCTG 0.986591 -133 AAGACAGGGAGGCGGTCACGGTGCATGAGGAGTGTAA 3 77 1 GGCCACGGTG 0.998572 -101 AATTTTCAGGGCCTCACAGGGATGCTTGCGCCCCGGA 3 112 1 GCCCAGGGTT 0.978947 -66 TGCGATAATCGGCCCCCGGGGAGGGCGAGCG 3 157 1 GGCCGGGGCG 0.976863 -21 GCATGCCACAGGCGCCTACGCTCCCTATTCTTACCCA 4 11 0 GGCTACGCTA 0.86593 -78 GCCTGTGGCATGCAATCAGGCATTGATCCATTTAGCA 4 35 1 TGCCAGGCAT 0.799072 -54 ATTTCACCGAGGTTATGACGCAAGTTTGCTAAATGGA 4 61 0 GGTGACGCTT 0.811604 -28 TCGCACAAAAGGCAAACACGCCGTATAACGGTACT 5 9 0 GGCCACGCTA 0.991883 -84 TTGCCTTTTGTGCGAGCACGATGTGTGGGAGCTGTCA 5 31 1 TGCCACGATG 0.963222 -62 CTTCCTACACGCCCCCCATGCTATGTGTTACACTGAC 5 64 0 GCCCATGCTG 0.960569 -29 *** ***** ** Masking position 10 Map Score: 28.2712 Number of sites scoring better than the average of aligned sites = 1317 Number in coding regions = 1193 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 2 TCCCCGCGCGCAGAGAGCGGACAACAAC 1 9 0 CAGAGAGCGG 0.900489 -22 GATGTGTTCAAAGGCGGGCGCGATCTCTGT 2 55 1 AAGGCGGGCG 0.995762 -80 GACAGTATGCTAGACAGGGGGGAAGGTGAG 2 103 1 TAGACAGGGG 0.828342 -32 GACAGGGGGGAAGGTGAGCGGCGCGTCACC 2 115 1 AAGGTGAGCG 0.901109 -20 TCCTACCACGCAGGATGCCGCTTCACGCGG 3 42 0 CAGGATGCCG 0.936804 -136 TCCTGCGTGGTAGGAAGGGGAAGACAGGGA 3 57 1 TAGGAAGGGG 0.952199 -121 AAGGGGAAGACAGGGAGGCGGTCACGGTGC 3 71 1 CAGGGAGGCG 0.996151 -107 TGCTTGCGCCCCGGAGGGGGATGTGCGATA 3 134 1 CCGGAGGGGG 0.988137 -44 CTCGCCCTCCCCGGGGGCCGATTATCGCAC 3 156 0 CCGGGGGCCG 0.991051 -22 GCCCCCGGGGAGGGCGAGCG 3 168 1 AGGGCGAGCG 0.905796 -10 AACACATAGCATGGGGGGCGTGTAGGAAGG 5 72 1 ATGGGGGGCG 0.982243 -21 ********** Masking position 3 Map Score: 14.3664 Number of sites scoring better than the average of aligned sites = 801 Number in coding regions = 687 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 3 ATAGGGAAAAGAGGTATGCAGGGGATGTGT 2 32 1 GAGGTATGCA 0.935009 -103 GTATGCAGGGGATGTGTTCAAAGGCGGGCG 2 45 1 GATGTGTTCA 0.668982 -90 GATGTGTTCAAAGGCGGGCGCGATCTCTGT 2 55 1 AAGGCGGGCG 0.901036 -80 GGTCGCCGCGGGTGCTGACAGTATGCTAGA 2 87 1 GGTGCTGACA 0.828175 -48 GCTAGACAGGGGGGAAGGTGAGCGGCGCGT 2 111 1 GGGGAAGGTG 0.892236 -24 GCTTCACGCGGTTGATTGCACAGACAGGTT 3 23 0 GTTGATTGCA 0.686551 -155 GTGGTAGGAAGGGGAAGACAGGGAGGCGGT 3 63 1 GGGGAAGACA 0.893797 -115 GGAAGACAGGGAGGCGGTCACGGTGCATGA 3 75 1 GAGGCGGTCA 0.975003 -103 CACGGTGCATGAGGAGTGTAATTTTCAGGG 3 93 1 GAGGAGTGTA 0.912698 -85 GCCTCACAGGGATGCTTGCGCCCCGGAGGG 3 122 1 GATGCTTGCG 0.915657 -56 GCCCCGGAGGGGGATGTGCGATAATCGGCC 3 141 1 GGGATGTGCG 0.771855 -37 ATCGGCCCCCGGGGAGGGCGAGCG 3 164 1 GGGGAGGGCG 0.992669 -14 GTAGGCGCCTGTGGCATGCAATCAGGCATT 4 29 1 GTGGCATGCA 0.949151 -60 ACGATGTGTGGGAGCTGTCAGTGTAACACA 5 48 1 GGAGCTGTCA 0.677334 -45 CATAGCATGGGGGGCGTGTAGGAAGGT 5 76 1 GGGGCGTGTA 0.977241 -17 ********** Masking position 4 Map Score: 14.8349 Number of sites scoring better than the average of aligned sites = 3098 Number in coding regions = 2812 Number in noncoding regions = 286 Number of orfs with sites within 600 bp upstream = 205 Fraction of orfs with sites within 600 bp upstream = 0.0329264 Motif number 4 CGCGATCTCTGTGAGGTCGCCGCGGGTGCT 2 73 1 GTGAGGTCGC 0.983258 -62 GGTGACGCGCCGCTCACCTTC 2 124 0 GTGACGCGCC 0.992038 -11 AATCAACCGCGTGAAGCGGCATCCTGCGTG 3 36 1 GTGAAGCGGC 0.993656 -142 GGGGAAGACAGGGAGGCGGTCACGGTGCAT 3 73 1 GGGAGGCGGT 0.992036 -105 AAGCATCCCTGTGAGGCCCTGAAAATTACA 3 109 0 GTGAGGCCCT 0.992325 -69 ********** Masking position 4 Map Score: 6.20356 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 78 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 5 TTGTTGTCCGCTCTCTGCGCGCGGGGAAA 1 12 1 CTCTCTGCGC 0.971105 -19 GCCGCGGGTGCTGACAGTATGCTAGACAGG 2 91 1 CTGACAGTAT 0.956428 -44 CATAAAAAACCTGTCTGTGCAATCAACCGC 3 16 1 CTGTCTGTGC 0.99096 -162 GGATCAATGCCTGATTGCATGCCACAGGCG 4 34 0 CTGATTGCAT 0.866764 -55 TGTGTGGGAGCTGTCAGTGTAACACATAGC 5 52 1 CTGTCAGTGT 0.986086 -41 ********** Masking position 2 Map Score: 1.13539 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 251 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 6 ********** No masking Map Score: -3.24418e-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: -3.24418e-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: -3.24418e-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