AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00252_mgen_reg_300.orf -o00252_mgen_300.ace -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -g0.32 -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 = 0.32 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: MG035 28 histidyl-tRNA synthetase Input sequences: #1 MG109 59 serine/threonine protein kinase, putative #2 MG292 57 alanyl-tRNA synthetase (alaS) #3 MG294 117 conserved hypothetical protein #4 MG296 119 conserved hypothetical protein #5 MG298 202 P115 protein #6 MG301 30 glyceraldehyde-3-phosphate dehydrogenase (gap) #7 MG304 176 ABC transporter, ATP binding protein #8 MG305 87 heat shock protein 70 (dnaK) #9 MG309 53 lipoprotein, putative Motif number 1 ATTTAAAAGCTTTTCAATTTGATACTTATTT 1 30 0 TTTTCAATTG 0.707489 -30 GTAAATTGCATTTAAAATTAAGCA 2 44 1 TTTAAAATAA 0.942962 -14 AAAAAATAGTTTTTCTAGTAAACATTATTTT 3 12 1 TTTTCTATAA 0.790175 -106 TATTTTTCTTTTTAAAAGTAAGTGAAGAACG 3 37 1 TTTAAAATAA 0.943002 -81 TCCATCCACTTTTATTATTAGATGTATATTT 3 75 1 TTTATTATAG 0.863967 -43 ATTAGATGTATATTTAATTTATCCCACTTTA 3 91 1 TATTTAATTA 0.690447 -27 TTTTTAAATTAAACCTTTTAC 4 1 1 TTTTTAATTA 0.948827 -119 GTTAGTAGTTTATTTAAGTAATACTGAAATA 4 41 1 TATTTAATAA 0.752324 -79 ATTAATGTAATTTTTAAATTAAATAAACTAG 5 44 1 TTTTTAATTA 0.948827 -159 GCTTCTATGTTTTAATAGTAACTAGTTTATT 5 65 0 TTTAATATAA 0.894196 -138 CATAGAAGCTTTTTTAAATGAAGCGTTATTA 5 87 1 TTTTTAATGA 0.889145 -116 TATTAGCTTATTTTTTAGTAACCTAATAATT 5 113 1 TTTTTTATAA 0.928289 -90 ACTTTAATTTAATAATTAGATTTTAATA 6 13 0 TTTAATATTA 0.861292 -18 TGTGCTGCTCTTTTTTATTTGGAATATGTTC 7 23 0 TTTTTTATTG 0.809754 -154 ATTTATAAATTTTAAAAATAAGTCAGAGCTA 7 96 0 TTTAAAATAA 0.942965 -81 ATTTTTAAAATTTATAAATAAGCTTAGTTTG 7 108 1 TTTATAATAA 0.962716 -69 AAAACTGAGGTTTTTAACTTGTAGCAAACTA 7 132 0 TTTTTAATTG 0.892849 -45 GTTTTGGGTATTTAAAACTGAGGTTTTTAAC 7 145 0 TTTAAAATGA 0.839409 -32 CTAATTTTTGTTTATAATTACTGAGTAATTG 8 46 1 TTTATAATAC 0.866673 -42 AATTTATATTTTTATTATTACCAC 9 4 0 TTTATTATAC 0.768542 -50 TTTCAATAATTTTAAAATTTATATTTTTATT 9 19 0 TTTAAAATTA 0.923986 -35 ******* *** Masking position 3 Map Score: 29.6293 Number of sites scoring better than the average of aligned sites = 626 Number in coding regions = 516 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 2 TCAAATTGAAAAGCTTTTAAATAGGGGTGG 1 39 1 AAGCTTTTAA 0.956798 -21 TTTACTAGAAAAACTATTTTTTC 3 4 0 AAACTATTTT 0.877817 -114 TTTTTAAATTAAACCTTTTACAGTATTTTG 4 11 1 AAACCTTTTA 0.741407 -109 TTACTTAAATAAACTACTAACCAAAATACT 4 32 0 AAACTACTAA 0.774352 -88 ATACTGAAATAAACTGTTTAAGGATTGCTA 4 61 1 AAACTGTTTA 0.916985 -59 AGAAGTGTTAAAACTTTTTAGACTGGTGTA 4 100 1 AAACTTTTTA 0.957618 -20 AAACTTTTAAATGATATTGC 5 1 1 AAACTTTTAA 0.94128 -202 GCTTTTCTAAAAGCAATTAATGTAATTTTT 5 29 1 AAGCAATTAA 0.682968 -174 TAAATTAAATAAACTAGTTACTATTAAAAC 5 58 1 AAACTAGTTA 0.806866 -145 TAAAACATAGAAGCTTTTTTAAATGAAGCG 5 82 1 AAGCTTTTTT 0.910006 -121 ACTAAAAAATAAGCTAATAACGCTTCATTT 5 102 0 AAGCTAATAA 0.928402 -101 ATTTTTTAGTAACCTAATAATTAGCCTAGT 5 122 1 AACCTAATAA 0.7137 -81 CAACTAGTATAATCTAATAACAACATCCAA 5 163 1 AATCTAATAA 0.809516 -40 ATCCAAATTAAAGCTTTTTAGAACAA 5 187 1 AAGCTTTTTA 0.968979 -16 AGTATTAAAATCTAATTATTAAATTAAA 6 9 1 AATCTAATTA 0.857013 -22 CAGAGCTAAAAATCTGTTTTTTGGTAGATA 7 74 0 AATCTGTTTT 0.618355 -103 GTAGCAAACTAAGCTTATTTATAAATTTTA 7 113 0 AAGCTTATTT 0.838934 -64 ********** Masking position 8 Map Score: 17.7226 Number of sites scoring better than the average of aligned sites = 536 Number in coding regions = 484 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 3 TGATATTGTTGAAAATAAGTATCAAATTGA 1 18 1 GAAAATAAGT 0.752633 -42 CAAATAAAAGAACTATAGTTA 2 2 1 AAATAAAAGA 0.560791 -56 TACCAGTGATAAAAATAACTATAGTTCTTT 2 17 0 AAAAATAACT 0.841584 -41 AATTGCATTTAAAATTAAGCA 2 47 1 AAAATTAAGC 0.901968 -11 GAAAAAATAGTTTTTCTAGTA 3 2 1 AAAAAATAGT 0.68212 -116 TTTAAAAAGAAAAATAATGTTTACTAGAAA 3 23 0 AAAATAATGT 0.671025 -95 TTTTCTTTTTAAAAGTAAGTGAAGAACGTT 3 40 1 AAAAGTAAGT 0.710569 -78 ATACATCTAATAATAAAAGTGGATGGAAGT 3 72 0 TAATAAAAGT 0.797014 -46 TTTTTAAATTAAACCTTTTACAGTA 4 6 1 AAATTAAACC 0.800453 -114 CAGTATTACTTAAATAAACTACTAACCAAA 4 37 0 TAAATAAACT 0.783954 -83 AAGTAATACTGAAATAAACTGTTTAAGGAT 4 56 1 GAAATAAACT 0.750517 -64 ATTTTTAAATTAAATAAACTAGTTACTATT 5 53 1 TAAATAAACT 0.783954 -150 TAGGTTACTAAAAAATAAGCTAATAACGCT 5 108 0 AAAAATAAGC 0.901968 -95 TAGTTGAAGTAAACTAAACTAGGCTAATTA 5 139 0 AAACTAAACT 0.636214 -64 AACAACATCCAAATTAAAGCTTTTTAGAAC 5 181 1 AAATTAAAGC 0.907777 -22 TCTAATTATTAAATTAAAGT 6 21 1 AAATTAAAGT 0.933085 -10 TATTCCAAATAAAAAAGAGCAGCACAACAG 7 28 1 AAAAAAGAGC 0.691797 -149 TAGATAAAAAACAAAAAAGCAGCTGTTGTG 7 50 0 ACAAAAAAGC 0.680923 -127 TATAAATTTTAAAAATAAGTCAGAGCTAAA 7 94 0 AAAAATAAGT 0.928757 -83 CTAAAAGTGCTAATTAAAGTTTGTT 8 6 0 TAATTAAAGT 0.797014 -82 TATTGATCTAAAAAAAAAGT 8 78 1 AAAAAAAAGT 0.969354 -10 ********** Masking position 3 Map Score: 21.3777 Number of sites scoring better than the average of aligned sites = 785 Number in coding regions = 698 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 4 ********** No masking Map Score: -4.87842e-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 5 ********** No masking Map Score: -4.87842e-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 ATCAAATTGAAAAGCTTTTAAATAGGGGTG 1 38 1 AAAGCTTTTA 0.922637 -22 GTAAGTGAAGAACGTTTCACTTCCATCCAC 3 54 1 AACGTTTCAC 0.799078 -64 AAATACTGTAAAAGGTTTAATTTAAAAA 4 9 0 AAAGGTTTAA 0.914666 -111 ACCAGTCTAAAAAGTTTTAACACTTCTTGT 4 97 0 AAAGTTTTAA 0.959667 -23 AAACTTTTAAATGATATTGC 5 1 1 AAACTTTTAA 0.79749 -202 TTCATTTAAAAAAGCTTCTATGTTTTAATA 5 79 0 AAAGCTTCTA 0.938854 -124 ATAAGCTAATAACGCTTCATTTAAAAAAGC 5 94 0 AACGCTTCAT 0.809749 -109 TTGTTCTAAAAAGCTTTAATTTGGATGTT 5 184 0 AAAGCTTTAA 0.974187 -19 TGCACAGTCAAAAATTTCAATAATTTTAAA 9 34 0 AAAATTTCAA 0.773795 -20 ********** Masking position 6 Map Score: 5.91815 Number of sites scoring better than the average of aligned sites = 225 Number in coding regions = 194 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 ********** No masking Map Score: -4.87842e-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: -4.87842e-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 9 ********** No masking Map Score: -4.87842e-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