AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -igalR_mtub_opreg_100.orf -g0.656 -x5 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 = 0.656 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 galT' 128 galT' #2 Rv3329 59 hypothetical protein Rv3329 #3 Rv3330 68 hypothetical protein Rv3330 #4 sugI 95 sugI #5 rmlB2 22 rmlB2 Motif number 1 GCGGCTCGCCGCGCCGCCGGGAGACGATGC 1 14 0 GCGCCGCCGG 0.929335 -115 GTTGGTTTTGGGGCGGCTCGCCGCGCCGCC 1 26 0 GGGCGGCTCG 0.997736 -103 AAACCAACGATTGGGCCACGATGCGTAGGC 1 48 1 TTGGGCCACG 0.772581 -81 GCATAGCTGAGGTGGCGTCGCGGCCCTCAC 1 76 1 GGTGGCGTCG 0.97143 -53 GGTGTCGCCGGTGAGGGCCGCGACGCCACC 1 86 0 GTGAGGGCCG 0.954805 -43 CGAGATCCTCTGTGGTGTCGCCGGTGAGGG 1 99 0 TGTGGTGTCG 0.892029 -30 CCACAGAGGATCTCGGGCCGATCCG 1 114 1 TCTCGGGCCG 0.990817 -15 CGAGCGCAGCGCTAGGCTCGGGCAATGACC 2 14 0 GCTAGGCTCG 0.967113 -46 CGAGCCTAGCGCTGCGCTCGCCAACACGAC 2 24 1 GCTGCGCTCG 0.970648 -36 CCAAAGGTTTCGTGTCGTCGTGTTGGC 2 43 0 TTTCGTGTCG 0.794737 -17 GCGCTGTGACTGGCGGGACGAAAG 3 5 0 TGGCGGGACG 0.985956 -64 GCCAGTCACAGCGCGGCTCCTCGCGGTCGG 3 21 1 GCGCGGCTCC 0.974259 -48 GGCTCCTCGCGGTCGGGCCGCCGATCACCT 3 35 1 GGTCGGGCCG 0.977828 -34 CCCCGATACCTTCGGCGTCGTTTGCGGGCG 4 18 1 TTCGGCGTCG 0.751394 -78 CCGGCTAGGATGCCCGCCCGCAAACGACGC 4 32 0 TGCCCGCCCG 0.972542 -64 TGCCGACCAAGGCCGGCTAGGATGCCCGCC 4 44 0 GGCCGGCTAG 0.922384 -52 AGCCGGCCTTGGTCGGCACCGAAATCGGGG 4 56 1 GGTCGGCACC 0.741773 -40 GGCACCGAAATCGGGGCTTGACCAGCGGTT 4 70 1 TCGGGGCTTG 0.854372 -26 GGGCCGCCGGTATGGTGGGC 5 1 1 GGGCCGCCGG 0.875197 -22 GCCGCCGGTATGGTGGGCCG 5 13 1 TGGTGGGCCG 0.959235 -10 ********** Masking position 10 Map Score: 37.0021 Number of sites scoring better than the average of aligned sites = 45440 Number in coding regions = 41947 Number in noncoding regions = 3493 Number of orfs with sites within 600 bp upstream = 1373 Fraction of orfs with sites within 600 bp upstream = 0.220527 Motif number 2 GCATCGTCTCCCGGCGGCGCGGCGAGCCGC 1 14 1 CCGGCGGCGC 0.987251 -115 CGTTGGTTTTGGGGCGGCTCGCCGCGCCGC 1 27 0 GGGGCGGCTC 0.988108 -102 CCAAAACCAACGATTGGGCCACGATGCGTA 1 45 1 CGATTGGGCC 0.931704 -84 CTGAGGTGGCGTCGCGGCCCTCACCGGCGA 1 82 1 GTCGCGGCCC 0.969549 -47 ACCACAGAGGATCTCGGGCCGATCCG 1 113 1 ATCTCGGGCC 0.972648 -16 GCGAGCGCAGCGCTAGGCTCGGGCAATGAC 2 15 0 CGCTAGGCTC 0.850107 -45 CGCGCTGTGACTGGCGGGACGAAAG 3 6 0 CTGGCGGGAC 0.992722 -63 CGCCAGTCACAGCGCGGCTCCTCGCGGTCG 3 20 1 AGCGCGGCTC 0.982185 -49 CGGCTCCTCGCGGTCGGGCCGCCGATCACC 3 34 1 CGGTCGGGCC 0.997442 -35 GCGTCGTTTGCGGGCGGGCATCCTAGCCGG 4 32 1 CGGGCGGGCA 0.99041 -64 GGCGGGCATCCTAGCCGGCCTTGGTCGGCA 4 44 1 CTAGCCGGCC 0.925561 -52 TAGCCGGCCTTGGTCGGCACCGAAATCGGG 4 55 1 TGGTCGGCAC 0.910316 -41 GCCCACCATACCGGCGGCCC 5 1 0 CCGGCGGCCC 0.997867 -22 GGCCGCCGGTATGGTGGGCCG 5 12 1 ATGGTGGGCC 0.961515 -11 ********** Masking position 7 Map Score: 32.6125 Number of sites scoring better than the average of aligned sites = 14486 Number in coding regions = 13492 Number in noncoding regions = 994 Number of orfs with sites within 600 bp upstream = 692 Fraction of orfs with sites within 600 bp upstream = 0.111147 Motif number 3 CGGCGAGCCGCCCCAAAACCAACGATTGGG 1 33 1 CCCCAAAACC 0.975842 -96 AACGATTGGGCCACGATGCGTAGGCATAGC 1 53 1 CCACGATGCG 0.96414 -76 CCGGTGAGGGCCGCGACGCCACCTCAGCTA 1 79 0 CCGCGACGCC 0.993998 -50 CGGCCCTCACCGGCGACACCACAGAGGATC 1 96 1 CGGCGACACC 0.977007 -33 CGGATCGGCCCGAGATCCTCTGTGGTG 1 112 0 GCCCGAGATC 0.908329 -17 CAACACGACGACACGAAACCTTTGG 2 45 1 ACACGAAACC 0.951356 -15 CTGCTTACCCCGATACCTTCGGCGTCG 4 8 1 CCCCGATACC 0.99852 -88 GCTGGTCAAGCCCCGATTTCGGTGCCGACC 4 66 0 CCCCGATTTC 0.965023 -30 CGGCCCACCATACCGGCGGCCC 5 9 0 CCACCATACC 0.981846 -14 ********** Masking position 6 Map Score: 13.0499 Number of sites scoring better than the average of aligned sites = 4427 Number in coding regions = 4126 Number in noncoding regions = 301 Number of orfs with sites within 600 bp upstream = 255 Fraction of orfs with sites within 600 bp upstream = 0.0409573 Motif number 4 CATCGTGGCCCAATCGTTGGTTTTGGGGCG 1 41 0 CAATCGTTGG 0.977132 -88 TTGCCCGAGCCTAGCGCTGCGCTCGCCAAC 2 19 1 CTAGCGCTGC 0.921125 -41 CGACGACACGAAACCTTTGG 2 50 1 AAACCTTTGG 0.944644 -10 GCGGTCAACCGCTGGTCAAGCCCCG 4 81 0 CAACCGCTGG 0.926257 -15 ********** Masking position 3 Map Score: 0.862396 Number of sites scoring better than the average of aligned sites = 790 Number in coding regions = 731 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 5 ********** No masking Map Score: -2.60469e-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: -2.60469e-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: -2.60469e-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