AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -iglpR_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 Rv0110 147 hypothetical protein Rv0110 #2 Rv1903 89 hypothetical protein Rv1903 #3 Rv2250c 120 hypothetical protein Rv2250c #4 lpdA 202 lpdA #5 glpK 49 glpK #6 Rv3697c 250 hypothetical protein Rv3697c Motif number 1 TGTTGCATCCCGCCCAACGGCGCAGGCAAC 1 14 1 CGCCCAACGG 0.950047 -134 CCGATGAGCTGGCGCCACTCATCGCACCAT 1 45 0 GGCGCCACTC 0.782763 -103 TCATCGGAGTCGCCCACCTGCTATCGCCAT 1 68 1 CGCCCACCTG 0.94256 -80 ACGTAGGTCCGGCGCCCGGGATGGCGATAG 1 88 0 GGCGCCCGGG 0.965941 -60 GATCACATCGGGTGCAGCGGACGTAGGTCC 1 108 0 GGTGCAGCGG 0.982141 -40 TCTGCATCGTGGCGTACCGGGCGCGGCACC 2 12 1 GGCGTACCGG 0.9646 -78 CCGGACTCGCGGTGCCGCGCCCGGTACGCC 2 22 0 GGTGCCGCGC 0.984886 -68 CGCGGCACCGCGAGTCCGGGGACATGGCGA 2 33 1 CGAGTCCGGG 0.75293 -57 CACGGACATGCGAGCCGCCGCTGTTCGCCA 2 57 0 CGAGCCGCCG 0.987747 -33 AGGGCGGACGGGCGCAGCTGCACCTGCGCG 3 28 1 GGCGCAGCTG 0.975028 -93 GCCCGAACTCGACCCCGCGCAGGTGCAGCT 3 43 0 GACCCCGCGC 0.961334 -78 TAGCGGACTCGGAGCAGCCCGAACTCGACC 3 59 0 GGAGCAGCCC 0.973416 -62 GCAGGTTGTGGGCCTAGCGGACTCGGAGCA 3 73 0 GGCCTAGCGG 0.963963 -48 CCTGCTTCAGCAACGACCGGACGCCATCAG 3 98 1 CAACGACCGG 0.789688 -23 GGGTACCACCCGAGCCCCCGCCGTCTAAGC 4 19 0 CGAGCCCCCG 0.980232 -184 TGGTACCCATCGCGCCGCGCTGCGGTGCGG 4 41 1 CGCGCCGCGC 0.997912 -162 TTGACGATGACCCGCACCGCAGCGCGGCGC 4 52 0 CCCGCACCGC 0.894715 -151 GCCGAGCAGTCAAGCACAGCTTGACGATGA 4 72 0 CAAGCACAGC 0.64883 -131 GGCGTGAGGAGGAGCCGAGCAGTCAAGCAC 4 85 0 GGAGCCGAGC 0.97647 -118 CGATGCACGCCGCGCAGCGGCGTGAGGAGG 4 103 0 CGCGCAGCGG 0.997532 -100 CGTGCATCGTCGCCGAGCTGTGTTGGACTG 4 124 1 CGCCGAGCTG 0.899662 -79 GGCGTGAGGAGGAGCCGAGCAGTCCAACAC 4 143 0 GGAGCCGAGC 0.97647 -60 CGATGCACGCCGCGCAGCGGCGTGAGGAGG 4 161 0 CGCGCAGCGG 0.997532 -42 CGGCGTCGGACCCGCCGCTGCGGTGGA 5 8 1 GGACCCGCCG 0.977287 -42 CGTCCATGATGGTCCACCGCAGCGGCGGGT 5 20 0 GGTCCACCGC 0.940951 -30 GGCGTCGTTTCAACGCCCGCAGTATGTCGT 6 65 0 CAACGCCCGC 0.816496 -186 GGCGTTGAAACGACGCCAGCGCGAGGAGCG 6 78 1 CGACGCCAGC 0.854112 -173 GACGCCAGCGCGAGGAGCGCAAAACGTTAG 6 89 1 CGAGGAGCGC 0.987812 -162 CAAGCAATTCGGAGGCGAGCTGCCCTAACG 6 113 0 GGAGGCGAGC 0.93327 -138 AACGTTTGGAGGAGGCTCGGCCGCCAGAGC 6 148 0 GGAGGCTCGG 0.860498 -103 AGTCGGCAGTCGACCAGCGGATGTCAACGT 6 173 0 CGACCAGCGG 0.994629 -78 GGTCGACTGCCGACTTGCGGCCCCGTGTGG 6 188 1 CGACTTGCGG 0.649647 -63 ********** Masking position 2 Map Score: 70.1191 Number of sites scoring better than the average of aligned sites = 47570 Number in coding regions = 43987 Number in noncoding regions = 3583 Number of orfs with sites within 600 bp upstream = 1309 Fraction of orfs with sites within 600 bp upstream = 0.210247 Motif number 2 TCCCGCCCAACGGCGCAGGCAACAATGGTG 1 21 1 CGGCGCAGGC 0.984122 -127 GGCGCCAGCTCATCGGAGTCGCCCACCTGC 1 59 1 CATCGGAGTC 0.78358 -89 CTGCTATCGCCATCCCGGGCGCCGGACCTA 1 85 1 CATCCCGGGC 0.936328 -63 GCCGGACCTACGTCCGCTGCACCCGATGTG 1 105 1 CGTCCGCTGC 0.901007 -43 GTCTGCATCGTGGCGTACCGGGCGC 2 6 1 CATCGTGGCG 0.746021 -84 CGTGGCGTACCGGGCGCGGCACCGCGAGTC 2 19 1 CGGGCGCGGC 0.894058 -71 ACATGGCGAACAGCGGCGGCTCGCATGTCC 2 54 1 CAGCGGCGGC 0.995565 -36 CCGTCCGCCCTGTCGGGGGCAGACCACG 3 9 0 TGTCGGGGGC 0.737179 -112 CGCGCAGGTGCAGCTGCGCCCGTCCGCCCT 3 28 0 CAGCTGCGCC 0.943885 -93 GCAGCTGCACCTGCGCGGGGTCGAGTTCGG 3 41 1 CTGCGCGGGG 0.913714 -80 CTAGCGGACTCGGAGCAGCCCGAACTCGAC 3 60 0 CGGAGCAGCC 0.700638 -61 TTTCTGATGGCGTCCGGTCGTTGCTGAAGC 3 101 0 CGTCCGGTCG 0.75605 -20 AAAGCTTAGACGGCGGGGGCTCGGGTGGTA 4 16 1 CGGCGGGGGC 0.996356 -187 ACCCGCACCGCAGCGCGGCGCGATGGGTAC 4 43 0 CAGCGCGGCG 0.980599 -160 CTTGACTGCTCGGCTCCTCCTCACGCCGCT 4 88 1 CGGCTCCTCC 0.796614 -115 GCACGCCGCGCAGCGGCGTGAGGAGGAGCC 4 99 0 CAGCGGCGTG 0.982322 -104 CGGCGTGCATCGTCGCCGAGCTGTGTTGGA 4 121 1 CGTCGCCGAG 0.950258 -82 TTGGACTGCTCGGCTCCTCCTCACGCCGCT 4 146 1 CGGCTCCTCC 0.796614 -57 GCACGCCGCGCAGCGGCGTGAGGAGGAGCC 4 157 0 CAGCGGCGTG 0.982322 -46 CGGCGTGCATCGTCGCCGAGCTAGGTTATG 4 179 1 CGTCGCCGAG 0.950258 -24 CGGCGTCGGACCCGCCGCTG 5 1 1 CGGCGTCGGA 0.718424 -49 TGGTCCACCGCAGCGGCGGGTCCGACGCCG 5 11 0 CAGCGGCGGG 0.995229 -39 AGTATGTCGTCATCGAGGTCGATCGTAGTG 6 45 0 CATCGAGGTC 0.416127 -206 GAAACGACGCCAGCGCGAGGAGCGCAAAAC 6 84 1 CAGCGCGAGG 0.781154 -167 GCAAGCAATTCGGAGGCGAGCTGCCCTAAC 6 114 0 CGGAGGCGAG 0.797139 -137 CAAGCTCTGGCGGCCGAGCCTCCTCCAAAC 6 145 1 CGGCCGAGCC 0.95428 -106 CAAACGTTGACATCCGCTGGTCGACTGCCG 6 170 1 CATCCGCTGG 0.80777 -81 TGCCGACTTGCGGCCCCGTGTGGATCTTGA 6 195 1 CGGCCCCGTG 0.971843 -56 ********** Masking position 1 Map Score: 52.8261 Number of sites scoring better than the average of aligned sites = 86129 Number in coding regions = 81366 Number in noncoding regions = 4763 Number of orfs with sites within 600 bp upstream = 1425 Fraction of orfs with sites within 600 bp upstream = 0.228879 Motif number 3 GCCTGCGCCGTTGGGCGGGATGCAACACGC 1 11 0 TTGGGCGGGA 0.776597 -137 CCCGCCCAACGGCGCAGGCAACAATGGTGC 1 22 1 GGCGCAGGCA 0.874561 -126 TGCGATGAGTGGCGCCAGCTCATCGGAGTC 1 49 1 GGCGCCAGCT 0.858868 -99 GCGATAGCAGGTGGGCGACTCCGATGAGCT 1 65 0 GTGGGCGACT 0.702307 -83 TCGCCATCCCGGGCGCCGGACCTACGTCCG 1 91 1 GGGCGCCGGA 0.854324 -57 CCGGACCTACGTCCGCTGCACCCGATGTGA 1 106 1 GTCCGCTGCA 0.919319 -42 GTGGCGTACCGGGCGCGGCACCGCGAGTCC 2 20 1 GGGCGCGGCA 0.872177 -70 CATGGCGAACAGCGGCGGCTCGCATGTCCG 2 55 1 AGCGGCGGCT 0.547288 -35 CGGCTCGCATGTCCGTGGCAGGATCGGGCA 2 70 1 GTCCGTGGCA 0.837518 -20 CGTCCGCCCTGTCGGGGGCAGACCACG 3 8 0 GTCGGGGGCA 0.975363 -113 CAGGGCGGACGGGCGCAGCTGCACCTGCGC 3 27 1 GGGCGCAGCT 0.888742 -94 CAGCTGCACCTGCGCGGGGTCGAGTTCGGG 3 42 1 TGCGCGGGGT 0.677765 -79 TTCTGATGGCGTCCGGTCGTTGCTGAAGCA 3 100 0 GTCCGGTCGT 0.43982 -21 AAGCTTAGACGGCGGGGGCTCGGGTGGTAC 4 17 1 GGCGGGGGCT 0.96567 -186 CGCACCGCAGCGCGGCGCGATGGGTACCAC 4 40 0 CGCGGCGCGA 0.827019 -163 CCGCGCTGCGGTGCGGGTCATCGTCAAGCT 4 55 1 GTGCGGGTCA 0.703537 -148 CACGCCGCGCAGCGGCGTGAGGAGGAGCCG 4 98 0 AGCGGCGTGA 0.915301 -105 CACGCCGCGCAGCGGCGTGAGGAGGAGCCG 4 156 0 AGCGGCGTGA 0.915301 -47 GGTCCACCGCAGCGGCGGGTCCGACGCCG 5 10 0 AGCGGCGGGT 0.932603 -40 AAGCTCTGGCGGCCGAGCCTCCTCCAAACG 6 146 1 GGCCGAGCCT 0.845325 -105 AAACGTTGACATCCGCTGGTCGACTGCCGA 6 171 1 ATCCGCTGGT 0.686372 -80 GCCGACTTGCGGCCCCGTGTGGATCTTGAC 6 196 1 GGCCCCGTGT 0.900948 -55 ********** Masking position 5 Map Score: 26.2584 Number of sites scoring better than the average of aligned sites = 54806 Number in coding regions = 51316 Number in noncoding regions = 3490 Number of orfs with sites within 600 bp upstream = 1374 Fraction of orfs with sites within 600 bp upstream = 0.220687 Motif number 4 GTCCGGCGCCCGGGATGGCGATAGCAGGTG 1 82 0 CGGGATGGCG 0.922108 -66 CGTGGCGTACCGGGCGCGGCACCGCGAGTC 2 19 1 CGGGCGCGGC 0.964328 -71 CGCGGCACCGCGAGTCCGGGGACATGGCGA 2 33 1 CGAGTCCGGG 0.89686 -57 ATGTCCGTGGCAGGATCGGGCA 2 78 1 CAGGATCGGG 0.969623 -12 TGCGCGGGGTCGAGTTCGGGCTGCTCCGAG 3 52 1 CGAGTTCGGG 0.982515 -69 GTTGCTGAAGCAGGTTGTGGGCCTAGCGGA 3 82 0 CAGGTTGTGG 0.885013 -39 TTAGACGGCGGGGGCTCGGGTGGTACCCAT 4 21 1 GGGGCTCGGG 0.984978 -182 CGCAGCGCGGCGCGATGGGTACCACCCGAG 4 35 0 CGCGATGGGT 0.86936 -168 CCCATCGCGCCGCGCTGCGGTGCGGGTCAT 4 46 1 CGCGCTGCGG 0.95751 -157 GGGTCATCGTCAAGCTGTGCTTGACTGCTC 4 69 1 CAAGCTGTGC 0.908522 -134 GCATCGTCGCCGAGCTGTGTTGGACTGCTC 4 127 1 CGAGCTGTGT 0.904547 -76 AGCCCATAACCTAGCTCGGCGACGATGCAC 4 183 0 CTAGCTCGGC 0.914927 -20 TTGCGCTCCTCGCGCTGGCGTCGTTTCAAC 6 81 0 CGCGCTGGCG 0.956106 -170 ATTGCTTGCGCAAGCTCTGGCGGCCGAGCC 6 135 1 CAAGCTCTGG 0.960615 -116 ACGTTTGGAGGAGGCTCGGCCGCCAGAGCT 6 147 0 GAGGCTCGGC 0.9206 -104 ********** Masking position 4 Map Score: 20.7969 Number of sites scoring better than the average of aligned sites = 13515 Number in coding regions = 12499 Number in noncoding regions = 1016 Number of orfs with sites within 600 bp upstream = 694 Fraction of orfs with sites within 600 bp upstream = 0.111468 Motif number 5 TGGCGATAGCAGGTGGGCGACTCCGATGAG 1 67 0 AGGTGGGCGA 0.916449 -81 GCGCAGGTGCAGCTGCGCCCGTCCGCCCTG 3 27 0 AGCTGCGCCC 0.929956 -94 GCGGACTCGGAGCAGCCCGAACTCGACCCC 3 57 0 AGCAGCCCGA 0.988296 -64 CGCACCGCAGCGCGGCGCGATGGGTACCAC 4 40 0 CGCGGCGCGA 0.984231 -163 GTCATCGTCAAGCTGTGCTTGACTGCTCGG 4 71 1 AGCTGTGCTT 0.67729 -132 CACGCCGCGCAGCGGCGTGAGGAGGAGCCG 4 98 0 AGCGGCGTGA 0.981039 -105 GGAGGAGCCGAGCAGTCCAACACAGCTCGG 4 136 0 AGCAGTCCAA 0.819375 -67 CACGCCGCGCAGCGGCGTGAGGAGGAGCCG 4 156 0 AGCGGCGTGA 0.981039 -47 CGCCAGCGCGAGGAGCGCAAAACGTTAGGG 6 91 1 AGGAGCGCAA 0.932813 -160 TTCGGAGGCGAGCTGCCCTAACGTTTTGCG 6 106 0 AGCTGCCCTA 0.967738 -145 ********** Masking position 5 Map Score: 9.58892 Number of sites scoring better than the average of aligned sites = 5240 Number in coding regions = 4804 Number in noncoding regions = 436 Number of orfs with sites within 600 bp upstream = 335 Fraction of orfs with sites within 600 bp upstream = 0.0538066 Motif number 6 ********** No masking Map Score: 2.227e-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: 2.227e-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: 2.227e-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