AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -imalT_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 Rv1234 149 hypothetical protein Rv1234 #2 Rv1781c 263 hypothetical protein Rv1781c #3 Rv2041c 37 hypothetical protein Rv2041c #4 pncA 40 pncA #5 Rv2044c 85 hypothetical protein Rv2044c #6 lipT 48 lipT #7 ugpA 86 ugpA #8 infB 85 infB #9 Rv2840c 126 hypothetical protein Rv2840c Motif number 1 GCTCGCCGTTCGGTGGGCCTCGGTCGCTCG 1 37 1 CGGTGGGCCT 0.977031 -113 CGGTGGGCCTCGGTCGCTCGCGGGTTGAGT 1 47 1 CGGTCGCTCG 0.668985 -103 GCGCTGAAAAAGGGGGGCGGAGGAGAATGA 1 124 1 AGGGGGGCGG 0.922153 -26 GGGTATTTGCCACTGCGCGGATCCCCCAAG 2 56 1 CACTGCGCGG 0.993875 -208 GTCGTGTCTTCACTGGGCATGGTAGCGGCG 2 91 1 CACTGGGCAT 0.851021 -173 GCGAATGACCGAGTCCGCCTGTGGAACTGT 2 118 1 GAGTCCGCCT 0.707513 -146 TGGAACTGTCCGCTCCGCAGTCTACCTCGT 2 139 1 CGCTCCGCAG 0.974494 -125 CAGATTCCTGCGCTCGCCCGCACACGGGTG 2 224 1 CGCTCGCCCG 0.981016 -40 CGCCCGCACACGGGTGCCGGACGCAAGATG 2 238 1 CGGGTGCCGG 0.910733 -26 GCAAACTGCCCGGGCAGTCGCCC 4 4 1 AACTGCCCGG 0.885234 -37 ACTGCCCGGGCAGTCGCCCGAACGTATGGT 4 15 1 CAGTCGCCCG 0.960926 -26 CCTTTTCTGTCAGTGGCCGGAGCGCCGCGA 5 12 1 CAGTGGCCGG 0.989008 -74 GTTGCCTTTCCAGGTCGCGGCGCTCCGGCC 5 26 0 CAGGTCGCGG 0.954101 -60 CAGGAATGGGGGCGGGGCGGCTAGCCTGTC 6 14 0 GGCGGGGCGG 0.968946 -35 CCCATTCCTGCACTGCGCATGCCGC 6 34 1 CACTGCGCAT 0.838758 -15 TACGGAGCTACACTGCGCCG 7 77 1 CACTGCGCCG 0.99446 -10 TAGCTAAACCCGAGGCGCGGCCCACGACTG 8 43 1 CGAGGCGCGG 0.966397 -43 CGGGCAAGCCCGATTGCCCGGCTATCTGCC 9 29 0 CGATTGCCCG 0.92409 -98 CGGGCAATCGGGCTTGCCCGGTGACGCTAC 9 39 1 GGCTTGCCCG 0.92231 -88 GGTGACGCTACACTTAGCCGTGATCCAGCG 9 58 1 CACTTAGCCG 0.804805 -69 ATCCGGGCGTCGATGCGCCGAGGCCGAAGG 9 92 0 CGATGCGCCG 0.982947 -35 CGGTCCGCGGGGATTATCCG 9 117 0 CGGTCCGCGG 0.992364 -10 ********** Masking position 8 Map Score: 39.4262 Number of sites scoring better than the average of aligned sites = 36326 Number in coding regions = 33735 Number in noncoding regions = 2591 Number of orfs with sites within 600 bp upstream = 1211 Fraction of orfs with sites within 600 bp upstream = 0.194507 Motif number 2 CCGCGAGCGACCGAGGCCCACCGAACGGCGAGCATCG 1 33 0 CGAGCCCGCG 0.960178 -117 TCCAGGTGTTCTGAGCAGACCGGAAGGTGATCTAGC 2 10 0 CGAGGCGGGG 0.907462 -254 ACGACGAATCCTTGGGGGATCCGCGCAGTGGCAAATA 2 59 0 CTGGGCCGCA 0.776215 -205 CTACCATGCCCAGTGAAGACACGACGAATCCTTGGGG 2 79 0 CGTGGACGGA 0.992833 -185 CGGTAGCCAACCGTGCTGTGCTGACGGAAGGCTCAGA 2 191 1 CGTGGCTGGG 0.983702 -73 CGTCCGGCACCCGTGTGCGGGCGAGCGCAGGAATCTG 2 224 0 CGTGCGCGCG 0.964067 -40 ATTTTGGGTCCTGTGGTACAACGACCG 3 1 0 CGTGAACGCG 0.992305 -37 TACCACCGTTGATACAACGACGGTTTCGTACAT 5 63 0 CTTGAACGGG 0.946103 -23 GCGGCATGCGCAGTGCAGGAATGGGGGCGGGGCGGCT 6 22 0 CGTGGATGGG 0.985638 -27 CTGGCCGACATTGCCGTGACGGCGGTGATTGGTTC 7 9 1 CTTGGACGGG 0.989924 -78 GGTTCATCGACCGTGGCGGCAAACTCGCCGACAGAAT 7 41 1 CGTGGAAACG 0.863586 -46 CGGCGCAGTGTAGCTCCGTATTCTGTCGGCGA 7 65 0 CGTGGCCGTT 0.890386 -22 GCACACCGTGAAGTCCCGATGACAATGCGTCA 8 6 1 CGTGGCCGGA 0.992686 -80 CATCTCCTGTCCATGAGGCGACAGTCGTGGGCCGCGC 8 57 0 CATGGACACG 0.863707 -29 CGGCTATCTGCCGTGGGATAACGCACGGCG 9 4 0 CGTGAACGCG 0.992335 -123 CGGGCTTGCCCGGTGACGCTACACTTAGCCGTGATCC 9 47 1 CGTGGACATA 0.795938 -80 CCTTCGGCCTCGGCGCATCGACGCCCGGATAATCCCC 9 92 1 CGCGTACGCG 0.884018 -35 * *** * *** ** Masking position 5 Map Score: 24.1402 Number of sites scoring better than the average of aligned sites = 8297 Number in coding regions = 7660 Number in noncoding regions = 637 Number of orfs with sites within 600 bp upstream = 496 Fraction of orfs with sites within 600 bp upstream = 0.0796659 Motif number 3 GCGAGCATCGTTGCCGGGATAGGTTGATCACC 1 10 0 TGCCGGAAGG 0.988655 -140 CCGAGGCCCACCGAACGGCGAGCATCGTTGCCG 1 27 0 CGAAGGCAGC 0.907589 -123 CGCTCGCGGGTTGAGTGGATAGTGTGCCGGGAG 1 61 1 TGAGGGAAGT 0.909275 -89 GTAGCTGGACCTGACTGGACATGAAACGATGGC 1 93 1 CGACGGAATG 0.985106 -57 GTGTTCTGAGCAGACCGGAAGGTGATCTAGC 2 9 0 CGACGGAGGT 0.979119 -255 AGGTAGACTGCGGAGCGGACAGTTCCACAGGCG 2 133 0 CGAGGGAAGT 0.969117 -131 CCGTGCTGTGCTGACGGAAGGCTCAGATTCCTG 2 201 1 CGACGAAGCT 0.62647 -63 GTTCGGGCGACTGCCCGGGCAGTTTGC 4 5 0 CGCCGGGAGT 0.964307 -36 GCTCCGGCCACTGACAGAAAAGGT 5 2 0 CGACGAAAGG 0.982234 -84 CGGAGCGCCGCGACCTGGAAAGGCAACCCGAGA 5 29 1 CACCGGAAGG 0.966984 -57 CCCGACAGGCTAGCCGCCCCGCCC 6 2 1 CGACGGCAGC 0.993338 -47 GGCAAACTCGCCGACAGAATACGGAGCTACACT 7 58 1 CGACGAAACG 0.922375 -29 TGTCGCCTCATGGACAGGAGATGTA 8 71 1 TGACGGAATG 0.9548 -15 GCAAGCCCGATTGCCCGGCTATCTGCCGTGGGA 9 23 0 TGCCGGCATC 0.886198 -104 AAGTGTAGCGTCACCGGGCAAGCCCGATTGCCC 9 40 0 TACCGGCAGC 0.807637 -87 * *** *** *** Masking position 7 Map Score: 19.7114 Number of sites scoring better than the average of aligned sites = 7790 Number in coding regions = 7208 Number in noncoding regions = 582 Number of orfs with sites within 600 bp upstream = 464 Fraction of orfs with sites within 600 bp upstream = 0.0745262 Motif number 4 GGTGATCAACCTATCCCGGCA 1 1 1 GGGATCAACC 0.966043 -149 CCACTCAACCCGCGAGCGACCGAGGCCCACC 1 48 0 CGGAGCGACC 0.863161 -102 GGGGGGCGGAGGAGAATGAGAACCG 1 135 1 GGGAATGAGA 0.788069 -15 CAGACCGGAAGGTGATCTAGC 2 1 0 GGGATCTAGC 0.838252 -263 CAGAACACCTGGACATTGACCTGGGTATTTG 2 34 1 GGCATTGACC 0.527316 -230 GCATGGTAGCGGCGAATGACCGAGTCCGCCT 2 107 1 GGGAATGACC 0.942571 -157 CTACGTTGCAGGTCAACGAGGTAGACTGCGG 2 153 0 GGCAACGAGG 0.880064 -111 GGGTCCTGTGGTACAACGACCG 3 2 0 GTCAACGACC 0.940404 -36 CATACGTTCGGGCGACTGCCCGGGCAGTTTG 4 12 0 GGGACTGCCC 0.90302 -29 GCGGCGCTCCGGCCACTGACAGAAAAGGT 5 9 0 GGCACTGACA 0.883514 -77 GCGGTGATTGGTTCATCGACCGTGGCGGCAA 7 32 1 GTCATCGACC 0.935527 -55 TTCGGCCTCGGCGCATCGACGCCCGGATAAT 9 94 1 GCCATCGACG 0.827694 -33 CGGTCCGCGGGGATTATCCGGGCGTCGAT 9 108 0 GGGATTATCC 0.641226 -19 ** ******** Masking position 5 Map Score: 10.0941 Number of sites scoring better than the average of aligned sites = 7306 Number in coding regions = 6883 Number in noncoding regions = 423 Number of orfs with sites within 600 bp upstream = 343 Fraction of orfs with sites within 600 bp upstream = 0.0550916 Motif number 5 ATCCCGGCAACGATGCTCGCCGTTCGGTGG 1 23 1 CGATGCTCGC 0.947222 -127 GGTGGGCCTCGGTCGCTCGCGGGTTGAGTG 1 48 1 GGTCGCTCGC 0.886703 -102 TCAGGTCCAGCTACTCCCGGCACACTATCC 1 77 0 CTACTCCCGG 0.968684 -73 GCTCAGATTCCTGCGCTCGCCCGCACACGG 2 221 1 CTGCGCTCGC 0.963008 -43 CGCCCGCACACGGGTGCCGGACGCAAGATG 2 238 1 CGGGTGCCGG 0.938651 -26 TACGTTCGGGCGACTGCCCGGGCAGTTTGC 4 11 0 CGACTGCCCG 0.943158 -30 TTCCAGGTCGCGGCGCTCCGGCCACTGACA 5 19 0 CGGCGCTCCG 0.754396 -67 CGGTTTCGTACATCTCTCGGGTTGCCTTTC 5 46 0 CATCTCTCGG 0.855662 -40 TAGCTAAACCCGAGGCGCGGCCCACGACTG 8 43 1 CGAGGCGCGG 0.938676 -43 GCGCGGCCCACGACTGTCGCCTCATGGACA 8 57 1 CGACTGTCGC 0.974021 -29 CTCGGCGCATCGACGCCCGGATAATCCCCG 9 100 1 CGACGCCCGG 0.995083 -27 ********** Masking position 8 Map Score: 12.7658 Number of sites scoring better than the average of aligned sites = 11237 Number in coding regions = 10333 Number in noncoding regions = 904 Number of orfs with sites within 600 bp upstream = 682 Fraction of orfs with sites within 600 bp upstream = 0.109541 Motif number 6 GGCAACGATGCTCGCCGTTCGGTGGGCCTC 1 28 1 CTCGCCGTTC 0.874308 -122 CTCATTCTCCTCCGCCCCCCTTTTTCAGCG 1 125 0 TCCGCCCCCC 0.945662 -25 GACTCGGTCATTCGCCGCTACCATGCCCAG 2 103 0 TTCGCCGCTA 0.864361 -161 GGAATCTGAGCCTTCCGTCAGCACAGCACG 2 202 0 CCTTCCGTCA 0.541708 -62 GATTCCTGCGCTCGCCCGCACACGGGTGCC 2 226 1 CTCGCCCGCA 0.932712 -38 CACACGGGTGCCGGACGCAAGATGGGCGAC 2 244 1 CCGGACGCAA 0.540723 -20 GGCTAGCCGCCCCGCCCCCATTCCTGCACT 6 18 1 CCCGCCCCCA 0.992471 -31 CTGGCCGACATTGCCGTGAC 7 1 1 CTGGCCGACA 0.965937 -86 TGAACCAATCACCGCCGTCACGGCAATGTC 7 17 0 ACCGCCGTCA 0.958229 -70 TGTCGGCGAGTTTGCCGCCACGGTCGATGA 7 44 0 TTTGCCGCCA 0.874086 -43 TGGCGGCAAACTCGCCGACAGAATACGGAG 7 54 1 CTCGCCGACA 0.993146 -33 ACCGTGAAGTCCCGATGACAATGCGTCATA 8 15 1 CCCGATGACA 0.847962 -71 ATCGGGCTTGCCCGGTGACGCTACACTTAG 9 45 1 CCCGGTGACG 0.381224 -82 GCCTCGGCGCATCGACGCCCGGATAATCCC 9 98 1 ATCGACGCCC 0.821526 -29 CCGGATAATCCCCGCGGACCG 9 116 1 CCCGCGGACC 0.944889 -11 ********** Masking position 4 Map Score: 10.5389 Number of sites scoring better than the average of aligned sites = 32481 Number in coding regions = 30445 Number in noncoding regions = 2036 Number of orfs with sites within 600 bp upstream = 1119 Fraction of orfs with sites within 600 bp upstream = 0.17973 Motif number 7 AGGTCAACGAGGTAGACTGCGGAGCGGACA 2 145 0 GGTAGACTGC 0.948393 -119 CGACTGCCCGGGCAGTTTGC 4 1 0 GGCAGTTTGC 0.987005 -40 CCATACGTTCGGGCGACTGCCCGGGCAGTT 4 14 0 GGGCGACTGC 0.983775 -27 ATGGGGGCGGGGCGGCTAGCCTGTCGGG 6 9 0 GGCGGCTAGC 0.908887 -40 TATTCTGTCGGCGAGTTTGCCGCCACGGTC 7 49 0 GCGAGTTTGC 0.918861 -38 GTTATCCCACGGCAGATAGCCGGGCAATCG 9 19 1 GGCAGATAGC 0.986481 -108 CACCGGGCAAGCCCGATTGCCCGGCTATCT 9 32 0 GCCCGATTGC 0.986528 -95 GATGCGCCGAGGCCGAAGGCTCGCGCTGGA 9 81 0 GGCCGAAGGC 0.950632 -46 ********** Masking position 5 Map Score: 7.48663 Number of sites scoring better than the average of aligned sites = 1795 Number in coding regions = 1640 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 8 CGAACGGCGAGCATCGTTGCCGGGATAGGT 1 19 0 GCATCGTTGC 0.535569 -131 TTTTTCAGCGCCATCGTTTCATGTCCAGTC 1 105 0 CCATCGTTTC 0.901745 -45 TCTTCACTGGGCATGGTAGCGGCGAATGAC 2 97 1 GCATGGTAGC 0.892222 -167 TCGTTGACCTGCAACGTAGTGGTGTTCGGT 2 165 1 GCAACGTAGT 0.796219 -99 CGGTCGTTGTACCACAGGAC 3 1 1 CGGTCGTTGT 0.901527 -37 ATGTACGAAACCGTCGTTGTATCAACGGTG 5 63 1 CCGTCGTTGT 0.98405 -23 CTGGCCGACATTGCCGTGACGGCG 7 5 1 CCGACATTGC 0.92163 -82 CGATGACAATGCGTCATAGCTAAACCCGAG 8 27 1 GCGTCATAGC 0.960462 -59 GATTATCCGGGCGTCGATGCGCCGAGGCCG 9 96 0 GCGTCGATGC 0.659016 -31 ********** Masking position 7 Map Score: 9.54234 Number of sites scoring better than the average of aligned sites = 5542 Number in coding regions = 5043 Number in noncoding regions = 499 Number of orfs with sites within 600 bp upstream = 341 Fraction of orfs with sites within 600 bp upstream = 0.0547703 Motif number 9 ********** No masking Map Score: -8.07587e-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 10 ********** No masking Map Score: -8.07587e-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 11 ********** No masking Map Score: -8.07587e-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