AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00562_mtub_reg_300.orf -o00562_mtub_300.ace -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -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 = 0.66 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ppp 88 ppp #2 Rv0019c 123 hypothetical protein Rv0019c #3 Rv0020c 300 hypothetical protein Rv0020c #4 pknD 21 pknD #5 pstS 215 pstS Motif number 1 CTGCATCGTCGCCAGCGCGGG 1 2 0 GCCAGCGCGG 0.993754 -87 GAGAAGCGGTGGGGGCGCGCCCCCACAAGT 1 38 1 GGGGGCGCGC 0.991007 -51 CCGCAAGCGGGTGGGGGTACCCCCCACTTG 1 63 0 GTGGGGGTAC 0.869296 -26 CCACCCGCTTGCGGGGGAGA 1 79 1 GCGGGGGAGA 0.89725 -10 GCTCGAAGCTGCCGGGGTTGACCCGCGCCG 2 20 1 GCCGGGGTTG 0.964155 -104 TTTGACGGTGGTCGGCGCGGGTCAACCCCG 2 32 0 GTCGGCGCGG 0.997734 -92 TGACGTGCTCGGCAGCGCGGGGCCGGAGCA 2 77 1 GGCAGCGCGG 0.980451 -47 GCAGCGCGGGGCCGGAGCAGACGGTGCAGG 2 88 1 GCCGGAGCAG 0.884597 -36 TCACAGTACGGTGGGCGAAGGGGGACTTGA 3 18 1 GTGGGCGAAG 0.977487 -283 CCTTCGGGACGTGGGGGTTCAAGTCCCCCT 3 36 0 GTGGGGGTTC 0.91248 -265 GGCACCTGAAGCCAGCGCGTCTGCCATTCC 3 71 1 GCCAGCGCGT 0.945005 -230 TCCGGTTGTTGCGGGCGAGTGGCGGAATGG 3 94 0 GCGGGCGAGT 0.962489 -207 TACCACTGTAGTAGCCGCAGGCCCCATCCG 3 130 1 GTAGCCGCAG 0.844317 -171 GGCGCCCCTGGCAGCGGATGGGGCCTGCGG 3 144 0 GCAGCGGATG 0.629625 -157 TGCCAGGGGCGCCGGCGGGCTCAGTGGGCG 3 161 1 GCCGGCGGGC 0.981433 -140 GGCGGGCTCAGTGGGCGTGGCCGGCCCTTT 3 174 1 GTGGGCGTGG 0.991599 -127 TCGGGACAGTGTGAGCGAGCGGAAAGGGCC 3 196 0 GTGAGCGAGC 0.961222 -105 CTGGTGCATCGTCGGCGCAAGGCAAACGAC 3 258 0 GTCGGCGCAA 0.926896 -43 GAACAGTGAGGCGAGCGCTGAAAG 3 287 1 GCGAGCGCTG 0.98397 -14 ACTGAGGGTCGACGGCGCGCTTTGTCCAAG 5 45 0 GACGGCGCGC 0.967229 -171 GCGTTCAGGAGGGGCCGCTGATACTGAGGG 5 67 0 GGGGCCGCTG 0.968623 -149 TATTCGAGCCGTCACCGTTGTGCATCGAAA 5 120 0 GTCACCGTTG 0.839615 -96 GCCACCGGTGGTCGCCGAGCCACCGACCCG 5 157 0 GTCGCCGAGC 0.977511 -59 GGATCCACTCGCCACCGGTGGTCGCCGAGC 5 167 0 GCCACCGGTG 0.838144 -49 GGGGGTCGTGGTGGCGGATCCACTCGCCAC 5 182 0 GTGGCGGATC 0.850192 -34 ********** Masking position 7 Map Score: 50.593 Number of sites scoring better than the average of aligned sites = 48718 Number in coding regions = 45785 Number in noncoding regions = 2933 Number of orfs with sites within 600 bp upstream = 1261 Fraction of orfs with sites within 600 bp upstream = 0.202538 Motif number 2 CTGCGCTCTGCATCGTCGCCAGCGCGGG 1 6 0 CAGCGCCAGC 0.972535 -83 CAGAGCGCAGAGAAGCGGTGGGGGCGCGCCCCC 1 29 1 AGGGGTGGGG 0.88173 -60 TCTCCCCCGCAAGCGGGTGGGGGTACCCCCCA 1 67 0 CACGGTGGGG 0.930234 -22 CTACTGGGCTCGAAGCTGCCGGGGTTGACCCGC 2 13 1 CGGTGCCGGG 0.99006 -111 ACGATACTTTGACGGTGGTCGGCGCGGGTCAAC 2 36 0 GAGGGTCGGC 0.982568 -88 CTGACGTGCTCGGCAGCGCGGGGCCGGAGCAGA 2 76 1 CGACGCGGGG 0.981672 -48 CGGTGCAGGACGGAAAGGACGCCAG 2 109 1 CGAGGACGCC 0.704406 -15 ACTCGTCTCACAGTACGGTGGGCGAAGGGGGAC 3 11 1 CAAGGTGGGC 0.940642 -290 GGCGGAATGGCAGACGCGCTGGCTTCAGGTGCC 3 71 0 CACCGCTGGC 0.79253 -230 ATGGTCCTCCGGTTGTTGCGGGCGAGTGGCGGA 3 98 0 GGGTGCGGGC 0.988911 -203 CCCTGGCAGCGGATGGGGCCTGCGGCTACTACA 3 136 0 GGGGGCCTGC 0.941321 -165 CATCCGCTGCCAGGGGCGCCGGCGGGCTCAGTG 3 154 1 CAGCGCCGGC 0.995664 -147 CGGGCTCAGTGGGCGTGGCCGGCCCTTTCCGCT 3 176 1 GGGGGCCGGC 0.997053 -125 CATGGTATCGGGACAGTGTGAGCGAGCGGAAAG 3 200 0 GGATGTGAGC 0.430589 -101 TCTGGTGCATCGTCGGCGCAAGGCAAACGACTC 3 256 0 CGGCGCAAGG 0.785167 -45 TGCACCAGAACAGTGAGGCGAGCGCTGAAAG 3 280 1 CAGGGCGAGC 0.977846 -21 CGCTGATACTGAGGGTCGACGGCGCGCTTTGTC 5 49 0 GAGCGACGGC 0.968811 -167 GAAATCCTAGCGTTCAGGAGGGGCCGCTGATAC 5 73 0 CGCGGAGGGG 0.946147 -143 TTTCGATGCACAACGGTGACGGCTCGAATACCG 5 120 1 CAGTGACGGC 0.941643 -96 GTCGCCGAGCCACCGACCCGGGGTCGGTATTCG 5 144 0 CAGCCCGGGG 0.899847 -72 ACTCGCCACCGGTGGTCGCCGAGCCACCGACCC 5 158 0 GGGCGCCGAG 0.888433 -58 CTCTCGAGGGGGTCGTGGTGGCGGATCCACTCG 5 186 0 GGGGGTGGCG 0.88604 -30 ** * ******* Masking position 8 Map Score: 36.3567 Number of sites scoring better than the average of aligned sites = 64058 Number in coding regions = 60736 Number in noncoding regions = 3322 Number of orfs with sites within 600 bp upstream = 1288 Fraction of orfs with sites within 600 bp upstream = 0.206874 Motif number 3 CTTCTCTGCGCTCTGCATCGTCGCCAGCGC 1 14 0 CTCTGCATCG 0.922409 -75 GTGGGGGCGCGCCCCCACCGCTTCTCTGCG 1 34 0 GCCCCCACCG 0.894858 -55 GGTCAACCCCGGCAGCTTCGAGCCCAGTAG 2 13 0 GGCAGCTTCG 0.773563 -111 TTGACCCGCGCCGACCACCGTCAAAGTATC 2 37 1 CCGACCACCG 0.821905 -87 GACTTTGCTGACGTGCTCGGCAGCGCGGGG 2 69 1 ACGTGCTCGG 0.62911 -55 GTCCTTTCCGTCCTGCACCGTCTGCTCCGG 2 99 0 TCCTGCACCG 0.97263 -25 GGGGTTCAAGTCCCCCTTCGCCCACCGTAC 3 23 0 TCCCCCTTCG 0.88128 -278 TCAGGTGCCAGTGTCCTTCGGGACGTGGGG 3 50 0 GTGTCCTTCG 0.812624 -251 TACAGTGGTATGGTCCTCCGGTTGTTGCGG 3 110 0 TGGTCCTCCG 0.963109 -191 ATCCGCTGCCAGGGGCGCCGGCGGGCTCAG 3 155 1 AGGGGCGCCG 0.780078 -146 GAGTCGTTTGCCTTGCGCCGACGATGCACC 3 256 1 CCTTGCGCCG 0.757871 -45 CTCACTGTTCTGGTGCATCGTCGGCGCAAG 3 267 0 TGGTGCATCG 0.933708 -34 GCATGTAGTACCCTGCGCCG 5 1 0 CCCTGCGCCG 0.934969 -215 GGGTACTACATGCTCCTTGGGATGCTCCTT 5 18 1 TGCTCCTTGG 0.83149 -198 CTCCTTGGGATGCTCCTTGGACAAAGCGCG 5 30 1 TGCTCCTTGG 0.83149 -186 TTGGACAAAGCGCGCCGTCGACCCTCAGTA 5 46 1 CGCGCCGTCG 0.933201 -170 GCCGTCACCGTTGTGCATCGAAAGAGGTCT 5 113 0 TTGTGCATCG 0.858869 -103 GGCGGATCCACTCGCCACCGGTGGTCGCCG 5 170 0 CTCGCCACCG 0.898366 -46 ********** Masking position 6 Map Score: 20.5455 Number of sites scoring better than the average of aligned sites = 32647 Number in coding regions = 30548 Number in noncoding regions = 2099 Number of orfs with sites within 600 bp upstream = 1090 Fraction of orfs with sites within 600 bp upstream = 0.175072 Motif number 4 CGCTCTGCATCGTCGCCAGCGCGGG 1 4 0 CGTCCCAGGC 0.932767 -85 TGTGGGGGCGCGCCCCCACCGCTTCTCTGCGC 1 33 0 CGCCCCACGC 0.979233 -56 GGGGGCGCGCCCCCACAAGTGGGGGGTACCCC 1 48 1 CCCCCAAGGG 0.993364 -41 TCTCCCCCGCAAGCGGGTGGGGGTAC 1 73 0 CCCCCAAGGG 0.944215 -16 TGACGTGCTCGGCAGCGCGGGGCCGGAGCAGA 2 77 1 GGCACGCGGG 0.812798 -47 GCCACTCGCCCGCAACAACCGGAGGACCATAC 3 101 1 CGCACAACGG 0.958411 -200 AGGCCCCATCCGCTGCCAGGGGCGCCGGCGGG 3 148 1 CGCTCCAGGG 0.992892 -153 CGTCGAATTCCCTTCACTAGG 4 1 0 CCCTCACTGG 0.832998 -21 TCGCCGAGCCACCGACCCGGGGTCGGTATTCG 5 144 0 ACCGCCCGGG 0.880359 -72 CGGATCCACTCGCCACCGGTGGTCGCCGAGCC 5 166 0 CGCCCCGGGG 0.994881 -50 CCACCACGACCCCCTCGAGAGGAGTTGC 5 198 1 CCCCCGAGGG 0.510785 -18 **** **** ** Masking position 6 Map Score: 15.8281 Number of sites scoring better than the average of aligned sites = 4772 Number in coding regions = 4291 Number in noncoding regions = 481 Number of orfs with sites within 600 bp upstream = 348 Fraction of orfs with sites within 600 bp upstream = 0.0558946 Motif number 5 GCGACGATGCAGAGCGCAGAGAAGCGGTGG 1 20 1 AGAGCGCAGA 0.550572 -69 CCGGCAGCTTCGAGCCCAGTAGGT 2 5 0 CGAGCCCAGT 0.923847 -119 TGACGGTGGTCGGCGCGGGTCAACCCCGGC 2 30 0 CGGCGCGGGT 0.758015 -94 ACTTTGCTGACGTGCTCGGCAGCGCGGGGC 2 70 1 CGTGCTCGGC 0.887761 -54 CTCGGCAGCGCGGGGCCGGAGCAGACGGTG 2 84 1 CGGGGCCGGA 0.99716 -40 CCGGAGCAGACGGTGCAGGACGGAAAGGAC 2 99 1 CGGTGCAGGA 0.824304 -25 CGCTGGCTTCAGGTGCCAGTGTCCTTCGGG 3 58 0 AGGTGCCAGT 0.860687 -243 TGGCAGCGGATGGGGCCTGCGGCTACTACA 3 136 0 TGGGGCCTGC 0.921054 -165 GGGGCGCCGGCGGGCTCAGTGGGCGTGGCC 3 166 1 CGGGCTCAGT 0.937902 -135 GCTCAGTGGGCGTGGCCGGCCCTTTCCGCT 3 179 1 CGTGGCCGGC 0.981436 -122 AACAGTGAGGCGAGCGCTGAAAG 3 288 1 CGAGCGCTGA 0.784055 -13 AGCGTTCAGGAGGGGCCGCTGATACTGAGG 5 68 0 AGGGGCCGCT 0.874651 -148 GTGCATCGAAAGAGGTCTGATCATTGAAAT 5 101 0 AGAGGTCTGA 0.626934 -115 CGATGCACAACGGTGACGGCTCGAATACCG 5 123 1 CGGTGACGGC 0.89803 -93 GCCACCGACCCGGGGTCGGTATTCGAGCCG 5 139 0 CGGGGTCGGT 0.99125 -77 GAGGGGGTCGTGGTGGCGGATCCACTCGCC 5 184 0 TGGTGGCGGA 0.81776 -32 ********** Masking position 2 Map Score: 17.335 Number of sites scoring better than the average of aligned sites = 27683 Number in coding regions = 25958 Number in noncoding regions = 1725 Number of orfs with sites within 600 bp upstream = 959 Fraction of orfs with sites within 600 bp upstream = 0.154031 Motif number 6 ********** No masking Map Score: 9.40348e-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: 9.40348e-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: 9.40348e-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