AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i316_mixed3_mtub_reg_300.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -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 = 0.66 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 ppp 88 ppp #2 Rv0019c 123 hypothetical protein Rv0019c #3 Rv0020c 300 hypothetical protein Rv0020c #4 accD5 49 accD5 Motif number 1 CCCGCGCTGGCGACGATGCA 1 1 1 CCCGCGCTGG 0.755619 -88 TGGGGGCGCGCCCCCACCGCTTCTCTGCGC 1 33 0 CCCCCACCGC 0.996893 -56 GTGGGGGTACCCCCCACTTGTGGGGGCGCG 1 53 0 CCCCCACTTG 0.973021 -36 GTGGGGGGTACCCCCACCCGCTTGCGGGGG 1 66 1 CCCCCACCCG 0.982632 -23 TCTCCCCCGCAAGCGGGTGGGGG 1 76 0 CCCCCGCAAG 0.978053 -13 CGCGGGTCAACCCCGGCAGCTTCGAGCCCA 2 17 0 CCCCGGCAGC 0.992547 -107 CCGGGGTTGACCCGCGCCGACCACCGTCAA 2 31 1 CCCGCGCCGA 0.97872 -93 CTGCTCCGGCCCCGCGCTGCCGAGCACGTC 2 78 0 CCCGCGCTGC 0.988784 -46 AGTCCCCCTTCGCCCACCGTACTGTGAGAC 3 15 0 CGCCCACCGT 0.975963 -286 GGGACTTGAACCCCCACGTCCCGAAGGACA 3 39 1 CCCCCACGTC 0.980552 -262 ATGGCAGACGCGCTGGCTTCAGGTGCCAGT 3 68 0 CGCTGGCTTC 0.940429 -233 TTCCGCCACTCGCCCGCAACAACCGGAGGA 3 97 1 CGCCCGCAAC 0.987642 -204 CTGTAGTAGCCGCAGGCCCCATCCGCTGCC 3 135 1 CGCAGGCCCC 0.930115 -166 CCGCCGGCGCCCCTGGCAGCGGATGGGGCC 3 149 0 CCCTGGCAGC 0.966513 -152 CTGCCAGGGGCGCCGGCGGGCTCAGTGGGC 3 160 1 CGCCGGCGGG 0.984608 -141 GGGCCGGCCACGCCCACTGAGCCCGCCGGC 3 171 0 CGCCCACTGA 0.979255 -130 CGGCCCTTTCCGCTCGCTCACACTGTCCCG 3 195 1 CGCTCGCTCA 0.901909 -106 GTTTGCCTTGCGCCGACGATGCACCAGAAC 3 261 1 CGCCGACGAT 0.693135 -40 CTTTCAGCGCTCGCCTCACTGTTCTGG 3 284 0 CGCTCGCCTC 0.983073 -17 CGCCCCAGCCTAAGGAAGTAGT 4 3 1 CCCCAGCCTA 0.811921 -47 TATCGGCTGCCGCACACTACTTCCTTAGGC 4 18 0 CGCACACTAC 0.858743 -32 ********** Masking position 7 Map Score: 46.4932 Number of sites scoring better than the average of aligned sites = 21568 Number in coding regions = 20054 Number in noncoding regions = 1514 Number of orfs with sites within 600 bp upstream = 889 Fraction of orfs with sites within 600 bp upstream = 0.142788 Motif number 2 AGAAGCGGTGGGGGCGCGCCCCCACAAGTGGG 1 39 1 GGCGCGCCCC 0.499977 -50 CCACAAGTGGGGGGTACCCCCACCCGCTTGCG 1 60 1 GGTACCCCCA 0.907499 -29 AACCCCGGCAGCTTCGAGCCCAGTAGGT 2 7 0 GCCGAGCCCA 0.989837 -117 TGGTCGGCGCGGGTCAACCCCGGCAGCTTCGA 2 22 0 GGCAACCCCG 0.92983 -102 TGCACCGTCTGCTCCGGCCCCGCGCTGCCGAG 2 84 0 GCCGGCCCCG 0.99274 -40 GGTTCAAGTCCCCCTTCGCCCACCGTACTGTG 3 19 0 CCTTCGCCCA 0.953669 -282 GACTTGAACCCCCACGTCCCGAAGGACACTGG 3 41 1 CCCGTCCCGA 0.825497 -260 GCACCTGAAGCCAGCGCGTCTGCCATTCCGCC 3 72 1 CCCGCGTCTG 0.864649 -229 CTGCCATTCCGCCACTCGCCCGCAACAACCGG 3 91 1 GCCTCGCCCG 0.993747 -210 CACTGTAGTAGCCGCAGGCCCCATCCGCTGCC 3 133 1 GCCAGGCCCC 0.96816 -168 ACTGAGCCCGCCGGCGCCCCTGGCAGCGGATG 3 154 0 CCCGCCCCTG 0.943981 -147 CGGAAAGGGCCGGCCACGCCCACTGAGCCCGC 3 175 0 CGCACGCCCA 0.972101 -126 CGCAAGGCAAACGACTCGCCTGTATGTCGTGT 3 241 0 ACCTCGCCTG 0.860519 -60 CGAGTCGTTTGCCTTGCGCCGACGATGCACCA 3 255 1 GCTGCGCCGA 0.964823 -46 ** ******** Masking position 10 Map Score: 20.1045 Number of sites scoring better than the average of aligned sites = 19174 Number in coding regions = 17730 Number in noncoding regions = 1444 Number of orfs with sites within 600 bp upstream = 872 Fraction of orfs with sites within 600 bp upstream = 0.140058 Motif number 3 GCGACGATGCAGAGCGCAGAGAAGCGGTGGG 1 20 1 AGGCGCAGAG 0.990319 -69 CAGACGGTGCAGGACGGAAAGGACGCCAG 2 105 1 AGACGGAAAG 0.982707 -19 CTTCGCCCACCGTACTGTGAGACGAGT 3 7 0 CGACTGTGAG 0.965804 -294 GGGGCGCCGGCGGGCTCAGTGGGCGTGGCCG 3 166 1 CGGCTCAGTG 0.942227 -135 ACAGTGTGAGCGAGCGGAAAGGGCCGGCCAC 3 190 0 CGGCGGAAAG 0.992992 -111 ACGATGCACCAGAACAGTGAGGCGAGCGCTG 3 276 1 AGACAGTGAG 0.92775 -25 CAGTGAGGCGAGCGCTGAAAG 3 290 1 AGGCTGAAAG 0.986774 -11 ** ******** Masking position 5 Map Score: 7.03791 Number of sites scoring better than the average of aligned sites = 619 Number in coding regions = 552 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 4 TCTGCGCTCTGCATCGTCGCCAGCGCGGG 1 9 0 GCATCGCGCC 0.993617 -80 TTGTGGGGGCGCGCCCCCACCGCTTCTCTGC 1 35 0 GCGCCCCACC 0.976873 -54 GGGTTGACCCGCGCCGACCACCGTCAAAGTA 2 34 1 GCGCCGCCAC 0.943259 -90 GACTTTGCTGACGTGCTCGGCAGCGCGGGGC 2 69 1 ACGTGCCGGC 0.941795 -55 TTTCCGTCCTGCACCGTCTGCTCCGGCCCCG 2 94 0 GCACCGCTGC 0.988297 -30 CTGGCGTCCTTTCCGTCCTGCACC 2 110 0 GCGTCCTTCC 0.974812 -14 CCTGAAGCCAGCGCGTCTGCCATTCCGCCAC 3 75 1 GCGCGTTGCC 0.87486 -226 GAGCCCGCCGGCGCCCCTGGCAGCGGATGGG 3 152 0 GCGCCCTGGC 0.991217 -149 GGCTCAGTGGGCGTGGCCGGCCCTTTCCGCT 3 178 1 GCGTGGCGGC 0.994513 -123 ACATACAGGCGAGTCGTTTGCCTTGCGCCGA 3 246 1 GAGTCGTTGC 0.850424 -55 CTGTTCTGGTGCATCGTCGGCGCAAGGCAAA 3 262 0 GCATCGCGGC 0.994576 -39 GCAGCCGATAACATCGACTCCC 4 38 1 ACATCGCTCC 0.902265 -12 ****** **** Masking position 11 Map Score: 20.9568 Number of sites scoring better than the average of aligned sites = 34332 Number in coding regions = 32583 Number in noncoding regions = 1749 Number of orfs with sites within 600 bp upstream = 884 Fraction of orfs with sites within 600 bp upstream = 0.141985 Motif number 5 TCTCTGCGCTCTGCATCGTCGCCAGCGCGG 1 12 0 CTGCATCGTC 0.996373 -77 GACCCGCGCCGACCACCGTCAAAGTATCGT 2 39 1 GACCACCGTC 0.979483 -85 CCGAGCACGTCAGCAAAGTCACGATACTTT 2 59 0 CAGCAAAGTC 0.954257 -65 CCTTTCCGTCCTGCACCGTCTGCTCCGGCC 2 97 0 CTGCACCGTC 0.997655 -27 CACTGTTCTGGTGCATCGTCGGCGCAAGGC 3 265 0 GTGCATCGTC 0.994601 -36 ********** Masking position 5 Map Score: 7.49986 Number of sites scoring better than the average of aligned sites = 642 Number in coding regions = 558 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 6 GAGAAGCGGTGGGGGCGCGCCCCCACAAGT 1 38 1 GGGGGCGCGC 0.530727 -51 TGGGGGGTACCCCCACCCGCTTGCGGGGGA 1 67 1 CCCCACCCGC 0.865234 -22 TCTCCCCCGCAAGCGGGTGG 1 79 0 TCTCCCCCGC 0.777549 -10 AGCTGCCGGGGTTGACCCGCGCCGACCACC 2 26 1 GTTGACCCGC 0.887549 -98 TCGTGACTTTGCTGACGTGCTCGGCAGCGC 2 65 1 GCTGACGTGC 0.952216 -59 ACCGTCTGCTCCGGCCCCGCGCTGCCGAGC 2 83 0 CCGGCCCCGC 0.746513 -41 CAGTGTCCTTCGGGACGTGGGGGTTCAAGT 3 42 0 CGGGACGTGG 0.589587 -259 TGGCGGAATGGCAGACGCGCTGGCTTCAGG 3 75 0 GCAGACGCGC 0.828172 -226 TCCGGTTGTTGCGGGCGAGTGGCGGAATGG 3 94 0 GCGGGCGAGT 0.629339 -207 TGGCAGCGGATGGGGCCTGCGGCTACTACA 3 136 0 TGGGGCCTGC 0.787058 -165 CACTGAGCCCGCCGGCGCCCCTGGCAGCGG 3 157 0 GCCGGCGCCC 0.70597 -144 GCGGAAAGGGCCGGCCACGCCCACTGAGCC 3 178 0 CCGGCCACGC 0.952469 -123 TCGGGACAGTGTGAGCGAGCGGAAAGGGCC 3 196 0 GTGAGCGAGC 0.477334 -105 GATGTTATCGGCTGCCGCACACTACTTCCT 4 23 0 GCTGCCGCAC 0.90058 -27 ********** Masking position 6 Map Score: 13.0107 Number of sites scoring better than the average of aligned sites = 36298 Number in coding regions = 33575 Number in noncoding regions = 2723 Number of orfs with sites within 600 bp upstream = 1222 Fraction of orfs with sites within 600 bp upstream = 0.196274 Motif number 7 CAAGTGGGGGGTACCCCCACCCGCTTGCGG 1 63 1 GTACCCCCAC 0.881682 -26 TGCCGGGGTTGACCCGCGCCGACCACCGTC 2 29 1 GACCCGCGCC 0.942646 -95 CGTCAGCAAAGTCACGATACTTTGACGGTG 2 52 0 GTCACGATAC 0.891527 -72 CGTCCTTTCCGTCCTGCACCGTCTGCTCCG 2 100 0 GTCCTGCACC 0.944956 -24 GGGGGTTCAAGTCCCCCTTCGCCCACCGTA 3 24 0 GTCCCCCTTC 0.962063 -277 GAACCCCCACGTCCCGAAGGACACTGGCAC 3 46 1 GTCCCGAAGG 0.78316 -255 TTCCGCCACTCGCCCGCAACAACCGGAGGA 3 97 1 CGCCCGCAAC 0.950064 -204 AGTAGCCGCAGGCCCCATCCGCTGCCAGGG 3 139 1 GGCCCCATCC 0.972037 -162 GAGCGGAAAGGGCCGGCCACGCCCACTGAG 3 180 0 GGCCGGCCAC 0.95798 -121 CGCTCACACTGTCCCGATACCATGATTGAT 3 209 1 GTCCCGATAC 0.984344 -92 ********** Masking position 4 Map Score: 6.48459 Number of sites scoring better than the average of aligned sites = 6896 Number in coding regions = 6282 Number in noncoding regions = 614 Number of orfs with sites within 600 bp upstream = 465 Fraction of orfs with sites within 600 bp upstream = 0.0746868 Motif number 8 ********** No masking Map Score: 1.48747e-12 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: 1.48747e-12 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: 1.48747e-12 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