AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i012_Glycogen_Biosynthesis_mtub_reg_100.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 glgC 174 glgC #2 Rv1327c 30 hypothetical protein Rv1327c #3 glgX 38 glgX #4 Rv1565c 98 hypothetical protein Rv1565c #5 Rv1566c 239 hypothetical protein Rv1566c #6 Rv1781c 263 hypothetical protein Rv1781c Motif number 1 GCCCGCCACGCGGGCCGCCCCGTCACCGCACT 1 23 0 CGGCGCCCCG 0.662219 -152 GCCTCCTCCTCGGCCCGCCACGCGGGCCGCCC 1 35 0 CGCCGCCACG 0.969019 -140 TGTGCCGCCTCCGCCTCCTCCTCGGCCCGCCA 1 47 0 CGCCCCTCCT 0.96729 -128 TCAAGGTGTTTGGCCCCGTTCGACGGGTGCTG 1 77 0 TGCCCGTTCG 0.933987 -98 GAATCCGCCCCTGGCTACTGCTCTGACGGGCT 1 114 0 CGGCACTGCT 0.949086 -61 CTCAAACCTATCGGCCCCCGCAAACCACTGCC 1 151 0 TGGCCCCGCA 0.969155 -24 TCCAGGTTCTCCGGCGGGTGTAGGCG 3 5 0 CGGCGGTGTA 0.804591 -34 CGGTCCCGCTTGCTTTCTCGCC 4 1 1 CGTCCGCTTG 0.90113 -98 CCTCCCAAACCCGCCTCCTGCTTCCCGCTGCT 4 31 1 CGCCCCTGCT 0.986286 -68 CTGCTTCCCGCTGCTCAGCGCGCGAAGCAGGA 4 48 1 CGCTAGCGCG 0.879149 -51 TTACCCAAACCAGCCTCCTGCTTCGCGCGCTG 4 63 0 CGCCCCTGCT 0.986286 -36 GTTGTGATTTCAGTCACGCGCGA 5 2 0 CGTCCGCGCG 0.994423 -238 CGGACGGTGACTGCCGCGCTCAATCTTTGATC 5 38 0 CGCCCGCTCA 0.984504 -202 CAACAGATGCCGGCCGCGTCCATAGCTGGCCA 5 103 0 CGCCCGTCCA 0.952713 -137 TGTAACCTCCTTGGCACTCTCGGGTGGTGTGT 5 213 0 TGGCCTCTCG 0.762205 -27 GACAGTTCCACAGGCGGACTCGGTCATTCGCC 6 117 0 CGGCGACTCG 0.895165 -147 GCCTGTGGAACTGTCCGCTCCGCAGTCTACCT 6 134 1 CGTCGCTCCG 0.947895 -130 GTCCGCTCCGCAGTCTACCTCGTTGACCTGCA 6 146 1 CGTCACCTCG 0.964615 -118 TGGTGTTCGGTAGCCAACCGTGCTGTGCTGAC 6 184 1 TGCCACCGTG 0.855135 -80 CACCCGTGTGCGGGCGAGCGCAGGAATCTGAG 6 222 0 CGGCAGCGCA 0.788514 -42 CATCTTGCGTCCGGCACCCGTGTGCGGGCGAG 6 236 0 CGGCCCCGTG 0.991572 -28 * *** ****** Masking position 3 Map Score: 35.9808 Number of sites scoring better than the average of aligned sites = 32141 Number in coding regions = 30047 Number in noncoding regions = 2094 Number of orfs with sites within 600 bp upstream = 1068 Fraction of orfs with sites within 600 bp upstream = 0.171539 Motif number 2 GTCACCGCACTACGGTGCGGGGT 1 3 0 TACGTGCGGG 0.985619 -172 CGCACCGTAGTGCGGTGACGGGGCGGCCCGC 1 15 1 TGCGTGACGG 0.984226 -160 CGGGGCGGCCCGCGTGGCGGGCCGAGGAGGA 1 33 1 CGCGGGCGGG 0.995851 -142 GTTCGACGGGTGCTGTGCCGCCTCCGCCTCC 1 61 0 TGCTTGCCGC 0.937518 -114 CCCTGGCTACTGCTCTGACGGGCTGTCCGTC 1 107 0 TGCTTGACGG 0.930878 -68 CCCTTGGCAGTGGTTTGCGGGGGCCGATAGG 1 146 1 TGGTTGCGGG 0.973798 -29 GAGGCGGGTTTGGGAGGCGAGAAAGCAAGCG 4 17 0 TGGGGGCGAG 0.835351 -82 CGCTGAGCAGCGGGAAGCAGGAGGCGGGTTT 4 37 0 CGGGAGCAGG 0.954729 -62 CTGCTCAGCGCGCGAAGCAGGAGGCTGGTTT 4 58 1 CGCGAGCAGG 0.980229 -41 GCCAGCTATGGACGCGGCCGGCATCTGTTGT 5 105 1 GACGGGCCGG 0.835328 -135 GGTGAAGTCACGTGCTGAGGCACACACCACC 5 192 1 CGTGTGAGGC 0.793327 -48 TTGGGGGATCCGCGCAGTGGCAAATACCCAG 6 54 0 CGCGAGTGGC 0.796149 -210 CGAGGTAGACTGCGGAGCGGACAGTTCCACA 6 137 0 TGCGAGCGGA 0.926814 -127 CGAACACCACTACGTTGCAGGTCAACGAGGT 6 162 0 TACGTGCAGG 0.94507 -102 CCAACCGTGCTGTGCTGACGGAAGGCTCAGA 6 197 1 TGTGTGACGG 0.89635 -67 CGTCCGGCACCCGTGTGCGGGCGAGCGCAGG 6 230 0 CCGTTGCGGG 0.771062 -34 **** ****** Masking position 7 Map Score: 19.8164 Number of sites scoring better than the average of aligned sites = 22233 Number in coding regions = 20760 Number in noncoding regions = 1473 Number of orfs with sites within 600 bp upstream = 852 Fraction of orfs with sites within 600 bp upstream = 0.136845 Motif number 3 CCCGCACCGTAGTGCGGTGACGGGGCGGCC 1 13 1 AGTGCGGTGA 0.575048 -162 CGGGCCGAGGAGGAGGCGGAGGCGGCACAG 1 50 1 AGGAGGCGGA 0.858351 -125 CCCCGTTCGACGGGTGCTGTGCCGCCTCCG 1 66 0 CGGGTGCTGT 0.980893 -109 GAGCAGTAGCCAGGGGCGGATTCCCCTTGG 1 123 1 CAGGGGCGGA 0.918472 -52 CAGTGGTTTGCGGGGGCCGATAGGTTTGAG 1 153 1 CGGGGGCCGA 0.964694 -22 CCAGGTTCTCCGGCGGGTGTAGGCG 3 6 0 CGGCGGGTGT 0.969405 -33 CCTCCTGCTTCGCGCGCTGAGCAGCGGGAA 4 52 0 CGCGCGCTGA 0.972699 -47 AATCTTTGATCGGCAGTTGTGATTTCAGTC 5 19 0 CGGCAGTTGT 0.721531 -221 GTAACGTGACCGGACGGTGACTGCCGCGCT 5 50 0 CGGACGGTGA 0.987301 -190 TGGACGCGGCCGGCATCTGTTGTCAAAGTG 5 113 1 CGGCATCTGT 0.820191 -127 GCTGGAATGGCAGACGGTGAAGTCACGTGC 5 177 1 CAGACGGTGA 0.922824 -63 ACGGTGAAGTCACGTGCTGAGGCACACACC 5 190 1 CACGTGCTGA 0.681733 -50 TTGGCACTCTCGGGTGGTGTGTGCCTCAGC 5 205 0 CGGGTGGTGT 0.971892 -35 CTGAGCAGACCGGAAGGTGATCTAGC 6 7 0 CGGAAGGTGA 0.975351 -257 GTTCCACAGGCGGACTCGGTCATTCGCCGC 6 115 0 CGGACTCGGT 0.821231 -149 GGGCGAGCGCAGGAATCTGAGCCTTCCGTC 6 213 0 AGGAATCTGA 0.581548 -51 ********** Masking position 9 Map Score: 18.2097 Number of sites scoring better than the average of aligned sites = 16304 Number in coding regions = 15159 Number in noncoding regions = 1145 Number of orfs with sites within 600 bp upstream = 782 Fraction of orfs with sites within 600 bp upstream = 0.125602 Motif number 4 CCCCGTCACCGCACTACGGTGCGGGGT 1 8 0 GCACTACGGT 0.817263 -167 CGCCACGCGGGCCGCCCCGTCACCGCACTA 1 22 0 GCCGCCCCGT 0.945616 -153 GTTTGCGGGGGCCGATAGGTTTGAGCC 1 158 1 GCCGATAGGT 0.836187 -17 GGTGGCATCCTCAGTAAGGTAAGGACGC 2 9 0 TCAGTAAGGT 0.874308 -22 ATCCAGGTTCTCCGGCGGGTGTAGGCG 3 8 0 TCCGGCGGGT 0.765652 -31 CCGTAACGTGACCGGACGGTGACTGCCGCG 5 52 0 ACCGGACGGT 0.505441 -188 AAGTCTTTTTGCCGTAACGTGACCGGACGG 5 63 0 GCCGTAACGT 0.949606 -177 TTCTGAGCAGACCGGAAGGTGATCTAGC 6 9 0 ACCGGAAGGT 0.706508 -255 TTCCGTCAGCACAGCACGGTTGGCTACCGA 6 190 0 ACAGCACGGT 0.892265 -74 ********** Masking position 10 Map Score: 5.11904 Number of sites scoring better than the average of aligned sites = 5079 Number in coding regions = 4689 Number in noncoding regions = 390 Number of orfs with sites within 600 bp upstream = 317 Fraction of orfs with sites within 600 bp upstream = 0.0509155 Motif number 5 CGGGGCCAAACACCTTGACGGACAGCCCGT 1 91 1 CACCTTGACG 0.960324 -84 GGGGAATCCGCCCCTGGCTACTGCTCTGAC 1 119 0 CCCCTGGCTA 0.969138 -56 GGGGCGGATTCCCCTTGGCAGTGGTTTGCG 1 135 1 CCCCTTGGCA 0.986115 -40 CCCGCCGGAGAACCTGGATAAGGTCGTGTG 3 19 1 AACCTGGATA 0.896648 -20 ACTTCTGGTGGATCTGGCCAGCTATGGACG 5 89 1 GATCTGGCCA 0.854416 -151 TCACTACAGACACTTTGACAACAGATGCCG 5 123 0 CACTTTGACA 0.910589 -117 GGGTTGTAACCTCCTTGGCACTCTCGGGTG 5 219 0 CTCCTTGGCA 0.963021 -21 CTGCTCAGAACACCTGGACATTGACCTGGG 6 29 1 CACCTGGACA 0.995121 -235 CCTGGACATTGACCTGGGTATTTGCCACTG 6 41 1 GACCTGGGTA 0.966084 -223 ********** Masking position 5 Map Score: 8.80678 Number of sites scoring better than the average of aligned sites = 1994 Number in coding regions = 1845 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 6 ACCCCGCACCGTAGTGCGGTG 1 2 1 CCCCGCACCG 0.813418 -173 GCCGCCCCGTCACCGCACTACGGTGCGGGG 1 12 0 CACCGCACTA 0.864032 -163 GGCGGCACAGCACCCGTCGAACGGGGCCAA 1 70 1 CACCCGTCGA 0.894016 -105 CACCTTGACGGACAGCCCGTCAGAGCAGTA 1 101 1 GACAGCCCGT 0.911105 -74 CGCCTACACCCGCCGGAGAACCTGGA 3 7 1 CACCCGCCGG 0.985954 -32 CACACGACCTTATCCAGGTT 3 29 0 CACACGACCT 0.818081 -10 GCCGTAACGTGACCGGACGGTGACTGCCGC 5 53 0 GACCGGACGG 0.987153 -187 TGGCCAGATCCACCAGAAGTCTTTTTGCCG 5 79 0 CACCAGAAGT 0.675358 -161 TGGTGTGTGCCTCAGCACGTGACTTCACCG 5 191 0 CTCAGCACGT 0.783192 -49 CTGAGGCACACACCACCCGAGAGTGCCAAG 5 206 1 CACCACCCGA 0.918315 -34 GTTCTGAGCAGACCGGAAGGTGATCTAGC 6 10 0 GACCGGAAGG 0.906732 -254 GCCCAGTGAAGACACGACGAATCCTTGGGG 6 79 0 GACACGACGA 0.920887 -185 CGGACAGTTCCACAGGCGGACTCGGTCATT 6 121 0 CACAGGCGGA 0.81206 -143 CTTCCGTCAGCACAGCACGGTTGGCTACCG 6 191 0 CACAGCACGG 0.98522 -73 ********** Masking position 3 Map Score: 12.6516 Number of sites scoring better than the average of aligned sites = 12429 Number in coding regions = 11501 Number in noncoding regions = 928 Number of orfs with sites within 600 bp upstream = 657 Fraction of orfs with sites within 600 bp upstream = 0.105525 Motif number 7 ********** No masking Map Score: -6.939e-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: -6.939e-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 9 ********** No masking Map Score: -6.939e-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