AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i165_Nitrate_Reductase_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 narG 300 narG #2 narH 38 narH #3 narJ 56 narJ Motif number 1 CGGCGGCCACCGTCAACCACACCGT 1 6 0 CGTCAACCAC 0.970145 -295 ACCAAGTTGACGGCGGCCACCGTCAACCAC 1 16 0 CGGCGGCCAC 0.912696 -285 TAATCGCTACGGGCATGCAAACCCAAGTTA 1 67 0 GGGCATGCAA 0.689438 -234 TGTCGCCACGCGTCCAGAAAACCATCGTAA 1 94 0 CGTCCAGAAA 0.919017 -207 TTTCTGGACGCGTGGCGACAACTTCCGGGC 1 104 1 CGTGGCGACA 0.760501 -197 TGGGCGTCAGCGTCCTGCCCGGAAGTTGTC 1 120 0 CGTCCTGCCC 0.936057 -181 GGACCCCTCTCGTCAACATCGGGTATCTCG 1 155 0 CGTCAACATC 0.835291 -146 TCCGCCGGGTCGGGGACCCCTCTCGTCAAC 1 168 0 CGGGGACCCC 0.929589 -133 GCATTGCGCCCGTCAAGCCCCGGTCCGCCG 1 191 0 CGTCAAGCCC 0.969419 -110 GCGGCGCGGCCGGCCAGCCCGTAACGTCCA 1 219 1 CGGCCAGCCC 0.946887 -82 CAGCCCGTAACGTCCAGCGAGTGCGGTCGC 1 233 1 CGTCCAGCGA 0.987117 -68 CAGCGAGTGCGGTCGCGCGCCGACGGCCCG 1 247 1 GGTCGCGCGC 0.785011 -54 CGCGCGCCGACGGCCCGGCCCCACACCGCT 1 260 1 CGGCCCGGCC 0.967141 -41 TGACCCTCCTCGTCATGAGCGGTGTGGGGC 1 277 0 CGTCATGAGC 0.957532 -24 CCAATGAAGGGCCCGAGCGACGCTTGCG 2 9 1 GGGCCCGAGC 0.783899 -30 CGTCTCGCTCCGCAAGCGTC 2 29 0 CGTCTCGCTC 0.927806 -10 GTCCGAGAGCGGTCGAGCGCCACCACAATG 3 25 1 GGTCGAGCGC 0.941219 -32 ********** Masking position 2 Map Score: 29.6224 Number of sites scoring better than the average of aligned sites = 34461 Number in coding regions = 32246 Number in noncoding regions = 2215 Number of orfs with sites within 600 bp upstream = 1149 Fraction of orfs with sites within 600 bp upstream = 0.184549 Motif number 2 GTGTGGTTGACGGTGGCCGCCGTCAACTTGG 1 14 1 CGGTGGCCGC 0.904838 -287 ACTTGGGTTTGCATGCCCGTAGCGATTACGA 1 69 1 GCATGCCCGA 0.807616 -232 GGAAGTTGTCGCCACGCGTCCAGAAAACCAT 1 99 0 GCCACGCGTC 0.817641 -202 GCGTCAGCGTCCTGCCCGGAAGTTGTCGCCA 1 116 0 CCTGCCCGGA 0.849129 -185 TTGACGAGAGGGGTCCCCGACCCGGCGGACC 1 169 1 GGGTCCCCGC 0.946502 -132 CCCGTCAAGCCCCGGTCCGCCGGGTCGGGGA 1 182 0 CCCGGTCCGC 0.87028 -119 ACCGGGGCTTGACGGGCGCAATGCGGCGCGG 1 197 1 GACGGGCGCA 0.692445 -104 GGGCTGGCCGGCCGCGCCGCATTGCGCCCGT 1 208 0 GCCGCGCCGA 0.945454 -93 GGCGCGGCCGGCCAGCCCGTAACGTCCAGCG 1 221 1 GCCAGCCCGA 0.94739 -80 CCGGGCCGTCGGCGCGCGACCGCACTCGCTG 1 247 0 GGCGCGCGAC 0.933225 -54 GCGGTGTGGGGCCGGGCCGTCGGCGCGCGAC 1 258 0 GCCGGGCCGC 0.504828 -43 GGGATGACCCTCCTCGTCATGAGCGGTG 1 283 0 CCCTCCTCGC 0.874016 -18 CTCCGCAAGCGTCGCTCGGGCCCTTCATTGG 2 11 0 GTCGCTCGGC 0.978525 -28 CGTCTCGCTCCGCAAGCGTCGCTC 2 25 0 CTCGCTCCGA 0.956199 -14 GGCGCTCGACCGCTCTCGGACACGAGACAGC 3 15 0 CGCTCTCGGC 0.962376 -42 CAGTCGGTCCCTCATTGTGGTGG 3 44 0 GTCGGTCCCC 0.755462 -13 ********* * Masking position 7 Map Score: 20.4716 Number of sites scoring better than the average of aligned sites = 65279 Number in coding regions = 60793 Number in noncoding regions = 4486 Number of orfs with sites within 600 bp upstream = 1468 Fraction of orfs with sites within 600 bp upstream = 0.235785 Motif number 3 GTGTGGTTGACGGTGGCCGCCGTCAACTTG 1 14 1 CGGTGGCCGC 0.909183 -287 TCTCGATGGATGGGCGTCAGCGTCCTGCCC 1 130 0 TGGGCGTCAG 0.750691 -171 GAGAGGGGTCCCCGACCCGGCGGACCGGGG 1 174 1 CCCGACCCGG 0.856243 -127 TTGCGCCCGTCAAGCCCCGGTCCGCCGGGT 1 188 0 CAAGCCCCGG 0.75763 -113 CGGGGCTTGACGGGCGCAATGCGGCGCGGC 1 199 1 CGGGCGCAAT 0.830457 -102 TACGGGCTGGCCGGCCGCGCCGCATTGCGC 1 212 0 CCGGCCGCGC 0.972885 -89 CGAGTGCGGTCGCGCGCCGACGGCCCGGCC 1 250 1 CGCGCGCCGA 0.966133 -51 CGCCGACGGCCCGGCCCCACACCGCTCATG 1 264 1 CCGGCCCCAC 0.958921 -37 AAGCGTCGCTCGGGCCCTTCATTGG 2 6 0 CGGGCCCTTC 0.903395 -33 TCTCGCTCCGCAAGCGTCGCTCGGGCCCTT 2 17 0 CAAGCGTCGC 0.928329 -22 CGAGAGCGGTCGAGCGCCACCACAATGAGG 3 28 1 CGAGCGCCAC 0.992206 -29 ********** Masking position 1 Map Score: 10.5834 Number of sites scoring better than the average of aligned sites = 32560 Number in coding regions = 30381 Number in noncoding regions = 2179 Number of orfs with sites within 600 bp upstream = 1075 Fraction of orfs with sites within 600 bp upstream = 0.172663 Motif number 4 GGCCACCGTCAACCACACCGT 1 2 0 AACCACACCG 0.972906 -299 CGAGAGGGGTCCCCGACCCGGCGGACCGGG 1 173 1 CCCCGACCCG 0.986106 -128 GCCCGTCAAGCCCCGGTCCGCCGGGTCGGG 1 184 0 CCCCGGTCCG 0.986106 -117 TGGCCGGCCGCGCCGCATTGCGCCCGTCAA 1 205 0 CGCCGCATTG 0.951004 -96 GACGGCCCGGCCCCACACCGCTCATGACGA 1 268 1 CCCCACACCG 0.99809 -33 GGTCGAGCGCCACCACAATGAGGGACCGAC 3 35 1 CACCACAATG 0.937599 -22 ********** Masking position 4 Map Score: 4.45989 Number of sites scoring better than the average of aligned sites = 4735 Number in coding regions = 4345 Number in noncoding regions = 390 Number of orfs with sites within 600 bp upstream = 312 Fraction of orfs with sites within 600 bp upstream = 0.0501124 Motif number 5 GGTGGCCGCCGTCAACTTGGTTAGAACAAC 1 25 1 GTCAACTTGG 0.990071 -276 TTAACGTTTTGTCACGTTGTTCTAACCAAG 1 40 0 GTCACGTTGT 0.960399 -261 GTGACAAAACGTTAACTTGGGTTTGCATGC 1 55 1 GTTAACTTGG 0.971177 -246 GCCCGTAGCGATTACGATGGTTTTCTGGAC 1 83 1 ATTACGATGG 0.947096 -218 AACATCGGGTATCTCGATGGATGGGCGTCA 1 141 0 ATCTCGATGG 0.92893 -160 GACCCCTCTCGTCAACATCGGGTATCTCGA 1 154 0 GTCAACATCG 0.958095 -147 ********** Masking position 8 Map Score: 3.44248 Number of sites scoring better than the average of aligned sites = 2100 Number in coding regions = 1957 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 6 ********** No masking Map Score: 8.19556e-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: 8.19556e-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: 8.19556e-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