AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i232_formulase_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 def 300 def #2 fmt 196 fmt Motif number 1 CCGCCCGACGGTTCCTGGCGTGGTTCAATA 1 54 0 GTTCCTGGCG 0.723772 -247 GGCAGGATTACCGCCCGACGGTTCCTGGCG 1 64 0 CCGCCCGACG 0.996499 -237 GGGCGGTAATCCTGCCCGCGAGTCGGCCGA 1 78 1 CCTGCCCGCG 0.929707 -223 TGCAAGCAAGTCGGCCGACTCGCGGGCAGG 1 88 0 TCGGCCGACT 0.853782 -213 CGACTTGCTTGCACCCGACTGCCGATCGCG 1 105 1 GCACCCGACT 0.966574 -196 CTGCCGATCGCGGCGCGCCGGCTCATGCTC 1 123 1 CGGCGCGCCG 0.499927 -178 GTGAATCCTGCGACGCGACATGCCGGCCAG 1 158 1 CGACGCGACA 0.728019 -143 CACACGACGGCTGGCCGGCATGTCGCGTCG 1 168 0 CTGGCCGGCA 0.940268 -133 CGGGTGTGAACCACACGACGGCTGGCCGGC 1 179 0 CCACACGACG 0.941656 -122 CGTGTGGTTCACACCCGGCGATGATGCCCG 1 192 1 ACACCCGGCG 0.978822 -109 CCCGGCGATGATGCCCGCCGCCCCGCGGCG 1 205 1 ATGCCCGCCG 0.974848 -96 ATGCCCGCCGCCCCGCGGCGCGCCTAAGCC 1 215 1 CCCCGCGGCG 0.780925 -86 CCTAAGCCGATTGCCCGCCTCCTCAGCCCG 1 237 1 TTGCCCGCCT 0.842966 -64 CCCGCCTCCTCAGCCCGCCGCCTCGCGGCG 1 250 1 CAGCCCGCCG 0.976956 -51 CAGCCCGCCGCCTCGCGGCGCGTATCGTCG 1 260 1 CCTCGCGGCG 0.787764 -41 CTAGCTTAAGCGCGCCGACGATACGCGCCG 1 275 0 CGCGCCGACG 0.951153 -26 CTCCCGCCGTGCCCGCGACAACGATGTCGA 2 48 0 GCCCGCGACA 0.926735 -149 TACTGCCCAGGCTCCCGCCGTGCCCGCGAC 2 59 0 GCTCCCGCCG 0.994703 -138 CGTGCCTTGCGTACCCACCGGATACAGTAT 2 90 1 GTACCCACCG 0.78181 -107 TGTCGGAATTGTGGCCCACGCCACGTCGGC 2 156 1 GTGGCCCACG 0.902334 -41 TCTAAGAAGCGCCGCCGACGTGGCGTGGGC 2 169 0 GCCGCCGACG 0.99127 -28 ********** Masking position 9 Map Score: 40.611 Number of sites scoring better than the average of aligned sites = 40295 Number in coding regions = 37641 Number in noncoding regions = 2654 Number of orfs with sites within 600 bp upstream = 1186 Fraction of orfs with sites within 600 bp upstream = 0.190491 Motif number 2 GCCGAAGAAGCGCCTACGTAGGCCAAGTCAT 1 20 0 CGCCTACGAG 0.962569 -281 GTTCAATATTCGCCGAAGAAGCGCCTACGTA 1 31 0 CGCCGAAGAG 0.744739 -270 TCACACTCGGAGCATGAGCCGGCGCGCCGCG 1 131 0 AGCATGAGCG 0.961196 -170 CCGAGTGTGAATCCTGCGACGCGACATGCCG 1 152 1 ATCCTGCGCG 0.952726 -149 CCCCGCGGCGCGCCTAAGCCGATTGCCCGCC 1 225 1 CGCCTAAGCG 0.571816 -76 GCGAGGCGGCGGGCTGAGGAGGCGGGCAATC 1 245 0 GGGCTGAGAG 0.904163 -56 CAGGTCTCCTGAGAAGTAAGTGATGT 2 6 1 CTCCTGAGAG 0.730492 -191 GCACGGCGGGAGCCTGGGCAGTAGCGTGCCT 2 66 1 AGCCTGGGAG 0.987703 -131 GCCCACGCCACGTCGGCGGCGCTTCTTAGAC 2 169 1 CGTCGGCGCG 0.529222 -28 GCGCCCAGTCTAAGAAGCGCCGCCGAC 2 180 0 AGTCTAAGAG 0.947155 -17 ******** ** Masking position 8 Map Score: 17.1148 Number of sites scoring better than the average of aligned sites = 7781 Number in coding regions = 7321 Number in noncoding regions = 460 Number of orfs with sites within 600 bp upstream = 350 Fraction of orfs with sites within 600 bp upstream = 0.0562159 Motif number 3 GGAACCGTCGGGCGGTAATCCTGCCCGCGA 1 69 1 GGCGGTAATC 0.88009 -232 AAGCAAGTCGGCCGACTCGCGGGCAGGATT 1 85 0 GCCGACTCGC 0.846062 -216 ATCGGCAGTCGGGTGCAAGCAAGTCGGCCG 1 101 0 GGGTGCAAGC 0.949327 -200 CGGAGCATGAGCCGGCGCGCCGCGATCGGC 1 125 0 GCCGGCGCGC 0.841266 -176 GACGCGACATGCCGGCCAGCCGTCGTGTGG 1 169 1 GCCGGCCAGC 0.732561 -132 CATCATCGCCGGGTGTGAACCACACGACGG 1 188 0 GGGTGTGAAC 0.53355 -113 CGCGCCGCGGGGCGGCGGGCATCATCGCCG 1 207 0 GGCGGCGGGC 0.991257 -94 CCCGCCGCCCCGCGGCGCGCCTAAGCCGAT 1 218 1 CGCGGCGCGC 0.995363 -83 GGCTGAGGAGGCGGGCAATCGGCTTAGGCG 1 235 0 GCGGGCAATC 0.931771 -66 CGCGCCGCGAGGCGGCGGGCTGAGGAGGCG 1 252 0 GGCGGCGGGC 0.991257 -49 CCCGCCGCCTCGCGGCGCGTATCGTCGGCG 1 263 1 CGCGGCGCGT 0.958165 -38 GGCGCGTATCGTCGGCGCGCTTAAGCTAGC 1 276 1 GTCGGCGCGC 0.971813 -25 GGTGGGCTAGCTTAAGCGCGC 1 290 0 GTGGGCTAGC 0.939607 -11 TAAGTGATGTGGCTGCGAACTTCGACATCG 2 27 1 GGCTGCGAAC 0.935224 -170 CATCGTTGTCGCGGGCACGGCGGGAGCCTG 2 52 1 GCGGGCACGG 0.604577 -145 ACTGTATCCGGTGGGTACGCAAGGCACGCT 2 88 0 GTGGGTACGC 0.864467 -109 ACGCCACGTCGGCGGCGCTTCTTAGACTGG 2 173 1 GGCGGCGCTT 0.963556 -24 ********** Masking position 5 Map Score: 41.5689 Number of sites scoring better than the average of aligned sites = 20888 Number in coding regions = 19428 Number in noncoding regions = 1460 Number of orfs with sites within 600 bp upstream = 885 Fraction of orfs with sites within 600 bp upstream = 0.142146 Motif number 4 TGTGTACGAATGACTTGGCCTACGTAG 1 7 1 CGAAGACTTG 0.55597 -294 GCCCGCGAGTCGGCCGACTTGCTTGCACCCG 1 91 1 CGGCGACTTG 0.991261 -210 GCGCCGCGATCGGCAGTCGGGTGCAAGCAAG 1 108 0 CGGCGTCGGG 0.97274 -193 CTGCCGATCGCGGCGCGCCGGCTCATGCTCC 1 123 1 CGGCCGCCGG 0.643448 -178 AACCACACGACGGCTGGCCGGCATGTCGCGT 1 170 0 CGGCGGCCGG 0.945721 -131 GCGATGATGCCCGCCGCCCCGCGGCGCGCCT 1 209 1 CCGCGCCCCG 0.811012 -92 CCTCCTCAGCCCGCCGCCTCGCGGCGCGTAT 1 254 1 CCGCGCCTCG 0.961745 -47 ACTTACTTCTCAGGAGACCTG 2 1 0 CAGGGACCTG 0.726418 -196 ACATCGTTGTCGCGGGCACGGCGGGAGCCTG 2 51 1 CGCGGCACGG 0.779616 -146 GCGGGCACGGCGGGAGCCTGGGCAGTAGCGT 2 62 1 CGGGGCCTGG 0.920959 -135 CCTGGGCAGTAGCGTGCCTTGCGTACCCACC 2 78 1 AGCGGCCTTG 0.715313 -119 CTAAGAAGCGCCGCCGACGTGGCGTGGGCCA 2 167 0 CCGCGACGTG 0.964794 -30 **** ****** Masking position 11 Map Score: 17.694 Number of sites scoring better than the average of aligned sites = 18045 Number in coding regions = 16919 Number in noncoding regions = 1126 Number of orfs with sites within 600 bp upstream = 731 Fraction of orfs with sites within 600 bp upstream = 0.117411 Motif number 5 ********** No masking Map Score: 2.72438e-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 6 ********** No masking Map Score: 2.72438e-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: 2.72438e-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