AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i152_Xanthine_Dehydrogenase_tpal_reg_300.orf -o152_tpal_300.ace -a/home/amcguire/alignace/lib/ORF_tpal.txt -z/skink1/amcguire/genomes/tpal.fna -g0.53 -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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTP00395 300 AE000520 #2 RTP00396 118 AE000520 #3 RTP01065 39 AE000520 #4 RTP00398 40 AE000520 Motif number 1 AGGAGTGACTGGCGCGTCGG 1 1 0 GGCGCGTCGG 0.990746 -300 TGCGCGCGGTGGAGCAGGGGGGAGGAGTGA 1 23 0 GGAGCAGGGG 0.993396 -278 GTGTTGTCTTTGCGCGCGGTGGAGCAGGGG 1 33 0 TGCGCGCGGT 0.975317 -268 CAACCGCTTTTGAGCGTGTTGTCTTTGCGC 1 48 0 TGAGCGTGTT 0.573749 -253 TATTGCTGCTGGCGGGGGTGTACCAACCGC 1 71 0 GGCGGGGGTG 0.983863 -230 CGCAGGGGCGCTAGCGGCGGCGGCAATGCT 1 127 0 CTAGCGGCGG 0.889792 -174 GGCGACCGTGTGCGCAGGGGCGCTAGCGGC 1 139 0 TGCGCAGGGG 0.996094 -162 GCCACAAATCCGCGCGTGTGTGCAGTAGTA 1 166 1 CGCGCGTGTG 0.973736 -135 AGTCTGAACAGACGCAGGGGCGGTCGCAGA 1 207 1 GACGCAGGGG 0.990497 -94 CGCAGGGGCGGTCGCAGAGGATGCGTCACG 1 219 1 GTCGCAGAGG 0.873653 -82 GAGGATGCGTCACGCGCGTGCTGCATGCGA 1 235 1 CACGCGCGTG 0.499626 -66 TCCATATGGACGTGCAGGTGAAAGTCGTTC 2 12 0 CGTGCAGGTG 0.955677 -107 TTTTGCAGGAGGCGCGCGGCTACGATGTTG 2 69 0 GGCGCGCGGC 0.963088 -50 CAACGAACACCGCGCAGGAGGAGGAACAA 2 100 1 CGCGCAGGAG 0.985252 -19 GTTGATCTTGCGCGCGCGGTCTGTCGTGT 3 10 0 CGCGCGCGGT 0.984773 -30 GTTCAGCACTGGCGCAGCTGGC 4 3 0 GGCGCAGCTG 0.990054 -38 ********** Masking position 4 Map Score: 36.4393 Number of sites scoring better than the average of aligned sites = 2708 Number in coding regions = 2508 Number in noncoding regions = 200 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 2 TCACTCCTCCCCCCTGCTCCACCGCGCGCAA 1 23 1 CCCTGCTCCA 0.933907 -278 GGTACACCCCCGCCAGCAGCAATACCAATGA 1 77 1 CGCAGCAGCA 0.884182 -224 GGGGCGCTAGCGGCGGCGGCAATGCTCACGC 1 122 0 CGCGGCGGCA 0.971023 -179 ACCGTGTGCGCAGGGGCGCTAGCGGCGGCGG 1 134 0 CAGGGCGCTA 0.974113 -167 CCCCTGCGCACACGGTCGCCACAAATCCGCG 1 149 1 CAGGTCGCCA 0.966644 -152 TCTGTTCAGACTACGGCGGTCCTTACTACTG 1 188 0 CTCGGCGGTC 0.924966 -113 TGAACAGACGCAGGGGCGGTCGCAGAGGATG 1 211 1 CAGGGCGGTC 0.966858 -90 ATGCGTCACGCGCGTGCTGCATGCGAGAAAA 1 239 1 CGGTGCTGCA 0.986577 -62 TCAAGTGGCACGTCGTCTCCATATGGACGTG 2 28 0 CGCGTCTCCA 0.980215 -91 CGTAGCCGCGCGCCTCCTGCAAAAGCAACGA 2 75 1 CGCTCCTGCA 0.936584 -44 ATCTTGCGCGCGCGGTCTGTCGTGT 3 5 0 CGGGTCTGTC 0.89935 -35 GCCAGCTGCGCCAGTGCTGAACC 4 3 1 CACTGCGCCA 0.983373 -38 ** ******** Masking position 7 Map Score: 17.7468 Number of sites scoring better than the average of aligned sites = 1097 Number in coding regions = 1024 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 3 CGACGCGCCAGTCACTCCTCCCCCCTGCTCC 1 12 1 GTCACTCTCC 0.922687 -289 ACTCCTCCCCCCTGCTCCACCGCGCGCAAAG 1 25 1 CCTGCTCACC 0.888091 -276 CTCAAAAGCGGTTGGTACACCCCCGCCAGCA 1 64 1 GTTGGTCACC 0.973165 -237 TTTCCGGTTCATTGGTATTGCTGCTGGCGGG 1 85 0 ATTGGTTTGC 0.914321 -216 TACGGCGGTCCTTACTACTGCACACACGCGC 1 177 0 CTTACTCTGC 0.977314 -124 TTATTTTCTTTGTGCTGCTTGGGTTTGT 1 283 0 CTTTGTCTGC 0.966845 -18 TGAACGACTTTCACCTGCACGTCCATAT 2 8 1 CTTTCACTGC 0.845531 -111 CGCGGTGTTCGTTGCTTTTGCAGGAGGCGCG 2 83 0 GTTGCTTTGC 0.982934 -36 TTGTTCCTCCTCCTGCGCGGTGT 2 106 0 GTTCCTCTCC 0.963146 -13 TGGTTTTGATGTTGATCTTGCGCGCGCGGTC 3 19 0 GTTGATTTGC 0.882032 -21 CCCCACTTATATCGGTTCAGCACTGGCGCAG 4 16 0 ATCGGTCAGC 0.868167 -25 ****** **** Masking position 11 Map Score: 7.70082 Number of sites scoring better than the average of aligned sites = 826 Number in coding regions = 786 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 4 ACCCCCGCCAGCAGCAATACCAATGAACCGG 1 82 1 GCAGCAATCC 0.971766 -219 GCACACGGTCGCCACAAATCCGCGCGTGTGT 1 156 1 GCCACAAACC 0.994948 -145 CGCACACACTGCCACAAACCCAAGCAGCACA 1 270 1 GCCACAAACC 0.994954 -31 TAACAGCTCAACATCGTAGCCGCGCGCCTCC 2 61 1 ACATCGTACC 0.919816 -58 TCCTGCAAAAGCAACGAACACCGCGCAGGAG 2 89 1 GCAACGAAAC 0.968258 -30 CGCAAGATCAACATCAAAACCA 3 28 1 ACATCAAACC 0.982483 -12 ******** ** Masking position 5 Map Score: 4.54626 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 122 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 ********** No masking Map Score: 4.35863e-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: 4.35863e-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: 4.35863e-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