AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i300_mixed15_tpal_reg_100.orf -o300_tpal_100.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 RTP00609 300 AE000520 Motif number 1 AGGTACGCGTGCGCAGGCGAT 1 1 0 GCGCAGGCGT 0.998775 -300 GCTAGGAAGTGTGCATGCGGTGCCGCATATA 1 109 0 GTGCATGCGT 0.995049 -192 GGTATGGGAAATGCATGCGATGGTGTCGCGC 1 176 1 ATGCATGCGT 0.957342 -125 CGATGGTGTCGCGCAGGATGTGCACGTACCC 1 193 1 GCGCAGGATT 0.995049 -108 TTTCAGTCTTGTGCTtCCGCTTTTAGGATAT 1 242 1 GTGCTtCCGT 0.981434 -59 GGCTGCCACAGCGCTGCATATCCTAAAAGCG 1 259 0 GCGCTGCATT 0.981434 -42 TCAGCGCCCCGTGCAGGCTGCCACAGCGCTG 1 274 0 GTGCAGGCTC 0.988518 -27 CCTGCACGGGGCGCTGAATCTGT 1 288 1 GCGCTGAATT 0.950933 -13 ********* * Masking position 4 Map Score: 13.5169 Number of sites scoring better than the average of aligned sites = 955 Number in coding regions = 904 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 2 AACCCCCAAAGGTACGCGTGCGCAGGCGAT 1 10 0 GGTACGGTGC 0.996626 -291 TTGGGGGTTTGGAATGAGCGCGGAAATAAAG 1 32 1 GGAATGGCGC 0.995846 -269 TTCTTATGTTGGTATATGCGGCACCGCATGC 1 97 1 GGTATAGCGG 0.973947 -204 ATAACCAAATGGAACGCTAGGAAGTGTGCAT 1 124 0 GGAACGTAGG 0.897079 -177 CTTCGGATCAGTTATGGGTGCGGTATGGGAA 1 155 1 GTTATGGTGC 0.969284 -146 TTATGGGTGCGGTATGGGAAATGCATGCGAT 1 166 1 GGTATGGAAA 0.927495 -135 AAAACCAGTGGGTACGTGCACATCCTGCGCG 1 202 0 GGTACGGCAC 0.994524 -99 ****** **** Masking position 4 Map Score: 7.64337 Number of sites scoring better than the average of aligned sites = 691 Number in coding regions = 627 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 3 CGCTCATTCCAAACCCCCAAAGGTACGCGT 1 22 0 AAACCCCCAA 0.917868 -279 GGTTTGGAATGAGCGCGGAAATAAAGAGGC 1 37 1 GAGCGCGGAA 0.99692 -264 AGAATAGTTGGAACGCCGAAAAAAAAGATT 1 71 0 GAACGCCGAA 0.996806 -230 TGCATATCCTAAAAGCGGaAGCACAAGACT 1 246 0 AAAAGCGGaA 0.963695 -55 AGCCTGCACGGGGCGCTGAATCTGT 1 286 1 GGGCGCTGAA 0.982327 -15 ********** Masking position 9 Map Score: 3.43227 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 206 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 4 GCCGAAAAAAAAGATTAACAGCCTCTTTAT 1 57 0 AAGATTAACA 0.801257 -244 CGCATATACCAACATAAGAATAGTTGGAAC 1 87 0 AACATAAGAA 0.823559 -214 AACTGATCCGAAGATAACCAAATGGAACGC 1 138 0 AAGATAACCA 0.977948 -163 GGTGCGGTATGGGAAATGCATGCGATGGTG 1 171 1 GGGAAATGCA 0.905656 -130 GGTGTCGCGCAGGATGTGCACGTACCCACT 1 197 1 AGGATGTGCA 0.964535 -104 GAAAGGGATCAACAAAACCAGTGGGTACGT 1 216 0 AACAAAACCA 0.891049 -85 TtCCGCTTTTAGGATATGCAGCGCTGTGGC 1 256 1 AGGATATGCA 0.954072 -45 ********** Masking position 4 Map Score: 2.37287 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 308 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 AAGGTACGCGTGCGCAGGCGAT 1 3 0 TGCGCAGGCG 0.868129 -298 TAAGAATAGTTGGAACGCCGAAAAAAAAGA 1 73 0 TGGAACGCCG 0.931165 -228 TGTTGGTATATGCGGCACCGCATGCACACT 1 103 1 TGCGGCACCG 0.979232 -198 GATAACCAAATGGAACGCTAGGAAGTGTGC 1 126 0 TGGAACGCTA 0.808438 -175 CGCATGCATTTCCCATACCGCACCCATAAC 1 165 0 TCCCATACCG 0.734791 -136 GCACATCCTGCGCGACACCATCGCATGCAT 1 186 0 CGCGACACCA 0.955416 -115 CCGTGCAGGCTGCCACAGCGCTGCATATCC 1 267 0 TGCCACAGCG 0.917532 -34 GCAGCCTGCACGGGGCGCTGAATCTGT 1 284 1 CGGGGCGCTG 0.905416 -17 ********** Masking position 2 Map Score: 2.9935 Number of sites scoring better than the average of aligned sites = 2087 Number in coding regions = 1928 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 6 ********** No masking Map Score: 7.91135e-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: 7.91135e-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: 7.91135e-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