AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i210_trans4_tpal_reg_300.orf -o210_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 RTP00665 147 AE000520 #2 RTP00669 175 AE000520 #3 RTP00670 49 AE000520 #4 RTP00971 174 AE000520 #5 RTP00672 21 AE000520 #6 RTP00676 38 AE000520 #7 RTP00677 40 AE000520 Motif number 1 AAGACGACACGCGCGTCACTGCAGCAGTTCCTAC 1 101 0 GCGCGTACTG 0.993553 -47 GAAGGTGTTGGCATGTATCTAATGCACGGTGTTA 2 42 0 GCATGTTCTG 0.968143 -134 GTGTGCAAGCGTGTGCGTCCGTGGTTTCCTGAAG 2 72 0 GTGTGCTCCG 0.987046 -104 GTTGCAATGGGCGTGCCTCTCGTGGGTATTTTTT 2 126 0 GCGTGCTCTG 0.998566 -50 GAGGAGATCTGCGCGCAACTTTTGTCTGAAAAGA 3 17 0 GCGCGCACTG 0.99747 -33 ATCCGGGGGAGCGTGCTATCTTCGTTCAAGGGCG 4 90 0 GCGTGCATCG 0.993634 -85 ACACGGTGCTGCGTGCATCCTTCGTGCTCAAGAT 6 13 0 GCGTGCTCCG 0.998537 -26 TACGCGTGTAATTACTGCACATTGGAG 7 4 1 GCGTGTATTG 0.984189 -37 ****** *** * Masking position 5 Map Score: 16.5507 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 226 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 2 CCAAGATGGCTAATGAGCACTACGTGTCGCGG 1 44 1 TATGAGCATA 0.913029 -104 TGCGGTACATCATCGAGCAGGGGCCGCGACAC 1 67 0 CACGAGCAGG 0.957655 -81 TGCGTGATGGTATGGTGCAAGACGACACGCGC 1 121 0 TAGGTGCAGA 0.976358 -27 ATTTCGATAACACCGTGCATTAGATACATGCC 2 35 1 CACGTGCATA 0.984571 -141 GGAACCATGATAGTGTGCACAACAGAAGGAGT 4 131 1 TATGTGCAAA 0.944992 -44 AGTGTTAGGGACCGTGCAGGAGACTCCTTCT 4 154 0 GACGTGCAGA 0.980815 -21 TCATCTTGAGCACGAAGGATGCACG 6 4 1 TCTGAGCAGA 0.909955 -35 TGTTGAACTCCAATGTGCAGTAATTACACGCG 7 13 0 CATGTGCATA 0.966567 -28 ** ****** ** Masking position 9 Map Score: 7.41644 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 153 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 3 CTTTATCCGCATCACGGGTAGGGTCTCCAA 1 18 1 ATCACGGGTA 0.878185 -130 CTCATTAGCCATCTTGGAGACCCTACCCGT 1 31 0 ATCTTGGAGA 0.907736 -117 TCTGCGGTACATCATCGAGCAGGGGCCGCG 1 71 0 ATCATCGAGC 0.967204 -77 GCACCATACCATCACGCATCGGT 1 135 1 ATCACGCATC 0.84493 -13 CCATTTCGATAACACCGTGCATTAGATACA 2 33 1 AACACCGTGC 0.950613 -143 GGACGCACTGATCTTGGTGAGCCGCTTTTT 4 31 0 ATCTTGGTGA 0.940417 -144 GGAGCGTGCTATCTTCGTTCAAGGGCGCAG 4 87 0 ATCTTCGTTC 0.926643 -88 TGTGCACACTATCATGGTTCCTCCTGACAT 4 122 0 ATCATGGTTC 0.979048 -53 GCACACGGTGCTGCGTGCATC 6 28 0 CACACGGTGC 0.897189 -11 ********** Masking position 3 Map Score: 5.53803 Number of sites scoring better than the average of aligned sites = 421 Number in coding regions = 401 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 4 ATCCGCATCACGGGTAGGGTCTCCAAGATG 1 22 1 CGGGTAGGGT 0.944417 -126 TCATCGAGCAGGGGCCGCGACACGTAGTGC 1 60 0 GGGGCCGCGA 0.986567 -88 CAGTGACGCGCGTGTCGTCTTGCACCATAC 1 114 1 CGTGTCGTCT 0.788756 -34 TGGTCGATGTGGTGTCGGGATTTTT 2 6 0 GGTGTCGGGA 0.977025 -170 GTTTCCTGAAGGTGTTGGCATGTATCTAAT 2 53 0 GGTGTTGGCA 0.943254 -123 CGGTTGCAATGGGCGTGCCTCTCGTGGGTA 2 132 0 GGGCGTGCCT 0.88239 -44 CCTGACATCCGGGGGAGCGTGCTATCTTCG 4 100 0 GGGGGAGCGT 0.981223 -75 GCACACGGTGCTGCGTGCATCCTTCG 6 23 0 GGTGCTGCGT 0.979272 -16 ********** Masking position 7 Map Score: 3.3382 Number of sites scoring better than the average of aligned sites = 901 Number in coding regions = 800 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 5 CGTGTCGCGGCCCCTGCTCGATGATGTACC 1 66 1 CCCCTGCTCG 0.943517 -82 CCTTCAGGAAACCACGGACGCACACGCTTG 2 71 1 ACCACGGACG 0.96926 -105 ACAAAAAATACCCACGAGAGGCACGCCCAT 2 124 1 CCCACGAGAG 0.94854 -52 CGCATCAAAGACCCCGAATGGAATTC 2 160 1 ACCCCGAATG 0.979092 -16 CGCGCAGATCTCCTCGATTGTACT 3 36 1 TCCTCGATTG 0.863399 -14 AGCACCTGCGCCCTTGAACGAAGATAGCAC 4 82 1 CCCTTGAACG 0.963486 -93 ATAGCACGCTCCCCCGGATGTCAGGAGGAA 4 105 1 CCCCCGGATG 0.983426 -70 GTCAGGAGGAACCATGATAGTGTGCACAAC 4 124 1 ACCATGATAG 0.861948 -51 ********** Masking position 6 Map Score: 5.01232 Number of sites scoring better than the average of aligned sites = 426 Number in coding regions = 396 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 ********** No masking Map Score: -1.07049e-12 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: -1.07049e-12 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: -1.07049e-12 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