AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i210_trans4_tpal_reg_100.orf -o210_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 RTP00665 147 AE000520 #2 RTP00669 175 AE000520 #3 RTP00670 49 AE000520 #4 RTP00971 174 AE000520 Motif number 1 TCATTAGCCATCTTGGAGACCCTACCCGTGATGCG 1 25 0 TCTAGCCTAC 0.982323 -123 GAGCACTACGTGTCGCGGCCCCTGCTCGATGATGT 1 58 1 TGTGGCCTGC 0.998694 -90 CGCGCGTCACTGCAGCAGTTCCTACTCTGCGGTAC 1 91 0 TGCAGCCTAC 0.986768 -57 TTGGAGCGTGTGTGCAAGCGTGTGCGTCCGTGGTT 2 80 0 TGTAGTGTGC 0.970704 -96 CTTCATCTATTGTGTAAGCACCTGCGCCCTTGAAC 4 66 1 TGTAGCCTGC 0.997933 -109 CCTCCTGACATCCGGGGGAGCGTGCTATCTTCGTT 4 98 0 TCCGGCGTGC 0.991186 -77 TTGTGCACACTATCATGGTTCCTCCTGACATCCGG 4 118 0 TATGGCCTCC 0.96449 -57 AGTGTTAGGGACCGTGCAGGAGACTCC 4 158 0 TGTGGCGTGC 0.99788 -17 *** ** ***** Masking position 13 Map Score: 12.0259 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 158 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 2 ACGGGTAGGGTCTCCAAGATGGCTAATGAGCAC 1 31 1 TCCCAGATGC 0.981037 -117 CGCGGCCCCTGCTCGATGATGTACCGCAGAGTA 1 71 1 GCCGAGATTA 0.973653 -77 TGTATCTAATGCACGGTGTTATCGAAATGGTCG 2 30 0 GCCGGGTTTC 0.906142 -146 TTGCACACACGCTCCAAAAACTCTTGACAAAAA 2 98 1 GCCCAAAATC 0.838709 -78 CCCACGAGAGGCACGCCCATTGCAACCGCATCA 2 134 1 GCCGCCATGC 0.98448 -42 CCGCATCAAAGACCCCGAATGGAATTC 2 159 1 GACCCAATGA 0.808265 -17 GACAAAAGTTGCGCGCAGATCTCCTCGATTGTA 3 25 1 GCCGCGATTC 0.995796 -25 CTGCGCCCTTGAACGAAGATAGCACGCTCCCCC 4 87 1 GACGAGATGC 0.988292 -88 GATAGCACGCTCCCCCGGATGTCAGGAGGAACC 4 104 1 TCCCCGATTC 0.976603 -71 ATGTCAGGAGGAACCATGATAGTGTGCACAACA 4 122 1 GACCAGATGT 0.904123 -53 ** *** *** ** Masking position 4 Map Score: 7.48067 Number of sites scoring better than the average of aligned sites = 651 Number in coding regions = 616 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 3 GACCCTACCCGTGATGCGGATAAAGCAGAGG 1 12 0 GTGATGCGGT 0.995056 -136 TGAGCACTACGTGTCGCGGCCCCTGCTCGAT 1 57 1 GTGTCGCGGC 0.996203 -91 AACTGCTGCAGTGACGCGCGTGTCGTCTTGC 1 106 1 GTGACGCGCT 0.988996 -42 GGTCGATGTGGTGTCGGGATTTTT 2 4 0 GTGTCGGGAT 0.969417 -172 TTCGGGGTCTTTGATGCGGTTGCAATGGGCG 2 147 0 TTGATGCGGT 0.968883 -29 AGTGTTAGGGACCGTGCAGGAG 4 163 0 GTGTTAGGGC 0.930986 -12 ********* * Masking position 2 Map Score: 4.59785 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 156 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 4 TGGTATGGTGCAAGACGACACGCGCGTCACTG 1 114 0 CAGACACACG 0.980705 -34 CGTCTTGCACCATACCATCACGCATCGGT 1 129 1 CAACCTCACG 0.970814 -19 GCATTAGATACATGCCAACACCTTCAGGAAAC 2 51 1 CAGCCACACC 0.972661 -125 CCAACACCTTCAGGAAACCACGGACGCACACG 2 65 1 CAGAACCACG 0.986216 -111 GACGCACACGCTTGCACACACGCTCCAAAAAC 2 87 1 CTGCAACACG 0.948887 -89 CTCTTGACAAAAAATACCCACGAGAGGCACGC 2 118 1 AAATACCACG 0.760454 -58 AAGTTGCGCGCAGATCTCCTCGATTGTACT 3 30 1 CAATCCCTCG 0.924151 -20 ACGAAGATAGCACGCTCCCCCGGATGTCAGGA 4 99 1 CAGCTCCCCG 0.963248 -76 ** *** ***** Masking position 9 Map Score: 3.3784 Number of sites scoring better than the average of aligned sites = 422 Number in coding regions = 387 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 TCCAAGATGGCTAATGAGCACTACGTGTCG 1 43 1 CTAATGAGCA 0.96165 -105 ATGCGTGATGGTATGGTGCAAGACGACACG 1 124 0 GTATGGTGCA 0.972246 -24 ATTTCTTCATCTATTGTGTAAGCACCTGCG 4 62 1 CTATTGTGTA 0.975783 -113 GAGACTCCTTCTGTTGTGCACACTATCATG 4 136 0 CTGTTGTGCA 0.989463 -39 ********** Masking position 2 Map Score: 0.0134807 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 61 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 ********** No masking Map Score: -1.04207e-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: -1.04207e-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: -1.04207e-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