AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i303_mixed18_tpal_reg_300.orf -o303_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 RTP00417 194 AE000520 #2 RTP00981 170 AE000520 #3 RTP00980 169 AE000520 #4 RTP00594 46 AE000520 #5 RTP00593 104 AE000520 #6 RTP00592 140 AE000520 Motif number 1 ATAGATCTGCAACCCGCCGATCGGGAAGCAATCCGC 1 84 1 AACCGCCGGA 0.934906 -111 CCGCACGTGGAAGGAGCGTGTGGGGCAGGTGATTGT 1 140 0 AAGAGCGGGC 0.785747 -55 GCTCCTTCCACGTGCGGTAAAAGGGCTCGAGCTCTT 1 159 1 CGGCGGAGGC 0.994357 -36 CTCGGATCAGCGTGCGCACGTCGGTCAGGTCGAGGG 2 40 1 CGGCGCCGGC 0.997223 -131 GATTTTTTCGCCGCCGCGGTTGCGCCCCTCGACCTG 2 65 0 CCCCGCGCGC 0.963314 -106 TTCTTCTGAGCGAGCTCTGCTAGGGCATCGGCAAGC 2 126 1 CGGCTCAGGC 0.92251 -45 ACGTGCGGTTTAAGGAAGTGCTTGCCG 2 154 0 CGGCGGAGGA 0.994472 -17 ACTGAGTGTGCAGGCGGCGAACGGTATCTACTCCGC 3 25 0 CAGCGGCGGA 0.994451 -145 CCGACGTTATCCAGCGCATTCGCGAACTGAGTGTGC 3 50 0 CCGCGCGCGA 0.991053 -120 GGCGTCTACAAACGCGCAGAACGGCATCTCCTTCAT 3 118 0 AAGCGCCGGA 0.983438 -52 GCAGATGTGGTGCGCGGTGGTACGGATGACTTTGGT 5 11 1 TGGCGGACGA 0.901295 -94 AAAACATTCACGGGCGGACATGAGGAACCTGCGCGG 5 53 1 CGGCGGGAGA 0.960859 -52 ACATGAGGAACCTGCGCGGGCGGAGACGTCACGTAC 5 70 1 CCGCGCGGAA 0.93443 -35 CTTTAAGAAAACGGCGGAAACAGGCACAATGGGTAC 6 26 1 ACGCGGAGGA 0.969292 -115 TCCGGACAACCATGCGGGCTTGCGTACCCATTGTGC 6 49 0 CAGCGGGCGA 0.987655 -92 CTCACCGTCTTACCCGCCTTCCGGACAACCATGCGG 6 68 0 TACCGCCGGC 0.882899 -73 ** **** *** * Masking position 6 Map Score: 25.6573 Number of sites scoring better than the average of aligned sites = 1668 Number in coding regions = 1543 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 2 CCGATCGGCGGGTTGCAGATCTATCTCCTTT 1 77 0 GGTTGCGATC 0.995247 -118 TGTGCGGATTGCTTCCCGATCGGCGGGTTGC 1 92 0 GCTTCCGATC 0.988875 -103 ACCGACGTGCGCACGCTGATCCGAGTTTGCG 2 34 0 GCACGCGATC 0.979039 -137 TCGCCGCCGCGGTTGCGCCCCTCGACCTGAC 2 63 0 GGTTGCCCCC 0.916735 -108 TTAAGGAAGTGCTTGCCGATGCCCTAGCAGA 2 141 0 GCTTGCGATG 0.989431 -30 CCTTCATTCAGGTTGCGGAGGCGTTTTTACA 3 94 0 GGTTGCGAGG 0.966147 -76 CGGAGCCAGATCCGTGGTTTGA 3 158 0 GGAGCCGATC 0.918489 -12 AATATTTCCTGCACGCAGACCAAGG 4 5 0 GCACGCGACC 0.974215 -42 CGCCCGCGCAGGTTCCTCATGTCCGCCCGTG 5 61 0 GGTTCCCATG 0.926815 -44 AACCATGCGGGCTTGCGTACCCATTGTGCCT 6 47 0 GCTTGCTACC 0.95054 -94 ****** **** Masking position 6 Map Score: 10.8163 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 268 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 3 TATTTTCACTGATGGTCGAGTTCCGCT 1 3 0 GTGGTCGTCG 0.974562 -192 GCGTGCGCACGTCGGTCAGGTCGAGGGGCGCAACC 2 49 1 GCGGTCGTGG 0.988703 -122 GGAAGTGCTTGCCGATGCCCTAGCAGAGCTCGCTC 2 133 0 GCGATGCTGA 0.829048 -38 AGAGACGGTCTTCTGCGGAGTAGATACC 3 4 1 GCGGTCCTCG 0.992225 -166 CTTCTGCGGAGTAGATACCGTTCGCCGCCTGCACA 3 20 1 GAGATAGTCC 0.814382 -150 GCTGGATAACGTCGGTGGTCTCCTGTAAAAACGCC 3 71 1 GCGGTGCTCG 0.995207 -99 CCTGAATGAAGGAGATGCCGTTCTGCGCGTTTGTA 3 113 1 GAGATGGTCG 0.987679 -57 GCAGATGTGGTGCGCGGTGGTACGG 5 1 1 GAGATGGTCC 0.96594 -104 AACCTGCGCGGGCGGAGACGTCACGTACTTCCTTG 5 78 1 GCGGAGGTAG 0.891755 -27 * ***** ** * * Masking position 11 Map Score: 4.60117 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 282 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 4 GAAATAGAACGCACAATCTTTTCGCAAACT 2 12 1 GCACAATCTT 0.793556 -159 CAATCTTTTCGCAAACTCGGATCAGCGTGC 2 25 1 GCAAACTCGG 0.929055 -146 ACCGACGTGCGCACGCTGATCCGAGTTTGC 2 35 0 GCACGCTGAT 0.976213 -136 CCCTAGCAGAGCTCGCTCAGAAGAAAATCC 2 121 0 GCTCGCTCAG 0.986722 -50 TTCGCCGCCTGCACACTCAGTTCGCGAATG 3 40 1 GCACACTCAG 0.994295 -130 GGAACAACACGCTCACTGATAATATTTCCT 4 26 0 GCTCACTGAT 0.947957 -21 TGACGTCTCCGCCCGCGCAGGTTCCTCATG 5 71 0 GCCCGCGCAG 0.943128 -34 GCGGAAACAGGCACAATGGGTACGCAAGCC 6 39 1 GCACAATGGG 0.942813 -102 ********** Masking position 2 Map Score: 6.66959 Number of sites scoring better than the average of aligned sites = 625 Number in coding regions = 578 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 5 TTTAGATGCCAACACGGATACCTCTCCAAA 1 50 1 AACACGGATA 0.885041 -145 CACGTGCGGTAAAAGGGCTCGAGCTCTTTT 1 167 1 AAAAGGGCTC 0.982351 -28 GAAAACGAAAAAGAGCTCGAGCCCTTTT 1 177 0 AAAAGAGCTC 0.927171 -18 TCTTTTCGCAAACTCGGATCAGCGTGCGCA 2 28 1 AACTCGGATC 0.925121 -143 CCGATGCCCTAGCAGAGCTCGCTCAGAAGA 2 127 0 AGCAGAGCTC 0.922532 -44 GTCTCCTGTAAAAACGCCTCCGCAACCTGA 3 88 1 AAAACGCCTC 0.951672 -82 CGTGGTTTGAACCAGGCGTCTACAAACGCG 3 138 0 ACCAGGCGTC 0.905908 -32 CCTGGTTCAAACCACGGATCTGGCTCCG 3 152 1 ACCACGGATC 0.9789 -18 ********** Masking position 1 Map Score: 3.35467 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 175 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 TGGCATCTAAAACGAGATATGATTATTTTC 1 31 0 AACGAGATAT 0.884124 -164 TACCTCTCCAAAGGAGATAGATCTGCAACC 1 68 1 AAGGAGATAG 0.965481 -127 CGTGCGGTTTAAGGAAGTGCTTGCCGATGC 2 150 0 AAGGAAGTGC 0.97039 -21 AACCTGAATGAAGGAGATGCCGTTCTGCGC 3 111 1 AAGGAGATGC 0.984167 -59 GGTCTGCGTGCAGGAAATATTATCAGTGAG 4 15 1 CAGGAAATAT 0.885557 -32 GCCAAGGAAGTACGTGACGTCTC 5 92 0 AAGGAAGTAC 0.975327 -13 ********** Masking position 5 Map Score: 2.01152 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 102 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 ********** No masking Map Score: -1.58918e-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: -1.58918e-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 9 ********** No masking Map Score: -1.58918e-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