AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i207_holliday_junction_tpal_reg_100.orf -o207_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 RTP00323 174 AE000520 #2 RTP00235 300 AE000520 #3 RTP00092 41 AE000520 #4 RTP00091 24 AE000520 #5 RTP00090 84 AE000520 #6 RTP00984 143 AE000520 Motif number 1 TTGTGACTGTGCAGGTGAAGAGGTAGGTAATGGGGT 1 49 1 GCAGAAGGTG 0.994315 -126 ATATTTGCCAGCAGTGCATACGCGCGCCTTGTGTAA 1 146 0 GCAGATAGGG 0.942215 -29 CGCCTGCAACACCAGTGGTTCTGGAACTGTC 2 6 1 GCAACAGGTC 0.880165 -295 GCGTAGGTCTGCAAGCTGCCAGCTCGACAGTTCCAG 2 31 0 GCAAGCCGTG 0.93051 -270 ATCTCCGGGCGCAGCAGACCGGCGTGGTGTACAGTG 2 87 0 GCAGACCGGG 0.99758 -214 AAGCTACGTGGCAGACAAACAGGTGCTATACGCACA 2 177 1 GCAGAACGTC 0.985063 -124 GCTGTGTAACGCAGATGACGGGTGGGGACCCCGCTT 2 234 1 GCAGACGGGG 0.99704 -67 TCTGCGCTTCGCAGGCAAAGCGGGGTCCCCACCCGT 2 251 0 GCAGAAGGGT 0.978619 -50 CCTGCGAAGCGCAGAAAAACGGAGTGCGCGTCTTTT 2 272 1 GCAGAACGGG 0.998034 -29 TGCAAGAGCACAGGGTGCATAATCAAA 5 2 1 GCAACACGGG 0.98592 -83 **** *** * * * Masking position 3 Map Score: 14.2732 Number of sites scoring better than the average of aligned sites = 341 Number in coding regions = 318 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 2 TTTTTTTCTTACCTCTTTGTCGCGGTTTTT 1 90 1 ACCTCTTTGT 0.946986 -85 ACCTCTTTGTCGCGGTTTTTGTTTTCGACG 1 100 1 CGCGGTTTTT 0.86013 -75 AGTGCATACGCGCGCCTTGTGTAAAACTTT 1 140 0 CGCGCCTTGT 0.970981 -35 TGCGTATAGCACCTGTTTGTCTGCCACGTA 2 181 0 ACCTGTTTGT 0.882869 -120 GGGGTCCCCACCCGTCATCTGCGTTACACA 2 236 0 CCCGTCATCT 0.81769 -65 GGGTGGGGACCCCGCTTTGCCTGCGAAGCG 2 253 1 CCCGCTTTGC 0.962728 -48 GACGCGCACTCCGTTTTTCTGCGCTTCGCA 2 274 0 CCGTTTTTCT 0.775809 -27 AAACGGAGTGCGCGTCTTTTGGT 2 288 1 CGCGTCTTTT 0.822878 -13 GTACTGCTATCCCTCTTTCTATTTTTTCTC 5 46 0 CCCTCTTTCT 0.983113 -39 GAGAGATGATACCGCTTTCTGCACGTATTA 6 21 1 ACCGCTTTCT 0.964824 -123 ATGAGAAAATCCCTTTTTGTAAGAGCGTTC 6 86 0 CCCTTTTTGT 0.973478 -58 ********** Masking position 8 Map Score: 10.4845 Number of sites scoring better than the average of aligned sites = 480 Number in coding regions = 436 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 3 TTTCAGTGCGGATCGCACTACCC 1 4 1 CAGTGCGGAT 0.878706 -171 TTTACACAAGGCGCGCGTATGCACTGCTGG 1 145 1 GCGCGCGTAT 0.992822 -30 TGTGCATCGACTGCGCGTAGGTCTGCAAGC 2 51 0 CTGCGCGTAG 0.737095 -250 CCGGTCTGCTGCGCCCGGAGATTGCCATCA 2 101 1 GCGCCCGGAG 0.980285 -200 ATCAAAACTGGTATGCGGATATGGAAAGCT 2 152 1 GTATGCGGAT 0.818226 -149 GCGTTCCCTGGTGTGCGTATAGCACCTGTT 2 194 0 GTGTGCGTAT 0.979395 -107 CTCCGTTTTTCTGCGCTTCGCAGGCAAAGC 2 266 0 CTGCGCTTCG 0.822319 -35 GAAAAACGGAGTGCGCGTCTTTTGGT 2 285 1 GTGCGCGTCT 0.986344 -16 CCGGATGGCGCCTGGAGCCATAAT 4 8 1 GCGCCTGGAG 0.812909 -17 ATACCGCTTTCTGCACGTATTACGAGCATC 6 29 1 CTGCACGTAT 0.925318 -115 ********** Masking position 6 Map Score: 9.89362 Number of sites scoring better than the average of aligned sites = 2071 Number in coding regions = 1935 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 4 CGTCATGGGTAGTGCGATCCGCACTGAAA 1 10 0 AGTGCGATCC 0.99355 -165 CGTGGTGTACAGTGTGGTCCTGTGCATCGA 2 71 0 AGTGTGGTCC 0.951506 -230 AGCAGACCGGCGTGGTGTACAGTGTGGTCC 2 81 0 CGTGGTGTAC 0.795258 -220 CAGACAAACAGGTGCTATACGCACACCAGG 2 188 1 GGTGCTATAC 0.884918 -113 AGCAGTGTATCGTGCGTTCCCTGGTGTGCG 2 207 0 CGTGCGTTCC 0.974359 -94 TCGCAGGCAAAGCGGGGTCCCCACCCGTCA 2 249 0 AGCGGGGTCC 0.984684 -52 TATGGCTCCAGGCGCCATCCGG 4 3 0 GGCGCCATCC 0.94266 -22 TGTTGTCAGTACTGCTATCCCTCTTTCTAT 5 54 0 ACTGCTATCC 0.910486 -31 ACGTGCAGAAAGCGGTATCATCTCTCCTTC 6 17 0 AGCGGTATCA 0.744717 -127 CCTTTTTGTAAGAGCGTTCCATACGCAATG 6 75 0 AGAGCGTTCC 0.932677 -69 ********** Masking position 8 Map Score: 6.97387 Number of sites scoring better than the average of aligned sites = 576 Number in coding regions = 529 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 5 CACAATGGTCATGTCGTCATGGGTAGTGCGAT 1 22 0 ATGTCTATGG 0.974323 -153 TTCACCTGCACAGTCACAATGGTCATGTCGTC 1 36 0 CAGTCCATGG 0.97353 -139 AGGCGCGCGTATGCACTGCTGGCAAATATAGC 1 153 1 ATGCATCTGG 0.799756 -22 CCTGCAACACCAGTGGTTCTGGAACTGTCGAG 2 13 1 CAGTGTCTGG 0.97654 -288 GGTTCTGGAACTGTCGAGCTGGCAGCTTGCAG 2 27 1 CTGTCACTGG 0.96701 -274 GCCATAATGGGAGTCATGATGGCAATCTCCGG 2 115 0 GAGTCTATGG 0.964815 -186 TTTTGATGGTCAGCCATAATGGGAGTCATGAT 2 127 0 CAGCCTATGG 0.989964 -174 ATCCGCATACCAGTTTTGATGGTCAGCCATAA 2 140 0 CAGTTTATGG 0.948689 -161 CAAAACTGGTATGCGGATATGGAAAGCTACGT 2 154 1 ATGCGAATGG 0.828619 -147 ***** * **** Masking position 10 Map Score: 6.59802 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 131 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 ACAAAAACCGCGACAAAGAGGTAAGAAAAA 1 92 0 CGACAAAGAG 0.765429 -83 TTGTGTAAAACTTTAAACAGAATACGTCGA 1 124 0 CTTTAAACAG 0.770854 -51 CAAGGCGCGCGTATGCACTGCTGGCAAATA 1 151 1 GTATGCACTG 0.621756 -24 GCTTGCAGACCTACGCGCAGTCGATGCACA 2 51 1 CTACGCGCAG 0.951934 -250 TACGCGCAGTCGATGCACAGGACCACACTG 2 62 1 CGATGCACAG 0.988789 -239 GCTACGTGGCAGACAAACAGGTGCTATACG 2 179 1 AGACAAACAG 0.709405 -122 CAAACAGGTGCTATACGCACACCAGGGAAC 2 192 1 CTATACGCAC 0.816082 -109 AGGGAACGCACGATACACTGCTGTGTAACG 2 215 1 CGATACACTG 0.962732 -86 CCGTCATCTGCGTTACACAGCAGTGTATCG 2 225 0 CGTTACACAG 0.96271 -76 GCTTTGCCTGCGAAGCGCAGAAAAACGGAG 2 266 1 CGAAGCGCAG 0.92676 -35 CATGAACAAACTACACACATGATTTTAGAA 6 113 1 CTACACACAT 0.838196 -31 ********** Masking position 8 Map Score: 5.98287 Number of sites scoring better than the average of aligned sites = 975 Number in coding regions = 899 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 7 ********** No masking Map Score: -1.51102e-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: -1.51102e-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: -1.51102e-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