AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i207_holliday_junction_tpal_reg_300.orf -o207_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 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 ACCCCATTACCTACCTCTTCACCTGCACAGTCACAA 1 49 0 CACCTTCTGC 0.994362 -126 TTACACAAGGCGCGCGTATGCACTGCTGGCAAATAT 1 146 1 CCCTATCTGC 0.942667 -29 GACAGTTCCAGAACCACTGGTGTTGCAGGCG 2 6 0 GACCTGTTGC 0.88104 -295 CTGGAACTGTCGAGCTGGCAGCTTGCAGACCTACGC 2 31 1 CACGGCTTGC 0.931047 -270 CACTGTACACCACGCCGGTCTGCTGCGCCCGGAGAT 2 87 1 CCCGGTCTGC 0.997599 -214 TGTGCGTATAGCACCTGTTTGTCTGCCACGTAGCTT 2 177 0 GACGTTCTGC 0.985185 -124 AAGCGGGGTCCCCACCCGTCATCTGCGTTACACAGC 2 234 0 CCCCGTCTGC 0.997065 -67 ACGGGTGGGGACCCCGCTTTGCCTGCGAAGCGCAGA 2 251 1 ACCCTTCTGC 0.978793 -50 AAAAGACGCGCACTCCGTTTTTCTGCGCTTCGCAGG 2 272 0 CCCGTTCTGC 0.998051 -29 TTTGATTATGCACCCTGTGCTCTTGCA 5 2 0 CCCGTGTTGC 0.986035 -83 * * * *** **** Masking position 14 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 TTTCAGTGCGGATCGCACTACCCATGACG 1 9 1 CGGATGCACT 0.980218 -166 TAAAGTTTTACACAAGGCGCGCGTATGCACT 1 139 1 CACAAGCGCG 0.944031 -36 TTTCCATATCCGCATACCAGTTTTGATGGTC 2 148 0 CGCATCCAGT 0.738723 -153 CCCTGGTGTGCGTATAGCACCTGTTTGTCTG 2 188 0 CGTATGCACC 0.86982 -113 ACGCACACCAGGGAACGCACGATACACTGCT 2 206 1 GGGAAGCACG 0.966029 -95 CTGTGTAACGCAGATGACGGGTGGGGACCCC 2 235 1 CAGATACGGG 0.694414 -66 GCGCTTCGCAGGCAAAGCGGGGTCCCCACCC 2 253 0 GGCAAGCGGG 0.956969 -48 CGCAGAAAAACGGAGTGCGCGTCTTTTGGT 2 281 1 CGGAGGCGCG 0.979563 -20 CCGGATGGCGCCTGGAGCCATA 4 2 1 CGGATGCGCC 0.989665 -23 AATAGAAAGAGGGATAGCAGTACTGACAACA 5 53 1 GGGATGCAGT 0.935154 -32 GTAATACGTGCAGAAAGCGGTATCATCTCTC 6 21 0 CAGAAGCGGT 0.925109 -123 GCGTTCCATACGCAATGCATCATATACATCG 6 61 0 CGCAAGCATC 0.791935 -83 ***** ***** Masking position 4 Map Score: 10.7687 Number of sites scoring better than the average of aligned sites = 1314 Number in coding regions = 1214 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 3 ATCGCACTACCCATGACGACATGACCATTGTG 1 22 1 CCATAGACAT 0.975202 -153 GACGACATGACCATTGTGACTGTGCAGGTGAA 1 36 1 CCATGGACTG 0.974435 -139 GCTATATTTGCCAGCAGTGCATACGCGCGCCT 1 153 0 CCAGATGCAT 0.805418 -22 CTCGACAGTTCCAGAACCACTGGTGTTGCAGG 2 13 0 CCAGACACTG 0.977345 -288 CTGCAAGCTGCCAGCTCGACAGTTCCAGAACC 2 27 0 CCAGTGACAG 0.968131 -274 CCGGAGATTGCCATCATGACTCCCATTATGGC 2 115 1 CCATAGACTC 0.966008 -186 ATCATGACTCCCATTATGGCTGACCATCAAAA 2 127 1 CCATAGGCTG 0.990313 -174 TTATGGCTGACCATCAAAACTGGTATGCGGAT 2 140 1 CCATAAACTG 0.950399 -161 ACGTAGCTTTCCATATCCGCATACCAGTTTTG 2 154 0 CCATTCGCAT 0.833634 -147 **** * ***** Masking position 3 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 4 GGGTAGTGCGATCCGCACTGAAA 1 4 0 ATCCGCACTG 0.8156 -171 CCAGCAGTGCATACGCGCGCCTTGTGTAAA 1 145 0 ATACGCGCGC 0.992581 -30 GCTTGCAGACCTACGCGCAGTCGATGCACA 2 51 1 CTACGCGCAG 0.881873 -250 TGATGGCAATCTCCGGGCGCAGCAGACCGG 2 101 0 CTCCGGGCGC 0.98052 -200 AACAGGTGCTATACGCACACCAGGGAACGC 2 194 1 ATACGCACAC 0.964182 -107 GCTTTGCCTGCGAAGCGCAGAAAAACGGAG 2 266 1 CGAAGCGCAG 0.871766 -35 ACCAAAAGACGCGCACTCCGTTTTTC 2 285 0 AGACGCGCAC 0.985241 -16 ATTATGGCTCCAGGCGCCATCCGG 4 8 0 CTCCAGGCGC 0.831543 -17 GATGCTCGTAATACGTGCAGAAAGCGGTAT 6 29 0 ATACGTGCAG 0.934118 -115 ********** Masking position 8 Map Score: 9.20144 Number of sites scoring better than the average of aligned sites = 1775 Number in coding regions = 1656 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 5 CAAAAACCGCGACAAAGAGGTAAGAAAAAA 1 91 0 GACAAAGAGG 0.994791 -84 CTACGTGGCAGACAAACAGGTGCTATACGC 2 180 1 GACAAACAGG 0.981897 -121 GCGCTTCGCAGGCAAAGCGGGGTCCCCACC 2 254 0 GGCAAAGCGG 0.98302 -47 AGAGAAAAAATAGAAAGAGGGATAGCAGTA 5 45 1 TAGAAAGAGG 0.977926 -40 GTAATACGTGCAGAAAGCGGTATCATCTCT 6 22 0 CAGAAAGCGG 0.968623 -122 GGAACGCTCTTACAAAAAGGGATTTTCTCA 6 85 1 TACAAAAAGG 0.942004 -59 ********** Masking position 5 Map Score: 6.43997 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 50 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 TTTTTCTTACCTCTTTGTCGCGGTTTTTGT 1 92 1 CTCTTTGTCG 0.777805 -83 TCGACGTATTCTGTTTAAAGTTTTACACAA 1 124 1 CTGTTTAAAG 0.783022 -51 TATTTGCCAGCAGTGCATACGCGCGCCTTG 1 151 0 CAGTGCATAC 0.638111 -24 TGTGCATCGACTGCGCGTAGGTCTGCAAGC 2 51 0 CTGCGCGTAG 0.952344 -250 CAGTGTGGTCCTGTGCATCGACTGCGCGTA 2 62 0 CTGTGCATCG 0.989395 -239 CGTATAGCACCTGTTTGTCTGCCACGTAGC 2 179 0 CTGTTTGTCT 0.72367 -122 GTTCCCTGGTGTGCGTATAGCACCTGTTTG 2 192 0 GTGCGTATAG 0.826381 -109 CGTTACACAGCAGTGTATCGTGCGTTCCCT 2 215 0 CAGTGTATCG 0.965172 -86 CGATACACTGCTGTGTAACGCAGATGACGG 2 225 1 CTGTGTAACG 0.965148 -76 CTCCGTTTTTCTGCGCTTCGCAGGCAAAGC 2 266 0 CTGCGCTTCG 0.931382 -35 TTCTAAAATCATGTGTGTAGTTTGTTCATG 6 113 0 ATGTGTGTAG 0.847494 -31 ********** Masking position 3 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 AAGCTGCCAGCTCGACAGTTCCAGAACCACT 2 24 0 CTCGACGTTC 0.943543 -277 ATGCACAGGACCACACTGTACACCACGCCGG 2 74 1 CCACACGTAC 0.975323 -227 ACACTGTACACCACGCCGGTCTGCTGCGCCC 2 86 1 CCACGCGGTC 0.988972 -215 AAAGCGGGGTCCCCACCCGTCATCTGCGTTA 2 240 0 CCCCACCGTC 0.979831 -61 CGGGTGGGGACCCCGCTTTGCCTGCGAAGCG 2 252 1 CCCCGCTTGC 0.936616 -49 TGTCCAGACTGTTCTAAAATCATG 6 130 0 CCAGACGTTC 0.985636 -14 ****** **** Masking position 6 Map Score: 1.14538 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 171 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 CACTACCCATGACGACATGACCATTGTGAC 1 26 1 GACGACATGA 0.930538 -149 AGCCATAATGGGAGTCATGATGGCAATCTC 2 118 0 GGAGTCATGA 0.98542 -183 GATGGCGCCTGGAGCCATAAT 4 14 1 GGAGCCATAA 0.950484 -11 GGTGGGATGATTGTTGTCAG 5 75 0 GGTGGGATGA 0.964561 -10 AAATTGGAAGGAGAGATGATACCGCTTTC 6 10 1 GGAGAGATGA 0.987926 -134 ********** Masking position 7 Map Score: 0.925448 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 36 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 AGAGGTAAGAAAAAAATAGCAACCCCATTA 1 76 0 AAAAAATAGC 0.969467 -99 ACGTCGAAAACAAAAACCGCGACAAAGAGG 1 101 0 CAAAAACCGC 0.938022 -74 GCACTGCTGGCAAATATAGC 1 165 1 CAAATATAGC 0.933811 -10 GTGCATAATCAAAATATCCCAGAGAAAAAA 5 25 1 AAAATATCCC 0.933269 -60 TATCCCAGAGAAAAAATAGAAAGAGGGATA 5 39 1 AAAAAATAGA 0.830854 -46 TTTGTTCATGAGAAAATCCCTTTTTGTAAG 6 93 0 AGAAAATCCC 0.905137 -51 ********** Masking position 6 Map Score: 0.248772 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 182 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 10 ********** 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 11 ********** 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 12 ********** 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