AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i224_Holliday_Junction_enzyme_tpal_reg_300.orf -o224_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 0.993465 -126 TTACACAAGGCGCGCGTATGCACTGCTGGCAAATAT 1 146 1 CCCTATCTGC 0.934087 -29 GACAGTTCCAGAACCACTGGTGTTGCAGGCG 2 6 0 GACCTGTTGC 0.864575 -295 CTGGAACTGTCGAGCTGGCAGCTTGCAGACCTACGC 2 31 1 CACGGCTTGC 0.920877 -270 CACTGTACACCACGCCGGTCTGCTGCGCCCGGAGAT 2 87 1 CCCGGTCTGC 0.997227 -214 TGTGCGTATAGCACCTGTTTGTCTGCCACGTAGCTT 2 177 0 GACGTTCTGC 0.982855 -124 AAGCGGGGTCCCCACCCGTCATCTGCGTTACACAGC 2 234 0 CCCCGTCTGC 0.996599 -67 ACGGGTGGGGACCCCGCTTTGCCTGCGAAGCGCAGA 2 251 1 ACCCTTCTGC 0.975478 -50 AAAAGACGCGCACTCCGTTTTTCTGCGCTTCGCAGG 2 272 0 CCCGTTCTGC 0.997739 -29 TTTGATTATGCACCCTGTGCTCTTGCA 5 2 0 CCCGTGTTGC 0.983834 -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 AAAAACCGCGACAAAGAGGTAAGAAAAAAA 1 90 0 ACAAAGAGGT 0.952833 -85 CGTCGAAAACAAAAACCGCGACAAAGAGGT 1 100 0 AAAAACCGCG 0.874286 -75 AAAGTTTTACACAAGGCGCGCGTATGCACT 1 140 1 ACAAGGCGCG 0.974254 -35 TACGTGGCAGACAAACAGGTGCTATACGCA 2 181 1 ACAAACAGGT 0.895004 -120 TGTGTAACGCAGATGACGGGTGGGGACCCC 2 236 1 AGATGACGGG 0.835319 -65 CGCTTCGCAGGCAAAGCGGGGTCCCCACCC 2 253 0 GCAAAGCGGG 0.966899 -48 TGCGAAGCGCAGAAAAACGGAGTGCGCGTC 2 274 1 AGAAAAACGG 0.79648 -27 ACCAAAAGACGCGCACTCCGTTT 2 288 0 AAAAGACGCG 0.840103 -13 GAGAAAAAATAGAAAGAGGGATAGCAGTAC 5 46 1 AGAAAGAGGG 0.985039 -39 TAATACGTGCAGAAAGCGGTATCATCTCTC 6 21 0 AGAAAGCGGT 0.968769 -123 GAACGCTCTTACAAAAAGGGATTTTCTCAT 6 86 1 ACAAAAAGGG 0.976476 -58 ********** Masking position 3 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 0.884441 -171 TTTACACAAGGCGCGCGTATGCACTGCTGG 1 145 1 GCGCGCGTAT 0.993199 -30 TGTGCATCGACTGCGCGTAGGTCTGCAAGC 2 51 0 CTGCGCGTAG 0.730607 -250 CCGGTCTGCTGCGCCCGGAGATTGCCATCA 2 101 1 GCGCCCGGAG 0.981318 -200 ATCAAAACTGGTATGCGGATATGGAAAGCT 2 152 1 GTATGCGGAT 0.826247 -149 GCGTTCCCTGGTGTGCGTATAGCACCTGTT 2 194 0 GTGTGCGTAT 0.980473 -107 CTCCGTTTTTCTGCGCTTCGCAGGCAAAGC 2 266 0 CTGCGCTTCG 0.830148 -35 GAAAAACGGAGTGCGCGTCTTTTGGT 2 285 1 GTGCGCGTCT 0.987059 -16 CCGGATGGCGCCTGGAGCCATAAT 4 8 1 GCGCCTGGAG 0.821122 -17 ATACCGCTTTCTGCACGTATTACGAGCATC 6 29 1 CTGCACGTAT 0.928821 -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 TTTCAGTGCGGATCGCACTACCCATGACG 1 10 1 GGATCGCACT 0.993052 -165 TCGATGCACAGGACCACACTGTACACCACG 2 71 1 GGACCACACT 0.947917 -230 GGACCACACTGTACACCACGCCGGTCTGCT 2 81 1 GTACACCACG 0.782746 -220 CCTGGTGTGCGTATAGCACCTGTTTGTCTG 2 188 0 GTATAGCACC 0.877038 -113 CGCACACCAGGGAACGCACGATACACTGCT 2 207 1 GGAACGCACG 0.972414 -94 TGACGGGTGGGGACCCCGCTTTGCCTGCGA 2 249 1 GGACCCCGCT 0.983508 -52 CCGGATGGCGCCTGGAGCCATA 4 3 1 GGATGGCGCC 0.938501 -22 ATAGAAAGAGGGATAGCAGTACTGACAACA 5 54 1 GGATAGCAGT 0.904168 -31 GAAGGAGAGATGATACCGCTTTCTGCACGT 6 17 1 TGATACCGCT 0.730165 -127 CATTGCGTATGGAACGCTCTTACAAAAAGG 6 75 1 GGAACGCTCT 0.927856 -69 ********** Masking position 3 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 ATCGCACTACCCATGACGACATGACCATTGTG 1 22 1 CCATAGACAT 0.972988 -153 GACGACATGACCATTGTGACTGTGCAGGTGAA 1 36 1 CCATGGACTG 0.972157 -139 GCTATATTTGCCAGCAGTGCATACGCGCGCCT 1 153 0 CCAGATGCAT 0.79129 -22 CTCGACAGTTCCAGAACCACTGGTGTTGCAGG 2 13 0 CCAGACACTG 0.975318 -288 CTGCAAGCTGCCAGCTCGACAGTTCCAGAACC 2 27 0 CCAGTGACAG 0.965308 -274 CCGGAGATTGCCATCATGACTCCCATTATGGC 2 115 1 CCATAGACTC 0.963005 -186 ATCATGACTCCCATTATGGCTGACCATCAAAA 2 127 1 CCATAGGCTG 0.989434 -174 TTATGGCTGACCATCAAAACTGGTATGCGGAT 2 140 1 CCATAAACTG 0.946099 -161 ACGTAGCTTTCCATATCCGCATACCAGTTTTG 2 154 0 CCATTCGCAT 0.821101 -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 6 ACAAAAACCGCGACAAAGAGGTAAGAAAAA 1 92 0 CGACAAAGAG 0.762353 -83 TTGTGTAAAACTTTAAACAGAATACGTCGA 1 124 0 CTTTAAACAG 0.767829 -51 CAAGGCGCGCGTATGCACTGCTGGCAAATA 1 151 1 GTATGCACTG 0.617742 -24 GCTTGCAGACCTACGCGCAGTCGATGCACA 2 51 1 CTACGCGCAG 0.951802 -250 TACGCGCAGTCGATGCACAGGACCACACTG 2 62 1 CGATGCACAG 0.988634 -239 GCTACGTGGCAGACAAACAGGTGCTATACG 2 179 1 AGACAAACAG 0.705877 -122 CAAACAGGTGCTATACGCACACCAGGGAAC 2 192 1 CTATACGCAC 0.813512 -109 AGGGAACGCACGATACACTGCTGTGTAACG 2 215 1 CGATACACTG 0.962116 -86 CCGTCATCTGCGTTACACAGCAGTGTATCG 2 225 0 CGTTACACAG 0.962094 -76 GCTTTGCCTGCGAAGCGCAGAAAAACGGAG 2 266 1 CGAAGCGCAG 0.925596 -35 CATGAACAAACTACACACATGATTTTAGAA 6 113 1 CTACACACAT 0.835872 -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