AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i150_ATP_synthase_1_tpal_reg_100.orf -o150_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 RTP00149 141 AE000520 #2 RTP00108 94 AE000520 #3 RTP00103 300 AE000520 #4 RTP00098 140 AE000520 Motif number 1 TCTCTGTGATTGTGTGCAAGGGCACGTGGTGCGTGTGTATGAAGG 1 20 1 TGGGGCGGGG 0.996941 -122 ATGAAGGTACTGCACGGTGTGTACCTGGGGAGGGGAAAATAGCAG 1 58 1 TGGTGCGGGG 0.99782 -84 TAGCAGGGGCTGTGCGTACTCCGTATTGAGTAGCGACAGACGGGT 1 97 1 TGGTCAGAGG 0.994441 -45 TGCTGTTTTGTGGGAGCCGTGGACCGCGAATGGGGATTATAAGTC 2 16 0 TGGTGCGAGG 0.998445 -79 CAGTTTGAAGAGATGGATGTGTACACTGACACGCGTCGTGCGGCA 3 105 0 AGGTGAGAGG 0.991156 -196 GCGAATCGGCTTGTGGACTGGAATATCGATGTGAAGACAGAGAGT 3 150 0 TTGGGAGAGA 0.914553 -151 TGTTGCTGAAAGCCAGCTGTCTATCGCGATAGGAAAGCAAGGTTT 3 208 0 AGGTCCGAGA 0.971295 -93 GCTGAGGTGCTGAACGTCGTGGTACTTGATGAGGAGAAGCGTTCT 3 264 0 TGGTGCGAGA 0.996285 -37 GTTTCATCCCTGTAAGCGCGCCGCATCGGAAAGAGCGGCATCCTT 4 69 1 TGGGCAGGGG 0.989093 -72 TGCGCGGAGATGAAGGAGGTGTCGAGGAAACTGAAGGATGCCGCT 4 102 0 TGGTGAAAGA 0.937627 -39 ** * ** * ** * * Masking position 6 Map Score: 14.8209 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 222 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 2 ACGTGGTGCGTGTGTATGAAGGTACTGCACGGTGTGTACC 1 43 1 TGGAGCGCAC 0.994942 -99 TACTGCACGGTGTGTACCTGGGGAGGGGAAAATAGCAGGG 1 65 1 TGGAGGGGAA 0.985177 -77 TACTCCGTATTGAGTAGCGACAGACGGGTAGGAAGAGTG 1 113 1 TGGACCGGTA 0.9527 -29 TTGTGGGAGCCGTGGACCGCGAATGGGGATTATAAGTCTA 2 14 0 CGGAGGGGAT 0.962772 -81 TCTTCATACGTGGGATTTACGCCGGAGCTCATTAAGATTC 3 23 0 TGGTGGGCTC 0.983828 -278 AAGAGATGGATGTGTACACTGACACGCGTCGTGCGGCAGA 3 103 0 TGGAGCCGTC 0.945643 -198 GGTTTGAACGTGCGTTTAGCGAATCGGCTTGTGGACTGGA 3 173 0 TGGTGCGCTT 0.974589 -128 TGGTACTTGATGAGGAGAAGCGTTCTGCACTTGCCATTGT 3 250 0 TGGACCGCAC 0.988671 -51 TGCGCTATTTCTGCGCGGATATGCTCCCCC 4 1 1 TGGTCGGGAT 0.961409 -140 CAGTTAAGGGTGCGCAAATTGGGGGAGCATATCCGCGCAG 4 21 0 TGGAGGGCAT 0.992001 -120 ** * * * * **** Masking position 4 Map Score: 9.22445 Number of sites scoring better than the average of aligned sites = 339 Number in coding regions = 325 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 3 GGTACACACCGTGCAGTACCTTCATACACA 1 53 0 GTGCAGTACC 0.984892 -89 CGTTGTCCTGCAGAATCTTAATGAGCT 3 8 1 CTGCAGAATC 0.959161 -293 AAAAGATTTTCTGCCGCACGACGCGTGTCA 3 94 1 CTGCCGCACG 0.980476 -207 ACAATGGCAAGTGCAGAACGCTTCTCCTCA 3 250 1 GTGCAGAACG 0.979801 -51 GTACCACGACGTTCAGCACCTCAGCAG 3 284 1 GTTCAGCACC 0.977838 -17 CCCTGTAAGCGCGCCGCATCGGAAAGAGCG 4 76 1 GCGCCGCATC 0.980346 -65 GCATCGGAAAGAGCGGCATCCTTCAGTTTC 4 91 1 GAGCGGCATC 0.948199 -50 ********** Masking position 8 Map Score: 5.7048 Number of sites scoring better than the average of aligned sites = 514 Number in coding regions = 479 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 4 GGTGAAGCTTCTCTGTGATTGTGTGC 1 7 1 GCTTCTCTGT 0.974031 -135 CACTCTTCCTACCCGTCTGTCGCTAC 1 126 0 TCCTACCCGT 0.951111 -16 GCCTACCTGACCATTGGGAA 2 85 0 GCCTACCTGA 0.905078 -10 TCTTCAAACTGACTCTCTGTCTTCACATCG 3 139 1 GACTCTCTGT 0.852582 -162 AGTGCAGAACGCTTCTCCTCATCAAGTACC 3 259 1 GCTTCTCCTC 0.822739 -42 AATTGGGGGAGCATATCCGCGCAGAAATAG 4 15 0 GCATATCCGC 0.959 -126 CCCTTAACTGACTTACCTGTTTCATCCCTG 4 51 1 ACTTACCTGT 0.791804 -90 CTTACCTGTTTCATCCCTGTAAGCGCGCCG 4 62 1 TCATCCCTGT 0.949698 -79 GACACCTCCTTCATCTCCGCGCATTCA 4 124 1 TCATCTCCGC 0.948718 -17 ********** Masking position 4 Map Score: 4.56048 Number of sites scoring better than the average of aligned sites = 616 Number in coding regions = 564 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 5 GATTGTGTGCAAGGGCACGTGGTGCGTGTGTATG 1 27 1 AAGGCAGGTG 0.996969 -115 TGTATGAAGGTACTGCACGGTGTGTACCTGGGGA 1 55 1 TATGCAGTTG 0.925347 -87 GGGAGGGGAAAATAGCAGGGGCTGTGCGTACTCC 1 85 1 AAAGCAGGTG 0.996701 -57 GCTCCCACAAAACAGCAAACGTTGACTTAAAATC 2 44 1 AAAGCAAGTG 0.979224 -51 ATCGCGATAGGAAAGCAAGGTTTGAACGTGCGTT 3 197 0 GAAGCAGTTG 0.978588 -104 TTTCAGCAACAATGGCAAGTGCAGAACGCTTCTC 3 242 1 AAGGCAGGAG 0.987844 -59 ** **** * * ** Masking position 7 Map Score: 3.68658 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 55 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 ********** No masking Map Score: -1.09891e-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: -1.09891e-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: -1.09891e-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