Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: scaffold2271 Parameters: 2 7 7 80 10 50 1000 Pmatch=0.80,Pindel=0.10 tuple sizes 0,4,5,7 tuple distances 0, 29, 159, 605 Length: 1009 ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35 Found at i:727 original size:7 final size:7 Alignment explanation
Indices: 715--819 Score: 53 Period size: 7 Copynumber: 15.4 Consensus size: 7 705 AACCCTGAAT 715 CCTTAAA 1 CCTTAAA 722 CCTTAAA 1 CCTTAAA * 729 CC-TGAA 1 CCTTAAA * 735 CCCTAAA 1 CCTTAAA * 742 CCCTAAA 1 CCTTAAA 749 -CTCTAAA 1 CCT-TAAA * 756 TCCTTGAA 1 -CCTTAAA 764 -CTCTAAA 1 CCT-TAAA 771 CC-TAAA 1 CCTTAAA * 777 CTTTAAA 1 CCTTAAA * 784 CC-TCAA 1 CCTTAAA 790 CAC-TAAA 1 C-CTTAAA 797 -CTTAAA 1 CCTTAAA 803 CCTTAAA 1 CCTTAAA * * 810 TCTCAAA 1 CCTTAAA 817 CCT 1 CCT 820 AAATCCTAAA Statistics Matches: 76, Mismatches: 12, Indels: 20 0.70 0.11 0.19 Matches are distributed among these distances: 5 1 0.01 6 21 0.28 7 48 0.63 8 4 0.05 9 2 0.03 ACGTcount: A:0.41, C:0.31, G:0.02, T:0.26 Consensus pattern (7 bp): CCTTAAA Found at i:741 original size:13 final size:13 Alignment explanation
Indices: 725--829 Score: 70 Period size: 13 Copynumber: 7.8 Consensus size: 13 715 CCTTAAACCT * * 725 TAAACCTGAACCC 1 TAAACCTAAACTC 738 TAAACCCTAAACTC 1 TAAA-CCTAAACTC * 752 TAAATCCTTGAACTC 1 TAAA-CC-TAAACTC * 767 TAAACCTAAACTT 1 TAAACCTAAACTC * * 780 TAAACCTCAACAC 1 TAAACCTAAACTC * 793 TAAACTTAAAC-C 1 TAAACCTAAACTC * 805 TTAAATCTCAAAC-C 1 -TAAACCT-AAACTC 819 TAAATCCTAAA 1 TAAA-CCTAAA 830 TCTCGAGGTT Statistics Matches: 73, Mismatches: 14, Indels: 10 0.75 0.14 0.10 Matches are distributed among these distances: 12 1 0.01 13 40 0.55 14 22 0.30 15 10 0.14 ACGTcount: A:0.44, C:0.30, G:0.02, T:0.25 Consensus pattern (13 bp): TAAACCTAAACTC Done.