Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_788 ID=scaffold_788-JGI_221_v2.0

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, 1000

Length: 4139
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.28

Warning! 422 characters in sequence are not A, C, G, or T


Found at i:2158 original size:11 final size:11

Alignment explanation

Indices: 2136--2202 Score: 53 Period size: 11 Copynumber: 5.5 Consensus size: 11 2126 ATTTTAAAAA 2136 TTAAAAAGTATT 1 TTAAAAA-TATT 2148 TTAAAAATATT 1 TTAAAAATATT * 2159 TTAAAATTAAAAATT 1 TT--AA--AAATATT ** 2174 AAAAAAAGTATT 1 TTAAAAA-TATT 2186 TTAAAAATATT 1 TTAAAAATATT 2197 TTAAAA 1 TTAAAA 2203 TTTTAAAAAA Statistics Matches: 44, Mismatches: 6, Indels: 11 0.72 0.10 0.18 Matches are distributed among these distances: 11 19 0.43 12 15 0.34 13 4 0.09 15 6 0.14 ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39 Consensus pattern (11 bp): TTAAAAATATT Found at i:2159 original size:38 final size:39 Alignment explanation

Indices: 2117--2238 Score: 171 Period size: 38 Copynumber: 3.1 Consensus size: 39 2107 CCCCATTTTT 2117 TATTTTAAAATTTTAAAAATT-AAAAAGTATTTTAAAAA 1 TATTTTAAAATTTTAAAAATTAAAAAAGTATTTTAAAAA 2155 TATTTTAAAA--TTAAAAATTAAAAAAAGTATTTTAAAAA 1 TATTTTAAAATTTTAAAAATT-AAAAAAGTATTTTAAAAA * 2193 TATTTTAAAATTTTAAAAAAAATTAAAAAAGTA-TGTAAAAA 1 TATTTTAAAATTTT---AAAAATTAAAAAAGTATTTTAAAAA 2234 TATTT 1 TATTT 2239 AAATTAAAAA Statistics Matches: 76, Mismatches: 1, Indels: 11 0.86 0.01 0.12 Matches are distributed among these distances: 36 9 0.12 38 37 0.49 40 2 0.03 41 12 0.16 42 9 0.12 43 7 0.09 ACGTcount: A:0.57, C:0.00, G:0.03, T:0.39 Consensus pattern (39 bp): TATTTTAAAATTTTAAAAATTAAAAAAGTATTTTAAAAA Found at i:2221 original size:19 final size:19 Alignment explanation

Indices: 2183--2221 Score: 51 Period size: 19 Copynumber: 2.1 Consensus size: 19 2173 TAAAAAAAGT * * * 2183 ATTTTAAAAATATTTTAAA 1 ATTTTAAAAAAAATTAAAA 2202 ATTTTAAAAAAAATTAAAA 1 ATTTTAAAAAAAATTAAAA 2221 A 1 A 2222 AGTATGTAAA Statistics Matches: 17, Mismatches: 3, Indels: 0 0.85 0.15 0.00 Matches are distributed among these distances: 19 17 1.00 ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38 Consensus pattern (19 bp): ATTTTAAAAAAAATTAAAA Done.