Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005245.1 Corchorus capsularis cultivar CVL-1 contig05263, whole genome shotgun sequence

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: 14141
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29


Found at i:191 original size:17 final size:18

Alignment explanation


    Indices: 169--207  Score: 53
    Period size: 17  Copynumber: 2.2  Consensus size: 18

        159 TAATTAAATG

                    *    *    
        169 AAAATAAAGTT-TTTATT
          1 AAAATAAAATTGTATATT

                              
        186 AAAATAAAATTGTATATT
          1 AAAATAAAATTGTATATT

                
        204 AAAA
          1 AAAA

        208 ATTTTAATAT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  17   10  0.53
  18    9  0.47

ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38


Consensus pattern (18 bp):   
AAAATAAAATTGTATATT

Found at i:11180 original size:24 final size:24

Alignment explanation


    Indices: 11149--11196  Score: 87
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      11139 TCACCACTGT

                          *         
      11149 GGGGGTGATGTTAGGTTTGCTCTA
          1 GGGGGTGATGTTAGATTTGCTCTA

                                    
      11173 GGGGGTGATGTTAGATTTGCTCTA
          1 GGGGGTGATGTTAGATTTGCTCTA

      11197 TGGTCGATGA


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   23  1.00

ACGTcount: A:0.15, C:0.08, G:0.40, T:0.38


Consensus pattern (24 bp):   
GGGGGTGATGTTAGATTTGCTCTA

Found at i:13596 original size:2 final size:2

Alignment explanation


    Indices: 13589--13632  Score: 88
    Period size: 2  Copynumber: 22.0  Consensus size: 2

      13579 GTCCGTCAGA

                                                                          
      13589 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

              
      13631 AG
          1 AG

      13633 CTGTTTGCTT


Statistics
Matches: 42,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   42  1.00

ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00


Consensus pattern (2 bp):   
AG

Found at i:13673 original size:3 final size:3

Alignment explanation


    Indices: 13665--13691  Score: 54
    Period size: 3  Copynumber: 9.0  Consensus size: 3

      13655 GATCATTGAT

                                               
      13665 TGA TGA TGA TGA TGA TGA TGA TGA TGA
          1 TGA TGA TGA TGA TGA TGA TGA TGA TGA

      13692 GGAAGGTGAG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   24  1.00

ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33


Consensus pattern (3 bp):   
TGA

Done.