Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010559.1 Corchorus capsularis cultivar CVL-1 contig10580, 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: 3764
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Found at i:285 original size:24 final size:25

Alignment explanation


    Indices: 253--301  Score: 73
    Period size: 25  Copynumber: 2.0  Consensus size: 25

        243 TTGAATGATT

                *                    
        253 GAGATTTG-AAAGTTTGAAGGTTGA
          1 GAGAATTGAAAAGTTTGAAGGTTGA

                                *    
        277 GAGAATTGAAAAGTTTGAAGTTTGA
          1 GAGAATTGAAAAGTTTGAAGGTTGA

        302 TGGAAAATAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  24    7  0.32
  25   15  0.68

ACGTcount: A:0.37, C:0.00, G:0.31, T:0.33


Consensus pattern (25 bp):   
GAGAATTGAAAAGTTTGAAGGTTGA

Found at i:857 original size:28 final size:28

Alignment explanation


    Indices: 817--872  Score: 103
    Period size: 28  Copynumber: 2.0  Consensus size: 28

        807 ACGTTTCGGT

                         *              
        817 ATCGGACATTTGGTTTGATGATATAGAC
          1 ATCGGACATTTGGCTTGATGATATAGAC

                                        
        845 ATCGGACATTTGGCTTGATGATATAGAC
          1 ATCGGACATTTGGCTTGATGATATAGAC

        873 TTGCTTTGAC


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  28   27  1.00

ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34


Consensus pattern (28 bp):   
ATCGGACATTTGGCTTGATGATATAGAC

Found at i:2718 original size:22 final size:21

Alignment explanation


    Indices: 2693--2740  Score: 60
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       2683 CCATACCGAC

                   *      *       
       2693 AACCGACTCGCTAACCCGAATA
          1 AACCGACAC-CTAAACCGAATA

                     *           
       2715 AACCGACACTTAAACCGAATA
          1 AACCGACACCTAAACCGAATA

                 
       2736 AACCG
          1 AACCG

       2741 CGAAACCGAT


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  21   15  0.65
  22    8  0.35

ACGTcount: A:0.42, C:0.33, G:0.12, T:0.12


Consensus pattern (21 bp):   
AACCGACACCTAAACCGAATA
Done.