Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005252.1 Corchorus capsularis cultivar CVL-1 contig05270, 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: 2419
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31


Found at i:1555 original size:24 final size:25

Alignment explanation


    Indices: 1528--1576  Score: 82
    Period size: 24  Copynumber: 2.0  Consensus size: 25

       1518 TTTTAGAAAA

                                     
       1528 CGCAAATTTTTT-TCTTTTTCTTTT
          1 CGCAAATTTTTTCTCTTTTTCTTTT

                                *    
       1552 CGCAAATTTTTTCTCTTTTTTTTTT
          1 CGCAAATTTTTTCTCTTTTTCTTTT

       1577 AAATCGCAAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  24   12  0.52
  25   11  0.48

ACGTcount: A:0.12, C:0.16, G:0.04, T:0.67


Consensus pattern (25 bp):   
CGCAAATTTTTTCTCTTTTTCTTTT

Found at i:1562 original size:25 final size:24

Alignment explanation


    Indices: 1528--1576  Score: 71
    Period size: 25  Copynumber: 2.0  Consensus size: 24

       1518 TTTTAGAAAA

                       *            
       1528 CGCAAATTTTTTTCTTTTTCTTTT
          1 CGCAAATTTTTCTCTTTTTCTTTT

                                *    
       1552 CGCAAATTTTTTCTCTTTTTTTTTT
          1 CGCAAA-TTTTTCTCTTTTTCTTTT

       1577 AAATCGCAAA


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

Matches are distributed among these distances:
  24    6  0.27
  25   16  0.73

ACGTcount: A:0.12, C:0.16, G:0.04, T:0.67


Consensus pattern (24 bp):   
CGCAAATTTTTCTCTTTTTCTTTT

Found at i:1631 original size:22 final size:22

Alignment explanation


    Indices: 1590--1632  Score: 68
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       1580 TCGCAAAAAG

                          **      
       1590 CAATTTTTTTTTAGGGAAAACA
          1 CAATTTTTTTTTAGAAAAAACA

                                 
       1612 CAATTTTTTTTTAGAAAAAAC
          1 CAATTTTTTTTTAGAAAAAAC

       1633 GCAAAAACAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42


Consensus pattern (22 bp):   
CAATTTTTTTTTAGAAAAAACA

Found at i:1917 original size:21 final size:20

Alignment explanation


    Indices: 1878--1922  Score: 54
    Period size: 20  Copynumber: 2.2  Consensus size: 20

       1868 ACAGATTAAT

                  *       *     
       1878 TAAAAAGAAAGCAATTAAAC
          1 TAAAAACAAAGCAAGTAAAC

                                *
       1898 TAAAAACAAAGCAAAGTAAAT
          1 TAAAAACAAAGC-AAGTAAAC

                
       1919 TAAA
          1 TAAA

       1923 TCTAAACTAT


Statistics
Matches: 21,  Mismatches: 3, Indels: 1
        0.84            0.12        0.04

Matches are distributed among these distances:
  20   11  0.52
  21   10  0.48

ACGTcount: A:0.67, C:0.09, G:0.09, T:0.16


Consensus pattern (20 bp):   
TAAAAACAAAGCAAGTAAAC
Done.