Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005433.1 Corchorus capsularis cultivar CVL-1 contig05451, 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: 1964
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38


Found at i:1529 original size:12 final size:13

Alignment explanation


    Indices: 1488--1532  Score: 74
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       1478 AATTATTGTT

                         
       1488 TGCTTTATTAATC
          1 TGCTTTATTAATC

                        *
       1501 TGCTTTATTAATT
          1 TGCTTTATTAATC

                         
       1514 TGCTTTA-TAATC
          1 TGCTTTATTAATC

                   
       1526 TGCTTTA
          1 TGCTTTA

       1533 GATTTAGATT


Statistics
Matches: 30,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  12   11  0.37
  13   19  0.63

ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56


Consensus pattern (13 bp):   
TGCTTTATTAATC

Found at i:1566 original size:28 final size:25

Alignment explanation


    Indices: 1526--1579  Score: 63
    Period size: 28  Copynumber: 2.0  Consensus size: 25

       1516 CTTTATAATC

                                        
       1526 TGCTTTAGATTTAGATTTAGATTTGTTT
          1 TGCTTTAGATTTAG-TTTA-A-TTGTTT

                   **                
       1554 TGCTTTATTTTTAGTTTAATTGTTT
          1 TGCTTTAGATTTAGTTTAATTGTTT

             
       1579 T
          1 T

       1580 CTTCATAATT


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  25    7  0.29
  26    1  0.04
  27    4  0.17
  28   12  0.50

ACGTcount: A:0.19, C:0.04, G:0.15, T:0.63


Consensus pattern (25 bp):   
TGCTTTAGATTTAGTTTAATTGTTT

Found at i:1598 original size:14 final size:15

Alignment explanation


    Indices: 1570--1602  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       1560 ATTTTTAGTT

                    *      
       1570 TAATTGTTTTCTTCA
          1 TAATTGTTATCTTCA

                           
       1585 TAATTGTTAT-TTCA
          1 TAATTGTTATCTTCA

                
       1599 TAAT
          1 TAAT

       1603 CCCTGTTTTC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  14    8  0.47
  15    9  0.53

ACGTcount: A:0.27, C:0.09, G:0.06, T:0.58


Consensus pattern (15 bp):   
TAATTGTTATCTTCA
Done.