Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000731.1 Corchorus capsularis cultivar CVL-1 contig00731, 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: 6466
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35


Found at i:1446 original size:26 final size:26

Alignment explanation


    Indices: 1417--1484  Score: 93
    Period size: 26  Copynumber: 2.6  Consensus size: 26

       1407 TACTTAGTTT

                                      
       1417 ATTAGTTTATGTTTAATTAGTATCTA
          1 ATTAGTTTATGTTTAATTAGTATCTA

                            *       *  
       1443 ATTAGTTTAT-TATTAGTTAGTATTTA
          1 ATTAGTTTATGT-TTAATTAGTATCTA

                       *    
       1469 ATTAGTTTATGATTAA
          1 ATTAGTTTATGTTTAA

       1485 AATGAAGGAA


Statistics
Matches: 36,  Mismatches: 4, Indels: 4
        0.82            0.09        0.09

Matches are distributed among these distances:
  25    1  0.03
  26   35  0.97

ACGTcount: A:0.32, C:0.01, G:0.12, T:0.54


Consensus pattern (26 bp):   
ATTAGTTTATGTTTAATTAGTATCTA

Found at i:1484 original size:15 final size:13

Alignment explanation


    Indices: 1417--1478  Score: 51
    Period size: 11  Copynumber: 4.8  Consensus size: 13

       1407 TACTTAGTTT

                           
       1417 ATTAGTTTATGTTTA
          1 ATTAGTTTA--TTTA

                      *  
       1432 ATTAG--TATCTA
          1 ATTAGTTTATTTA

                         
       1443 ATTAGTTTA-TT-
          1 ATTAGTTTATTTA

                           
       1454 ATTAGTTAGTATTTA
          1 ATTAGTT--TATTTA

                      
       1469 ATTAGTTTAT
          1 ATTAGTTTAT

       1479 GATTAAAATG


Statistics
Matches: 39,  Mismatches: 2, Indels: 14
        0.71            0.04        0.25

Matches are distributed among these distances:
  11   15  0.38
  12    1  0.03
  13    9  0.23
  14    2  0.05
  15   12  0.31

ACGTcount: A:0.31, C:0.02, G:0.11, T:0.56


Consensus pattern (13 bp):   
ATTAGTTTATTTA

Found at i:1528 original size:24 final size:25

Alignment explanation


    Indices: 1494--1552  Score: 95
    Period size: 25  Copynumber: 2.4  Consensus size: 25

       1484 AAATGAAGGA

                             *       
       1494 AAATGAA-TTTGAAG-ATTTGTTAG
          1 AAATGAAGTTTGAAGAAGTTGTTAG

                                     
       1517 AAATGAAGTTTGAAGAAGTTGTTAG
          1 AAATGAAGTTTGAAGAAGTTGTTAG

                       
       1542 AAATGAAGTTT
          1 AAATGAAGTTT

       1553 AGGGTTTGAA


Statistics
Matches: 33,  Mismatches: 1, Indels: 2
        0.92            0.03        0.06

Matches are distributed among these distances:
  23    7  0.21
  24    7  0.21
  25   19  0.58

ACGTcount: A:0.41, C:0.00, G:0.24, T:0.36


Consensus pattern (25 bp):   
AAATGAAGTTTGAAGAAGTTGTTAG

Found at i:1648 original size:20 final size:20

Alignment explanation


    Indices: 1623--1685  Score: 108
    Period size: 20  Copynumber: 3.1  Consensus size: 20

       1613 CAAAAGTGTA

                                
       1623 AAAAGGGGGCGGTATTTAGC
          1 AAAAGGGGGCGGTATTTAGC

                                
       1643 AAAAGGGGGCGGTATTTAGC
          1 AAAAGGGGGCGGTATTTAGC

                          *      
       1663 AAAAGGGGAGCGGTGTTTAGC
          1 AAAAGGGG-GCGGTATTTAGC

              
       1684 AA
          1 AA

       1686 TCCAGTTTGG


Statistics
Matches: 41,  Mismatches: 1, Indels: 1
        0.95            0.02        0.02

Matches are distributed among these distances:
  20   28  0.68
  21   13  0.32

ACGTcount: A:0.32, C:0.10, G:0.40, T:0.19


Consensus pattern (20 bp):   
AAAAGGGGGCGGTATTTAGC
Done.