Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011249.1 Corchorus capsularis cultivar CVL-1 contig11270, 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: 5423
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35


Found at i:873 original size:14 final size:14

Alignment explanation


    Indices: 842--900  Score: 59
    Period size: 14  Copynumber: 4.1  Consensus size: 14

        832 AGAGACAATC

                          
        842 TATCT-TATATCTA
          1 TATCTATATATCTA

                          
        855 TATCTATATAT-TA
          1 TATCTATATATCTA

                              
        868 TAATCTATCTATATTCTA
          1 T-ATCTA--TATA-TCTA

                   *      
        886 TATCTATCTATCTA
          1 TATCTATATATCTA

             
        900 T
          1 T

        901 CTATAAAATA


Statistics
Matches: 39,  Mismatches: 1, Indels: 11
        0.76            0.02        0.22

Matches are distributed among these distances:
  13    8  0.21
  14   15  0.38
  15    3  0.08
  16    4  0.10
  17    6  0.15
  18    3  0.08

ACGTcount: A:0.32, C:0.15, G:0.00, T:0.53


Consensus pattern (14 bp):   
TATCTATATATCTA

Found at i:878 original size:18 final size:19

Alignment explanation


    Indices: 855--906  Score: 74
    Period size: 18  Copynumber: 2.9  Consensus size: 19

        845 CTTATATCTA

                               
        855 TATCTATATAT-TATAATC
          1 TATCTATATATCTATAATC

                               
        873 TATCTATAT-TCTAT-ATC
          1 TATCTATATATCTATAATC

                   *         
        890 TATCTATCTATCTATAA
          1 TATCTATATATCTATAA

        907 AATAAAAATA


Statistics
Matches: 30,  Mismatches: 1, Indels: 5
        0.83            0.03        0.14

Matches are distributed among these distances:
  17   12  0.40
  18   17  0.57
  19    1  0.03

ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50


Consensus pattern (19 bp):   
TATCTATATATCTATAATC

Found at i:3536 original size:30 final size:31

Alignment explanation


    Indices: 3475--3549  Score: 100
    Period size: 30  Copynumber: 2.5  Consensus size: 31

       3465 AAAATGAGTT

                              *            
       3475 AGGGACCCAATTGCTCAATTAATTCCACTTC
          1 AGGGACCCAATTGCTCAACTAATTCCACTTC

                  *                         
       3506 AGGGACTCAATTGCTC-ACTAAGTT-CACTTC
          1 AGGGACCCAATTGCTCAACTAA-TTCCACTTC

                     *    
       3536 AGGGACCCATTTGC
          1 AGGGACCCAATTGC

       3550 ACATTTTAAT


Statistics
Matches: 39,  Mismatches: 4, Indels: 3
        0.85            0.09        0.07

Matches are distributed among these distances:
  30   22  0.56
  31   17  0.44

ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28


Consensus pattern (31 bp):   
AGGGACCCAATTGCTCAACTAATTCCACTTC
Done.