Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013160.1 Corchorus capsularis cultivar CVL-1 contig13181, 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: 11946
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30


Found at i:2457 original size:30 final size:30

Alignment explanation


    Indices: 2421--2478  Score: 100
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       2411 CATCTTCAAG

                                           
       2421 TCCATGATAAGTCCTT-GGCGCATCATTCCA
          1 TCCATGATAAG-CCTTGGGCGCATCATTCCA

                                        
       2451 TCCATGATAAGCCTTGGGCGCATCATTC
          1 TCCATGATAAGCCTTGGGCGCATCATTC

       2479 TCACCCTTGT


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  29    4  0.15
  30   23  0.85

ACGTcount: A:0.22, C:0.29, G:0.19, T:0.29


Consensus pattern (30 bp):   
TCCATGATAAGCCTTGGGCGCATCATTCCA

Found at i:7649 original size:21 final size:21

Alignment explanation


    Indices: 7611--7650  Score: 55
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       7601 AGAAAAAAGA

                       *         
       7611 AAAAAAAATATTTGTTTTTCT
          1 AAAAAAAATATCTGTTTTTCT

                                
       7632 AAAAAAAAT-TCTGATTTTT
          1 AAAAAAAATATCTG-TTTTT

       7651 ATTTATTTAT


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    3  0.18
  21   14  0.82

ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45


Consensus pattern (21 bp):   
AAAAAAAATATCTGTTTTTCT

Found at i:10593 original size:21 final size:21

Alignment explanation


    Indices: 10563--10604  Score: 59
    Period size: 23  Copynumber: 2.0  Consensus size: 21

      10553 ATAGTAAGAA

                                 
      10563 TAAATTAATT-ATAAAAATAT
          1 TAAATTAATTAATAAAAATAT

                                  
      10583 TAAATTTAATTGAATAAAAATA
          1 TAAA-TTAATT-AATAAAAATA

      10605 GAGTTTTTAG


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  20    4  0.21
  21    6  0.32
  23    9  0.47

ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38


Consensus pattern (21 bp):   
TAAATTAATTAATAAAAATAT
Done.