Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008923.1 Corchorus capsularis cultivar CVL-1 contig08944, 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: 6227
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30


Found at i:3787 original size:16 final size:16

Alignment explanation


    Indices: 3758--3808  Score: 68
    Period size: 16  Copynumber: 3.2  Consensus size: 16

       3748 TAATAAATTT

                *           
       3758 ATAACAAAAATAAATA
          1 ATAATAAAAATAAATA

               *     *      
       3774 ATACTAAAAGTAAATA
          1 ATAATAAAAATAAATA

                            
       3790 ATAATAAAAAT-AATA
          1 ATAATAAAAATAAATA

                
       3805 ATAA
          1 ATAA

       3809 CCTAAATCTA


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

Matches are distributed among these distances:
  15    8  0.27
  16   22  0.73

ACGTcount: A:0.71, C:0.04, G:0.02, T:0.24


Consensus pattern (16 bp):   
ATAATAAAAATAAATA

Found at i:5516 original size:19 final size:19

Alignment explanation


    Indices: 5479--5527  Score: 59
    Period size: 19  Copynumber: 2.7  Consensus size: 19

       5469 AGAATAACAA

                        *      
       5479 AAATAATTAA-TAAATATT
          1 AAATAATTAATTTAATATT

                                
       5497 ATAATAATTAATTTAA-ATT
          1 A-AATAATTAATTTAATATT

                         
       5516 AAATAA-TAATTT
          1 AAATAATTAATTT

       5528 TTTTTTAAAA


Statistics
Matches: 28,  Mismatches: 1, Indels: 5
        0.82            0.03        0.15

Matches are distributed among these distances:
  17    6  0.21
  18    6  0.21
  19   13  0.46
  20    3  0.11

ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43


Consensus pattern (19 bp):   
AAATAATTAATTTAATATT

Found at i:5597 original size:33 final size:33

Alignment explanation


    Indices: 5559--5633  Score: 87
    Period size: 33  Copynumber: 2.3  Consensus size: 33

       5549 GTCACGACCG

                     *       *               
       5559 ACCCGTGGTTAGGTCACGACCAGATCGCGACTC
          1 ACCCGTGGTGAGGTCACAACCAGATCGCGACTC

            *              **    *          *
       5592 GCCCGTGGTGAGGTCGTAACCGGATCGCGACTT
          1 ACCCGTGGTGAGGTCACAACCAGATCGCGACTC

                     
       5625 ACCCGTGGT
          1 ACCCGTGGT

       5634 CAAGTCGTGA


Statistics
Matches: 34,  Mismatches: 8, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  33   34  1.00

ACGTcount: A:0.17, C:0.31, G:0.32, T:0.20


Consensus pattern (33 bp):   
ACCCGTGGTGAGGTCACAACCAGATCGCGACTC
Done.