Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010193.1 Corchorus capsularis cultivar CVL-1 contig10214, 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: 7173
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28


Found at i:5708 original size:25 final size:25

Alignment explanation


    Indices: 5678--5732  Score: 73
    Period size: 21  Copynumber: 2.4  Consensus size: 25

       5668 ACAAGCGCCA

                                     
       5678 GCACCAGCCAGCCCGCGTCCCGCGC
          1 GCACCAGCCAGCCCGCGTCCCGCGC

                           *         
       5703 G---CA-CCAGCCCGTGTCCCGCGC
          1 GCACCAGCCAGCCCGCGTCCCGCGC

                     
       5724 GCACCAGCC
          1 GCACCAGCC

       5733 CGCGCTACCG


Statistics
Matches: 25,  Mismatches: 1, Indels: 8
        0.74            0.03        0.24

Matches are distributed among these distances:
  21   18  0.72
  22    2  0.08
  24    2  0.08
  25    3  0.12

ACGTcount: A:0.13, C:0.55, G:0.27, T:0.05


Consensus pattern (25 bp):   
GCACCAGCCAGCCCGCGTCCCGCGC

Found at i:5711 original size:21 final size:21

Alignment explanation


    Indices: 5685--5736  Score: 95
    Period size: 21  Copynumber: 2.5  Consensus size: 21

       5675 CCAGCACCAG

                                 
       5685 CCAGCCCGCGTCCCGCGCGCA
          1 CCAGCCCGCGTCCCGCGCGCA

                    *            
       5706 CCAGCCCGTGTCCCGCGCGCA
          1 CCAGCCCGCGTCCCGCGCGCA

                      
       5727 CCAGCCCGCG
          1 CCAGCCCGCG

       5737 CTACCGCCAG


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  21   29  1.00

ACGTcount: A:0.10, C:0.56, G:0.29, T:0.06


Consensus pattern (21 bp):   
CCAGCCCGCGTCCCGCGCGCA

Found at i:6959 original size:24 final size:27

Alignment explanation


    Indices: 6932--6984  Score: 67
    Period size: 26  Copynumber: 2.1  Consensus size: 27

       6922 TTCTAGTGAT

                                 *     
       6932 GAGAAT-AAG-GAAGGAAAA-GAGGAG
          1 GAGAATCAAGAGAAGGAAAATAAGGAG

                   *                   
       6956 GAGAATCGAGAGAAGGAAAATAAGGAG
          1 GAGAATCAAGAGAAGGAAAATAAGGAG

              
       6983 GA
          1 GA

       6985 ATTTCATCCT


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

Matches are distributed among these distances:
  24    6  0.25
  25    2  0.08
  26    9  0.38
  27    7  0.29

ACGTcount: A:0.53, C:0.02, G:0.40, T:0.06


Consensus pattern (27 bp):   
GAGAATCAAGAGAAGGAAAATAAGGAG
Done.