Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013374.1 Corchorus capsularis cultivar CVL-1 contig13395, 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: 7963
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.34


Found at i:195 original size:2 final size:2

Alignment explanation


    Indices: 190--234  Score: 90
    Period size: 2  Copynumber: 22.5  Consensus size: 2

        180 CATATATATA

                                                                          
        190 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
          1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG

                
        232 TG T
          1 TG T

        235 ATAGCCCCAC


Statistics
Matches: 43,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   43  1.00

ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51


Consensus pattern (2 bp):   
TG

Found at i:3806 original size:2 final size:2

Alignment explanation


    Indices: 3799--3824  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       3789 GTCATGCCAC

                                                  
       3799 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

       3825 TTTCCAACTT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:4019 original size:26 final size:28

Alignment explanation


    Indices: 3971--4029  Score: 104
    Period size: 26  Copynumber: 2.2  Consensus size: 28

       3961 CACAAAAAAC

                                        
       3971 TAATTTTATTTATATTGTAGTAGTAATT
          1 TAATTTTATTTATATTGTAGTAGTAATT

                                        
       3999 TAATTTTA-TT-TATTGTAGTAGTAATT
          1 TAATTTTATTTATATTGTAGTAGTAATT

                 
       4025 TAATT
          1 TAATT

       4030 AGCTAGTAAG


Statistics
Matches: 31,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
  26   21  0.68
  27    2  0.06
  28    8  0.26

ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58


Consensus pattern (28 bp):   
TAATTTTATTTATATTGTAGTAGTAATT
Done.