Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008483.1 Corchorus capsularis cultivar CVL-1 contig08504, 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: 43206
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32


Found at i:2851 original size:17 final size:17

Alignment explanation


    Indices: 2829--2861  Score: 66
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       2819 AGAAAACTTC

                             
       2829 TAAATATTTATTAACAG
          1 TAAATATTTATTAACAG

                            
       2846 TAAATATTTATTAACA
          1 TAAATATTTATTAACA

       2862 TCAGAAAGTC


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42


Consensus pattern (17 bp):   
TAAATATTTATTAACAG

Found at i:16357 original size:2 final size:2

Alignment explanation


    Indices: 16350--16384  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

      16340 CAGCACCAAA

                                                                
      16350 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      16385 ATAACACAGC


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:37134 original size:3 final size:3

Alignment explanation


    Indices: 37126--37165  Score: 80
    Period size: 3  Copynumber: 13.3  Consensus size: 3

      37116 TTATGTTATG

                                                                 
      37126 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T

      37166 TAATTAAACG


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   37  1.00

ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35


Consensus pattern (3 bp):   
TAA

Found at i:41703 original size:6 final size:6

Alignment explanation


    Indices: 41692--41724  Score: 66
    Period size: 6  Copynumber: 5.5  Consensus size: 6

      41682 CACGGCTGCA

                                                  
      41692 GGCTGT GGCTGT GGCTGT GGCTGT GGCTGT GGC
          1 GGCTGT GGCTGT GGCTGT GGCTGT GGCTGT GGC

      41725 GAGTAAGGAG


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   27  1.00

ACGTcount: A:0.00, C:0.18, G:0.52, T:0.30


Consensus pattern (6 bp):   
GGCTGT

Found at i:41775 original size:12 final size:12

Alignment explanation


    Indices: 41758--41783  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

      41748 TGCATGGCCT

                        
      41758 TGAGGCTGGGGC
          1 TGAGGCTGGGGC

                        
      41770 TGAGGCTGGGGC
          1 TGAGGCTGGGGC

              
      41782 TG
          1 TG

      41784 GACAGGAGGA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.08, C:0.15, G:0.58, T:0.19


Consensus pattern (12 bp):   
TGAGGCTGGGGC
Done.