Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016449.1 Corchorus capsularis cultivar CVL-1 contig16470, 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: 13007
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35


Found at i:851 original size:12 final size:12

Alignment explanation


    Indices: 834--866  Score: 57
    Period size: 12  Copynumber: 2.8  Consensus size: 12

        824 CCAAAATCCA

                  *     
        834 TAAAACTAAGCC
          1 TAAAACCAAGCC

                        
        846 TAAAACCAAGCC
          1 TAAAACCAAGCC

                     
        858 TAAAACCAA
          1 TAAAACCAA

        867 ATGTTAGAAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  12   20  1.00

ACGTcount: A:0.55, C:0.27, G:0.06, T:0.12


Consensus pattern (12 bp):   
TAAAACCAAGCC

Found at i:7453 original size:13 final size:13

Alignment explanation


    Indices: 7435--7460  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       7425 CCCATTGCTT

                         
       7435 GGTTGACAAGAAG
          1 GGTTGACAAGAAG

                         
       7448 GGTTGACAAGAAG
          1 GGTTGACAAGAAG

       7461 ATTTACTGAA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.38, C:0.08, G:0.38, T:0.15


Consensus pattern (13 bp):   
GGTTGACAAGAAG

Found at i:7582 original size:12 final size:12

Alignment explanation


    Indices: 7565--7589  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       7555 AGATGTAGTC

                        
       7565 TAAGGTTAGATT
          1 TAAGGTTAGATT

                        
       7577 TAAGGTTAGATT
          1 TAAGGTTAGATT

             
       7589 T
          1 T

       7590 GGGTGGAGGC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44


Consensus pattern (12 bp):   
TAAGGTTAGATT

Found at i:9413 original size:2 final size:2

Alignment explanation


    Indices: 9402--9455  Score: 58
    Period size: 2  Copynumber: 28.0  Consensus size: 2

       9392 TAATGACCAC

                                              *        *        *        *
       9402 TA TA -A TA TA TA TA TA TA TA TA TC TA TA TC TA TA TC TA TA TC
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                                
       9443 TA TA TA T- TA TA TA
          1 TA TA TA TA TA TA TA

       9456 AGTCTAAACT


Statistics
Matches: 42,  Mismatches: 8, Indels: 4
        0.78            0.15        0.07

Matches are distributed among these distances:
   1    2  0.05
   2   40  0.95

ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:9845 original size:18 final size:19

Alignment explanation


    Indices: 9796--9845  Score: 52
    Period size: 21  Copynumber: 2.6  Consensus size: 19

       9786 TCAAACTTTT

                               
       9796 ATTATTATTA-TAATAATA
          1 ATTATTATTAGTAATAATA

                                  
       9814 ATTA-TATTAGTAGTAGTAA-A
          1 ATTATTATTAGTA--A-TAATA

                        
       9834 ATTATTATTAGT
          1 ATTATTATTAGT

       9846 TATACTTTCA


Statistics
Matches: 27,  Mismatches: 0, Indels: 7
        0.79            0.00        0.21

Matches are distributed among these distances:
  17    5  0.19
  18    6  0.22
  20    6  0.22
  21   10  0.37

ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48


Consensus pattern (19 bp):   
ATTATTATTAGTAATAATA
Done.