Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005947.1 Corchorus capsularis cultivar CVL-1 contig05965, 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: 3454
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.40


Found at i:453 original size:2 final size:2

Alignment explanation


    Indices: 446--478  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

        436 TAATGATGTG

                                                             
        446 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

        479 TCAATGGTTA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:1378 original size:37 final size:37

Alignment explanation


    Indices: 1337--1410  Score: 148
    Period size: 37  Copynumber: 2.0  Consensus size: 37

       1327 GAAATGGTCA

                                                 
       1337 AAAATGCTATAATTTTATCAATAGTCTCAATATTTTG
          1 AAAATGCTATAATTTTATCAATAGTCTCAATATTTTG

                                                 
       1374 AAAATGCTATAATTTTATCAATAGTCTCAATATTTTG
          1 AAAATGCTATAATTTTATCAATAGTCTCAATATTTTG

       1411 CGAAAAACAA


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

Matches are distributed among these distances:
  37   37  1.00

ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43


Consensus pattern (37 bp):   
AAAATGCTATAATTTTATCAATAGTCTCAATATTTTG

Found at i:1649 original size:22 final size:22

Alignment explanation


    Indices: 1623--1664  Score: 75
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       1613 AAGAAAGTTA

                                  
       1623 TACCAATCTTCTTATTCAAGGT
          1 TACCAATCTTCTTATTCAAGGT

                 *              
       1645 TACCATTCTTCTTATTCAAG
          1 TACCAATCTTCTTATTCAAG

       1665 TTTAAAAAAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.26, C:0.24, G:0.07, T:0.43


Consensus pattern (22 bp):   
TACCAATCTTCTTATTCAAGGT
Done.