Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009051.1 Corchorus capsularis cultivar CVL-1 contig09072, 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: 6251
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33


Found at i:563 original size:16 final size:16

Alignment explanation


    Indices: 544--584  Score: 66
    Period size: 15  Copynumber: 2.6  Consensus size: 16

        534 AAATTTTCAA

                          * 
        544 TTTCAAAAATAAATTT
          1 TTTCAAAAATAAATCT

                            
        560 TTTCAAAAA-AAATCT
          1 TTTCAAAAATAAATCT

                      
        575 TTTCAAAAAT
          1 TTTCAAAAAT

        585 TGGAGAAAAT


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  15   14  0.61
  16    9  0.39

ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39


Consensus pattern (16 bp):   
TTTCAAAAATAAATCT

Found at i:1556 original size:32 final size:33

Alignment explanation


    Indices: 1520--1581  Score: 92
    Period size: 34  Copynumber: 1.9  Consensus size: 33

       1510 TTTGCTTCCA

                            *                 
       1520 AAAGTCGAC-T-TCCTTGTCGACTTGCTCCTTGT
          1 AAAGTCGACTTCTCCTAGTCGACTT-CTCCTTGT

                                          
       1552 AAAGTCGACTTCTCCTAGTCGACTTCTCCT
          1 AAAGTCGACTTCTCCTAGTCGACTTCTCCT

       1582 CTAATTGGCC


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  32    9  0.33
  33    6  0.22
  34   12  0.44

ACGTcount: A:0.18, C:0.31, G:0.16, T:0.35


Consensus pattern (33 bp):   
AAAGTCGACTTCTCCTAGTCGACTTCTCCTTGT

Found at i:1573 original size:14 final size:14

Alignment explanation


    Indices: 1554--1581  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

       1544 CTCCTTGTAA

                          
       1554 AGTCGACTTCTCCT
          1 AGTCGACTTCTCCT

                          
       1568 AGTCGACTTCTCCT
          1 AGTCGACTTCTCCT

       1582 CTAATTGGCC


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

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.14, C:0.36, G:0.14, T:0.36


Consensus pattern (14 bp):   
AGTCGACTTCTCCT
Done.