Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012100.1 Corchorus capsularis cultivar CVL-1 contig12121, 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: 10551
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32


Found at i:6423 original size:12 final size:13

Alignment explanation


    Indices: 6382--6426  Score: 65
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       6372 AATTATTGTT

                     *   
       6382 TGCTTTATTGATC
          1 TGCTTTATTAATC

                        *
       6395 TGCTTTATTAATT
          1 TGCTTTATTAATC

                         
       6408 TGCTTTA-TAATC
          1 TGCTTTATTAATC

                   
       6420 TGCTTTA
          1 TGCTTTA

       6427 GATTTAGATT


Statistics
Matches: 29,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  12   11  0.38
  13   18  0.62

ACGTcount: A:0.20, C:0.13, G:0.11, T:0.56


Consensus pattern (13 bp):   
TGCTTTATTAATC

Found at i:6434 original size:6 final size:6

Alignment explanation


    Indices: 6423--6449  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

       6413 TATAATCTGC

                                           
       6423 TTTAGA TTTAGA TTTAGA TTTAGA TTT
          1 TTTAGA TTTAGA TTTAGA TTTAGA TTT

       6450 GCTTTGCTTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56


Consensus pattern (6 bp):   
TTTAGA

Found at i:9906 original size:14 final size:15

Alignment explanation


    Indices: 9887--9921  Score: 54
    Period size: 15  Copynumber: 2.4  Consensus size: 15

       9877 GATGAAAAAG

                       *   
       9887 AAAAAGA-AAAGGAA
          1 AAAAAGAGAAACGAA

                           
       9901 AAAAAGAGAAACGAA
          1 AAAAAGAGAAACGAA

                  
       9916 AAAAAG
          1 AAAAAG

       9922 CAACGATGGT


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  14    7  0.37
  15   12  0.63

ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00


Consensus pattern (15 bp):   
AAAAAGAGAAACGAA

Done.