Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008026.1 Corchorus capsularis cultivar CVL-1 contig08047, 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: 11982
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:6665 original size:10 final size:10

Alignment explanation


    Indices: 6652--6687  Score: 54
    Period size: 10  Copynumber: 3.6  Consensus size: 10

       6642 CCTTATATCG

                   *  
       6652 AAAAATATAA
          1 AAAAATAAAA

                *     
       6662 AAAATTAAAA
          1 AAAAATAAAA

                      
       6672 AAAAATAAAA
          1 AAAAATAAAA

                  
       6682 AAAAAT
          1 AAAAAT

       6688 TTCAACCAGA


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  10   23  1.00

ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17


Consensus pattern (10 bp):   
AAAAATAAAA

Found at i:11821 original size:36 final size:36

Alignment explanation


    Indices: 11781--11857  Score: 138
    Period size: 36  Copynumber: 2.1  Consensus size: 36

      11771 AGTTTTTGTT

                                                 
      11781 TTTTTCCGTTTTTTCTAAAAAAAAAAAGT-TTTTCCG
          1 TTTTTCCGTTTTTTCTAAAAAAAAAAA-TATTTTCCG

                                                
      11817 TTTTTCCGTTTTTTCTAAAAAAAAAAATATTTTCCG
          1 TTTTTCCGTTTTTTCTAAAAAAAAAAATATTTTCCG

                 
      11853 TTTTT
          1 TTTTT

      11858 AATTTTAGGG


Statistics
Matches: 40,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
  35    1  0.03
  36   39  0.98

ACGTcount: A:0.30, C:0.13, G:0.06, T:0.51


Consensus pattern (36 bp):   
TTTTTCCGTTTTTTCTAAAAAAAAAAATATTTTCCG

Found at i:11948 original size:41 final size:42

Alignment explanation


    Indices: 11875--11963  Score: 108
    Period size: 41  Copynumber: 2.1  Consensus size: 42

      11865 GGGTTTCCGA

                              *        *           *   
      11875 TTTTCTTTAAAAAAAAATTTAATTTTCCTTTTTCCGTTTTTCC
          1 TTTT-TTTAAAAAAAAATATAATTTTCATTTTTCCGTTTCTCC

                                     *       *      * 
      11918 TTTTTTTAAAAAAAAATAT-ATTTTTATTTTTCTGTTTCTGC
          1 TTTTTTTAAAAAAAAATATAATTTTCATTTTTCCGTTTCTCC

                 
      11959 TTTTT
          1 TTTTT

      11964 ATTTAAGAAC


Statistics
Matches: 40,  Mismatches: 6, Indels: 2
        0.83            0.12        0.04

Matches are distributed among these distances:
  41   22  0.55
  42   14  0.35
  43    4  0.10

ACGTcount: A:0.26, C:0.11, G:0.03, T:0.60


Consensus pattern (42 bp):   
TTTTTTTAAAAAAAAATATAATTTTCATTTTTCCGTTTCTCC
Done.