Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010201.1 Corchorus capsularis cultivar CVL-1 contig10222, 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: 13428
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:225 original size:1 final size:1

Alignment explanation


    Indices: 219--257  Score: 60
    Period size: 1  Copynumber: 39.0  Consensus size: 1

        209 TTGTTTCCGC

                           **                      
        219 TTTTTTTTTTTTTTTAATTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

        258 AATTTTAGAA


Statistics
Matches: 36,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   1   36  1.00

ACGTcount: A:0.05, C:0.00, G:0.00, T:0.95


Consensus pattern (1 bp):   
T

Found at i:241 original size:12 final size:12

Alignment explanation


    Indices: 224--263  Score: 62
    Period size: 12  Copynumber: 3.3  Consensus size: 12

        214 TCCGCTTTTT

                        
        224 TTTTTTTTTTAA
          1 TTTTTTTTTTAA

                      **
        236 TTTTTTTTTTTT
          1 TTTTTTTTTTAA

                        
        248 TTTTTTTTTTAA
          1 TTTTTTTTTTAA

                
        260 TTTT
          1 TTTT

        264 AGAAGAGGCT


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  12   24  1.00

ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90


Consensus pattern (12 bp):   
TTTTTTTTTTAA

Found at i:241 original size:13 final size:13

Alignment explanation


    Indices: 223--263  Score: 68
    Period size: 13  Copynumber: 3.3  Consensus size: 13

        213 TTCCGCTTTT

                         
        223 TTTTTTTTTTTAA
          1 TTTTTTTTTTTAA

                         
        236 TTTTTTTTTTT--
          1 TTTTTTTTTTTAA

                         
        247 TTTTTTTTTTTAA
          1 TTTTTTTTTTTAA

                
        260 TTTT
          1 TTTT

        264 AGAAGAGGCT


Statistics
Matches: 26,  Mismatches: 0, Indels: 4
        0.87            0.00        0.13

Matches are distributed among these distances:
  11   11  0.42
  13   15  0.58

ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90


Consensus pattern (13 bp):   
TTTTTTTTTTTAA

Found at i:1757 original size:14 final size:14

Alignment explanation


    Indices: 1738--1766  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       1728 TTCCCCTTGA

                          
       1738 ACATTTATTAGCAT
          1 ACATTTATTAGCAT

                          
       1752 ACATTTATTAGCAT
          1 ACATTTATTAGCAT

             
       1766 A
          1 A

       1767 TTTGTTAAGA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41


Consensus pattern (14 bp):   
ACATTTATTAGCAT
Done.