Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011029.1 Corchorus capsularis cultivar CVL-1 contig11050, 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: 19278
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:590 original size:32 final size:32

Alignment explanation


    Indices: 554--616  Score: 101
    Period size: 32  Copynumber: 2.0  Consensus size: 32

        544 GTCAGGTTGG

                                             
        554 GTTAAATTT-AGGTCAGCTTGATTCGGGTTCGA
          1 GTTAAATTTGA-GTCAGCTTGATTCGGGTTCGA

                            *              
        586 GTTAAATTTGAGTCAGGTTGATTCGGGTTCG
          1 GTTAAATTTGAGTCAGCTTGATTCGGGTTCG

        617 GGTTGGGTTT


Statistics
Matches: 29,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  32   28  0.97
  33    1  0.03

ACGTcount: A:0.21, C:0.11, G:0.30, T:0.38


Consensus pattern (32 bp):   
GTTAAATTTGAGTCAGCTTGATTCGGGTTCGA

Found at i:828 original size:29 final size:31

Alignment explanation


    Indices: 771--834  Score: 105
    Period size: 29  Copynumber: 2.1  Consensus size: 31

        761 AACTTTATGT

                 *                         
        771 TTTCCGATTGTATCCTTATTTTTAAAACATA
          1 TTTCCAATTGTATCCTTATTTTTAAAACATA

                                           
        802 TTTCCAATTGTA-CCTT-TTTTTAAAACATA
          1 TTTCCAATTGTATCCTTATTTTTAAAACATA

                
        831 TTTC
          1 TTTC

        835 TAAATTGTCA


Statistics
Matches: 32,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  29   17  0.53
  30    4  0.12
  31   11  0.34

ACGTcount: A:0.28, C:0.17, G:0.05, T:0.50


Consensus pattern (31 bp):   
TTTCCAATTGTATCCTTATTTTTAAAACATA

Found at i:1943 original size:2 final size:2

Alignment explanation


    Indices: 1932--1966  Score: 63
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       1922 GAAAAATGAA

                                                                 
       1932 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       1967 GAACTAATAA


Statistics
Matches: 32,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   31  0.97

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
AT

Done.