Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001136.1 Corchorus capsularis cultivar CVL-1 contig01136, 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: 2242
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29


Found at i:1885 original size:29 final size:29

Alignment explanation


    Indices: 1843--1923  Score: 101
    Period size: 29  Copynumber: 2.8  Consensus size: 29

       1833 TGGTTCCGAT

                                *  **    
       1843 TTTGTGGAGAAGGCGAAGCATAGTCGGTG
          1 TTTGTGGAGAAGGCGAAGCAGAGAAGGTG

                             *   *       
       1872 TTTGTGGAGAAGGCGAAACAGCGAAGGTG
          1 TTTGTGGAGAAGGCGAAGCAGAGAAGGTG

                                    
       1901 TTTGTGGA-ACAGGCGAAGCAGAG
          1 TTTGTGGAGA-AGGCGAAGCAGAG

       1924 GCGGCGCTTG


Statistics
Matches: 44,  Mismatches: 7, Indels: 2
        0.83            0.13        0.04

Matches are distributed among these distances:
  28    1  0.02
  29   43  0.98

ACGTcount: A:0.28, C:0.11, G:0.41, T:0.20


Consensus pattern (29 bp):   
TTTGTGGAGAAGGCGAAGCAGAGAAGGTG

Found at i:2022 original size:15 final size:13

Alignment explanation


    Indices: 2001--2041  Score: 55
    Period size: 13  Copynumber: 3.0  Consensus size: 13

       1991 AGAAATTAGG

                          
       2001 AAAAGAAAAAAGAA
          1 AAAAGAAAAAA-AA

                          
       2015 AGAAAGAAAAAAAA
          1 A-AAAGAAAAAAAA

              *          
       2029 AACAGAAAAAAAA
          1 AAAAGAAAAAAAA

       2042 GCTTTAGATG


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  13   11  0.44
  14    4  0.16
  15   10  0.40

ACGTcount: A:0.85, C:0.02, G:0.12, T:0.00


Consensus pattern (13 bp):   
AAAAGAAAAAAAA
Done.