Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008214.1 Corchorus capsularis cultivar CVL-1 contig08235, 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: 2343
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.36


Found at i:1571 original size:22 final size:23

Alignment explanation


    Indices: 1546--1597  Score: 79
    Period size: 23  Copynumber: 2.3  Consensus size: 23

       1536 AAGGGTTAAA

                                   
       1546 AAAATTAAA-CCCTTTCAGCCCG
          1 AAAATTAAACCCCTTTCAGCCCG

                               *   
       1568 AAAATTAAACCCCTTTCAGTCCG
          1 AAAATTAAACCCCTTTCAGCCCG

                   
       1591 AGAAATT
          1 A-AAATT

       1598 CTCTTTTCTC


Statistics
Matches: 27,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  22    9  0.33
  23   13  0.48
  24    5  0.19

ACGTcount: A:0.38, C:0.27, G:0.10, T:0.25


Consensus pattern (23 bp):   
AAAATTAAACCCCTTTCAGCCCG

Found at i:1613 original size:11 final size:11

Alignment explanation


    Indices: 1597--1632  Score: 54
    Period size: 11  Copynumber: 3.3  Consensus size: 11

       1587 TCCGAGAAAT

                       
       1597 TCTCTTTTCTC
          1 TCTCTTTTCTC

                       
       1608 TCTCTTTTCTC
          1 TCTCTTTTCTC

               *  *    
       1619 TCTGTTCTCTC
          1 TCTCTTTTCTC

               
       1630 TCT
          1 TCT

       1633 TCGAACTCGA


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  11   23  1.00

ACGTcount: A:0.00, C:0.36, G:0.03, T:0.61


Consensus pattern (11 bp):   
TCTCTTTTCTC

Found at i:2061 original size:40 final size:40

Alignment explanation


    Indices: 2006--2086  Score: 153
    Period size: 40  Copynumber: 2.0  Consensus size: 40

       1996 ATGTTATATA

                                          *         
       2006 TTTCTGGGATTGAAATATGACTATATTTCTTGGTTTGAAT
          1 TTTCTGGGATTGAAATATGACTATATTTCTGGGTTTGAAT

                                                    
       2046 TTTCTGGGATTGAAATATGACTATATTTCTGGGTTTGAAT
          1 TTTCTGGGATTGAAATATGACTATATTTCTGGGTTTGAAT

             
       2086 T
          1 T

       2087 GTTATGTTAT


Statistics
Matches: 40,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  40   40  1.00

ACGTcount: A:0.25, C:0.07, G:0.21, T:0.47


Consensus pattern (40 bp):   
TTTCTGGGATTGAAATATGACTATATTTCTGGGTTTGAAT
Done.