Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001626.1 Corchorus capsularis cultivar CVL-1 contig01626, 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: 5145
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.35


Found at i:2352 original size:2 final size:2

Alignment explanation


    Indices: 2345--2382  Score: 69
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       2335 GTGAGCCATT

                                                                      
       2345 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       2383 GATGGACTAT


Statistics
Matches: 35,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   34  0.97

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
TA

Found at i:3694 original size:57 final size:58

Alignment explanation


    Indices: 3601--3721  Score: 181
    Period size: 57  Copynumber: 2.1  Consensus size: 58

       3591 ATCCCAATGG

                             *      *      *           *              
       3601 AAACATGTACAATACTATAAATATTGCATCATATCTTTGCTTTGAAAAAAATGTA-AA
          1 AAACATGTACAATACTACAAATATCGCATCACATCTTTGCTTTAAAAAAAATGTAGAA

                       *                                              
       3658 AAACATGTACACTACTACAAATATCGCATCACATCTTTGCTTTAAAAAAAATGTAGAA
          1 AAACATGTACAATACTACAAATATCGCATCACATCTTTGCTTTAAAAAAAATGTAGAA

                  
       3716 AGAACA
          1 A-AACA

       3722 AAATATACTG


Statistics
Matches: 57,  Mismatches: 5, Indels: 2
        0.89            0.08        0.03

Matches are distributed among these distances:
  57   50  0.88
  58    3  0.05
  59    4  0.07

ACGTcount: A:0.46, C:0.16, G:0.09, T:0.29


Consensus pattern (58 bp):   
AAACATGTACAATACTACAAATATCGCATCACATCTTTGCTTTAAAAAAAATGTAGAA

Found at i:4519 original size:33 final size:33

Alignment explanation


    Indices: 4482--4544  Score: 90
    Period size: 33  Copynumber: 1.9  Consensus size: 33

       4472 TTATCTTAAA

                      *       *              
       4482 ACCACCATAAGAAACCGGGTCATTTGCTTTGCG
          1 ACCACCATAACAAACCGGATCATTTGCTTTGCG

                    *            *        
       4515 ACCACCATGACAAACCGGATCTTTTGCTTT
          1 ACCACCATAACAAACCGGATCATTTGCTTT

       4545 TGCAAGAAGT


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

Matches are distributed among these distances:
  33   26  1.00

ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27


Consensus pattern (33 bp):   
ACCACCATAACAAACCGGATCATTTGCTTTGCG

Found at i:5017 original size:2 final size:2

Alignment explanation


    Indices: 5010--5036  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       5000 GAATACATAC

                                                    
       5010 AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A

       5037 ATTATAAGTC


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.