Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013104.1 Corchorus capsularis cultivar CVL-1 contig13125, 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: 2120
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.34


Found at i:1545 original size:33 final size:33

Alignment explanation


    Indices: 1457--1552  Score: 129
    Period size: 33  Copynumber: 2.9  Consensus size: 33

       1447 GTGTTTTAGA

                                  *   *   *  
       1457 TGTTGTTTGCGATGATACTAAACCTAATTTGAG
          1 TGTTGTTTGCGATGATACTAAATCTATTTTAAG

                      *    *                 
       1490 TGTTGTTTGCAATGACACTAAATCTATTTTAAG
          1 TGTTGTTTGCGATGATACTAAATCTATTTTAAG

                     *               *    
       1523 TGTTGTTTGTGATGATACTAAATCTGTTTT
          1 TGTTGTTTGCGATGATACTAAATCTATTTT

       1553 GGATGCTAAT


Statistics
Matches: 54,  Mismatches: 9, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  33   54  1.00

ACGTcount: A:0.26, C:0.10, G:0.19, T:0.45


Consensus pattern (33 bp):   
TGTTGTTTGCGATGATACTAAATCTATTTTAAG

Found at i:1615 original size:33 final size:33

Alignment explanation


    Indices: 1578--1716  Score: 194
    Period size: 33  Copynumber: 4.3  Consensus size: 33

       1568 TGAAAACAAA

                 *                           
       1578 TCTGTCTTGGTTGATCATAGCATTGCAAATAAT
          1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT

                    *                        
       1611 TCTGTTTTAGTTGATCATAGCATTGCAAATAAT
          1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT

             *                               
       1644 TTTGTTTTGGTTGATCATAGCATTGCAAATAAT
          1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT

            *                 *      *      *
       1677 CCTGTTTTGGTTG---ATGGCATTGAAAATAAA
          1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT

                      
       1707 TCTGTTTTGG
          1 TCTGTTTTGG

       1717 GTGAAAAGAA


Statistics
Matches: 96,  Mismatches: 10, Indels: 3
        0.88            0.09        0.03

Matches are distributed among these distances:
  30   23  0.24
  33   73  0.76

ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42


Consensus pattern (33 bp):   
TCTGTTTTGGTTGATCATAGCATTGCAAATAAT

Found at i:2095 original size:30 final size:30

Alignment explanation


    Indices: 2059--2117  Score: 102
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       2049 CAAGGGGGAG

                                           
       2059 GGAATGATGCGCCCAAGG-CTTATCATGGAA
          1 GGAATGATGCG-CCAAGGACTTATCATGGAA

                                         
       2089 GGAATGATGCGCCAAGGACTTATCATGGA
          1 GGAATGATGCGCCAAGGACTTATCATGGA

       2118 CTT


Statistics
Matches: 28,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  29    6  0.21
  30   22  0.79

ACGTcount: A:0.31, C:0.19, G:0.31, T:0.20


Consensus pattern (30 bp):   
GGAATGATGCGCCAAGGACTTATCATGGAA
Done.