Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006373.1 Corchorus capsularis cultivar CVL-1 contig06394, 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: 14241
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:612 original size:20 final size:20

Alignment explanation


    Indices: 571--612  Score: 57
    Period size: 20  Copynumber: 2.1  Consensus size: 20

        561 TTTAGAATAA

                       *     *  
        571 TAAATAATAATTATAAATAT
          1 TAAATAATAATAATAAACAT

                           *    
        591 TAAATAATAATAATATACAT
          1 TAAATAATAATAATAAACAT

              
        611 TA
          1 TA

        613 TCCTCTGTTT


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38


Consensus pattern (20 bp):   
TAAATAATAATAATAAACAT

Found at i:1601 original size:21 final size:20

Alignment explanation


    Indices: 1560--1611  Score: 70
    Period size: 21  Copynumber: 2.6  Consensus size: 20

       1550 AAGATCAACA

                                
       1560 TTTGGTGTAAT-GATACTTT
          1 TTTGGTGTAATGGATACTTT

                            *    
       1579 TTTGGTGTAATGGCATCCTTT
          1 TTTGGTGTAATGG-ATACTTT

              *         
       1600 TTAGGTGTAATG
          1 TTTGGTGTAATG

       1612 AAAAATCTCA


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  19   11  0.38
  20    1  0.03
  21   17  0.59

ACGTcount: A:0.19, C:0.08, G:0.25, T:0.48


Consensus pattern (20 bp):   
TTTGGTGTAATGGATACTTT

Found at i:3642 original size:23 final size:23

Alignment explanation


    Indices: 3616--3675  Score: 77
    Period size: 23  Copynumber: 2.6  Consensus size: 23

       3606 ACCTCATTTT

                        *          
       3616 CTTTTTCTTCTTTAGTAAAGCCC
          1 CTTTTTCTTCTTCAGTAAAGCCC

                *        *         
       3639 CTTTATCTTCTTCGGTAAAGCCC
          1 CTTTTTCTTCTTCAGTAAAGCCC

                           
       3662 CTTTATT-TTCTTCA
          1 CTTT-TTCTTCTTCA

       3676 TCACTTTCTT


Statistics
Matches: 31,  Mismatches: 5, Indels: 2
        0.82            0.13        0.05

Matches are distributed among these distances:
  23   30  0.97
  24    1  0.03

ACGTcount: A:0.17, C:0.27, G:0.08, T:0.48


Consensus pattern (23 bp):   
CTTTTTCTTCTTCAGTAAAGCCC

Found at i:12950 original size:20 final size:20

Alignment explanation


    Indices: 12913--12951  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      12903 TGACTCGAGA

                       *        
      12913 AAAATTCGAGTTCGGCTCGG
          1 AAAATTCGAGTCCGGCTCGG

                                
      12933 AAAATTCGAG-CCGAGCTCG
          1 AAAATTCGAGTCCG-GCTCG

      12952 AGCTCGAGCT


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  19    2  0.12
  20   15  0.88

ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21


Consensus pattern (20 bp):   
AAAATTCGAGTCCGGCTCGG

Found at i:14066 original size:23 final size:22

Alignment explanation


    Indices: 14020--14066  Score: 60
    Period size: 22  Copynumber: 2.1  Consensus size: 22

      14010 AGGAGAAGTT

                  *               
      14020 GAAAGGGAGAGAAGAGAAAGGA
          1 GAAAGGAAGAGAAGAGAAAGGA

                                    
      14042 GAAAGGAAGGAGAAGA-AAAGAGA
          1 GAAAGGAA-GAGAAGAGAAAG-GA

              
      14065 GA
          1 GA

      14067 TGGAAGTGGG


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  22   11  0.50
  23   11  0.50

ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00


Consensus pattern (22 bp):   
GAAAGGAAGAGAAGAGAAAGGA
Done.