Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005346.1 Corchorus capsularis cultivar CVL-1 contig05364, 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: 2551
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31


Found at i:76 original size:30 final size:31

Alignment explanation


    Indices: 30--89  Score: 88
    Period size: 31  Copynumber: 2.0  Consensus size: 31

         20 TGTCTTCAAG

                                  *        
         30 TCCATGATAAGTCCTT-GGCGCTTCATTCCC
          1 TCCATGATAAGTCCTTGGGCGCATCATTCCC

                                           
         60 TCCACTGATAA-TCCTTGGGCGCATCATTCC
          1 TCCA-TGATAAGTCCTTGGGCGCATCATTCC

         90 TCCCCCTTGA


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  30    9  0.33
  31   18  0.67

ACGTcount: A:0.18, C:0.33, G:0.17, T:0.32


Consensus pattern (31 bp):   
TCCATGATAAGTCCTTGGGCGCATCATTCCC

Found at i:836 original size:15 final size:16

Alignment explanation


    Indices: 816--846  Score: 55
    Period size: 15  Copynumber: 2.0  Consensus size: 16

        806 TCTGGTCGAA

                            
        816 ATTTTTTTT-TATTTT
          1 ATTTTTTTTATATTTT

                            
        831 ATTTTTTTTATATTTT
          1 ATTTTTTTTATATTTT

        847 TCGATATAAC


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  15    9  0.60
  16    6  0.40

ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84


Consensus pattern (16 bp):   
ATTTTTTTTATATTTT

Found at i:1996 original size:30 final size:30

Alignment explanation


    Indices: 1962--2024  Score: 101
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       1952 TGTCTTCAAG

                                  *        
       1962 TCCATGATAAGTCCTT-GGCGCTTCATTCCC
          1 TCCATGATAA-TCCTTGGGCGCATCATTCCC

                                          
       1992 TCCATGATAATCCTTGGGCGCATCATTCCC
          1 TCCATGATAATCCTTGGGCGCATCATTCCC

               
       2022 TCC
          1 TCC

       2025 CCCTTGAAGA


Statistics
Matches: 31,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  29    5  0.16
  30   26  0.84

ACGTcount: A:0.17, C:0.35, G:0.16, T:0.32


Consensus pattern (30 bp):   
TCCATGATAATCCTTGGGCGCATCATTCCC
Done.