Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017749.1 Corchorus olitorius cultivar O-4 contig17782, 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: 47400
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:26230 original size:6 final size:6

Alignment explanation


    Indices: 26219--26263  Score: 67
    Period size: 6  Copynumber: 7.8  Consensus size: 6

      26209 GATTTCCATC

                                                      *           
      26219 TCTTTT TCTTTT TCTTTT TCTTTT T-TTTT TCTTTT AC-TTT TCTTT
          1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTT

      26264 GCATTATGGA


Statistics
Matches: 35,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
   5    9  0.26
   6   26  0.74

ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82


Consensus pattern (6 bp):   
TCTTTT

Found at i:26234 original size:12 final size:12

Alignment explanation


    Indices: 26219--26263  Score: 67
    Period size: 11  Copynumber: 3.9  Consensus size: 12

      26209 GATTTCCATC

                        
      26219 TCTTTTTCTTTT
          1 TCTTTTTCTTTT

                        
      26231 TCTTTTTCTTTT
          1 TCTTTTTCTTTT

                        
      26243 T-TTTTTCTTTT
          1 TCTTTTTCTTTT

            *          
      26254 AC-TTTTCTTT
          1 TCTTTTTCTTT

      26264 GCATTATGGA


Statistics
Matches: 31,  Mismatches: 1, Indels: 3
        0.89            0.03        0.09

Matches are distributed among these distances:
  11   18  0.58
  12   13  0.42

ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82


Consensus pattern (12 bp):   
TCTTTTTCTTTT

Found at i:37938 original size:10 final size:11

Alignment explanation


    Indices: 37910--37948  Score: 53
    Period size: 11  Copynumber: 3.5  Consensus size: 11

      37900 ACTTCTTCCT

                        
      37910 TAAAAAAAACAA
          1 TAAAAAAAA-AA

                        
      37922 -AACAAAAAAAA
          1 TAA-AAAAAAAA

                       
      37933 TAAAAAAAAAA
          1 TAAAAAAAAAA

                 
      37944 TAAAA
          1 TAAAA

      37949 GATATTGGAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 5
        0.83            0.00        0.17

Matches are distributed among these distances:
  11   17  0.68
  12    8  0.32

ACGTcount: A:0.87, C:0.05, G:0.00, T:0.08


Consensus pattern (11 bp):   
TAAAAAAAAAA

Found at i:38398 original size:24 final size:26

Alignment explanation


    Indices: 38351--38398  Score: 64
    Period size: 24  Copynumber: 1.9  Consensus size: 26

      38341 AGTGTCGCGG

                           *   *      
      38351 TATATTTCACAATTTCTATTTTGATT
          1 TATATTTCACAATTTATATATTGATT

                                    
      38377 TATATTT-AC-ATTTATATATTGA
          1 TATATTTCACAATTTATATATTGA

      38399 ATAATTACAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  24   11  0.55
  25    2  0.10
  26    7  0.35

ACGTcount: A:0.31, C:0.08, G:0.04, T:0.56


Consensus pattern (26 bp):   
TATATTTCACAATTTATATATTGATT
Done.