Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013692.1 Corchorus olitorius cultivar O-4 contig13725, 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: 38583
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:138 original size:29 final size:28

Alignment explanation


    Indices: 97--152  Score: 85
    Period size: 29  Copynumber: 2.0  Consensus size: 28

         87 GTTATTCCAC

                  * *                    
         97 GTTCTTTAGCGTTCTTGAAGATTAGAAAT
          1 GTTCTTGAACGTTCTTGAA-ATTAGAAAT

                                       
        126 GTTCTTGAACGTTCTTGAAATTAGAAA
          1 GTTCTTGAACGTTCTTGAAATTAGAAA

        153 GTTTGAAGAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  28    8  0.32
  29   17  0.68

ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39


Consensus pattern (28 bp):   
GTTCTTGAACGTTCTTGAAATTAGAAAT

Found at i:781 original size:2 final size:2

Alignment explanation


    Indices: 774--799  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

        764 TCTTTCCCTC

                                                  
        774 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

        800 TTGTTAGGCG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:991 original size:12 final size:12

Alignment explanation


    Indices: 974--1000  Score: 54
    Period size: 12  Copynumber: 2.2  Consensus size: 12

        964 TTAACCGCTT

                        
        974 CTTCTTCTGTCC
          1 CTTCTTCTGTCC

                        
        986 CTTCTTCTGTCC
          1 CTTCTTCTGTCC

               
        998 CTT
          1 CTT

       1001 TGAAAAAGAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   15  1.00

ACGTcount: A:0.00, C:0.41, G:0.07, T:0.52


Consensus pattern (12 bp):   
CTTCTTCTGTCC

Found at i:27526 original size:2 final size:2

Alignment explanation


    Indices: 27519--27543  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      27509 CCCATCTTCA

                                                 
      27519 TC TC TC TC TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC TC T

      27544 ATTTTTATCT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

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


Consensus pattern (2 bp):   
TC

Found at i:38495 original size:17 final size:18

Alignment explanation


    Indices: 38473--38515  Score: 61
    Period size: 20  Copynumber: 2.3  Consensus size: 18

      38463 AGTCCAAAGA

                              
      38473 ATATATGA-TTCAAGTTC
          1 ATATATGATTTCAAGTTC

                                
      38490 ATATATGATTGTTCAAGTTC
          1 ATATATGA-T-TTCAAGTTC

                  
      38510 ATATAT
          1 ATATAT

      38516 AAGTACAAAG


Statistics
Matches: 23,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  17    8  0.35
  20   15  0.65

ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44


Consensus pattern (18 bp):   
ATATATGATTTCAAGTTC
Done.