Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002830.1 Corchorus capsularis cultivar CVL-1 contig02838, 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, 887

Length: 1479
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44


Found at i:861 original size:78 final size:78

Alignment explanation


    Indices: 779--947  Score: 252
    Period size: 78  Copynumber: 2.2  Consensus size: 78

        769 TTGTTTAGGT

                                                  *                  *       
        779 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATA-TTTATAAC
          1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATA-ACCTTATAAC

                           
        842 TATTATATTTTACCA
         64 TATTATATTTTACCA

                                                           *  *              
        857 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTATTAACCTTATAACTA
          1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATAACCTTATAACTA

                      ** 
        922 TTATATTTTAATA
         66 TTATATTTTACCA

                         
        935 TTTTACTATTTTA
          1 TTTTACTATTTTA

        948 ATTAAAAAAC


Statistics
Matches: 83,  Mismatches: 6, Indels: 4
        0.89            0.06        0.04

Matches are distributed among these distances:
  77    1  0.01
  78   80  0.96
  79    2  0.02

ACGTcount: A:0.37, C:0.11, G:0.01, T:0.51


Consensus pattern (78 bp):   
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATAACCTTATAACTA
TTATATTTTACCA

Found at i:1065 original size:23 final size:23

Alignment explanation


    Indices: 1038--1081  Score: 61
    Period size: 23  Copynumber: 1.9  Consensus size: 23

       1028 AAACTTTTGC

                       *           
       1038 AATTGAAAACACTATTTTTATTT
          1 AATTGAAAACAATATTTTTATTT

                   **            
       1061 AATTGAATTCAATATTTTTAT
          1 AATTGAAAACAATATTTTTAT

       1082 AATTATTTTA


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  23   18  1.00

ACGTcount: A:0.39, C:0.07, G:0.05, T:0.50


Consensus pattern (23 bp):   
AATTGAAAACAATATTTTTATTT
Done.