Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010023.1 Corchorus capsularis cultivar CVL-1 contig10044, 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: 8880
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35


Found at i:618 original size:2 final size:2

Alignment explanation


    Indices: 611--648  Score: 58
    Period size: 2  Copynumber: 19.0  Consensus size: 2

        601 ATCATGTCCC

                                 *     *                            
        611 AT AT AT AT AT AT AT GT AT GT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

        649 CCATTGTTGA


Statistics
Matches: 32,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:2655 original size:2 final size:2

Alignment explanation


    Indices: 2648--2685  Score: 60
    Period size: 2  Copynumber: 19.5  Consensus size: 2

       2638 ATCCCCTTGA

                                                *                     
       2648 AT AT AT AT AT -T AT AT AT AT AT AT GT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

       2686 CTCCCTCCGT


Statistics
Matches: 33,  Mismatches: 2, Indels: 2
        0.89            0.05        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   32  0.97

ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:7776 original size:26 final size:26

Alignment explanation


    Indices: 7737--7786  Score: 68
    Period size: 26  Copynumber: 1.9  Consensus size: 26

       7727 CACCAAAATA

                                       
       7737 ATAATAATAATAAT-AATAATTTATAC
          1 ATAATAATAATAATAAAT-ATTTATAC

                                     
       7763 ATAA-AATAATTAATAAATATTTAT
          1 ATAATAATAA-TAATAAATATTTAT

       7787 TTTGATTATT


Statistics
Matches: 22,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  25    5  0.23
  26   14  0.64
  27    3  0.14

ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40


Consensus pattern (26 bp):   
ATAATAATAATAATAAATATTTATAC

Found at i:8820 original size:30 final size:29

Alignment explanation


    Indices: 8759--8821  Score: 99
    Period size: 29  Copynumber: 2.1  Consensus size: 29

       8749 CATTTGGATG

                                         
       8759 TTTTGTCCCATAAACTTCAATTTTGGACA
          1 TTTTGTCCCATAAACTTCAATTTTGGACA

                  *    *                  
       8788 TTTTGTTCCATGAACTTCAATTTTGAGACA
          1 TTTTGTCCCATAAACTTCAATTTTG-GACA

                
       8818 TTTT
          1 TTTT

       8822 ATTGACTGGC


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

Matches are distributed among these distances:
  29   23  0.74
  30    8  0.26

ACGTcount: A:0.25, C:0.17, G:0.11, T:0.46


Consensus pattern (29 bp):   
TTTTGTCCCATAAACTTCAATTTTGGACA
Done.