Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006304.1 Corchorus capsularis cultivar CVL-1 contig06325, 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: 7020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35


Found at i:1932 original size:22 final size:20

Alignment explanation


    Indices: 1904--1949  Score: 62
    Period size: 20  Copynumber: 2.4  Consensus size: 20

       1894 TCCCTTGCAA

                                 
       1904 ATATATAT-TA-ATTACTA-T
          1 ATATATATATATA-TACTAGT

                                
       1922 ATATATATATATATACTAGT
          1 ATATATATATATATACTAGT

                    
       1942 ATATATAT
          1 ATATATAT

       1950 TTCCAGAATT


Statistics
Matches: 25,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
  18    8  0.32
  19    7  0.28
  20   10  0.40

ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48


Consensus pattern (20 bp):   
ATATATATATATATACTAGT

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

Alignment explanation


    Indices: 2648--2674  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       2638 GAATACATAC

                                                    
       2648 AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A

       2675 AAGGGAGAAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:6676 original size:30 final size:29

Alignment explanation


    Indices: 6614--6683  Score: 86
    Period size: 29  Copynumber: 2.4  Consensus size: 29

       6604 ACCGAACCGT

                                  ****   
       6614 CAAATAAGCCCCTGAACTATTATTTCGGC
          1 CAAATAAGCCCCTGAACTATTAAAAAGGC

                              *           
       6643 CAAATAAGCCCCTGAACTCTTAAAAAAGGC
          1 CAAATAAGCCCCTGAACTATT-AAAAAGGC

                       
       6673 CAAATAAGCCC
          1 CAAATAAGCCC

       6684 TGTTGCCAAG


Statistics
Matches: 35,  Mismatches: 5, Indels: 1
        0.85            0.12        0.02

Matches are distributed among these distances:
  29   20  0.57
  30   15  0.43

ACGTcount: A:0.39, C:0.29, G:0.13, T:0.20


Consensus pattern (29 bp):   
CAAATAAGCCCCTGAACTATTAAAAAGGC
Done.