Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014369.1 Corchorus capsularis cultivar CVL-1 contig14390, 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: 16334
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34


Found at i:4337 original size:6 final size:6

Alignment explanation


    Indices: 4326--4352  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

       4316 TTTCAAGTAT

                                           
       4326 GAAAAA GAAAAA GAAAAA GAAAAA GAA
          1 GAAAAA GAAAAA GAAAAA GAAAAA GAA

       4353 GCATAATTGG


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00


Consensus pattern (6 bp):   
GAAAAA

Found at i:15881 original size:20 final size:20

Alignment explanation


    Indices: 15856--15893  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      15846 AGATAGTGAA

                                
      15856 TTACTAAATACCGCCCCCTT
          1 TTACTAAATACCGCCCCCTT

                  **          
      15876 TTACTAGCTACCGCCCCC
          1 TTACTAAATACCGCCCCC

      15894 CTTTGGACTA


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.21, C:0.45, G:0.08, T:0.26


Consensus pattern (20 bp):   
TTACTAAATACCGCCCCCTT

Found at i:15903 original size:22 final size:20

Alignment explanation


    Indices: 15864--15903  Score: 53
    Period size: 21  Copynumber: 1.9  Consensus size: 20

      15854 AATTACTAAA

                         *      
      15864 TACCGCCCCCTTTTACTAGC
          1 TACCGCCCCCTTTGACTAGC

                                
      15884 TACCGCCCCCCTTTGGACTA
          1 TACCG-CCCCCTTT-GACTA

      15904 TTTTGCCCTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    5  0.29
  21    8  0.47
  22    4  0.24

ACGTcount: A:0.15, C:0.45, G:0.12, T:0.28


Consensus pattern (20 bp):   
TACCGCCCCCTTTGACTAGC
Done.