Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005980.1 Corchorus olitorius cultivar O-4 contig06005, 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, 742

Length: 1237
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30


Found at i:387 original size:17 final size:17

Alignment explanation


    Indices: 365--418  Score: 58
    Period size: 17  Copynumber: 3.3  Consensus size: 17

        355 CGGGCCTGGC

                             
        365 GCGCGCTGGGCCAGCTA
          1 GCGCGCTGGGCCAGCTA

                   **   * *  
        382 GCGCGC-AAGCCTGGT-
          1 GCGCGCTGGGCCAGCTA

                             
        397 GCGCGCTGGGCCAGCTA
          1 GCGCGCTGGGCCAGCTA

                 
        414 GCGCG
          1 GCGCG

        419 GGCCTGAGCA


Statistics
Matches: 27,  Mismatches: 8, Indels: 4
        0.69            0.21        0.10

Matches are distributed among these distances:
  15    6  0.22
  16   10  0.37
  17   11  0.41

ACGTcount: A:0.11, C:0.35, G:0.43, T:0.11


Consensus pattern (17 bp):   
GCGCGCTGGGCCAGCTA

Found at i:394 original size:32 final size:32

Alignment explanation


    Indices: 358--418  Score: 113
    Period size: 32  Copynumber: 1.9  Consensus size: 32

        348 AGCCTAGCGG

                                            
        358 GCCTGGCGCGCGCTGGGCCAGCTAGCGCGCAA
          1 GCCTGGCGCGCGCTGGGCCAGCTAGCGCGCAA

                  *                      
        390 GCCTGGTGCGCGCTGGGCCAGCTAGCGCG
          1 GCCTGGCGCGCGCTGGGCCAGCTAGCGCG

        419 GGCCTGAGCA


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  32   28  1.00

ACGTcount: A:0.10, C:0.36, G:0.43, T:0.11


Consensus pattern (32 bp):   
GCCTGGCGCGCGCTGGGCCAGCTAGCGCGCAA

Found at i:554 original size:2 final size:2

Alignment explanation


    Indices: 547--571  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

        537 ATGAAAAAGA

                                                 
        547 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 A

        572 ATAATAATAA


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


Consensus pattern (2 bp):   
AT

Found at i:577 original size:3 final size:3

Alignment explanation


    Indices: 569--596  Score: 56
    Period size: 3  Copynumber: 9.3  Consensus size: 3

        559 ATATATATAT

                                                 
        569 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A

        597 AAGGGAAAGG


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

Matches are distributed among these distances:
   3   25  1.00

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (3 bp):   
ATA

Done.