Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010305.1 Corchorus capsularis cultivar CVL-1 contig10326, 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: 38342
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33


Found at i:6243 original size:57 final size:57

Alignment explanation


    Indices: 6155--6268  Score: 228
    Period size: 57  Copynumber: 2.0  Consensus size: 57

       6145 GTACAGTAGA

                                                                     
       6155 ATGGTCCCACCACTATTTATGTGTAGTTTAGCTATAGAACACAGGATGACTAGTAAT
          1 ATGGTCCCACCACTATTTATGTGTAGTTTAGCTATAGAACACAGGATGACTAGTAAT

                                                                     
       6212 ATGGTCCCACCACTATTTATGTGTAGTTTAGCTATAGAACACAGGATGACTAGTAAT
          1 ATGGTCCCACCACTATTTATGTGTAGTTTAGCTATAGAACACAGGATGACTAGTAAT

       6269 GACACGTCAC


Statistics
Matches: 57,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  57   57  1.00

ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32


Consensus pattern (57 bp):   
ATGGTCCCACCACTATTTATGTGTAGTTTAGCTATAGAACACAGGATGACTAGTAAT

Found at i:6942 original size:19 final size:19

Alignment explanation


    Indices: 6918--6958  Score: 82
    Period size: 19  Copynumber: 2.2  Consensus size: 19

       6908 ACAGACACTG

                               
       6918 TATTATATATAAATCCTTC
          1 TATTATATATAAATCCTTC

                               
       6937 TATTATATATAAATCCTTC
          1 TATTATATATAAATCCTTC

               
       6956 TAT
          1 TAT

       6959 CAAACTGGTC


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   22  1.00

ACGTcount: A:0.37, C:0.15, G:0.00, T:0.49


Consensus pattern (19 bp):   
TATTATATATAAATCCTTC

Found at i:17208 original size:13 final size:13

Alignment explanation


    Indices: 17186--17218  Score: 50
    Period size: 13  Copynumber: 2.5  Consensus size: 13

      17176 GTTTTTAACC

                         
      17186 AAAA-AAAAAAGA
          1 AAAAGAAAAAAGA

                         
      17198 AAAAGAAAAAAGA
          1 AAAAGAAAAAAGA

                    
      17211 AGAAAGAA
          1 A-AAAGAA

      17219 TGAAAGATAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  12    4  0.21
  13    9  0.47
  14    6  0.32

ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00


Consensus pattern (13 bp):   
AAAAGAAAAAAGA

Found at i:26784 original size:20 final size:21

Alignment explanation


    Indices: 26761--26801  Score: 75
    Period size: 20  Copynumber: 2.0  Consensus size: 21

      26751 TTTTGAGTAA

                                 
      26761 AAATGGCTGCT-TTTTTTTTT
          1 AAATGGCTGCTATTTTTTTTT

                                 
      26781 AAATGGCTGCTATTTTTTTTT
          1 AAATGGCTGCTATTTTTTTTT

      26802 TGGAAAAAAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  20   11  0.55
  21    9  0.45

ACGTcount: A:0.17, C:0.10, G:0.15, T:0.59


Consensus pattern (21 bp):   
AAATGGCTGCTATTTTTTTTT
Done.