Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013307.1 Corchorus olitorius cultivar O-4 contig13340, 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: 10519
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33


Found at i:763 original size:27 final size:27

Alignment explanation


    Indices: 733--787  Score: 110
    Period size: 27  Copynumber: 2.0  Consensus size: 27

        723 GCACTTCTGT

                                       
        733 AGCTTTGGTTTAAGAACACTCTGCTTG
          1 AGCTTTGGTTTAAGAACACTCTGCTTG

                                       
        760 AGCTTTGGTTTAAGAACACTCTGCTTG
          1 AGCTTTGGTTTAAGAACACTCTGCTTG

             
        787 A
          1 A

        788 TAAGCAAGTC


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   28  1.00

ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36


Consensus pattern (27 bp):   
AGCTTTGGTTTAAGAACACTCTGCTTG

Found at i:4966 original size:30 final size:30

Alignment explanation


    Indices: 4932--4988  Score: 114
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       4922 GCCAAAACAT

                                          
       4932 TGAATACCCAATGACGTAAAATTTCAGAAA
          1 TGAATACCCAATGACGTAAAATTTCAGAAA

                                       
       4962 TGAATACCCAATGACGTAAAATTTCAG
          1 TGAATACCCAATGACGTAAAATTTCAG

       4989 TTTTTCATAC


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  30   27  1.00

ACGTcount: A:0.44, C:0.18, G:0.14, T:0.25


Consensus pattern (30 bp):   
TGAATACCCAATGACGTAAAATTTCAGAAA

Found at i:9238 original size:21 final size:21

Alignment explanation


    Indices: 9205--9248  Score: 52
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       9195 GTGGAAAGCA

                 *               
       9205 TTATAGCTATTTTAATAACTT
          1 TTATAACTATTTTAATAACTT

                    *     *   *  
       9226 TTATAACTTTTTTAGTAATTT
          1 TTATAACTATTTTAATAACTT

              
       9247 TT
          1 TT

       9249 GATTACGAGA


Statistics
Matches: 19,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.30, C:0.07, G:0.05, T:0.59


Consensus pattern (21 bp):   
TTATAACTATTTTAATAACTT

Found at i:10413 original size:14 final size:14

Alignment explanation


    Indices: 10387--10413  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

      10377 CGGGCCTGCG

                          
      10387 CACGCGGGCCAGTA
          1 CACGCGGGCCAGTA

                         
      10401 CACGCGGGCCAGT
          1 CACGCGGGCCAGT

      10414 GCAGCCCAAC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.19, C:0.37, G:0.37, T:0.07


Consensus pattern (14 bp):   
CACGCGGGCCAGTA
Done.