Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023424.1 Corchorus olitorius cultivar O-4 contig23457, 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: 2368
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:1688 original size:20 final size:20

Alignment explanation


    Indices: 1663--1702  Score: 71
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       1653 TTTTTTTAGA

                                
       1663 AAAAACGGAAAACAAAAATT
          1 AAAAACGGAAAACAAAAATT

                        *       
       1683 AAAAACGGAAAAGAAAAATT
          1 AAAAACGGAAAACAAAAATT

       1703 TTTTTTTCAG


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.70, C:0.07, G:0.12, T:0.10


Consensus pattern (20 bp):   
AAAAACGGAAAACAAAAATT

Found at i:1728 original size:40 final size:41

Alignment explanation


    Indices: 1684--1766  Score: 114
    Period size: 40  Copynumber: 2.0  Consensus size: 41

       1674 ACAAAAATTA

                       *                             
       1684 AAAACGGAAAAGAAAAATTTTTTTTTCAG-AAAAAACGCAG
          1 AAAACGGAAAACAAAAATTTTTTTTTCAGAAAAAAACGCAG

                           **         *               
       1724 AAAACGGAAAACAAATTTTTTTTTTTTAGATAAAAAACGCAG
          1 AAAACGGAAAACAAAAATTTTTTTTTCAGA-AAAAAACGCAG

             
       1766 A
          1 A

       1767 CACGCAGACA


Statistics
Matches: 37,  Mismatches: 4, Indels: 2
        0.86            0.09        0.05

Matches are distributed among these distances:
  40   25  0.68
  42   12  0.32

ACGTcount: A:0.51, C:0.10, G:0.13, T:0.27


Consensus pattern (41 bp):   
AAAACGGAAAACAAAAATTTTTTTTTCAGAAAAAAACGCAG

Found at i:2074 original size:16 final size:15

Alignment explanation


    Indices: 2036--2077  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       2026 ACAGAGGTTG

                           
       2036 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                           
       2051 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       2066 ACTAGAAAACAA
          1 AC-AGAAAACAA

       2078 AACAAAGTAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.