Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024499.1 Corchorus olitorius cultivar O-4 contig24532, 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: 6039
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:883 original size:21 final size:21

Alignment explanation


    Indices: 859--913  Score: 74
    Period size: 21  Copynumber: 2.6  Consensus size: 21

        849 CGCCCATTCA

                           **    
        859 CCGTGCCACCACCGGTTAAGC
          1 CCGTGCCACCACCGGCCAAGC

                              *  
        880 CCGTGCCACCACCGGCCATGC
          1 CCGTGCCACCACCGGCCAAGC

                    *    
        901 CCGTGCCATCACC
          1 CCGTGCCACCACC

        914 ATTCCAAGCC


Statistics
Matches: 30,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   30  1.00

ACGTcount: A:0.16, C:0.49, G:0.22, T:0.13


Consensus pattern (21 bp):   
CCGTGCCACCACCGGCCAAGC

Found at i:1551 original size:10 final size:10

Alignment explanation


    Indices: 1536--1564  Score: 51
    Period size: 10  Copynumber: 3.0  Consensus size: 10

       1526 TTCTTTAATC

                      
       1536 CTGAAAATTT
          1 CTGAAAATTT

                      
       1546 CTGAAAATTT
          1 CTGAAAATTT

                      
       1556 -TGAAAATTT
          1 CTGAAAATTT

       1565 TGCATGTATT


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

Matches are distributed among these distances:
   9    9  0.47
  10   10  0.53

ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41


Consensus pattern (10 bp):   
CTGAAAATTT

Found at i:1561 original size:9 final size:9

Alignment explanation


    Indices: 1537--1566  Score: 51
    Period size: 9  Copynumber: 3.2  Consensus size: 9

       1527 TCTTTAATCC

                     
       1537 TGAAAATTT
          1 TGAAAATTT

                      
       1546 CTGAAAATTT
          1 -TGAAAATTT

                     
       1556 TGAAAATTT
          1 TGAAAATTT

              
       1565 TG
          1 TG

       1567 CATGTATTGA


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

Matches are distributed among these distances:
   9   11  0.55
  10    9  0.45

ACGTcount: A:0.40, C:0.03, G:0.13, T:0.43


Consensus pattern (9 bp):   
TGAAAATTT

Found at i:3435 original size:11 final size:11

Alignment explanation


    Indices: 3419--3444  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

       3409 AGATATTTTC

                       
       3419 TTTTCTTCTAG
          1 TTTTCTTCTAG

                       
       3430 TTTTCTTCTAG
          1 TTTTCTTCTAG

                
       3441 TTTT
          1 TTTT

       3445 TAGGCAAAGG


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69


Consensus pattern (11 bp):   
TTTTCTTCTAG

Found at i:4215 original size:15 final size:15

Alignment explanation


    Indices: 4185--4226  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       4175 TTACTTTGCT

                            
       4185 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
       4201 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

               *       
       4216 TTGCTTTCTGT
          1 TTGTTTTCTGT

       4227 CAATCTCTGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA
Done.