Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021572.1 Corchorus olitorius cultivar O-4 contig21605, 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: 15389
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33


Found at i:1709 original size:12 final size:10

Alignment explanation


    Indices: 1677--1712  Score: 54
    Period size: 10  Copynumber: 3.4  Consensus size: 10

       1667 TTAAAAAGCA

                      
       1677 AAAATTTTTG
          1 AAAATTTTTG

                      
       1687 AAAATTTTTG
          1 AAAATTTTTG

                        
       1697 AAAATTGTTTTG
          1 AAAA-T-TTTTG

                
       1709 AAAA
          1 AAAA

       1713 GCCTTCTCTA


Statistics
Matches: 24,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  10   14  0.58
  11    1  0.04
  12    9  0.38

ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44


Consensus pattern (10 bp):   
AAAATTTTTG

Found at i:2404 original size:22 final size:21

Alignment explanation


    Indices: 2362--2407  Score: 58
    Period size: 22  Copynumber: 2.1  Consensus size: 21

       2352 ACAAGTGTCT

                                  
       2362 TTTTTTTTTCAATTTTCTTTTC
          1 TTTTTTTTTC-ATTTTCTTTTC

                                   
       2384 TTTTTTTTTC-TTTTCAATTTTC
          1 TTTTTTTTTCATTTTC--TTTTC

              
       2406 TT
          1 TT

       2408 GGTGGTTGCA


Statistics
Matches: 22,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  20    5  0.23
  22   17  0.77

ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78


Consensus pattern (21 bp):   
TTTTTTTTTCATTTTCTTTTC

Found at i:8624 original size:2 final size:2

Alignment explanation


    Indices: 8619--8683  Score: 130
    Period size: 2  Copynumber: 32.5  Consensus size: 2

       8609 TATATATATA

                                                                          
       8619 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
          1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG

                                              
       8661 TG TG TG TG TG TG TG TG TG TG TG T
          1 TG TG TG TG TG TG TG TG TG TG TG T

       8684 ACTGAATCTT


Statistics
Matches: 63,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   63  1.00

ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51


Consensus pattern (2 bp):   
TG

Found at i:9060 original size:24 final size:25

Alignment explanation


    Indices: 9019--9066  Score: 80
    Period size: 24  Copynumber: 2.0  Consensus size: 25

       9009 CAAGTCTCTA

                      *              
       9019 ATCTACCATGTAGTATAACAATGCC
          1 ATCTACCATGAAGTATAACAATGCC

                                    
       9044 ATCTACC-TGAAGTATAACAATGC
          1 ATCTACCATGAAGTATAACAATGC

       9067 TATGCAAATT


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  24   15  0.68
  25    7  0.32

ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27


Consensus pattern (25 bp):   
ATCTACCATGAAGTATAACAATGCC
Done.