Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013394.1 Corchorus olitorius cultivar O-4 contig13427, 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: 9504
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--39  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

                                                                      
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

         40 GTGTGTGTGT


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:3762 original size:11 final size:11

Alignment explanation


    Indices: 3742--3776  Score: 52
    Period size: 11  Copynumber: 3.2  Consensus size: 11

       3732 TTGATAGCGC

                       
       3742 AACAAAAACAA
          1 AACAAAAACAA

               *       
       3753 AACGAAAACAA
          1 AACAAAAACAA

                    *  
       3764 AACAAAAATAA
          1 AACAAAAACAA

              
       3775 AA
          1 AA

       3777 AACAGAAAAA


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  11   21  1.00

ACGTcount: A:0.80, C:0.14, G:0.03, T:0.03


Consensus pattern (11 bp):   
AACAAAAACAA

Found at i:7593 original size:28 final size:28

Alignment explanation


    Indices: 7553--7641  Score: 160
    Period size: 28  Copynumber: 3.2  Consensus size: 28

       7543 TGAAACGACT

                           *            
       7553 AAAATGCCCCTGGACGTGCAAAATGACC
          1 AAAATGCCCCTGGACATGCAAAATGACC

                                        
       7581 AAAATGCCCCTGGACATGCAAAATGACC
          1 AAAATGCCCCTGGACATGCAAAATGACC

                              *         
       7609 AAAATGCCCCTGGACATGTAAAATGACC
          1 AAAATGCCCCTGGACATGCAAAATGACC

                 
       7637 AAAAT
          1 AAAAT

       7642 AAGAAGTAAA


Statistics
Matches: 59,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  28   59  1.00

ACGTcount: A:0.40, C:0.26, G:0.18, T:0.16


Consensus pattern (28 bp):   
AAAATGCCCCTGGACATGCAAAATGACC

Found at i:8974 original size:31 final size:32

Alignment explanation


    Indices: 8936--8995  Score: 86
    Period size: 31  Copynumber: 1.9  Consensus size: 32

       8926 CTACAAAAAT

                      *                     
       8936 TGTCAATTGAGTCCCTCTACTTG-CAATTTAG
          1 TGTCAATTGAATCCCTCTACTTGTCAATTTAG

                    *    *               
       8967 TGTCAATTTAATCTCTCTACTTGTCAATT
          1 TGTCAATTGAATCCCTCTACTTGTCAATT

       8996 GGGTCAATCG


Statistics
Matches: 25,  Mismatches: 3, Indels: 1
        0.86            0.10        0.03

Matches are distributed among these distances:
  31   20  0.80
  32    5  0.20

ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43


Consensus pattern (32 bp):   
TGTCAATTGAATCCCTCTACTTGTCAATTTAG
Done.