Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005711.1 Corchorus capsularis cultivar CVL-1 contig05729, 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: 11170
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:1492 original size:2 final size:2

Alignment explanation


    Indices: 1485--1520  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       1475 TTGCCGCCCC

                                                                 
       1485 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       1521 TTGGTACCGA


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:8650 original size:12 final size:12

Alignment explanation


    Indices: 8633--8671  Score: 51
    Period size: 12  Copynumber: 3.2  Consensus size: 12

       8623 CTAGTATGAT

                      * 
       8633 TAAATATATAAA
          1 TAAATATATATA

                  *     
       8645 TAAATAAATATA
          1 TAAATATATATA

              *         
       8657 TATATATATATA
          1 TAAATATATATA

               
       8669 TAA
          1 TAA

       8672 TGTAAGAGAT


Statistics
Matches: 22,  Mismatches: 5, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  12   22  1.00

ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38


Consensus pattern (12 bp):   
TAAATATATATA

Found at i:8670 original size:8 final size:8

Alignment explanation


    Indices: 8633--8666  Score: 50
    Period size: 8  Copynumber: 4.2  Consensus size: 8

       8623 CTAGTATGAT

                    
       8633 TAAATATA
          1 TAAATATA

                  * 
       8641 TAAATAAA
          1 TAAATATA

                    
       8649 TAAATATA
          1 TAAATATA

              *     
       8657 TATATATA
          1 TAAATATA

              
       8665 TA
          1 TA

       8667 TATAATGTAA


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   8   23  1.00

ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38


Consensus pattern (8 bp):   
TAAATATA

Found at i:9284 original size:28 final size:28

Alignment explanation


    Indices: 9249--9308  Score: 102
    Period size: 28  Copynumber: 2.1  Consensus size: 28

       9239 CTTTTAAGAC

                        *               
       9249 AAATATGCTAAATTTGCATAAATTAAAT
          1 AAATATGCTAAACTTGCATAAATTAAAT

                                *       
       9277 AAATATGCTAAACTTGCATAGATTAAAT
          1 AAATATGCTAAACTTGCATAAATTAAAT

                
       9305 AAAT
          1 AAAT

       9309 CTTTAACAAT


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  28   30  1.00

ACGTcount: A:0.50, C:0.08, G:0.08, T:0.33


Consensus pattern (28 bp):   
AAATATGCTAAACTTGCATAAATTAAAT
Done.