Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012297.1 Corchorus capsularis cultivar CVL-1 contig12318, 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: 15900
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31


Found at i:663 original size:27 final size:28

Alignment explanation


    Indices: 633--705  Score: 112
    Period size: 27  Copynumber: 2.6  Consensus size: 28

        623 CCTAAATGCC

                     *                * 
        633 AAAATGACCTAAATGCCCCTGGAT-GTG
          1 AAAATGACCAAAATGCCCCTGGATGGAG

                                  *     
        660 AAAATGACCAAAATGCCCCTGGGTGGAG
          1 AAAATGACCAAAATGCCCCTGGATGGAG

                              
        688 AAAATGACCAAAATGCCC
          1 AAAATGACCAAAATGCCC

        706 TTGGGCGACC


Statistics
Matches: 42,  Mismatches: 3, Indels: 1
        0.91            0.07        0.02

Matches are distributed among these distances:
  27   22  0.52
  28   20  0.48

ACGTcount: A:0.38, C:0.23, G:0.22, T:0.16


Consensus pattern (28 bp):   
AAAATGACCAAAATGCCCCTGGATGGAG

Found at i:698 original size:28 final size:27

Alignment explanation


    Indices: 633--710  Score: 111
    Period size: 28  Copynumber: 2.9  Consensus size: 27

        623 CCTAAATGCC

                     *            *  * 
        633 AAAATGACCTAAATGCCCCTGGATGTG
          1 AAAATGACCAAAATGCCCCTGGGTGAG

                                        
        660 AAAATGACCAAAATGCCCCTGGGTGGAG
          1 AAAATGACCAAAATGCCCCTGGGT-GAG

                              *    
        688 AAAATGACCAAAATGCCCTTGGG
          1 AAAATGACCAAAATGCCCCTGGG

        711 CGACCCTAAT


Statistics
Matches: 46,  Mismatches: 4, Indels: 1
        0.90            0.08        0.02

Matches are distributed among these distances:
  27   22  0.48
  28   24  0.52

ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18


Consensus pattern (27 bp):   
AAAATGACCAAAATGCCCCTGGGTGAG

Found at i:12254 original size:19 final size:18

Alignment explanation


    Indices: 12215--12254  Score: 53
    Period size: 19  Copynumber: 2.2  Consensus size: 18

      12205 TCCTTGAAAT

                          *   
      12215 AATTCTTCAATGATTTTC
          1 AATTCTTCAATGATCTTC

                        *      
      12233 AATTCTTCAAATTATCTTC
          1 AATTCTTC-AATGATCTTC

               
      12252 AAT
          1 AAT

      12255 AAATCTTCAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  18    8  0.42
  19   11  0.58

ACGTcount: A:0.33, C:0.17, G:0.03, T:0.47


Consensus pattern (18 bp):   
AATTCTTCAATGATCTTC

Found at i:15869 original size:2 final size:2

Alignment explanation


    Indices: 15862--15900  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

      15852 CAAGGATTAT

                                                                      
      15862 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


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

Done.