Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011359.1 Corchorus capsularis cultivar CVL-1 contig11380, 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: 11944
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:2845 original size:14 final size:14

Alignment explanation


    Indices: 2826--2854  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       2816 TTGCCTATAA

                          
       2826 ACATTAAACTGAAG
          1 ACATTAAACTGAAG

                          
       2840 ACATTAAACTGAAG
          1 ACATTAAACTGAAG

             
       2854 A
          1 A

       2855 GGTACCAACA


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

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.52, C:0.14, G:0.14, T:0.21


Consensus pattern (14 bp):   
ACATTAAACTGAAG

Found at i:8301 original size:2 final size:2

Alignment explanation


    Indices: 8294--8318  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       8284 AATTTGTACA

                                                 
       8294 AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A

       8319 GTAAAATATG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:8716 original size:12 final size:12

Alignment explanation


    Indices: 8699--8777  Score: 131
    Period size: 12  Copynumber: 6.5  Consensus size: 12

       8689 TTAATACAGG

                        
       8699 TATCGACGGATA
          1 TATCGACGGATA

                         
       8711 TATCGAACGGATA
          1 TATCG-ACGGATA

                  *     
       8724 TATCGAAGGATA
          1 TATCGACGGATA

                        
       8736 TATCGACGGATA
          1 TATCGACGGATA

                  *     
       8748 TATCGAAGGATA
          1 TATCGACGGATA

                        
       8760 TATCGACGGATA
          1 TATCGACGGATA

                  
       8772 TATCGA
          1 TATCGA

       8778 GGTATCGATG


Statistics
Matches: 62,  Mismatches: 4, Indels: 2
        0.91            0.06        0.03

Matches are distributed among these distances:
  12   50  0.81
  13   12  0.19

ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25


Consensus pattern (12 bp):   
TATCGACGGATA

Found at i:9848 original size:3 final size:3

Alignment explanation


    Indices: 9840--9869  Score: 53
    Period size: 3  Copynumber: 10.3  Consensus size: 3

       9830 TCATTTCCCC

                                                     
       9840 CAT CAT CAT CAT CAT CAT CAT CAT CA- CAT C
          1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C

       9870 TTTCGTGAGC


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   2    2  0.08
   3   24  0.92

ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30


Consensus pattern (3 bp):   
CAT

Found at i:10475 original size:10 final size:10

Alignment explanation


    Indices: 10460--10485  Score: 52
    Period size: 10  Copynumber: 2.6  Consensus size: 10

      10450 AATTTAATAT

                      
      10460 GGATATTTAC
          1 GGATATTTAC

                      
      10470 GGATATTTAC
          1 GGATATTTAC

                  
      10480 GGATAT
          1 GGATAT

      10486 ATCGAGATTT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   16  1.00

ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38


Consensus pattern (10 bp):   
GGATATTTAC

Found at i:10613 original size:12 final size:12

Alignment explanation


    Indices: 10596--10634  Score: 50
    Period size: 12  Copynumber: 3.6  Consensus size: 12

      10586 GTACAAATAT

                        
      10596 CGGATATATCGA
          1 CGGATATATCGA

                        
      10608 CGGATATATCGA
          1 CGGATATATCGA

                        
      10620 -GG---TATCGA
          1 CGGATATATCGA

                   
      10628 CGGATAT
          1 CGGATAT

      10635 TTAATTCCAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 8
        0.74            0.00        0.26

Matches are distributed among these distances:
   8    6  0.26
   9    2  0.09
  11    2  0.09
  12   13  0.57

ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26


Consensus pattern (12 bp):   
CGGATATATCGA

Found at i:11088 original size:19 final size:20

Alignment explanation


    Indices: 11064--11103  Score: 64
    Period size: 20  Copynumber: 2.0  Consensus size: 20

      11054 GGGAATTCAA

                       *        
      11064 ATTGAA-TTAATGAAAAACT
          1 ATTGAATTTAACGAAAAACT

                                
      11083 ATTGAATTTAACGAAAAACT
          1 ATTGAATTTAACGAAAAACT

             
      11103 A
          1 A

      11104 ACTTCCGACG


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  19    6  0.32
  20   13  0.68

ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30


Consensus pattern (20 bp):   
ATTGAATTTAACGAAAAACT

Done.