Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005652.1 Corchorus capsularis cultivar CVL-1 contig05670, 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: 7220
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33


Found at i:667 original size:2 final size:2

Alignment explanation


    Indices: 662--701  Score: 73
    Period size: 2  Copynumber: 20.5  Consensus size: 2

        652 ATATACATTT

                                                                         
        662 TA TA TA -A 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 TA T

        702 TGGAAAAAAC


Statistics
Matches: 37,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   36  0.97

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


Consensus pattern (2 bp):   
TA

Found at i:3264 original size:6 final size:6

Alignment explanation


    Indices: 3253--3287  Score: 70
    Period size: 6  Copynumber: 5.8  Consensus size: 6

       3243 GAGGAGCATG

                                                    
       3253 CTGAGC CTGAGC CTGAGC CTGAGC CTGAGC CTGAG
          1 CTGAGC CTGAGC CTGAGC CTGAGC CTGAGC CTGAG

       3288 GGAGAATCGG


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   29  1.00

ACGTcount: A:0.17, C:0.31, G:0.34, T:0.17


Consensus pattern (6 bp):   
CTGAGC

Found at i:5727 original size:22 final size:22

Alignment explanation


    Indices: 5702--5747  Score: 67
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       5692 TTGGCATCGT

                                   
       5702 TTTCGTTTTTCGGTTT-TTTTTG
          1 TTTCGTTTTT-GGTTTGTTTTTG

                       *          
       5724 TTTCGTTTTTGTTTTGTTTTTG
          1 TTTCGTTTTTGGTTTGTTTTTG

              
       5746 TT
          1 TT

       5748 GCGCTGTCAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  21    4  0.18
  22   18  0.82

ACGTcount: A:0.00, C:0.07, G:0.17, T:0.76


Consensus pattern (22 bp):   
TTTCGTTTTTGGTTTGTTTTTG

Found at i:5732 original size:11 final size:11

Alignment explanation


    Indices: 5718--5747  Score: 51
    Period size: 11  Copynumber: 2.7  Consensus size: 11

       5708 TTTTCGGTTT

                       
       5718 TTTTTGTTTCG
          1 TTTTTGTTTCG

                     * 
       5729 TTTTTGTTTTG
          1 TTTTTGTTTCG

                    
       5740 TTTTTGTT
          1 TTTTTGTT

       5748 GCGCTGTCAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  11   18  1.00

ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80


Consensus pattern (11 bp):   
TTTTTGTTTCG

Found at i:5738 original size:16 final size:15

Alignment explanation


    Indices: 5709--5742  Score: 50
    Period size: 15  Copynumber: 2.2  Consensus size: 15

       5699 CGTTTTCGTT

                           
       5709 TTTCGGTTTTTTTTG
          1 TTTCGGTTTTTTTTG

                 *          
       5724 TTTCGTTTTTGTTTTG
          1 TTTCGGTTTT-TTTTG

               
       5740 TTT
          1 TTT

       5743 TTGTTGCGCT


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  15    9  0.53
  16    8  0.47

ACGTcount: A:0.00, C:0.06, G:0.18, T:0.76


Consensus pattern (15 bp):   
TTTCGGTTTTTTTTG

Found at i:6904 original size:13 final size:13

Alignment explanation


    Indices: 6886--6910  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       6876 CTAACTTAGA

                         
       6886 TAATTACAAATTC
          1 TAATTACAAATTC

                        
       6899 TAATTACAAATT
          1 TAATTACAAATT

       6911 GAATTTAAAC


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40


Consensus pattern (13 bp):   
TAATTACAAATTC
Done.