Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019943.1 Corchorus olitorius cultivar O-4 contig19976, 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: 21221
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35


Found at i:6581 original size:2 final size:2

Alignment explanation


    Indices: 6569--6619  Score: 75
    Period size: 2  Copynumber: 25.0  Consensus size: 2

       6559 CTAAATATTG

                                   *     *                                 
       6569 TA TA TA CTA TA TA TA TC TA TT TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                       
       6612 TA TA TA TA
          1 TA TA TA TA

       6620 CACTGATATT


Statistics
Matches: 44,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
   2   42  0.95
   3    2  0.05

ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:19327 original size:1 final size:1

Alignment explanation


    Indices: 19321--19350  Score: 51
    Period size: 1  Copynumber: 30.0  Consensus size: 1

      19311 CATGACCTAT

                                 *        
      19321 AAAAAAAAAAAAAAAAAAAAATAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

      19351 CCACATCAAC


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   1   27  1.00

ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03


Consensus pattern (1 bp):   
A

Found at i:20707 original size:21 final size:22

Alignment explanation


    Indices: 20681--20724  Score: 63
    Period size: 21  Copynumber: 2.0  Consensus size: 22

      20671 TCTTTGGGGG

                                  
      20681 TTGCTAAATACCGCCCC-CTTT
          1 TTGCTAAATACCGCCCCACTTT

                  **              
      20702 TTGCTAGTTACCGCCCCACTTT
          1 TTGCTAAATACCGCCCCACTTT

             
      20724 T
          1 T

      20725 GACACTTTTG


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  21   15  0.75
  22    5  0.25

ACGTcount: A:0.16, C:0.36, G:0.11, T:0.36


Consensus pattern (22 bp):   
TTGCTAAATACCGCCCCACTTT

Found at i:21128 original size:33 final size:31

Alignment explanation


    Indices: 21085--21164  Score: 112
    Period size: 28  Copynumber: 2.6  Consensus size: 31

      21075 CGTCCTCCGG

                                             
      21085 GGACGGCACGACCATGGGCGTGTCGCCCTGTGA
          1 GGACGGCACGACCATGGGCG-G-CGCCCTGTGA

                 *                         
      21118 GGACGACACGACCAT--G-GGCGCCCTGTGA
          1 GGACGGCACGACCATGGGCGGCGCCCTGTGA

                               
      21146 GGACGGCACGACCATGGGC
          1 GGACGGCACGACCATGGGC

      21165 ATGCCGTCCT


Statistics
Matches: 42,  Mismatches: 2, Indels: 8
        0.81            0.04        0.15

Matches are distributed among these distances:
  28   24  0.57
  29    1  0.02
  30    2  0.05
  31    1  0.02
  33   14  0.33

ACGTcount: A:0.19, C:0.31, G:0.39, T:0.11


Consensus pattern (31 bp):   
GGACGGCACGACCATGGGCGGCGCCCTGTGA

Done.