Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007659.1 Corchorus capsularis cultivar CVL-1 contig07680, 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: 13183
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31


Found at i:7157 original size:24 final size:25

Alignment explanation


    Indices: 7118--7164  Score: 78
    Period size: 24  Copynumber: 1.9  Consensus size: 25

       7108 GAGAGATACC

                                     
       7118 GAGATATTTTTCGTATACACTTTTT
          1 GAGATATTTTTCGTATACACTTTTT

                              *    
       7143 GAGATA-TTTTCGTATACTCTTT
          1 GAGATATTTTTCGTATACACTTT

       7165 CATTTTACAC


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  24   15  0.71
  25    6  0.29

ACGTcount: A:0.23, C:0.13, G:0.13, T:0.51


Consensus pattern (25 bp):   
GAGATATTTTTCGTATACACTTTTT

Found at i:7191 original size:2 final size:2

Alignment explanation


    Indices: 7184--7226  Score: 68
    Period size: 2  Copynumber: 21.5  Consensus size: 2

       7174 CGTGAAAGTT

                           *           *                                  
       7184 TC TC TC TC TC GC TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

             
       7226 T
          1 T

       7227 ATATATATAT


Statistics
Matches: 37,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.00, C:0.51, G:0.02, T:0.47


Consensus pattern (2 bp):   
TC

Found at i:8907 original size:22 final size:22

Alignment explanation


    Indices: 8879--8920  Score: 66
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       8869 GATAAAACCT

                       *   *      
       8879 TTTTATTTTTGTTTTTAAAGTC
          1 TTTTATTTTTGCTTTGAAAGTC

                                
       8901 TTTTATTTTTGCTTTGAAAG
          1 TTTTATTTTTGCTTTGAAAG

       8921 CTTCCATTTT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   18  1.00

ACGTcount: A:0.19, C:0.05, G:0.12, T:0.64


Consensus pattern (22 bp):   
TTTTATTTTTGCTTTGAAAGTC
Done.