Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006895.1 Corchorus capsularis cultivar CVL-1 contig06916, 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: 28473
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:9039 original size:19 final size:18

Alignment explanation


    Indices: 9015--9050  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       9005 TGAAGATTTC

                               
       9015 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
       9034 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

       9051 ATTATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT

Found at i:10949 original size:22 final size:24

Alignment explanation


    Indices: 10907--10950  Score: 65
    Period size: 24  Copynumber: 1.9  Consensus size: 24

      10897 AGAAGAAGTC

                                    
      10907 AAAGAATCAGAGGTGAAACTATCA
          1 AAAGAATCAGAGGTGAAACTATCA

                   *              
      10931 AAAGAATTAGA-G-GAAACTAT
          1 AAAGAATCAGAGGTGAAACTAT

      10951 TCTTGACTTA


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

Matches are distributed among these distances:
  22    8  0.42
  23    1  0.05
  24   10  0.53

ACGTcount: A:0.52, C:0.09, G:0.20, T:0.18


Consensus pattern (24 bp):   
AAAGAATCAGAGGTGAAACTATCA

Found at i:26583 original size:10 final size:12

Alignment explanation


    Indices: 26552--26582  Score: 62
    Period size: 12  Copynumber: 2.6  Consensus size: 12

      26542 GGCCTAATAG

                        
      26552 TGGCGCGCGGGT
          1 TGGCGCGCGGGT

                        
      26564 TGGCGCGCGGGT
          1 TGGCGCGCGGGT

                   
      26576 TGGCGCG
          1 TGGCGCG

      26583 GAGCTGGCCG


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   19  1.00

ACGTcount: A:0.00, C:0.26, G:0.58, T:0.16


Consensus pattern (12 bp):   
TGGCGCGCGGGT

Found at i:27462 original size:15 final size:15

Alignment explanation


    Indices: 27442--27499  Score: 89
    Period size: 15  Copynumber: 3.9  Consensus size: 15

      27432 TATACAAGTT

                       *   
      27442 GCTCATCTTCTTGTG
          1 GCTCATCTTCTGGTG

                           
      27457 GCTCATCTTCTGGTG
          1 GCTCATCTTCTGGTG

             *             
      27472 GTTCATCTTCTGGTG
          1 GCTCATCTTCTGGTG

                 *       
      27487 GCTCAACTTCTGG
          1 GCTCATCTTCTGG

      27500 CTTGGCAAGG


Statistics
Matches: 39,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  15   39  1.00

ACGTcount: A:0.09, C:0.26, G:0.24, T:0.41


Consensus pattern (15 bp):   
GCTCATCTTCTGGTG
Done.