Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020096.1 Corchorus olitorius cultivar O-4 contig20129, 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: 4935
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:3473 original size:19 final size:20

Alignment explanation


    Indices: 3443--3506  Score: 76
    Period size: 21  Copynumber: 3.1  Consensus size: 20

       3433 TTGACACTGT

                                 
       3443 TTAGCAACTGTACAGATGAGA
          1 TTAGC-ACTGTACAGATGAGA

                            *   
       3464 TTA-CACTGTACAGATTAGA
          1 TTAGCACTGTACAGATGAGA

                 *        *      
       3483 TTAGGTACTGTACATATGAGA
          1 TTA-GCACTGTACAGATGAGA

               
       3504 TTA
          1 TTA

       3507 TTAGAGCAGC


Statistics
Matches: 37,  Mismatches: 4, Indels: 4
        0.82            0.09        0.09

Matches are distributed among these distances:
  19   17  0.46
  20    1  0.03
  21   19  0.51

ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31


Consensus pattern (20 bp):   
TTAGCACTGTACAGATGAGA

Found at i:3494 original size:21 final size:19

Alignment explanation


    Indices: 3449--3506  Score: 71
    Period size: 19  Copynumber: 2.9  Consensus size: 19

       3439 CTGTTTAGCA

                               
       3449 ACTGTACAGATGAGATTAC
          1 ACTGTACAGATGAGATTAC

                       *        *
       3468 ACTGTACAGATTAGATTAGGT
          1 ACTGTACAGATGAGATTA--C

                    *         
       3489 ACTGTACATATGAGATTA
          1 ACTGTACAGATGAGATTA

       3507 TTAGAGCAGC


Statistics
Matches: 33,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  19   17  0.52
  21   16  0.48

ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31


Consensus pattern (19 bp):   
ACTGTACAGATGAGATTAC

Found at i:3875 original size:21 final size:19

Alignment explanation


    Indices: 3830--3887  Score: 80
    Period size: 19  Copynumber: 2.9  Consensus size: 19

       3820 CTGTTTAGCA

                               
       3830 ACTGTACAGATGAGATTAC
          1 ACTGTACAGATGAGATTAC

                       *        *
       3849 ACTGTACAGATTAGATTAGGT
          1 ACTGTACAGATGAGATTA--C

                              
       3870 ACTGTACAGATGAGATTA
          1 ACTGTACAGATGAGATTA

       3888 TTAGAGCAGC


Statistics
Matches: 34,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
  19   17  0.50
  21   17  0.50

ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29


Consensus pattern (19 bp):   
ACTGTACAGATGAGATTAC
Done.