Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020647.1 Corchorus olitorius cultivar O-4 contig20680, 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: 4880
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32


Found at i:510 original size:20 final size:20

Alignment explanation


    Indices: 485--526  Score: 75
    Period size: 20  Copynumber: 2.1  Consensus size: 20

        475 TGAAACCAGT

                                
        485 TTATGGTTGTTATTTTAATG
          1 TTATGGTTGTTATTTTAATG

                       *        
        505 TTATGGTTGTTGTTTTAATG
          1 TTATGGTTGTTATTTTAATG

              
        525 TT
          1 TT

        527 TATTTTGAAC


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   21  1.00

ACGTcount: A:0.17, C:0.00, G:0.21, T:0.62


Consensus pattern (20 bp):   
TTATGGTTGTTATTTTAATG

Found at i:2759 original size:29 final size:31

Alignment explanation


    Indices: 2715--2798  Score: 102
    Period size: 29  Copynumber: 2.8  Consensus size: 31

       2705 TGTACTATCA

                 *     *                   
       2715 GAAAAAGATCATTTTAGTCCCTCCATTA-T-
          1 GAAAACGATCAATTTAGTCCCTCCATTATTG

                *                   *       
       2744 GAAATCTG-TCAATTTAGTCCCTCTATTATTG
          1 GAAAAC-GATCAATTTAGTCCCTCCATTATTG

                                    
       2775 GAAAACGATCAATTTAGTCCCTCC
          1 GAAAACGATCAATTTAGTCCCTCC

       2799 GTTTAATTGA


Statistics
Matches: 45,  Mismatches: 6, Indels: 6
        0.79            0.11        0.11

Matches are distributed among these distances:
  29   22  0.49
  30    3  0.07
  31   20  0.44

ACGTcount: A:0.31, C:0.23, G:0.12, T:0.35


Consensus pattern (31 bp):   
GAAAACGATCAATTTAGTCCCTCCATTATTG

Found at i:3963 original size:22 final size:23

Alignment explanation


    Indices: 3915--3963  Score: 84
    Period size: 22  Copynumber: 2.2  Consensus size: 23

       3905 CCAAAAAATT

                                   
       3915 TTACCAAGAATACAATCATTAAA
          1 TTACCAAGAATACAATCATTAAA

                                   
       3938 -TACCAAGAATACAATCA-TAAA
          1 TTACCAAGAATACAATCATTAAA

                 
       3959 TTACC
          1 TTACC

       3964 TGGCGATCCT


Statistics
Matches: 25,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
  21    4  0.16
  22   21  0.84

ACGTcount: A:0.51, C:0.20, G:0.04, T:0.24


Consensus pattern (23 bp):   
TTACCAAGAATACAATCATTAAA
Done.