Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009681.1 Corchorus capsularis cultivar CVL-1 contig09702, 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: 19982
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32


Found at i:9 original size:4 final size:4

Alignment explanation


    Indices: 1--45  Score: 90
    Period size: 4  Copynumber: 11.2  Consensus size: 4

                                                                    
          1 CGTA CGTA CGTA CGTA CGTA CGTA CGTA CGTA CGTA CGTA CGTA C
          1 CGTA CGTA CGTA CGTA CGTA CGTA CGTA CGTA CGTA CGTA CGTA C

         46 TACTACTACT


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   41  1.00

ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24


Consensus pattern (4 bp):   
CGTA

Found at i:5636 original size:24 final size:26

Alignment explanation


    Indices: 5609--5657  Score: 75
    Period size: 27  Copynumber: 1.9  Consensus size: 26

       5599 TCTCAAACTC

                                      
       5609 TCTCTTTT-A-GATTTTTAGTTTAGA
          1 TCTCTTTTAATGATTTTTAGTTTAGA

                                     
       5633 TCTCTTTTAATTGATTTTTAGTTTA
          1 TCTCTTTTAA-TGATTTTTAGTTTA

       5658 ATTAATCTAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  24    8  0.36
  25    1  0.05
  27   13  0.59

ACGTcount: A:0.20, C:0.08, G:0.10, T:0.61


Consensus pattern (26 bp):   
TCTCTTTTAATGATTTTTAGTTTAGA

Found at i:10205 original size:20 final size:19

Alignment explanation


    Indices: 10182--10224  Score: 59
    Period size: 19  Copynumber: 2.2  Consensus size: 19

      10172 ATTTAAGAGA

                       *        
      10182 TTTTTATTTATTTTAAATTT
          1 TTTTTATTT-TATTAAATTT

                         *     
      10202 TTTTTATTTTATTGAATTT
          1 TTTTTATTTTATTAAATTT

                
      10221 TTTT
          1 TTTT

      10225 AATAGGTTAT


Statistics
Matches: 21,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  19   12  0.57
  20    9  0.43

ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77


Consensus pattern (19 bp):   
TTTTTATTTTATTAAATTT

Found at i:10207 original size:16 final size:17

Alignment explanation


    Indices: 10181--10212  Score: 57
    Period size: 16  Copynumber: 1.9  Consensus size: 17

      10171 AATTTAAGAG

                             
      10181 ATTTTTATTTATTTTAA
          1 ATTTTTATTTATTTTAA

                            
      10198 ATTTTT-TTTATTTTA
          1 ATTTTTATTTATTTTA

      10213 TTGAATTTTT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16    9  0.60
  17    6  0.40

ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75


Consensus pattern (17 bp):   
ATTTTTATTTATTTTAA
Done.