Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015686.1 Corchorus olitorius cultivar O-4 contig15719, 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: 28607
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36


Found at i:1534 original size:1 final size:1

Alignment explanation


    Indices: 1530--1556  Score: 54
    Period size: 1  Copynumber: 27.0  Consensus size: 1

       1520 GCTAAAGTTC

                                       
       1530 TTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTT

       1557 GGTTAAATGA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   26  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Found at i:6011 original size:15 final size:16

Alignment explanation


    Indices: 5985--6019  Score: 63
    Period size: 15  Copynumber: 2.2  Consensus size: 16

       5975 CAATATTTTT

                            
       5985 AAAGAGAAAAAAAAAG
          1 AAAGAGAAAAAAAAAG

                            
       6001 AAAGA-AAAAAAAAAG
          1 AAAGAGAAAAAAAAAG

                
       6016 AAAG
          1 AAAG

       6020 GGGGTCCTTC


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  15   14  0.74
  16    5  0.26

ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00


Consensus pattern (16 bp):   
AAAGAGAAAAAAAAAG

Found at i:11693 original size:21 final size:21

Alignment explanation


    Indices: 11668--11709  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      11658 ATACATGATA

                           *     
      11668 TTATAGCTTTGCTTAGTCATC
          1 TTATAGCTTTGCTTACTCATC

                                 
      11689 TTATAGCTTTGCTTACTCATC
          1 TTATAGCTTTGCTTACTCATC

      11710 ACTTAGCCTA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   20  1.00

ACGTcount: A:0.19, C:0.21, G:0.12, T:0.48


Consensus pattern (21 bp):   
TTATAGCTTTGCTTACTCATC

Found at i:15735 original size:21 final size:21

Alignment explanation


    Indices: 15689--15752  Score: 67
    Period size: 21  Copynumber: 3.0  Consensus size: 21

      15679 ATGTTTGGCT

                        * *      
      15689 AGATGAGTAAGCTAGGCTA-A
          1 AGATGAGTAAGCAAAGCTATA

             *                    
      15709 GTGATGAGTAAGCAAAGCTATA
          1 -AGATGAGTAAGCAAAGCTATA

                  * *            
      15731 AGATGACTGAGCAAAGCTATA
          1 AGATGAGTAAGCAAAGCTATA

             
      15752 A
          1 A

      15753 TATCATGTAT


Statistics
Matches: 36,  Mismatches: 6, Indels: 2
        0.82            0.14        0.05

Matches are distributed among these distances:
  21   35  0.97
  22    1  0.03

ACGTcount: A:0.42, C:0.11, G:0.27, T:0.20


Consensus pattern (21 bp):   
AGATGAGTAAGCAAAGCTATA

Found at i:26440 original size:60 final size:61

Alignment explanation


    Indices: 26329--26451  Score: 212
    Period size: 60  Copynumber: 2.0  Consensus size: 61

      26319 TCTTTTTTTC

                  *   *       *                                          
      26329 TTCCAGGTATGTTTGGCTTTAGAAATGTTTTCCATTTTAGATGATTTCATGTTTTGTTGTT
          1 TTCCAGATATATTTGGCTATAGAAATGTTTTCCATTTTAGATGATTTCATGTTTTGTTGTT

                                                                         
      26390 TTCCAGATATATTTGGCTATAGAAATG-TTTCCATTTTAGATGATTTCATGTTTTGTTGTT
          1 TTCCAGATATATTTGGCTATAGAAATGTTTTCCATTTTAGATGATTTCATGTTTTGTTGTT

              
      26450 TT
          1 TT

      26452 GCTTATGGTT


Statistics
Matches: 59,  Mismatches: 3, Indels: 1
        0.94            0.05        0.02

Matches are distributed among these distances:
  60   35  0.59
  61   24  0.41

ACGTcount: A:0.20, C:0.10, G:0.18, T:0.52


Consensus pattern (61 bp):   
TTCCAGATATATTTGGCTATAGAAATGTTTTCCATTTTAGATGATTTCATGTTTTGTTGTT
Done.