Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014726.1 Corchorus olitorius cultivar O-4 contig14759, 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: 11333
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.34

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:2535 original size:20 final size:21

Alignment explanation


    Indices: 2499--2543  Score: 58
    Period size: 20  Copynumber: 2.2  Consensus size: 21

       2489 ATGTTCTTAG

                        *        
       2499 ATTATACTACTATTATA-TAT
          1 ATTATACTACTAATATAGTAT

                                  
       2519 ATTATACT-CTAGATATAGTAT
          1 ATTATACTACTA-ATATAGTAT

                
       2540 ATTA
          1 ATTA

       2544 ATTTCTCAAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  19    3  0.14
  20   12  0.55
  21    7  0.32

ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47


Consensus pattern (21 bp):   
ATTATACTACTAATATAGTAT

Found at i:2694 original size:1 final size:1

Alignment explanation


    Indices: 2688--2732  Score: 63
    Period size: 1  Copynumber: 45.0  Consensus size: 1

       2678 CTGNCAAAGG

                                       ***               
       2688 TTTTTTTTTTTTTTTTTTTTTTTTTTTCCATTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

       2733 AAGAAAAAGA


Statistics
Matches: 41,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   1   41  1.00

ACGTcount: A:0.02, C:0.04, G:0.00, T:0.93


Consensus pattern (1 bp):   
T

Found at i:11304 original size:2 final size:2

Alignment explanation


    Indices: 11297--11333  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

      11287 ACATTTGGTC

                                                                   
      11297 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.