Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000920.1 Corchorus olitorius cultivar O-4 contig00920, 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, 631

Length: 1053
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.35


Found at i:589 original size:17 final size:17

Alignment explanation


    Indices: 567--620  Score: 76
    Period size: 17  Copynumber: 3.2  Consensus size: 17

        557 TCTTGGCCCA

                             
        567 TTTATTATTTATTTTTT
          1 TTTATTATTTATTTTTT

                               
        584 TTTATTATTT-TTATTATT
          1 TTTATTATTTATT-TT-TT

                             
        602 TTT-TTATTTATTTTTT
          1 TTTATTATTTATTTTTT

               
        618 TTT
          1 TTT

        621 TACACTGGGC


Statistics
Matches: 34,  Mismatches: 0, Indels: 7
        0.83            0.00        0.17

Matches are distributed among these distances:
  16    7  0.21
  17   20  0.59
  18    7  0.21

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


Consensus pattern (17 bp):   
TTTATTATTTATTTTTT

Found at i:600 original size:12 final size:11

Alignment explanation


    Indices: 575--618  Score: 63
    Period size: 12  Copynumber: 3.9  Consensus size: 11

        565 CATTTATTAT

                       
        575 TTATTTTTTT-
          1 TTATTTTTTTA

                        
        585 TTATTATTTTTA
          1 TTATT-TTTTTA

                       
        597 TTATTTTTTTA
          1 TTATTTTTTTA

                       
        608 TTTATTTTTTT
          1 -TTATTTTTTT

        619 TTTACACTGG


Statistics
Matches: 31,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
  10    5  0.16
  11   11  0.35
  12   15  0.48

ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84


Consensus pattern (11 bp):   
TTATTTTTTTA

Found at i:603 original size:20 final size:20

Alignment explanation


    Indices: 566--621  Score: 80
    Period size: 20  Copynumber: 2.8  Consensus size: 20

        556 GTCTTGGCCC

                                 
        566 ATTTATTATTTATTTTTTTTT
          1 ATTTATT-TTTATTTTTTTTT

                                 
        587 A-TTATTTTTATTATTTTTTT
          1 ATTTATTTTTATT-TTTTTTT

                            
        607 ATTTATTTTT-TTTTT
          1 ATTTATTTTTATTTTT

        622 ACACTGGGCC


Statistics
Matches: 33,  Mismatches: 0, Indels: 6
        0.85            0.00        0.15

Matches are distributed among these distances:
  19    9  0.27
  20   15  0.45
  21    9  0.27

ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82


Consensus pattern (20 bp):   
ATTTATTTTTATTTTTTTTT

Found at i:615 original size:9 final size:8

Alignment explanation


    Indices: 571--622  Score: 54
    Period size: 9  Copynumber: 6.4  Consensus size: 8

        561 GGCCCATTTA

                     
        571 TTATTTATT
          1 TTATTT-TT

                    
        580 TT-TTTTT
          1 TTATTTTT

                     
        587 ATTATTTTT
          1 -TTATTTTT

                     
        596 ATTATTTTT
          1 -TTATTTTT

                  * 
        605 TTATTTAT
          1 TTATTTTT

                    
        613 TT-TTTTT
          1 TTATTTTT

               
        620 TTA
          1 TTA

        623 CACTGGGCCT


Statistics
Matches: 38,  Mismatches: 2, Indels: 7
        0.81            0.04        0.15

Matches are distributed among these distances:
   7    8  0.21
   8   14  0.37
   9   16  0.42

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


Consensus pattern (8 bp):   
TTATTTTT
Done.