Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023833.1 Corchorus olitorius cultivar O-4 contig23866, 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: 16281
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35


Found at i:379 original size:10 final size:10

Alignment explanation


    Indices: 355--384  Score: 51
    Period size: 10  Copynumber: 2.9  Consensus size: 10

        345 TAAGGCTAGG

                       
        355 CCCGGCCCGAA
          1 CCCGGCCC-AA

                      
        366 CCCGGCCCAA
          1 CCCGGCCCAA

                     
        376 CCCGGCCCA
          1 CCCGGCCCA

        385 TGAACAGGTC


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

Matches are distributed among these distances:
  10   11  0.58
  11    8  0.42

ACGTcount: A:0.17, C:0.60, G:0.23, T:0.00


Consensus pattern (10 bp):   
CCCGGCCCAA

Found at i:658 original size:21 final size:20

Alignment explanation


    Indices: 634--676  Score: 50
    Period size: 20  Copynumber: 2.1  Consensus size: 20

        624 GAAATATTTC

                *                
        634 ATTAGAAATTATTTTCTAATA
          1 ATTACAAATTA-TTTCTAATA

                  *         *   
        655 ATTACATATTATTTCTGATA
          1 ATTACAAATTATTTCTAATA

              
        675 AT
          1 AT

        677 ATTTATTGCA


Statistics
Matches: 19,  Mismatches: 3, Indels: 1
        0.83            0.13        0.04

Matches are distributed among these distances:
  20   10  0.53
  21    9  0.47

ACGTcount: A:0.40, C:0.07, G:0.05, T:0.49


Consensus pattern (20 bp):   
ATTACAAATTATTTCTAATA

Found at i:735 original size:30 final size:31

Alignment explanation


    Indices: 673--738  Score: 91
    Period size: 30  Copynumber: 2.2  Consensus size: 31

        663 TTATTTCTGA

                       *                   
        673 TAATATTTATTGCATATTTAATAAATTATTC
          1 TAATATTTATTACATATTTAATAAATTATTC

                                *           
        704 TAATATTTATTACATA-TTACTAAA-TATTTC
          1 TAATATTTATTACATATTTAATAAATTA-TTC

                 
        734 TAATA
          1 TAATA

        739 AAATCAAAAT


Statistics
Matches: 32,  Mismatches: 2, Indels: 3
        0.86            0.05        0.08

Matches are distributed among these distances:
  29    2  0.06
  30   15  0.47
  31   15  0.47

ACGTcount: A:0.41, C:0.08, G:0.02, T:0.50


Consensus pattern (31 bp):   
TAATATTTATTACATATTTAATAAATTATTC

Found at i:8302 original size:42 final size:42

Alignment explanation


    Indices: 8243--8327  Score: 170
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       8233 GGGACTAGAT

                                                      
       8243 TGAAATATTTAAAACTTAATTAATTAAAAAAATGGACATGTG
          1 TGAAATATTTAAAACTTAATTAATTAAAAAAATGGACATGTG

                                                      
       8285 TGAAATATTTAAAACTTAATTAATTAAAAAAATGGACATGTG
          1 TGAAATATTTAAAACTTAATTAATTAAAAAAATGGACATGTG

             
       8327 T
          1 T

       8328 CAACTCCACG


Statistics
Matches: 43,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  42   43  1.00

ACGTcount: A:0.49, C:0.05, G:0.12, T:0.34


Consensus pattern (42 bp):   
TGAAATATTTAAAACTTAATTAATTAAAAAAATGGACATGTG
Done.