Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005768.1 Corchorus olitorius cultivar O-4 contig05792, 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, 633

Length: 1055
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28


Found at i:360 original size:10 final size:10

Alignment explanation


    Indices: 345--384  Score: 57
    Period size: 10  Copynumber: 4.1  Consensus size: 10

        335 TATGTTTAAT

                      
        345 TACTTATATA
          1 TACTTATATA

                       
        355 TACTTATACT-
          1 TACTTATA-TA

                      
        365 TACTTATATA
          1 TACTTATATA

                      
        375 TA-TTATATA
          1 TACTTATATA

             
        384 T
          1 T

        385 TCAATATAGA


Statistics
Matches: 28,  Mismatches: 0, Indels: 5
        0.85            0.00        0.15

Matches are distributed among these distances:
   9    9  0.32
  10   18  0.64
  11    1  0.04

ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53


Consensus pattern (10 bp):   
TACTTATATA

Found at i:369 original size:20 final size:19

Alignment explanation


    Indices: 344--381  Score: 67
    Period size: 20  Copynumber: 1.9  Consensus size: 19

        334 TTATGTTTAA

                                
        344 TTACTTATATATACTTATAC
          1 TTACTTATATATA-TTATAC

                              
        364 TTACTTATATATATTATA
          1 TTACTTATATATATTATA

        382 TATTCAATAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  19    5  0.28
  20   13  0.72

ACGTcount: A:0.37, C:0.11, G:0.00, T:0.53


Consensus pattern (19 bp):   
TTACTTATATATATTATAC

Found at i:498 original size:16 final size:17

Alignment explanation


    Indices: 477--511  Score: 63
    Period size: 17  Copynumber: 2.1  Consensus size: 17

        467 TCTATTATTC

                             
        477 ATTAAT-CTACCTGTAT
          1 ATTAATACTACCTGTAT

                             
        493 ATTAATACTACCTGTAT
          1 ATTAATACTACCTGTAT

              
        510 AT
          1 AT

        512 CTTAAGAATC


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  16    6  0.33
  17   12  0.67

ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43


Consensus pattern (17 bp):   
ATTAATACTACCTGTAT

Done.