Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022647.1 Corchorus olitorius cultivar O-4 contig22680, 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: 10255
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32


Found at i:332 original size:7 final size:7

Alignment explanation


    Indices: 320--345  Score: 52
    Period size: 7  Copynumber: 3.7  Consensus size: 7

        310 TAATAAGTGT

                   
        320 CTTGTGC
          1 CTTGTGC

                   
        327 CTTGTGC
          1 CTTGTGC

                   
        334 CTTGTGC
          1 CTTGTGC

                 
        341 CTTGT
          1 CTTGT

        346 ATATGGTGGC


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   19  1.00

ACGTcount: A:0.00, C:0.27, G:0.27, T:0.46


Consensus pattern (7 bp):   
CTTGTGC

Found at i:434 original size:1 final size:1

Alignment explanation


    Indices: 428--452  Score: 50
    Period size: 1  Copynumber: 25.0  Consensus size: 1

        418 GAAGAAGAAG

                                     
        428 AAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAA

        453 CTCATATAGA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   24  1.00

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


Consensus pattern (1 bp):   
A

Found at i:9348 original size:18 final size:18

Alignment explanation


    Indices: 9307--9352  Score: 56
    Period size: 18  Copynumber: 2.6  Consensus size: 18

       9297 CACTAGAAAT

                    *         
       9307 TTAATAATAATTATTCAA
          1 TTAATAATTATTATTCAA

            **             *  
       9325 AAAATAATTATTATTTAA
          1 TTAATAATTATTATTCAA

                      
       9343 TTAATAATTA
          1 TTAATAATTA

       9353 ATTAATTTCA


Statistics
Matches: 22,  Mismatches: 6, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  18   22  1.00

ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46


Consensus pattern (18 bp):   
TTAATAATTATTATTCAA
Done.