Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010297.1 Corchorus capsularis cultivar CVL-1 contig10318, 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: 29189
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33


Found at i:4578 original size:24 final size:24

Alignment explanation


    Indices: 4535--4586  Score: 79
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       4525 TAGAGAGAAT

                                     
       4535 AAAAATAAACTCAGTTTTTTTTTAA
          1 AAAAATAAACTCAG-TTTTTTTTAA

                                     
       4560 AAAAGATAAACTCAG-TTTTTTTAA
          1 AAAA-ATAAACTCAGTTTTTTTTAA

               
       4584 AAA
          1 AAA

       4587 TAAAAAATAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  24   12  0.46
  25    4  0.15
  26   10  0.38

ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38


Consensus pattern (24 bp):   
AAAAATAAACTCAGTTTTTTTTAA

Found at i:10730 original size:1 final size:1

Alignment explanation


    Indices: 10724--10755  Score: 64
    Period size: 1  Copynumber: 32.0  Consensus size: 1

      10714 TGCTAATAAC

                                            
      10724 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

      10756 CAAGAATTTA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   31  1.00

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


Consensus pattern (1 bp):   
A

Found at i:20933 original size:2 final size:2

Alignment explanation


    Indices: 20926--20960  Score: 52
    Period size: 2  Copynumber: 17.5  Consensus size: 2

      20916 ATTGCCTCTT

                        *        *                              
      20926 TA TA TA TA AA TA TA AA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      20961 TAAAAAAAGC


Statistics
Matches: 29,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46


Consensus pattern (2 bp):   
TA

Done.