Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003399.1 Corchorus capsularis cultivar CVL-1 contig03407, 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, 809

Length: 1349
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.30


Found at i:625 original size:33 final size:33

Alignment explanation


    Indices: 583--724  Score: 248
    Period size: 33  Copynumber: 4.3  Consensus size: 33

        573 TTCTCGTCAC

                             *    **         
        583 CCAAAACAGAATTATTTTCAATATTATGATCAA
          1 CCAAAACAGAATTATTTGCAATGCTATGATCAA

                                             
        616 CCAAAACAGAATTATTTGCAATGCTATGATCAA
          1 CCAAAACAGAATTATTTGCAATGCTATGATCAA

                     *                       
        649 CCAAAACAGTATTATTTGCAATGCTATGATCAA
          1 CCAAAACAGAATTATTTGCAATGCTATGATCAA

                                             
        682 CCAAAACAGAATTATTTGCAATGCTATGATCAA
          1 CCAAAACAGAATTATTTGCAATGCTATGATCAA

                      
        715 CCAAAACAGA
          1 CCAAAACAGA

        725 TTTGTTTTCA


Statistics
Matches: 104,  Mismatches: 5, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  33  104  1.00

ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27


Consensus pattern (33 bp):   
CCAAAACAGAATTATTTGCAATGCTATGATCAA

Found at i:752 original size:66 final size:66

Alignment explanation


    Indices: 583--757  Score: 210
    Period size: 66  Copynumber: 2.7  Consensus size: 66

        573 TTCTCGTCAC

                     *       *     **    *                                   
        583 CCAAAACAGAATTATTTTCAATATTATGATCAACCAAAACAGAATTATTTGCAATGCTATGATCA
          1 CCAAAACAGTATTATTTGCAATACAATGAGCAACCAAAACAGAATTATTTGCAATGCTATGATCA

             
        648 A
         66 A

                                  * *    *                                   
        649 CCAAAACAGTATTATTTGCAATGCTATGATCAACCAAAACAGAATTATTTGCAATGCTATGATCA
          1 CCAAAACAGTATTATTTGCAATACAATGAGCAACCAAAACAGAATTATTTGCAATGCTATGATCA

             
        714 A
         66 A

                          *   *          *    *          
        715 CCAAAACAG-ATTTGTTTTC-ATCACAATTAGCATCCAAAACAGA
          1 CCAAAACAGTA-TTATTTGCAAT-ACAATGAGCAACCAAAACAGA

        758 TTTAGTATCA


Statistics
Matches: 96,  Mismatches: 11, Indels: 4
        0.86            0.10        0.04

Matches are distributed among these distances:
  65    3  0.03
  66   93  0.97

ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29


Consensus pattern (66 bp):   
CCAAAACAGTATTATTTGCAATACAATGAGCAACCAAAACAGAATTATTTGCAATGCTATGATCA
A

Found at i:787 original size:33 final size:33

Alignment explanation


    Indices: 750--854  Score: 131
    Period size: 33  Copynumber: 3.2  Consensus size: 33

        740 ATTAGCATCC

                                *            
        750 AAAACAGATTTAGTATCATCACAAACAACACTT
          1 AAAACAGATTTAGTATCATCGCAAACAACACTT

                          *    *            *
        783 AAAACAGATTTAGTGTCATTGCAAACAACACTC
          1 AAAACAGATTTAGTATCATCGCAAACAACACTT

               **  *                          
        816 AAATTAGGTTTAGTATCATCGCAAACAACA-TCT
          1 AAAACAGATTTAGTATCATCGCAAACAACACT-T

                  
        849 AAAACA
          1 AAAACA

        855 CTCTTTGCAA


Statistics
Matches: 59,  Mismatches: 12, Indels: 2
        0.81            0.16        0.03

Matches are distributed among these distances:
  32    1  0.02
  33   58  0.98

ACGTcount: A:0.46, C:0.20, G:0.10, T:0.25


Consensus pattern (33 bp):   
AAAACAGATTTAGTATCATCGCAAACAACACTT
Done.