Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011920.1 Corchorus capsularis cultivar CVL-1 contig11941, 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: 40487
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32


Found at i:14734 original size:27 final size:21

Alignment explanation


    Indices: 14682--14745  Score: 112
    Period size: 21  Copynumber: 3.0  Consensus size: 21

      14672 TAAAGGAAAC

                                 
      14682 CTAAATATAAATAAGAAACCT
          1 CTAAATATAAATAAGAAACCT

                                 
      14703 CTAAATATAAATAAGAAACCT
          1 CTAAATATAAATAAGAAACCT

                                  
      14724 CT-AATAATAAATAAGAAACCT
          1 CTAAAT-ATAAATAAGAAACCT

             
      14745 C
          1 C

      14746 CAACATAGGA


Statistics
Matches: 42,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
  20    3  0.07
  21   39  0.93

ACGTcount: A:0.56, C:0.16, G:0.05, T:0.23


Consensus pattern (21 bp):   
CTAAATATAAATAAGAAACCT

Found at i:36130 original size:13 final size:12

Alignment explanation


    Indices: 36103--36159  Score: 51
    Period size: 13  Copynumber: 4.3  Consensus size: 12

      36093 TAATGCACCC

                          
      36103 AAAACATCTTAATA
          1 AAAACAT-TT-ATA

                         
      36117 AAAATCATTTATA
          1 AAAA-CATTTATA

                          
      36130 AAAACAATTTATTA
          1 AAAAC-ATTTA-TA

                  * *   
      36144 AAAACAGTAATA
          1 AAAACATTTATA

                
      36156 AAAA
          1 AAAA

      36160 TAAGTCCCTC


Statistics
Matches: 38,  Mismatches: 2, Indels: 8
        0.79            0.04        0.17

Matches are distributed among these distances:
  12    7  0.18
  13   15  0.39
  14   13  0.34
  15    3  0.08

ACGTcount: A:0.61, C:0.09, G:0.02, T:0.28


Consensus pattern (12 bp):   
AAAACATTTATA

Found at i:39729 original size:40 final size:40

Alignment explanation


    Indices: 39685--39765  Score: 162
    Period size: 40  Copynumber: 2.0  Consensus size: 40

      39675 AAAATTAATT

                                                    
      39685 ACTAAAATTGAGTATAAATGAAAAATAAGATACACTTTTC
          1 ACTAAAATTGAGTATAAATGAAAAATAAGATACACTTTTC

                                                    
      39725 ACTAAAATTGAGTATAAATGAAAAATAAGATACACTTTTC
          1 ACTAAAATTGAGTATAAATGAAAAATAAGATACACTTTTC

             
      39765 A
          1 A

      39766 GTATTGACTT


Statistics
Matches: 41,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  40   41  1.00

ACGTcount: A:0.51, C:0.10, G:0.10, T:0.30


Consensus pattern (40 bp):   
ACTAAAATTGAGTATAAATGAAAAATAAGATACACTTTTC
Done.