Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008972.1 Corchorus capsularis cultivar CVL-1 contig08993, 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: 3292
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31


Found at i:796 original size:20 final size:20

Alignment explanation


    Indices: 773--810  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

        763 CAAAATCCAG

                                
        773 AAAAAAAAATGAAAAAAATA
          1 AAAAAAAAATGAAAAAAATA

                  **          
        793 AAAAAATGATGAAAAAAA
          1 AAAAAAAAATGAAAAAAA

        811 ATGATGAGCA


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.82, C:0.00, G:0.08, T:0.11


Consensus pattern (20 bp):   
AAAAAAAAATGAAAAAAATA

Found at i:807 original size:17 final size:16

Alignment explanation


    Indices: 773--811  Score: 51
    Period size: 17  Copynumber: 2.2  Consensus size: 16

        763 CAAAATCCAG

                            
        773 AAAAAAAAATGAAAAA
          1 AAAAAAAAATGAAAAA

                               
        789 AATAAAAAAATGATGAAAA
          1 AA-AAAAAAATGA--AAAA

                
        808 AAAA
          1 AAAA

        812 TGATGAGCAG


Statistics
Matches: 20,  Mismatches: 0, Indels: 4
        0.83            0.00        0.17

Matches are distributed among these distances:
  16    2  0.10
  17   10  0.50
  18    2  0.10
  19    6  0.30

ACGTcount: A:0.82, C:0.00, G:0.08, T:0.10


Consensus pattern (16 bp):   
AAAAAAAAATGAAAAA

Found at i:808 original size:13 final size:13

Alignment explanation


    Indices: 792--817  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

        782 TGAAAAAAAT

                         
        792 AAAAAAATGATGA
          1 AAAAAAATGATGA

                         
        805 AAAAAAATGATGA
          1 AAAAAAATGATGA

        818 GCAGCACCCA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15


Consensus pattern (13 bp):   
AAAAAAATGATGA

Found at i:2176 original size:23 final size:23

Alignment explanation


    Indices: 2137--2181  Score: 56
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       2127 AGTGCTCTGT

                       *     *     
       2137 TTAGAGTTTATTCAATTTAGTCA
          1 TTAGAGTTTATGCAATTAAGTCA

                                   
       2160 TTAGA-TTTATGCTAATTAAGTC
          1 TTAGAGTTTATGC-AATTAAGTC

       2182 CAAGAGGTCA


Statistics
Matches: 19,  Mismatches: 2, Indels: 2
        0.83            0.09        0.09

Matches are distributed among these distances:
  22    6  0.32
  23   13  0.68

ACGTcount: A:0.31, C:0.09, G:0.13, T:0.47


Consensus pattern (23 bp):   
TTAGAGTTTATGCAATTAAGTCA
Done.