Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012180.1 Corchorus capsularis cultivar CVL-1 contig12201, 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: 14463
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33


Found at i:1758 original size:20 final size:20

Alignment explanation


    Indices: 1733--1773  Score: 82
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       1723 TGATGCCAAA

                                
       1733 AAAAAAATCAGGGGGTAACC
          1 AAAAAAATCAGGGGGTAACC

                                
       1753 AAAAAAATCAGGGGGTAACC
          1 AAAAAAATCAGGGGGTAACC

             
       1773 A
          1 A

       1774 CCAGGAGGAT


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   21  1.00

ACGTcount: A:0.51, C:0.15, G:0.24, T:0.10


Consensus pattern (20 bp):   
AAAAAAATCAGGGGGTAACC

Found at i:1960 original size:34 final size:34

Alignment explanation


    Indices: 1922--2016  Score: 163
    Period size: 34  Copynumber: 2.7  Consensus size: 34

       1912 ATTTGACAGT

                                        *     
       1922 ACTCCTTGTGAGAGTTTTTGTATTGGTTTTTGGG
          1 ACTCCTTGTGAGAGTTTTTGTATTGGTTATTGGG

                                              
       1956 ACTCCTTGTGAGAGTTTTTGTATTGGTTATTGGG
          1 ACTCCTTGTGAGAGTTTTTGTATTGGTTATTGGG

                                       
       1990 ACTCCTTGTGAGAGTATTTTTGTATTG
          1 ACTCCTTGTGAGAG--TTTTTGTATTG

       2017 TCTTTGTACA


Statistics
Matches: 58,  Mismatches: 1, Indels: 2
        0.95            0.02        0.03

Matches are distributed among these distances:
  34   47  0.81
  36   11  0.19

ACGTcount: A:0.15, C:0.09, G:0.27, T:0.48


Consensus pattern (34 bp):   
ACTCCTTGTGAGAGTTTTTGTATTGGTTATTGGG

Found at i:6304 original size:6 final size:6

Alignment explanation


    Indices: 6285--6322  Score: 67
    Period size: 6  Copynumber: 6.2  Consensus size: 6

       6275 AACGTGGGGG

                                                        
       6285 AAGCCA AAGCCCA AAGCCA AAGCCA AAGCCA AAGCCA A
          1 AAGCCA AAG-CCA AAGCCA AAGCCA AAGCCA AAGCCA A

       6323 GCTAATAAAA


Statistics
Matches: 31,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   6   25  0.81
   7    6  0.19

ACGTcount: A:0.50, C:0.34, G:0.16, T:0.00


Consensus pattern (6 bp):   
AAGCCA

Done.