Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005063.1 Corchorus capsularis cultivar CVL-1 contig05081, 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: 10300
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31


Found at i:186 original size:2 final size:2

Alignment explanation


    Indices: 179--211  Score: 57
    Period size: 2  Copynumber: 16.0  Consensus size: 2

        169 ATTGTTTTAA

                                                            
        179 AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT

        212 TAAGCATCAT


Statistics
Matches: 30,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   2   28  0.93
   3    2  0.07

ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:337 original size:26 final size:26

Alignment explanation


    Indices: 308--373  Score: 88
    Period size: 22  Copynumber: 2.7  Consensus size: 26

        298 GAAAGAATAA

                                      
        308 TCAAATTTGAGTTGGAGTTTTTTTGT
          1 TCAAATTTGAGTTGGAGTTTTTTTGT

                                       
        334 TCAAATTTGCA-----AGTTTTTTTGT
          1 TCAAATTTG-AGTTGGAGTTTTTTTGT

                              
        356 TCAAATTTGAGTTGGAGT
          1 TCAAATTTGAGTTGGAGT

        374 CGAGTAGTTG


Statistics
Matches: 34,  Mismatches: 0, Indels: 12
        0.74            0.00        0.26

Matches are distributed among these distances:
  21    1  0.03
  22   20  0.59
  26   12  0.35
  27    1  0.03

ACGTcount: A:0.23, C:0.06, G:0.21, T:0.50


Consensus pattern (26 bp):   
TCAAATTTGAGTTGGAGTTTTTTTGT

Found at i:10253 original size:2 final size:2

Alignment explanation


    Indices: 10248--10294  Score: 94
    Period size: 2  Copynumber: 23.5  Consensus size: 2

      10238 GTTTTGGGTA

                                                                          
      10248 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

                   
      10290 AG AG A
          1 AG AG A

      10295 AGAAGA


Statistics
Matches: 45,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   45  1.00

ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00


Consensus pattern (2 bp):   
AG

Done.