Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000862.1 Corchorus capsularis cultivar CVL-1 contig00862, 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: 16576
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:124 original size:2 final size:2

Alignment explanation


    Indices: 117--141  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

        107 TAGCATGCAA

                                                 
        117 AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A

        142 GCTAATCTTA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:1050 original size:15 final size:15

Alignment explanation


    Indices: 1026--1055  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       1016 AAGCAATATG

                 *         
       1026 TTATCTTCCAAATCA
          1 TTATCATCCAAATCA

                           
       1041 TTATCATCCAAATCA
          1 TTATCATCCAAATCA

       1056 ATTTTCACAA


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.37, C:0.27, G:0.00, T:0.37


Consensus pattern (15 bp):   
TTATCATCCAAATCA

Found at i:4105 original size:33 final size:32

Alignment explanation


    Indices: 4042--4104  Score: 103
    Period size: 33  Copynumber: 2.0  Consensus size: 32

       4032 ATGACATCGT

                                             
       4042 GAAATTTTGTTTTTAGCAAATGTCAAAAAAAAA
          1 GAAATTTTGTTTTTAGC-AATGTCAAAAAAAAA

                                            
       4075 GAAATTTTGTTTTTAGC-ATG-CAAAAAAAAA
          1 GAAATTTTGTTTTTAGCAATGTCAAAAAAAAA

       4105 ATGCTATAGC


Statistics
Matches: 30,  Mismatches: 0, Indels: 3
        0.91            0.00        0.09

Matches are distributed among these distances:
  30   10  0.33
  31    3  0.10
  33   17  0.57

ACGTcount: A:0.48, C:0.06, G:0.13, T:0.33


Consensus pattern (32 bp):   
GAAATTTTGTTTTTAGCAATGTCAAAAAAAAA

Found at i:15495 original size:1 final size:1

Alignment explanation


    Indices: 15489--15518  Score: 60
    Period size: 1  Copynumber: 30.0  Consensus size: 1

      15479 TAATAATAAT

                                          
      15489 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

      15519 CTGAAACAAA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   29  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Done.