Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015982.1 Corchorus capsularis cultivar CVL-1 contig16003, 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: 3862
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32


Found at i:337 original size:2 final size:2

Alignment explanation


    Indices: 330--374  Score: 54
    Period size: 2  Copynumber: 21.5  Consensus size: 2

        320 TGTTTGTTGC

                                     *               *                      
        330 AT AT AT AT AT AT AT AT AC ACT AT AT AT AC ACT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT

             
        374 A
          1 A

        375 CACACACACA


Statistics
Matches: 37,  Mismatches: 4, Indels: 4
        0.82            0.09        0.09

Matches are distributed among these distances:
   2   35  0.95
   3    2  0.05

ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42


Consensus pattern (2 bp):   
AT

Found at i:355 original size:11 final size:11

Alignment explanation


    Indices: 330--368  Score: 62
    Period size: 11  Copynumber: 3.6  Consensus size: 11

        320 TGTTTGTTGC

                   *   
        330 ATATATATA-T
          1 ATATATACACT

                       
        340 ATATATACACT
          1 ATATATACACT

                       
        351 ATATATACACT
          1 ATATATACACT

                   
        362 ATATATA
          1 ATATATA

        369 TATATACACA


Statistics
Matches: 27,  Mismatches: 1, Indels: 1
        0.93            0.03        0.03

Matches are distributed among these distances:
  10    8  0.30
  11   19  0.70

ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41


Consensus pattern (11 bp):   
ATATATACACT

Found at i:2304 original size:17 final size:17

Alignment explanation


    Indices: 2282--2315  Score: 68
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       2272 TGATTCTTAC

                             
       2282 AAGAAGCTTGTAAGGGT
          1 AAGAAGCTTGTAAGGGT

                             
       2299 AAGAAGCTTGTAAGGGT
          1 AAGAAGCTTGTAAGGGT

       2316 GTTGTTCTTA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.35, C:0.06, G:0.35, T:0.24


Consensus pattern (17 bp):   
AAGAAGCTTGTAAGGGT
Done.