Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009187.1 Corchorus capsularis cultivar CVL-1 contig09208, 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: 51367
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30


Found at i:4361 original size:6 final size:7

Alignment explanation


    Indices: 4343--4372  Score: 60
    Period size: 7  Copynumber: 4.3  Consensus size: 7

       4333 TGTATATTCT

                   
       4343 GAAAAAA
          1 GAAAAAA

                   
       4350 GAAAAAA
          1 GAAAAAA

                   
       4357 GAAAAAA
          1 GAAAAAA

                   
       4364 GAAAAAA
          1 GAAAAAA

              
       4371 GA
          1 GA

       4373 GGAGAATAAA


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

Matches are distributed among these distances:
   7   23  1.00

ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00


Consensus pattern (7 bp):   
GAAAAAA

Found at i:21824 original size:19 final size:21

Alignment explanation


    Indices: 21789--21831  Score: 63
    Period size: 19  Copynumber: 2.1  Consensus size: 21

      21779 CGGGACCAAC

                                 
      21789 AAAATAAAAATCAGAAAAAAG
          1 AAAATAAAAATCAGAAAAAAG

                               * 
      21810 AAAA-AAAAATC-GAAAAAGG
          1 AAAATAAAAATCAGAAAAAAG

               
      21829 AAA
          1 AAA

      21832 GTTGAGTAAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  19   10  0.48
  20    7  0.33
  21    4  0.19

ACGTcount: A:0.77, C:0.05, G:0.12, T:0.07


Consensus pattern (21 bp):   
AAAATAAAAATCAGAAAAAAG

Found at i:32373 original size:1 final size:1

Alignment explanation


    Indices: 32367--32396  Score: 60
    Period size: 1  Copynumber: 30.0  Consensus size: 1

      32357 GTACTAATGC

                                          
      32367 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

      32397 TCTAATGAGA


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

Found at i:39682 original size:22 final size:22

Alignment explanation


    Indices: 39654--39700  Score: 94
    Period size: 22  Copynumber: 2.1  Consensus size: 22

      39644 AATTAATGTC

                                  
      39654 CATGATCAGGAACAATTACATG
          1 CATGATCAGGAACAATTACATG

                                  
      39676 CATGATCAGGAACAATTACATG
          1 CATGATCAGGAACAATTACATG

               
      39698 CAT
          1 CAT

      39701 CACCTTTTTA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   25  1.00

ACGTcount: A:0.40, C:0.19, G:0.17, T:0.23


Consensus pattern (22 bp):   
CATGATCAGGAACAATTACATG

Found at i:49239 original size:11 final size:11

Alignment explanation


    Indices: 49223--49247  Score: 50
    Period size: 11  Copynumber: 2.3  Consensus size: 11

      49213 TTGATACATT

                       
      49223 GATTAAACAAA
          1 GATTAAACAAA

                       
      49234 GATTAAACAAA
          1 GATTAAACAAA

               
      49245 GAT
          1 GAT

      49248 ATGGAGGGGG


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   14  1.00

ACGTcount: A:0.60, C:0.08, G:0.12, T:0.20


Consensus pattern (11 bp):   
GATTAAACAAA
Done.