Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021874.1 Corchorus olitorius cultivar O-4 contig21907, 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: 10442
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35


Found at i:2474 original size:3 final size:3

Alignment explanation


    Indices: 2466--2509  Score: 52
    Period size: 3  Copynumber: 14.7  Consensus size: 3

       2456 GTTTTTGCAT

                              *   *   *   *                           
       2466 CAG CAG CAG CAG CAA CAA CAA CAA CAG CAG CAG CAG CAG CAG CA
          1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA

       2510 ATTGCTGCAT


Statistics
Matches: 39,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   3   39  1.00

ACGTcount: A:0.43, C:0.34, G:0.23, T:0.00


Consensus pattern (3 bp):   
CAG

Found at i:10183 original size:42 final size:43

Alignment explanation


    Indices: 10116--10202  Score: 167
    Period size: 42  Copynumber: 2.0  Consensus size: 43

      10106 GTACTTTTTC

                                                       
      10116 GAGGAGAGTGCTTTTCCAAGGATAGGGGATTAGGGAACAATTA
          1 GAGGAGAGTGCTTTTCCAAGGATAGGGGATTAGGGAACAATTA

                                                       
      10159 GAGGAGAGTGC-TTTCCAAGGATAGGGGATTAGGGAACAATTA
          1 GAGGAGAGTGCTTTTCCAAGGATAGGGGATTAGGGAACAATTA

              
      10201 GA
          1 GA

      10203 AATACTCGGT


Statistics
Matches: 44,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  42   33  0.75
  43   11  0.25

ACGTcount: A:0.33, C:0.09, G:0.36, T:0.22


Consensus pattern (43 bp):   
GAGGAGAGTGCTTTTCCAAGGATAGGGGATTAGGGAACAATTA

Found at i:10263 original size:26 final size:26

Alignment explanation


    Indices: 10227--10276  Score: 100
    Period size: 26  Copynumber: 1.9  Consensus size: 26

      10217 TCTATATTTC

                                      
      10227 AATGTCTAATAACAGAAGAAGTTGGG
          1 AATGTCTAATAACAGAAGAAGTTGGG

                                    
      10253 AATGTCTAATAACAGAAGAAGTTG
          1 AATGTCTAATAACAGAAGAAGTTG

      10277 AGAAATATGA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   24  1.00

ACGTcount: A:0.44, C:0.08, G:0.24, T:0.24


Consensus pattern (26 bp):   
AATGTCTAATAACAGAAGAAGTTGGG
Done.