Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006816.1 Corchorus olitorius cultivar O-4 contig06841, 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, 669

Length: 1116
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.35


Found at i:328 original size:28 final size:25

Alignment explanation


    Indices: 291--343  Score: 70
    Period size: 26  Copynumber: 2.0  Consensus size: 25

        281 AATCTATCCT

                      *                
        291 TCTACTCATCTATCATCAAGTTTTTCA
          1 TCTACTCATCCATCA--AAGTTTTTCA

                                      
        318 TCTATCTCATCCATCAAAGTTTTTCA
          1 TCTA-CTCATCCATCAAAGTTTTTCA

        344 AATTTTCTAG


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  26   10  0.42
  27    4  0.17
  28   10  0.42

ACGTcount: A:0.26, C:0.26, G:0.04, T:0.43


Consensus pattern (25 bp):   
TCTACTCATCCATCAAAGTTTTTCA

Found at i:474 original size:9 final size:9

Alignment explanation


    Indices: 456--489  Score: 50
    Period size: 9  Copynumber: 3.7  Consensus size: 9

        446 AGTTTAATCG

                 *   
        456 AAAAATATA
          1 AAAAAAATA

                     
        465 AAAAAAATA
          1 AAAAAAATA

                      
        474 AAAACAAATA
          1 AAAA-AAATA

                  
        484 AAAAAA
          1 AAAAAA

        490 TTTCGACCAG


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
   9   14  0.61
  10    9  0.39

ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12


Consensus pattern (9 bp):   
AAAAAAATA

Found at i:477 original size:10 final size:10

Alignment explanation


    Indices: 456--489  Score: 50
    Period size: 10  Copynumber: 3.3  Consensus size: 10

        446 AGTTTAATCG

                       
        456 AAAAATATAAA
          1 AAAAATA-AAA

                      
        467 AAAAATAAAA
          1 AAAAATAAAA

             *        
        477 ACAAATAAAA
          1 AAAAATAAAA

               
        487 AAA
          1 AAA

        490 TTTCGACCAG


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

Matches are distributed among these distances:
  10   14  0.67
  11    7  0.33

ACGTcount: A:0.85, C:0.03, G:0.00, T:0.12


Consensus pattern (10 bp):   
AAAAATAAAA
Done.