Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000906.1 Corchorus capsularis cultivar CVL-1 contig00906, 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: 1919
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35


Found at i:299 original size:13 final size:12

Alignment explanation


    Indices: 275--315  Score: 55
    Period size: 13  Copynumber: 3.2  Consensus size: 12

        265 TGCTTTATAA

                 *      
        275 TTATTGTTTGCT
          1 TTATTATTTGCT

                         
        287 TTATTAATTTGCT
          1 TTATT-ATTTGCT

                         
        300 TTATTATCTTGCT
          1 TTATTAT-TTGCT

               
        313 TTA
          1 TTA

        316 GATTTTAGAT


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  12    7  0.27
  13   19  0.73

ACGTcount: A:0.17, C:0.10, G:0.10, T:0.63


Consensus pattern (12 bp):   
TTATTATTTGCT

Found at i:324 original size:7 final size:7

Alignment explanation


    Indices: 312--353  Score: 61
    Period size: 7  Copynumber: 6.3  Consensus size: 7

        302 ATTATCTTGC

                   
        312 TTTAGAT
          1 TTTAGAT

                   
        319 TTTAGAT
          1 TTTAGAT

              *    
        326 TTAAGAT
          1 TTTAGAT

                   
        333 TTTAGA-
          1 TTTAGAT

                   
        339 TTTAGA-
          1 TTTAGAT

                   
        345 TTTAGAT
          1 TTTAGAT

              
        352 TT
          1 TT

        354 GATTTGCTTT


Statistics
Matches: 32,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
   6   12  0.38
   7   20  0.62

ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55


Consensus pattern (7 bp):   
TTTAGAT

Found at i:334 original size:14 final size:13

Alignment explanation


    Indices: 312--358  Score: 71
    Period size: 14  Copynumber: 3.7  Consensus size: 13

        302 ATTATCTTGC

                         
        312 TTTAGATTTTAGA
          1 TTTAGATTTTAGA

                          
        325 TTTAAGATTTTAGA
          1 TTT-AGATTTTAGA

                         
        339 TTTAGA-TTTAGA
          1 TTTAGATTTTAGA

                     
        351 TTT-GATTT
          1 TTTAGATTT

        359 GCTTTGTTTT


Statistics
Matches: 32,  Mismatches: 0, Indels: 5
        0.86            0.00        0.14

Matches are distributed among these distances:
  11    2  0.06
  12   11  0.34
  13    6  0.19
  14   13  0.41

ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55


Consensus pattern (13 bp):   
TTTAGATTTTAGA

Found at i:342 original size:6 final size:6

Alignment explanation


    Indices: 312--358  Score: 60
    Period size: 6  Copynumber: 7.5  Consensus size: 6

        302 ATTATCTTGC

                                                                   
        312 TTTAGA TTTTAGA TTTAAGA TTTTAGA TTTAGA TTTAGA TTT-GA TTT
          1 TTTAGA -TTTAGA TTT-AGA -TTTAGA TTTAGA TTTAGA TTTAGA TTT

        359 GCTTTGTTTT


Statistics
Matches: 38,  Mismatches: 0, Indels: 6
        0.86            0.00        0.14

Matches are distributed among these distances:
   5    5  0.13
   6   18  0.47
   7   12  0.32
   8    3  0.08

ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55


Consensus pattern (6 bp):   
TTTAGA
Done.