Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001095.1 Corchorus capsularis cultivar CVL-1 contig01095, 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: 13377
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35


Found at i:295 original size:2 final size:2

Alignment explanation


    Indices: 288--320  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

        278 GTAGGTAGGA

                                                             
        288 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

        321 AGACAAAATT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:4335 original size:2 final size:2

Alignment explanation


    Indices: 4328--4367  Score: 66
    Period size: 2  Copynumber: 21.0  Consensus size: 2

       4318 TTTATAGCTT

                                                                          
       4328 TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA T- TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       4368 AGTCTAAACT


Statistics
Matches: 36,  Mismatches: 0, Indels: 4
        0.90            0.00        0.10

Matches are distributed among these distances:
   1    2  0.06
   2   34  0.94

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:4350 original size:17 final size:17

Alignment explanation


    Indices: 4328--4360  Score: 66
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       4318 TTTATAGCTT

                             
       4328 TATATATATATATATAA
          1 TATATATATATATATAA

                            
       4345 TATATATATATATATA
          1 TATATATATATATATA

       4361 TATTATAAGT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (17 bp):   
TATATATATATATATAA

Found at i:4352 original size:19 final size:19

Alignment explanation


    Indices: 4328--4367  Score: 71
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       4318 TTTATAGCTT

                               
       4328 TATATATATATATATAATA
          1 TATATATATATATATAATA

                            *  
       4347 TATATATATATATATATTA
          1 TATATATATATATATAATA

              
       4366 TA
          1 TA

       4368 AGTCTAAACT


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  19   20  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (19 bp):   
TATATATATATATATAATA
Done.