Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013430.1 Corchorus capsularis cultivar CVL-1 contig13451, 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: 16696
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:2159 original size:16 final size:16

Alignment explanation


    Indices: 2138--2170  Score: 66
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       2128 TTTTAAAATG

                            
       2138 AATGCTGGCTTTTTTA
          1 AATGCTGGCTTTTTTA

                            
       2154 AATGCTGGCTTTTTTA
          1 AATGCTGGCTTTTTTA

             
       2170 A
          1 A

       2171 GAATTATATT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.21, C:0.12, G:0.18, T:0.48


Consensus pattern (16 bp):   
AATGCTGGCTTTTTTA

Found at i:8576 original size:31 final size:31

Alignment explanation


    Indices: 8535--8599  Score: 112
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       8525 GGTGGGCATC

                                           
       8535 TTTTAGTAATTTCACTACTCTATTAAGGTCA
          1 TTTTAGTAATTTCACTACTCTATTAAGGTCA

                 *      *                  
       8566 TTTTATTAATTTTACTACTCTATTAAGGTCA
          1 TTTTAGTAATTTCACTACTCTATTAAGGTCA

               
       8597 TTT
          1 TTT

       8600 GAGAAATGAC


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  31   32  1.00

ACGTcount: A:0.28, C:0.14, G:0.08, T:0.51


Consensus pattern (31 bp):   
TTTTAGTAATTTCACTACTCTATTAAGGTCA

Found at i:12381 original size:28 final size:29

Alignment explanation


    Indices: 12338--12393  Score: 87
    Period size: 28  Copynumber: 2.0  Consensus size: 29

      12328 AGACGTTCGT

                                         
      12338 CATGTTAGTTTATACTCAAGCGCGGAGTC
          1 CATGTTAGTTTATACTCAAGCGCGGAGTC

                       *       *        
      12367 CATG-TAGTTTGTACTCAATCGCGGAGT
          1 CATGTTAGTTTATACTCAAGCGCGGAGT

      12394 TATTGCCGAT


Statistics
Matches: 25,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  28   21  0.84
  29    4  0.16

ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32


Consensus pattern (29 bp):   
CATGTTAGTTTATACTCAAGCGCGGAGTC

Found at i:13240 original size:42 final size:42

Alignment explanation


    Indices: 13125--13229  Score: 210
    Period size: 42  Copynumber: 2.5  Consensus size: 42

      13115 GTGGACTAGC

                                                      
      13125 CGGCGCGTGGAGGAGGATGGCTGGCGTGTCGGCAGTGCGTGA
          1 CGGCGCGTGGAGGAGGATGGCTGGCGTGTCGGCAGTGCGTGA

                                                      
      13167 CGGCGCGTGGAGGAGGATGGCTGGCGTGTCGGCAGTGCGTGA
          1 CGGCGCGTGGAGGAGGATGGCTGGCGTGTCGGCAGTGCGTGA

                                 
      13209 CGGCGCGTGGAGGAGGATGGC
          1 CGGCGCGTGGAGGAGGATGGC

      13230 CAACGGGTCG


Statistics
Matches: 63,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  42   63  1.00

ACGTcount: A:0.12, C:0.19, G:0.53, T:0.15


Consensus pattern (42 bp):   
CGGCGCGTGGAGGAGGATGGCTGGCGTGTCGGCAGTGCGTGA
Done.