Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016504.1 Corchorus capsularis cultivar CVL-1 contig16525, 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: 18187
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:10334 original size:24 final size:24

Alignment explanation


    Indices: 10307--10352  Score: 67
    Period size: 24  Copynumber: 1.9  Consensus size: 24

      10297 ATTTTATTTG

                                     
      10307 TTTT-TAATTAAATTGACTAGTTTT
          1 TTTTGTAATT-AATTGACTAGTTTT

                  *               
      10331 TTTTGTTATTAATTGACTAGTT
          1 TTTTGTAATTAATTGACTAGTT

      10353 AAAATATTCA


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  24   16  0.80
  25    4  0.20

ACGTcount: A:0.26, C:0.04, G:0.11, T:0.59


Consensus pattern (24 bp):   
TTTTGTAATTAATTGACTAGTTTT

Found at i:10658 original size:17 final size:17

Alignment explanation


    Indices: 10633--10688  Score: 73
    Period size: 17  Copynumber: 3.4  Consensus size: 17

      10623 TTTTAGATAT

                              
      10633 AATATATATTATTAAATA
          1 AATA-ATATTATTAAATA

                        *    
      10651 AATAATATTA-TCAA-A
          1 AATAATATTATTAAATA

                             
      10666 AA-AATATTATTAAATA
          1 AATAATATTATTAAATA

                   
      10682 AATAATA
          1 AATAATA

      10689 AATATATTTT


Statistics
Matches: 33,  Mismatches: 2, Indels: 7
        0.79            0.05        0.17

Matches are distributed among these distances:
  14    7  0.21
  15    6  0.18
  16    6  0.18
  17   10  0.30
  18    4  0.12

ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38


Consensus pattern (17 bp):   
AATAATATTATTAAATA

Found at i:10973 original size:16 final size:16

Alignment explanation


    Indices: 10954--11006  Score: 54
    Period size: 16  Copynumber: 3.3  Consensus size: 16

      10944 GGTTTGAGTC

                            
      10954 AGGTCGGGTTGAATTT
          1 AGGTCGGGTTGAATTT

                 *          
      10970 AGGTCAGGTT-AATTT
          1 AGGTCGGGTTGAATTT

            *        *       
      10985 GGGTTCGGGCTGAATTT
          1 AGG-TCGGGTTGAATTT

            *    
      11002 GGGTC
          1 AGGTC

      11007 ATGTTAATTC


Statistics
Matches: 31,  Mismatches: 4, Indels: 4
        0.79            0.10        0.10

Matches are distributed among these distances:
  15    7  0.23
  16   16  0.52
  17    8  0.26

ACGTcount: A:0.17, C:0.09, G:0.38, T:0.36


Consensus pattern (16 bp):   
AGGTCGGGTTGAATTT

Found at i:10993 original size:32 final size:32

Alignment explanation


    Indices: 10957--11027  Score: 97
    Period size: 32  Copynumber: 2.2  Consensus size: 32

      10947 TTGAGTCAGG

                                       *    
      10957 TCGGGTTGAATTTAGGTCAGGTTAATTTGGGT
          1 TCGGGTTGAATTTAGGTCAGGTTAATTCGGGT

                 *       *     *            
      10989 TCGGGCTGAATTTGGGTCATGTTAATTCGGGT
          1 TCGGGTTGAATTTAGGTCAGGTTAATTCGGGT

              *    
      11021 TCAGGTT
          1 TCGGGTT

      11028 CGATCTGGAT


Statistics
Matches: 33,  Mismatches: 6, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  32   33  1.00

ACGTcount: A:0.17, C:0.10, G:0.34, T:0.39


Consensus pattern (32 bp):   
TCGGGTTGAATTTAGGTCAGGTTAATTCGGGT
Done.