Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012402.1 Corchorus capsularis cultivar CVL-1 contig12423, 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: 40235
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34


Found at i:9652 original size:5 final size:5

Alignment explanation


    Indices: 9637--9667  Score: 55
    Period size: 5  Copynumber: 6.4  Consensus size: 5

       9627 GCTGCAATGG

                                                  
       9637 GAAAA -AAAA GAAAA GAAAA GAAAA GAAAA GA
          1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GA

       9668 GAGAGATACA


Statistics
Matches: 25,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   4    4  0.16
   5   21  0.84

ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00


Consensus pattern (5 bp):   
GAAAA

Found at i:15471 original size:2 final size:2

Alignment explanation


    Indices: 15464--15494  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

      15454 TCTTGGAAAG

                                                          
      15464 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 A

      15495 GTGGATTAAT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:26258 original size:30 final size:30

Alignment explanation


    Indices: 26224--26318  Score: 72
    Period size: 30  Copynumber: 3.2  Consensus size: 30

      26214 TTCCTACATA

                                          
      26224 TCAAACAATTTAATTTGAATAGAAAATTGT
          1 TCAAACAATTTAATTTGAATAGAAAATTGT

                  * **                * *    *
      26254 TCAAA-GAGGTAGATTTCTGAAT-GCTACA-T-A
          1 TCAAACAATTTA-A-TT-TGAATAG-AAAATTGT

                                          
      26284 TCAAACAATTTAATTTGAATAGAAAATTGT
          1 TCAAACAATTTAATTTGAATAGAAAATTGT

                 
      26314 TCAAA
          1 TCAAA

      26319 AAGGTAGATT


Statistics
Matches: 45,  Mismatches: 12, Indels: 16
        0.62            0.16        0.22

Matches are distributed among these distances:
  28    7  0.16
  29    7  0.16
  30   17  0.38
  31    7  0.16
  32    7  0.16

ACGTcount: A:0.44, C:0.09, G:0.13, T:0.34


Consensus pattern (30 bp):   
TCAAACAATTTAATTTGAATAGAAAATTGT

Found at i:26310 original size:60 final size:60

Alignment explanation


    Indices: 26217--26334  Score: 227
    Period size: 60  Copynumber: 2.0  Consensus size: 60

      26207 TCGAAATTTC

                                                      *                 
      26217 CTACATATCAAACAATTTAATTTGAATAGAAAATTGTTCAAAGAGGTAGATTTCTGAATG
          1 CTACATATCAAACAATTTAATTTGAATAGAAAATTGTTCAAAAAGGTAGATTTCTGAATG

                                                                      
      26277 CTACATATCAAACAATTTAATTTGAATAGAAAATTGTTCAAAAAGGTAGATTTCTGAA
          1 CTACATATCAAACAATTTAATTTGAATAGAAAATTGTTCAAAAAGGTAGATTTCTGAA

      26335 CGCCTGACGC


Statistics
Matches: 57,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  60   57  1.00

ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33


Consensus pattern (60 bp):   
CTACATATCAAACAATTTAATTTGAATAGAAAATTGTTCAAAAAGGTAGATTTCTGAATG

Found at i:29964 original size:13 final size:13

Alignment explanation


    Indices: 29946--29972  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

      29936 GTCGGTTTTC

                         
      29946 ATTTGAGCCTTTG
          1 ATTTGAGCCTTTG

                         
      29959 ATTTGAGCCTTTG
          1 ATTTGAGCCTTTG

             
      29972 A
          1 A

      29973 GAGAGAATCC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.19, C:0.15, G:0.22, T:0.44


Consensus pattern (13 bp):   
ATTTGAGCCTTTG

Found at i:31204 original size:22 final size:24

Alignment explanation


    Indices: 31165--31208  Score: 65
    Period size: 22  Copynumber: 1.9  Consensus size: 24

      31155 CATTATTTTG

                 *                  
      31165 ATTTTTTGAAAAATAAGAAAAATC
          1 ATTTTATGAAAAATAAGAAAAATC

                                  
      31189 ATTTTATG-AAAA-AAGAAAAA
          1 ATTTTATGAAAAATAAGAAAAA

      31209 CGAAAAAAGG


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  22    8  0.42
  23    4  0.21
  24    7  0.37

ACGTcount: A:0.59, C:0.02, G:0.09, T:0.30


Consensus pattern (24 bp):   
ATTTTATGAAAAATAAGAAAAATC
Done.