Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007765.1 Corchorus capsularis cultivar CVL-1 contig07786, 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: 17594
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31


Found at i:5335 original size:2 final size:2

Alignment explanation


    Indices: 5328--5358  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       5318 GGAAAACCAA

                                                          
       5328 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

       5359 GAAAATGAAG


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:10417 original size:14 final size:14

Alignment explanation


    Indices: 10392--10431  Score: 53
    Period size: 14  Copynumber: 2.9  Consensus size: 14

      10382 ATATCTTCTA

                *         
      10392 AAAACAAAAATAAT
          1 AAAATAAAAATAAT

                   *    * 
      10406 AAAATAAGAATACT
          1 AAAATAAAAATAAT

                        
      10420 AAAATAAAAATA
          1 AAAATAAAAATA

      10432 TCTTCATCTA


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  14   22  1.00

ACGTcount: A:0.75, C:0.05, G:0.03, T:0.17


Consensus pattern (14 bp):   
AAAATAAAAATAAT

Found at i:10656 original size:13 final size:13

Alignment explanation


    Indices: 10640--10664  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      10630 TTTAGTAGTA

                         
      10640 CATTTTTTTATTC
          1 CATTTTTTTATTC

                        
      10653 CATTTTTTTATT
          1 CATTTTTTTATT

      10665 GTTTTATTGT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72


Consensus pattern (13 bp):   
CATTTTTTTATTC

Found at i:12042 original size:15 final size:15

Alignment explanation


    Indices: 12022--12058  Score: 74
    Period size: 15  Copynumber: 2.5  Consensus size: 15

      12012 TGGGCCGGGG

                           
      12022 ATTTGGGAATTGGGA
          1 ATTTGGGAATTGGGA

                           
      12037 ATTTGGGAATTGGGA
          1 ATTTGGGAATTGGGA

                   
      12052 ATTTGGG
          1 ATTTGGG

      12059 GAAATGAAAT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   22  1.00

ACGTcount: A:0.24, C:0.00, G:0.41, T:0.35


Consensus pattern (15 bp):   
ATTTGGGAATTGGGA

Found at i:12044 original size:8 final size:8

Alignment explanation


    Indices: 12022--12058  Score: 60
    Period size: 7  Copynumber: 4.9  Consensus size: 8

      12012 TGGGCCGGGG

                    
      12022 ATTTGGGA
          1 ATTTGGGA

                    
      12030 A-TTGGGA
          1 ATTTGGGA

                    
      12037 ATTTGGGA
          1 ATTTGGGA

                    
      12045 A-TTGGGA
          1 ATTTGGGA

                   
      12052 ATTTGGG
          1 ATTTGGG

      12059 GAAATGAAAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 4
        0.87            0.00        0.13

Matches are distributed among these distances:
   7   14  0.52
   8   13  0.48

ACGTcount: A:0.24, C:0.00, G:0.41, T:0.35


Consensus pattern (8 bp):   
ATTTGGGA

Found at i:13097 original size:6 final size:6

Alignment explanation


    Indices: 13086--13110  Score: 50
    Period size: 6  Copynumber: 4.2  Consensus size: 6

      13076 TTATAATTAG

                                         
      13086 TATAGA TATAGA TATAGA TATAGA T
          1 TATAGA TATAGA TATAGA TATAGA T

      13111 TAAAATATAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   19  1.00

ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36


Consensus pattern (6 bp):   
TATAGA

Done.