Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015996.1 Corchorus capsularis cultivar CVL-1 contig16017, 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: 8270
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37


Found at i:2155 original size:29 final size:29

Alignment explanation


    Indices: 2113--2175  Score: 81
    Period size: 29  Copynumber: 2.2  Consensus size: 29

       2103 TAATCATTAA

                  * *        *   *       
       2113 AATTCCGTCTACCAATATACGTGCTACAT
          1 AATTCCATATACCAATAAACGCGCTACAT

                                   *     
       2142 AATTCCATATACCAATAAACGCGTTACAT
          1 AATTCCATATACCAATAAACGCGCTACAT

                 
       2171 AATTC
          1 AATTC

       2176 TTTAGTTTGT


Statistics
Matches: 29,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  29   29  1.00

ACGTcount: A:0.37, C:0.25, G:0.08, T:0.30


Consensus pattern (29 bp):   
AATTCCATATACCAATAAACGCGCTACAT

Found at i:3620 original size:20 final size:19

Alignment explanation


    Indices: 3586--3623  Score: 58
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       3576 GATTACTAAA

                      *        
       3586 AAAACAATTAGAGGTTATC
          1 AAAACAATTAAAGGTTATC

                               
       3605 AAAACAATTATAAGGTTAT
          1 AAAACAATTA-AAGGTTAT

       3624 TAATAAATTC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  19   10  0.59
  20    7  0.41

ACGTcount: A:0.50, C:0.08, G:0.13, T:0.29


Consensus pattern (19 bp):   
AAAACAATTAAAGGTTATC

Found at i:5110 original size:6 final size:6

Alignment explanation


    Indices: 5099--5133  Score: 70
    Period size: 6  Copynumber: 5.8  Consensus size: 6

       5089 CTTATATAAT

                                                    
       5099 ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
          1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATA

       5134 TATTATATAA


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

Matches are distributed among these distances:
   6   29  1.00

ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34


Consensus pattern (6 bp):   
ATATAG

Done.