Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012324.1 Corchorus capsularis cultivar CVL-1 contig12345, 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: 6484
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32


Found at i:1652 original size:2 final size:2

Alignment explanation


    Indices: 1647--1680  Score: 50
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       1637 TAAAAAAGGA

                        *                           *         
       1647 AT AT AT AT CT AT AT AT AT AT AT AT AT AA AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       1681 TCGGTAGCAA


Statistics
Matches: 28,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   2   28  1.00

ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:1903 original size:29 final size:29

Alignment explanation


    Indices: 1869--1941  Score: 146
    Period size: 29  Copynumber: 2.5  Consensus size: 29

       1859 AGAGTTCAGT

                                         
       1869 GGCTTATTTGGCTGTAATAAAAGTTTAGG
          1 GGCTTATTTGGCTGTAATAAAAGTTTAGG

                                         
       1898 GGCTTATTTGGCTGTAATAAAAGTTTAGG
          1 GGCTTATTTGGCTGTAATAAAAGTTTAGG

                           
       1927 GGCTTATTTGGCTGT
          1 GGCTTATTTGGCTGT

       1942 CTTGTATAAA


Statistics
Matches: 44,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  29   44  1.00

ACGTcount: A:0.23, C:0.08, G:0.29, T:0.40


Consensus pattern (29 bp):   
GGCTTATTTGGCTGTAATAAAAGTTTAGG

Found at i:5895 original size:47 final size:46

Alignment explanation


    Indices: 5832--5924  Score: 134
    Period size: 47  Copynumber: 2.0  Consensus size: 46

       5822 TTGAAAAATG

                       *                           *        
       5832 GTAAAAATAAAGTAATTATAAAGATATT-AGATTTAATTGAATAAAAA
          1 GTAAAAATAAAATAATTATAAA-ATATTGA-ATTTAATTAAATAAAAA

                                                     *    
       5879 GTAAAAATAAAATAATTATAAAATATTGAATTTAATTAAATGAAAA
          1 GTAAAAATAAAATAATTATAAAATATTGAATTTAATTAAATAAAAA

       5925 TAGATTTTTT


Statistics
Matches: 42,  Mismatches: 3, Indels: 3
        0.88            0.06        0.06

Matches are distributed among these distances:
  46   20  0.48
  47   22  0.52

ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32


Consensus pattern (46 bp):   
GTAAAAATAAAATAATTATAAAATATTGAATTTAATTAAATAAAAA
Done.