Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020631.1 Corchorus olitorius cultivar O-4 contig20664, 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: 13209
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32


Found at i:111 original size:30 final size:28

Alignment explanation


    Indices: 41--101  Score: 95
    Period size: 29  Copynumber: 2.1  Consensus size: 28

         31 TAAAATACTA

                       *                
         41 AAAAAATCCCTAATGTTTTTTTTGGGAC
          1 AAAAAATCCCTTATGTTTTTTTTGGGAC

                                          
         69 AAAAAATACCCTTATGTTTTTCTTTGGGAC
          1 AAAAAAT-CCCTTATGTTTTT-TTTGGGAC

               
         99 AAA
          1 AAA

        102 TTAGTCCCTT


Statistics
Matches: 30,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  28    7  0.23
  29   12  0.40
  30   11  0.37

ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38


Consensus pattern (28 bp):   
AAAAAATCCCTTATGTTTTTTTTGGGAC

Found at i:282 original size:29 final size:30

Alignment explanation


    Indices: 245--318  Score: 105
    Period size: 29  Copynumber: 2.5  Consensus size: 30

        235 CTCATTTTTG

                *                   *     
        245 AAACGTAAGGGATTAATTTGTCCCGAAA-A
          1 AAACATAAGGGATTAATTTGTCCCAAAACA

                           *               
        274 AAACATAAGGGATTATTTTGTCCCAAAAGCA
          1 AAACATAAGGGATTAATTTGTCCCAAAA-CA

                          
        305 AAACATAAGGGATT
          1 AAACATAAGGGATT

        319 TTTCTGGGTA


Statistics
Matches: 40,  Mismatches: 3, Indels: 2
        0.89            0.07        0.04

Matches are distributed among these distances:
  29   25  0.62
  31   15  0.38

ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24


Consensus pattern (30 bp):   
AAACATAAGGGATTAATTTGTCCCAAAACA

Done.