Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020172.1 Corchorus olitorius cultivar O-4 contig20205, 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: 7648
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:604 original size:17 final size:17

Alignment explanation


    Indices: 582--615  Score: 68
    Period size: 17  Copynumber: 2.0  Consensus size: 17

        572 GGAAGGAAGG

                             
        582 AAAGGATTGAGAGGTGT
          1 AAAGGATTGAGAGGTGT

                             
        599 AAAGGATTGAGAGGTGT
          1 AAAGGATTGAGAGGTGT

        616 TTGAGAGAAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   17  1.00

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


Consensus pattern (17 bp):   
AAAGGATTGAGAGGTGT

Found at i:4632 original size:19 final size:18

Alignment explanation


    Indices: 4608--4643  Score: 54
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       4598 TGAAGACCAT

                               
       4608 TTGAAGATAATTTGAAGAC
          1 TTGAAGAT-ATTTGAAGAC

                    *        
       4627 TTGAAGATTTTTGAAGA
          1 TTGAAGATATTTGAAGA

       4644 TTTATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    8  0.50
  19    8  0.50

ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36


Consensus pattern (18 bp):   
TTGAAGATATTTGAAGAC

Found at i:6368 original size:34 final size:35

Alignment explanation


    Indices: 6330--6397  Score: 95
    Period size: 35  Copynumber: 2.0  Consensus size: 35

       6320 TGCGTTTTTC

                                                
       6330 TTTTTCTCTGCGT-TTT-ATTCTGAAAAAAAAAATA
          1 TTTTTCTCTGCGTCTTTAATT-TGAAAAAAAAAATA

                   *              *           
       6364 TTTTTCTTTGCGTCTTTAATTTTAAAAAAAAAAT
          1 TTTTTCTCTGCGTCTTTAATTTGAAAAAAAAAAT

       6398 TGTGTTGTGT


Statistics
Matches: 30,  Mismatches: 2, Indels: 3
        0.86            0.06        0.09

Matches are distributed among these distances:
  34   12  0.40
  35   15  0.50
  36    3  0.10

ACGTcount: A:0.35, C:0.10, G:0.07, T:0.47


Consensus pattern (35 bp):   
TTTTTCTCTGCGTCTTTAATTTGAAAAAAAAAATA
Done.