Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018968.1 Corchorus olitorius cultivar O-4 contig19001, 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: 27069
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32


Found at i:11634 original size:8 final size:9

Alignment explanation


    Indices: 11623--11654  Score: 50
    Period size: 8  Copynumber: 3.8  Consensus size: 9

      11613 GCAAAGGCAG

                     
      11623 TTTTGGAG-
          1 TTTTGGAGA

                     
      11631 TTTTGGAGA
          1 TTTTGGAGA

                     
      11640 TTTT-GAGA
          1 TTTTGGAGA

                   
      11648 TTTTGGA
          1 TTTTGGA

      11655 AATTGGTGAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
   8   16  0.73
   9    6  0.27

ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50


Consensus pattern (9 bp):   
TTTTGGAGA

Found at i:12647 original size:15 final size:16

Alignment explanation


    Indices: 12624--12653  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

      12614 GCTACTTTTC

                            
      12624 TTTTAGTTTAGTTTAG
          1 TTTTAGTTTAGTTTAG

                           
      12640 TTTT-GTTTAGTTTA
          1 TTTTAGTTTAGTTTA

      12654 TTATTTTTAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15   10  0.71
  16    4  0.29

ACGTcount: A:0.17, C:0.00, G:0.17, T:0.67


Consensus pattern (16 bp):   
TTTTAGTTTAGTTTAG

Found at i:25940 original size:17 final size:16

Alignment explanation


    Indices: 25892--25951  Score: 68
    Period size: 17  Copynumber: 3.8  Consensus size: 16

      25882 AATTTTGGGT

                   *       *
      25892 ACCCGAACCCGAAATT
          1 ACCCGAATCCGAAATG

               *            
      25908 ACCTGAATCC-AAATG
          1 ACCCGAATCCGAAATG

                             
      25923 ACCCGAATCCGAAAATG
          1 ACCCGAATCCG-AAATG

                   *    
      25940 ACCCGAAGCCGA
          1 ACCCGAATCCGA

      25952 TCAACCCAAC


Statistics
Matches: 37,  Mismatches: 5, Indels: 4
        0.80            0.11        0.09

Matches are distributed among these distances:
  15   13  0.35
  16    9  0.24
  17   15  0.41

ACGTcount: A:0.38, C:0.33, G:0.17, T:0.12


Consensus pattern (16 bp):   
ACCCGAATCCGAAATG

Found at i:26898 original size:19 final size:19

Alignment explanation


    Indices: 26858--26894  Score: 67
    Period size: 19  Copynumber: 2.0  Consensus size: 19

      26848 AATTTTTAAG

                               
      26858 TAAAAATATAATATATAAA
          1 TAAAAATATAATATATAAA

                               
      26877 TAAAAATATAATAT-TAAA
          1 TAAAAATATAATATATAAA

      26895 ATAATTAATT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  18    4  0.22
  19   14  0.78

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (19 bp):   
TAAAAATATAATATATAAA
Done.