Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019055.1 Corchorus olitorius cultivar O-4 contig19088, 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: 17940
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:12703 original size:13 final size:13

Alignment explanation


    Indices: 12669--12700  Score: 55
    Period size: 13  Copynumber: 2.4  Consensus size: 13

      12659 AAAACTCTTC

                         
      12669 TTTTCCTTTGATA
          1 TTTTCCTTTGATA

                         
      12682 TTTTCCTTTGATA
          1 TTTTCCTTTGATA

                  
      12695 TCTTTC
          1 T-TTTC

      12701 TTTCCTCTAC


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

Matches are distributed among these distances:
  13   14  0.78
  14    4  0.22

ACGTcount: A:0.12, C:0.19, G:0.06, T:0.62


Consensus pattern (13 bp):   
TTTTCCTTTGATA

Found at i:12797 original size:17 final size:16

Alignment explanation


    Indices: 12743--12793  Score: 57
    Period size: 17  Copynumber: 3.1  Consensus size: 16

      12733 ATCACCCCCC

                   *         
      12743 AGATCACTAGTGATCTA
          1 AGATCACCAGTGATC-A

                     *       
      12760 AGATCACCAATGATGCA
          1 AGATCACCAGTGAT-CA

                    *       
      12777 AGATCACCGGTGATCA
          1 AGATCACCAGTGATCA

             
      12793 A
          1 A

      12794 AGATTACATG


Statistics
Matches: 29,  Mismatches: 4, Indels: 3
        0.81            0.11        0.08

Matches are distributed among these distances:
  16    3  0.10
  17   25  0.86
  18    1  0.03

ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22


Consensus pattern (16 bp):   
AGATCACCAGTGATCA

Found at i:14889 original size:25 final size:25

Alignment explanation


    Indices: 14846--14896  Score: 61
    Period size: 23  Copynumber: 2.0  Consensus size: 25

      14836 AATGATAAAT

                                       
      14846 TTATATATAGTTATGATTTCTTAAAAA
          1 TTATATATAGTTATGA-TT-TTAAAAA

                  *                  
      14873 TTATATGTA-TTAT-ATTTTAAAAA
          1 TTATATATAGTTATGATTTTAAAAA

             
      14896 T
          1 T

      14897 AATGTAGAGA


Statistics
Matches: 23,  Mismatches: 1, Indels: 4
        0.82            0.04        0.14

Matches are distributed among these distances:
  23    8  0.35
  24    2  0.09
  25    1  0.04
  26    4  0.17
  27    8  0.35

ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51


Consensus pattern (25 bp):   
TTATATATAGTTATGATTTTAAAAA
Done.