Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019482.1 Corchorus olitorius cultivar O-4 contig19515, 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: 17915
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33


Found at i:16291 original size:62 final size:62

Alignment explanation


    Indices: 16194--16316  Score: 201
    Period size: 62  Copynumber: 2.0  Consensus size: 62

      16184 TGAATTTCTG

                     *        *    *   *         *                        
      16194 TTTTGGTCAGCTAATTATTAAAAGTAATGTTTTGGTCGCTTATATTTGCAATATTGAATATA
          1 TTTTGGTCACCTAATTATAAAAAATAACGTTTTGGTCACTTATATTTGCAATATTGAATATA

                                                                         
      16256 TTTTGGTCACCTAATTATAAAAAATAACGTTTTGGTCACTTATATTTGCAATATTGAATAT
          1 TTTTGGTCACCTAATTATAAAAAATAACGTTTTGGTCACTTATATTTGCAATATTGAATAT

      16317 TTTGATCACT


Statistics
Matches: 56,  Mismatches: 5, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  62   56  1.00

ACGTcount: A:0.33, C:0.10, G:0.14, T:0.44


Consensus pattern (62 bp):   
TTTTGGTCACCTAATTATAAAAAATAACGTTTTGGTCACTTATATTTGCAATATTGAATATA

Found at i:17578 original size:10 final size:10

Alignment explanation


    Indices: 17563--17589  Score: 54
    Period size: 10  Copynumber: 2.7  Consensus size: 10

      17553 GATGATGGGA

                      
      17563 TCCCTCCGTT
          1 TCCCTCCGTT

                      
      17573 TCCCTCCGTT
          1 TCCCTCCGTT

                   
      17583 TCCCTCC
          1 TCCCTCC

      17590 TAATAGCCAT


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

Matches are distributed among these distances:
  10   17  1.00

ACGTcount: A:0.00, C:0.56, G:0.07, T:0.37


Consensus pattern (10 bp):   
TCCCTCCGTT

Found at i:17798 original size:21 final size:24

Alignment explanation


    Indices: 17774--17824  Score: 65
    Period size: 21  Copynumber: 2.3  Consensus size: 24

      17764 CTCTCATCTC

                         *          
      17774 TTTTCTTG-TGAAGATTT-T-ATT
          1 TTTTCTTGTTGAAAATTTCTAATT

                                    
      17795 TTTT-TTGTTGAAAATTTCTAATT
          1 TTTTCTTGTTGAAAATTTCTAATT

                   
      17818 TTTTCTT
          1 TTTTCTT

      17825 TTGTTTTTTA


Statistics
Matches: 25,  Mismatches: 1, Indels: 5
        0.81            0.03        0.16

Matches are distributed among these distances:
  20    3  0.12
  21   12  0.48
  22    1  0.04
  23    7  0.28
  24    2  0.08

ACGTcount: A:0.20, C:0.06, G:0.10, T:0.65


Consensus pattern (24 bp):   
TTTTCTTGTTGAAAATTTCTAATT
Done.