Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012763.1 Corchorus olitorius cultivar O-4 contig12796, 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: 26717
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31


Found at i:15544 original size:51 final size:50

Alignment explanation


    Indices: 15443--15544  Score: 118
    Period size: 51  Copynumber: 2.0  Consensus size: 50

      15433 GTTCATCAAA

                                                     * **     
      15443 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGT
          1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT

                                      *     *                    
      15493 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
          1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGT

             
      15544 T
          1 T

      15545 CTTCATTCAG


Statistics
Matches: 44,  Mismatches: 5, Indels: 5
        0.81            0.09        0.09

Matches are distributed among these distances:
  50    7  0.16
  51   36  0.82
  52    1  0.02

ACGTcount: A:0.23, C:0.23, G:0.14, T:0.41


Consensus pattern (50 bp):   
TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT

Found at i:16674 original size:18 final size:18

Alignment explanation


    Indices: 16648--16693  Score: 58
    Period size: 18  Copynumber: 2.6  Consensus size: 18

      16638 GTTAAAAAAT

                *      *  *   
      16648 TTCTTAATTTTTGTTGGA
          1 TTCTCAATTTTGGTCGGA

                              
      16666 TTCTCAATTTTGGTCGGA
          1 TTCTCAATTTTGGTCGGA

                       
      16684 TTCTC-ATTTT
          1 TTCTCAATTTT

      16694 AATGTTTGGG


Statistics
Matches: 25,  Mismatches: 3, Indels: 1
        0.86            0.10        0.03

Matches are distributed among these distances:
  17    5  0.20
  18   20  0.80

ACGTcount: A:0.15, C:0.13, G:0.15, T:0.57


Consensus pattern (18 bp):   
TTCTCAATTTTGGTCGGA
Done.