Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016815.1 Corchorus olitorius cultivar O-4 contig16848, 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: 18255
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:1729 original size:49 final size:49

Alignment explanation


    Indices: 1634--1761  Score: 154
    Period size: 49  Copynumber: 2.7  Consensus size: 49

       1624 ATTTTGTTAC

                                             *      *  *     
       1634 AAAAATTGATAAAAAGG-GC-AGGAAATGTAAATGTTCAATTTTGTTGT
          1 AAAAATTGATAAAAAGGTGCAAGGAAATGTAAAGGTTCAAATTAGTTGT

                      *                   *                   
       1681 AAAAATTGATTAAAAGGTGCAAGGAAAT-TTAAGGATTCAAATTAGTTGT
          1 AAAAATTGATAAAAAGGTGCAAGGAAATGTAAAGG-TTCAAATTAGTTGT

                     *     *           *    
       1730 AAAAATTGAGAAAAATGTGCAAGGAAAAGTAA
          1 AAAAATTGATAAAAAGGTGCAAGGAAATGTAA

       1762 CGATTGCTTT


Statistics
Matches: 67,  Mismatches: 10, Indels: 5
        0.82            0.12        0.06

Matches are distributed among these distances:
  47   16  0.24
  48    6  0.09
  49   43  0.64
  50    2  0.03

ACGTcount: A:0.48, C:0.04, G:0.21, T:0.27


Consensus pattern (49 bp):   
AAAAATTGATAAAAAGGTGCAAGGAAATGTAAAGGTTCAAATTAGTTGT

Found at i:9296 original size:15 final size:16

Alignment explanation


    Indices: 9259--9296  Score: 53
    Period size: 15  Copynumber: 2.5  Consensus size: 16

       9249 GAGTATATCT

                           *
       9259 TTTATTTTTAGTTGTG
          1 TTTATTTTTAGTTGTC

                            
       9275 TTT-TTTTTAGTT-TC
          1 TTTATTTTTAGTTGTC

                    
       9289 TTTATTTT
          1 TTTATTTT

       9297 CTCTCTGCTT


Statistics
Matches: 20,  Mismatches: 1, Indels: 3
        0.83            0.04        0.12

Matches are distributed among these distances:
  14    4  0.20
  15   13  0.65
  16    3  0.15

ACGTcount: A:0.11, C:0.03, G:0.11, T:0.76


Consensus pattern (16 bp):   
TTTATTTTTAGTTGTC
Done.