Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015526.1 Corchorus olitorius cultivar O-4 contig15559, 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: 14916
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34


Found at i:1538 original size:33 final size:31

Alignment explanation


    Indices: 1462--1543  Score: 92
    Period size: 31  Copynumber: 2.6  Consensus size: 31

       1452 CATTAGCGTC

                  *        *  *    *       
       1462 TTGGTCTGACGTGGCCTTGCCACGTGGCATT
          1 TTGGTCCGACGTGGCATTCCCACATGGCATT

                   *                         
       1493 TTGGTCCAACGTGGCATTCCCACATGGCATTTT
          1 TTGGTCCGACGTGGCATTCCCACATGGCA--TT

                 *            
       1526 TTGGTTCGACGTGGCATT
          1 TTGGTCCGACGTGGCATT

       1544 GCTACGTCGG


Statistics
Matches: 42,  Mismatches: 7, Indels: 2
        0.82            0.14        0.04

Matches are distributed among these distances:
  31   24  0.57
  33   18  0.43

ACGTcount: A:0.13, C:0.24, G:0.28, T:0.34


Consensus pattern (31 bp):   
TTGGTCCGACGTGGCATTCCCACATGGCATT

Found at i:4802 original size:20 final size:20

Alignment explanation


    Indices: 4777--4814  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       4767 TCGTAGATTT

                   *            
       4777 AATTAAATATAAATTAATAA
          1 AATTAAAAATAAATTAATAA

                      *       
       4797 AATTAAAAATTAATTAAT
          1 AATTAAAAATAAATTAAT

       4815 TATATAATGG


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37


Consensus pattern (20 bp):   
AATTAAAAATAAATTAATAA

Found at i:4884 original size:31 final size:31

Alignment explanation


    Indices: 4846--4907  Score: 97
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       4836 TATGTTAGAA

                       *                   
       4846 AAATAAGGATATAATAGGCATTTCAAAAGTT
          1 AAATAAGGATACAATAGGCATTTCAAAAGTT

                    *          *           
       4877 AAATAAGGGTACAATAGGCGTTTCAAAAGTT
          1 AAATAAGGATACAATAGGCATTTCAAAAGTT

       4908 TTACAAAACT


Statistics
Matches: 28,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  31   28  1.00

ACGTcount: A:0.45, C:0.08, G:0.19, T:0.27


Consensus pattern (31 bp):   
AAATAAGGATACAATAGGCATTTCAAAAGTT
Done.