Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009545.1 Corchorus olitorius cultivar O-4 contig09577, 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: 10893
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:3890 original size:56 final size:56

Alignment explanation


    Indices: 3802--3914  Score: 217
    Period size: 56  Copynumber: 2.0  Consensus size: 56

       3792 TTGGCATGAA

                                                                    
       3802 GAGGAAACATACATGTGCATTGATGCTCTAATTGAAGCTTTTATGGACTTGAGGTT
          1 GAGGAAACATACATGTGCATTGATGCTCTAATTGAAGCTTTTATGGACTTGAGGTT

                                       *                            
       3858 GAGGAAACATACATGTGCATTGATGCTTTAATTGAAGCTTTTATGGACTTGAGGTT
          1 GAGGAAACATACATGTGCATTGATGCTCTAATTGAAGCTTTTATGGACTTGAGGTT

             
       3914 G
          1 G

       3915 TTGAATAATG


Statistics
Matches: 56,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  56   56  1.00

ACGTcount: A:0.28, C:0.12, G:0.26, T:0.35


Consensus pattern (56 bp):   
GAGGAAACATACATGTGCATTGATGCTCTAATTGAAGCTTTTATGGACTTGAGGTT

Found at i:6564 original size:69 final size:72

Alignment explanation


    Indices: 6453--6593  Score: 234
    Period size: 69  Copynumber: 2.0  Consensus size: 72

       6443 TTGAATTACA

                                   *                                      *  
       6453 AGCTTTCTAATACATATTTTTTTCAAATTAAA-T-TATATATATA-TTTTTAATAAATAACGGTC
          1 AGCTTTCTAATACATATTTTTTTAAAATTAAATTATATATATATATTTTTTAATAAATAACGATC

                   
       6515 AAATATT
         66 AAATATT

                    *                                                        
       6522 AGCTTTCTGATACATATTTTTTTAAAATTAAATTATATATATATATTTTTTAATAAATAACGATC
          1 AGCTTTCTAATACATATTTTTTTAAAATTAAATTATATATATATATTTTTTAATAAATAACGATC

                   
       6587 AAATATT
         66 AAATATT

       6594 GTGAGTAGTT


Statistics
Matches: 66,  Mismatches: 3, Indels: 3
        0.92            0.04        0.04

Matches are distributed among these distances:
  69   30  0.45
  70    1  0.02
  71   10  0.15
  72   25  0.38

ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47


Consensus pattern (72 bp):   
AGCTTTCTAATACATATTTTTTTAAAATTAAATTATATATATATATTTTTTAATAAATAACGATC
AAATATT

Found at i:7204 original size:28 final size:28

Alignment explanation


    Indices: 7163--7222  Score: 102
    Period size: 28  Copynumber: 2.1  Consensus size: 28

       7153 ATTTCTAAGA

                               *        
       7163 TTAAGGAAACAACATGGGGCACATATGC
          1 TTAAGGAAACAACATGGGGAACATATGC

                     *                  
       7191 TTAAGGAAAGAACATGGGGAACATATGC
          1 TTAAGGAAACAACATGGGGAACATATGC

                
       7219 TTAA
          1 TTAA

       7223 TTAATTAATT


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  28   30  1.00

ACGTcount: A:0.42, C:0.13, G:0.25, T:0.20


Consensus pattern (28 bp):   
TTAAGGAAACAACATGGGGAACATATGC
Done.