Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017916.1 Corchorus olitorius cultivar O-4 contig17949, 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: 6331
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31


Found at i:4533 original size:21 final size:21

Alignment explanation


    Indices: 4500--4548  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       4490 GAGAATTGTA

                          **     
       4500 GCTT-CTTGGAAATGGCTCTT
          1 GCTTCCTTGGAAATCCCTCTT

                    *            
       4520 GCTTCCTTTGAAATCCCTCTT
          1 GCTTCCTTGGAAATCCCTCTT

                    
       4541 GCATTCCT
          1 GC-TTCCT

       4549 AAAGCATTGA


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  20    4  0.17
  21   15  0.62
  22    5  0.21

ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41


Consensus pattern (21 bp):   
GCTTCCTTGGAAATCCCTCTT

Found at i:5695 original size:7 final size:8

Alignment explanation


    Indices: 5678--5728  Score: 50
    Period size: 8  Copynumber: 6.0  Consensus size: 8

       5668 AGTAACTAAG

                    
       5678 AAAAATAA
          1 AAAAATAA

                    
       5686 AAAAATAA
          1 AAAAATAA

                     
       5694 AAGAAA-AA
          1 AA-AAATAA

                     
       5702 GAAAAATAA
          1 -AAAAATAA

                      
       5711 CGAAAAATAA
          1 --AAAAATAA

               *    
       5721 AAAGATAA
          1 AAAAATAA

       5729 GGGTAAGAAA


Statistics
Matches: 38,  Mismatches: 1, Indels: 8
        0.81            0.02        0.17

Matches are distributed among these distances:
   8   22  0.58
   9    7  0.18
  10    9  0.24

ACGTcount: A:0.80, C:0.02, G:0.08, T:0.10


Consensus pattern (8 bp):   
AAAAATAA

Done.