Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024589.1 Corchorus olitorius cultivar O-4 contig24622, 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: 15938
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33


Found at i:2828 original size:19 final size:20

Alignment explanation


    Indices: 2789--2830  Score: 61
    Period size: 19  Copynumber: 2.1  Consensus size: 20

       2779 ACTAATGGAT

                                
       2789 TGTACGGACAACGACAAAGC
          1 TGTACGGACAACGACAAAGC

                                 
       2809 TGTACGGAC-ACG-CTAAAGC
          1 TGTACGGACAACGAC-AAAGC

               
       2828 TGT
          1 TGT

       2831 CAACAGCTTG


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  18    1  0.05
  19   11  0.52
  20    9  0.43

ACGTcount: A:0.33, C:0.24, G:0.26, T:0.17


Consensus pattern (20 bp):   
TGTACGGACAACGACAAAGC

Found at i:6809 original size:12 final size:12

Alignment explanation


    Indices: 6792--6816  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       6782 AATCGATAAC

                        
       6792 TTTTTTGAATTT
          1 TTTTTTGAATTT

                        
       6804 TTTTTTGAATTT
          1 TTTTTTGAATTT

             
       6816 T
          1 T

       6817 CACTATTTTT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76


Consensus pattern (12 bp):   
TTTTTTGAATTT

Found at i:12373 original size:29 final size:28

Alignment explanation


    Indices: 12337--12409  Score: 87
    Period size: 29  Copynumber: 2.6  Consensus size: 28

      12327 TTAGGATCAA

                                      *   
      12337 CTAGGGGCATTTTGGTCATTCT-CAAGAAT
          1 CTAGGGGCATTTTGGTCATT-TGC-ACAAT

                         *            * 
      12366 CTAGGGGCATTTTAGTCATTTGCACATT
          1 CTAGGGGCATTTTGGTCATTTGCACAAT

                             
      12394 C-AGGGGCATTTTGGTC
          1 CTAGGGGCATTTTGGTC

      12410 TTTTAAGTTC


Statistics
Matches: 39,  Mismatches: 4, Indels: 4
        0.83            0.09        0.09

Matches are distributed among these distances:
  27   14  0.36
  28    5  0.13
  29   20  0.51

ACGTcount: A:0.21, C:0.18, G:0.26, T:0.36


Consensus pattern (28 bp):   
CTAGGGGCATTTTGGTCATTTGCACAAT
Done.