Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011304.1 Corchorus olitorius cultivar O-4 contig11337, 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: 14095
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30


Found at i:281 original size:22 final size:22

Alignment explanation


    Indices: 256--308  Score: 63
    Period size: 22  Copynumber: 2.4  Consensus size: 22

        246 AAATCAAACT

                       **          
        256 AACAATTAAGACTATCT-AAGAA
          1 AACAATTAAGAAAAT-TAAAGAA

                  *               
        278 AACAATCAAGAAAATTAAAGAA
          1 AACAATTAAGAAAATTAAAGAA

                     
        300 AACAATTAA
          1 AACAATTAA

        309 TCAGAAAGCA


Statistics
Matches: 26,  Mismatches: 4, Indels: 2
        0.81            0.12        0.06

Matches are distributed among these distances:
  21    1  0.04
  22   25  0.96

ACGTcount: A:0.62, C:0.11, G:0.08, T:0.19


Consensus pattern (22 bp):   
AACAATTAAGAAAATTAAAGAA

Found at i:3864 original size:20 final size:18

Alignment explanation


    Indices: 3825--3860  Score: 54
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       3815 CTAACCCTAA

                          *   
       3825 AACTAGAAGAAAAACTAG
          1 AACTAGAAGAAAAAATAG

                              
       3843 AACTAGAAGAGAAAAATA
          1 AACTAGAAGA-AAAAATA

       3861 AGAAGAGAAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18   10  0.62
  19    6  0.38

ACGTcount: A:0.64, C:0.08, G:0.17, T:0.11


Consensus pattern (18 bp):   
AACTAGAAGAAAAAATAG

Found at i:4489 original size:19 final size:18

Alignment explanation


    Indices: 4456--4491  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       4446 TTGGGATAAT

                              
       4456 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       4474 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       4492 TAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA
Done.