Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005759.1 Corchorus capsularis cultivar CVL-1 contig05777, 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: 3022
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.35


Found at i:2021 original size:54 final size:54

Alignment explanation


    Indices: 1939--2046  Score: 200
    Period size: 54  Copynumber: 2.0  Consensus size: 54

       1929 TAGATTTCAG

                                                                  
       1939 CAAATCAGATCAAAATGTTAATAATATCTGATTTCTTTCTTCAAAATTAATTAT
          1 CAAATCAGATCAAAATGTTAATAATATCTGATTTCTTTCTTCAAAATTAATTAT

                                                                   
       1993 CAAATCAG-TCCAAAATGTTAATAATATCTGATTTCTTTCTTCAAAATTAATTAT
          1 CAAATCAGAT-CAAAATGTTAATAATATCTGATTTCTTTCTTCAAAATTAATTAT

       2047 TGATTTCTAT


Statistics
Matches: 53,  Mismatches: 0, Indels: 2
        0.96            0.00        0.04

Matches are distributed among these distances:
  53    1  0.02
  54   52  0.98

ACGTcount: A:0.40, C:0.14, G:0.06, T:0.41


Consensus pattern (54 bp):   
CAAATCAGATCAAAATGTTAATAATATCTGATTTCTTTCTTCAAAATTAATTAT

Found at i:2783 original size:11 final size:11

Alignment explanation


    Indices: 2767--2809  Score: 59
    Period size: 11  Copynumber: 3.9  Consensus size: 11

       2757 TATGCTATAT

                       
       2767 CTAATTAATAG
          1 CTAATTAATAG

                      *
       2778 CTAATTAATAT
          1 CTAATTAATAG

                     * 
       2789 CTAATTAATGG
          1 CTAATTAATAG

            *         
       2800 TTAATTAATA
          1 CTAATTAATA

       2810 ATGAATAAAT


Statistics
Matches: 27,  Mismatches: 5, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  11   27  1.00

ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42


Consensus pattern (11 bp):   
CTAATTAATAG

Found at i:2789 original size:22 final size:22

Alignment explanation


    Indices: 2763--2809  Score: 76
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       2753 CCATTATGCT

                                  
       2763 ATATCTAATTAATAGCTAATTA
          1 ATATCTAATTAATAGCTAATTA

                         * *      
       2785 ATATCTAATTAATGGTTAATTA
          1 ATATCTAATTAATAGCTAATTA

               
       2807 ATA
          1 ATA

       2810 ATGAATAAAT


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  22   23  1.00

ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43


Consensus pattern (22 bp):   
ATATCTAATTAATAGCTAATTA
Done.