Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012164.1 Corchorus capsularis cultivar CVL-1 contig12185, 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: 41392
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35


Found at i:16247 original size:33 final size:34

Alignment explanation


    Indices: 16193--16262  Score: 124
    Period size: 33  Copynumber: 2.1  Consensus size: 34

      16183 GTATCGTGTG

                                              
      16193 TCGAAATCTTATTTTTTAAATATCAATTATCGTA
          1 TCGAAATCTTATTTTTTAAATATCAATTATCGTA

                                    *         
      16227 TCGAAATCTTA-TTTTTAAATATCGATTATCGTA
          1 TCGAAATCTTATTTTTTAAATATCAATTATCGTA

               
      16260 TCG
          1 TCG

      16263 TAAGATACAA


Statistics
Matches: 35,  Mismatches: 1, Indels: 1
        0.95            0.03        0.03

Matches are distributed among these distances:
  33   24  0.69
  34   11  0.31

ACGTcount: A:0.33, C:0.13, G:0.09, T:0.46


Consensus pattern (34 bp):   
TCGAAATCTTATTTTTTAAATATCAATTATCGTA

Found at i:17788 original size:3 final size:3

Alignment explanation


    Indices: 17782--17810  Score: 58
    Period size: 3  Copynumber: 9.7  Consensus size: 3

      17772 ATGATGATGA

                                                  
      17782 TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
          1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TG

      17811 AAGGTGAACC


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   26  1.00

ACGTcount: A:0.00, C:0.00, G:0.66, T:0.34


Consensus pattern (3 bp):   
TGG

Found at i:26111 original size:2 final size:2

Alignment explanation


    Indices: 26104--26146  Score: 77
    Period size: 2  Copynumber: 21.0  Consensus size: 2

      26094 GACATGAAAC

                                                                           
      26104 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA

      26147 AAATTTGTAG


Statistics
Matches: 40,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   2   38  0.95
   3    2  0.05

ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:40924 original size:20 final size:20

Alignment explanation


    Indices: 40884--40932  Score: 64
    Period size: 20  Copynumber: 2.4  Consensus size: 20

      40874 AGAATGTAAG

                                 
      40884 ATATTACTAAATTTATTAATA
          1 ATATTA-TAAATTTATTAATA

                                 
      40905 ATATTATAACATTT-TTAATA
          1 ATATTATAA-ATTTATTAATA

              *     
      40925 ATTTTATA
          1 ATATTATA

      40933 CCTTTTGAAG


Statistics
Matches: 26,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  20   16  0.62
  21   10  0.38

ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51


Consensus pattern (20 bp):   
ATATTATAAATTTATTAATA
Done.