Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011355.1 Corchorus capsularis cultivar CVL-1 contig11376, 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: 15384
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34


Found at i:6468 original size:28 final size:28

Alignment explanation


    Indices: 6437--6491  Score: 85
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       6427 TTTCATTTGA

                                         
       6437 ATTATTTTAATATTTAT-TATTTATAAAG
          1 ATTATTTTAATATTTATGT-TTTATAAAG

                       *               
       6465 ATTATTTTAATTTTTATGTTTTATAAA
          1 ATTATTTTAATATTTATGTTTTATAAA

       6492 TTATTAAAGA


Statistics
Matches: 25,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  28   24  0.96
  29    1  0.04

ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60


Consensus pattern (28 bp):   
ATTATTTTAATATTTATGTTTTATAAAG

Found at i:7967 original size:75 final size:75

Alignment explanation


    Indices: 7855--8004  Score: 246
    Period size: 75  Copynumber: 2.0  Consensus size: 75

       7845 AAATTGCCGA

                              **            *                                
       7855 GTTGCTATAATGATTTGTGTCAAGTAGAATTCGATTATGATTATGATATAAACTAAATTTTACGT
          1 GTTGCTATAATGATTTGTACCAAGTAGAATTCAATTATGATTATGATATAAACTAAATTTTACGT

              *       
       7920 TTGCTTGAAT
         66 TTACTTGAAT

                  * *                                                        
       7930 GTTGCTGTCATGATTTGTACCAAGTAGAATTCAATTATGATTATGATATAAACTAAATTTTACGT
          1 GTTGCTATAATGATTTGTACCAAGTAGAATTCAATTATGATTATGATATAAACTAAATTTTACGT

                      
       7995 TTACTTGAAT
         66 TTACTTGAAT

       8005 CGGAGCTTGG


Statistics
Matches: 69,  Mismatches: 6, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  75   69  1.00

ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42


Consensus pattern (75 bp):   
GTTGCTATAATGATTTGTACCAAGTAGAATTCAATTATGATTATGATATAAACTAAATTTTACGT
TTACTTGAAT

Found at i:9550 original size:28 final size:27

Alignment explanation


    Indices: 9485--9551  Score: 70
    Period size: 24  Copynumber: 2.5  Consensus size: 27

       9475 TTTAGTCGAC

                                *       
       9485 TATTTCTTGTAAATTTGATTGCTTTATT
          1 TATTTC-TGTAAATTTGATTACTTTATT

                                        
       9513 T-TTTAC---AAATTTGATTACTTTATT
          1 TATTT-CTGTAAATTTGATTACTTTATT

                           
       9537 TATTTCTGGTAAATT
          1 TATTTCT-GTAAATT

       9552 ATCATGATTG


Statistics
Matches: 32,  Mismatches: 1, Indels: 12
        0.71            0.02        0.27

Matches are distributed among these distances:
  24   19  0.59
  25    3  0.09
  27    3  0.09
  28    7  0.22

ACGTcount: A:0.25, C:0.07, G:0.09, T:0.58


Consensus pattern (27 bp):   
TATTTCTGTAAATTTGATTACTTTATT
Done.