Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011341.1 Corchorus capsularis cultivar CVL-1 contig11362, 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: 6752
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.32

Warning! 2 characters in sequence are not A, C, G, or T


Found at i:6437 original size:28 final size:28

Alignment explanation


    Indices: 6386--6453  Score: 77
    Period size: 28  Copynumber: 2.5  Consensus size: 28

       6376 TTTTTCTTCT

                       *                 
       6386 TTTCTTACTCTTTTTTACCAATTACTC-C
          1 TTTCTTACTCTCTTTTACCAATTAC-CAC

                             ***        
       6414 TTTCTTACTCTCTTTTATTTATTACCAC
          1 TTTCTTACTCTCTTTTACCAATTACCAC

                         
       6442 TTT-TTACTCTCT
          1 TTTCTTACTCTCT

       6454 CTTTTCTTAT


Statistics
Matches: 35,  Mismatches: 4, Indels: 3
        0.83            0.10        0.07

Matches are distributed among these distances:
  27   10  0.29
  28   25  0.71

ACGTcount: A:0.16, C:0.26, G:0.00, T:0.57


Consensus pattern (28 bp):   
TTTCTTACTCTCTTTTACCAATTACCAC

Found at i:6554 original size:21 final size:21

Alignment explanation


    Indices: 6530--6569  Score: 55
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       6520 CTATTATCGC

                *                 
       6530 TTTTGCTCTTACC-GATTACTG
          1 TTTTACTCTT-CCTGATTACTG

                               
       6551 TTTTACTCTTCCTGATTAC
          1 TTTTACTCTTCCTGATTAC

       6570 CTTTTATTGA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    2  0.12
  21   15  0.88

ACGTcount: A:0.15, C:0.25, G:0.10, T:0.50


Consensus pattern (21 bp):   
TTTTACTCTTCCTGATTACTG

Found at i:6595 original size:15 final size:15

Alignment explanation


    Indices: 6562--6624  Score: 58
    Period size: 15  Copynumber: 4.1  Consensus size: 15

       6552 TTTACTCTTC

                     *     
       6562 CTGATTAC-CTTTTA
          1 CTGATTACTATTTTA

            *              
       6576 TTGATTACTATTTTA
          1 CTGATTACTATTTTA

                              
       6591 CTGATCTTTACT-TTTTA
          1 CTGA---TTACTATTTTA

                    *      
       6608 CTGATTACCATTTTA
          1 CTGATTACTATTTTA

              
       6623 CT
          1 CT

       6625 CTTTTTTCTG


Statistics
Matches: 40,  Mismatches: 4, Indels: 9
        0.75            0.08        0.17

Matches are distributed among these distances:
  14   11  0.28
  15   15  0.38
  17    9  0.22
  18    5  0.12

ACGTcount: A:0.22, C:0.17, G:0.06, T:0.54


Consensus pattern (15 bp):   
CTGATTACTATTTTA

Found at i:6693 original size:23 final size:23

Alignment explanation


    Indices: 6669--6752  Score: 70
    Period size: 22  Copynumber: 3.7  Consensus size: 23

       6659 TTACNGGTTA

                                    
       6669 CTTTTTACTTTTTACTGATTGTA-
          1 CTTTTTACTTTTTACTGATT-TAC

                  *                  
       6692 C-TTTTGCTTTTTANC-GTATTTAC
          1 CTTTTTACTTTTTA-CTG-ATTTAC

                         *        *
       6715 CTTTTTAC-TTTTGCTGA-TTAG
          1 CTTTTTACTTTTTACTGATTTAC

                     *       
       6736 CTTTTTACTCTTTACTG
          1 CTTTTTACTTTTTACTG


Statistics
Matches: 49,  Mismatches: 6, Indels: 13
        0.72            0.09        0.19

Matches are distributed among these distances:
  21   11  0.22
  22   22  0.45
  23   11  0.22
  24    5  0.10

ACGTcount: A:0.14, C:0.17, G:0.10, T:0.58


Consensus pattern (23 bp):   
CTTTTTACTTTTTACTGATTTAC
Done.