Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001177.1 Corchorus capsularis cultivar CVL-1 contig01177, 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: 11694
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35


Found at i:560 original size:12 final size:11

Alignment explanation


    Indices: 543--608  Score: 59
    Period size: 10  Copynumber: 6.3  Consensus size: 11

        533 ACGCGAATCT

                        
        543 TTCTCTCTCCTC
          1 TTCTCTCT-CTC

                       
        555 TTCTCTCTCTC
          1 TTCTCTCTCTC

                    *  
        566 TT-TCTCTTTC
          1 TTCTCTCTCTC

                   *   
        576 -TCTCTCCCT-
          1 TTCTCTCTCTC

               *  *    
        585 TTCCCTTTCTC
          1 TTCTCTCTCTC

                       
        596 TT-TCTCTCTC
          1 TTCTCTCTCTC

               
        606 TTC
          1 TTC

        609 GAAGTTCTAA


Statistics
Matches: 42,  Mismatches: 8, Indels: 9
        0.71            0.14        0.15

Matches are distributed among these distances:
   9    1  0.02
  10   26  0.62
  11    7  0.17
  12    8  0.19

ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56


Consensus pattern (11 bp):   
TTCTCTCTCTC

Found at i:571 original size:6 final size:6

Alignment explanation


    Indices: 540--602  Score: 65
    Period size: 6  Copynumber: 10.5  Consensus size: 6

        530 AAAACGCGAA

                      *              *                    *   *     
        540 TCTTTC TCTCTC -CTCTTC TCTCTC TCTTTC TCTTTC TCTCTC CCTTTC
          1 TCTTTC TCTTTC TCT-TTC TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC

            *                
        588 CCTTTC TCTTTC TCT
          1 TCTTTC TCTTTC TCT

        603 CTCTTCGAAG


Statistics
Matches: 47,  Mismatches: 8, Indels: 4
        0.80            0.14        0.07

Matches are distributed among these distances:
   5    2  0.04
   6   43  0.91
   7    2  0.04

ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57


Consensus pattern (6 bp):   
TCTTTC

Found at i:574 original size:30 final size:30

Alignment explanation


    Indices: 540--602  Score: 92
    Period size: 30  Copynumber: 2.1  Consensus size: 30

        530 AAAACGCGAA

                               *           
        540 TCTTTCTCTCT-CCTCTTCTCTCTCTCTTTC
          1 TCTTTCTCTCTCCCT-TTCCCTCTCTCTTTC

                                 *        
        570 TCTTTCTCTCTCCCTTTCCCTTTCTCTTTC
          1 TCTTTCTCTCTCCCTTTCCCTCTCTCTTTC

               
        600 TCT
          1 TCT

        603 CTCTTCGAAG


Statistics
Matches: 30,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  30   27  0.90
  31    3  0.10

ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57


Consensus pattern (30 bp):   
TCTTTCTCTCTCCCTTTCCCTCTCTCTTTC

Found at i:9399 original size:20 final size:20

Alignment explanation


    Indices: 9374--9413  Score: 80
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       9364 GGAATGGTAC

                                
       9374 GTATGTGTGTTAGAAGTCAT
          1 GTATGTGTGTTAGAAGTCAT

                                
       9394 GTATGTGTGTTAGAAGTCAT
          1 GTATGTGTGTTAGAAGTCAT

       9414 TTATATACTA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.25, C:0.05, G:0.30, T:0.40


Consensus pattern (20 bp):   
GTATGTGTGTTAGAAGTCAT

Found at i:10724 original size:2 final size:2

Alignment explanation


    Indices: 10717--10749  Score: 57
    Period size: 2  Copynumber: 16.5  Consensus size: 2

      10707 TGTTTTTGCT

                                                      *      
      10717 TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      10750 GTGTGTGTGT


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48


Consensus pattern (2 bp):   
TA

Found at i:11416 original size:16 final size:15

Alignment explanation


    Indices: 11395--11429  Score: 61
    Period size: 15  Copynumber: 2.3  Consensus size: 15

      11385 TAACTCTGAA

                            
      11395 AAAGAAAAGAAAAAAG
          1 AAAGAAAAG-AAAAAG

                           
      11411 AAAGAAAAGAAAAAG
          1 AAAGAAAAGAAAAAG

                
      11426 AAAG
          1 AAAG

      11430 GTATTGCCTA


Statistics
Matches: 19,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  15   10  0.53
  16    9  0.47

ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00


Consensus pattern (15 bp):   
AAAGAAAAGAAAAAG
Done.