Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013635.1 Corchorus capsularis cultivar CVL-1 contig13656, 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: 27791
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:13458 original size:2 final size:2

Alignment explanation


    Indices: 13451--13486  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

      13441 CAGAATATGC

                                                                 
      13451 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      13487 CAGAGAATGG


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:14560 original size:6 final size:6

Alignment explanation


    Indices: 14549--14581  Score: 57
    Period size: 6  Copynumber: 5.5  Consensus size: 6

      14539 CACTCTCCTC

                             *                    
      14549 CGCTGT CGCTGT CGCCGT CGCTGT CGCTGT CGC
          1 CGCTGT CGCTGT CGCTGT CGCTGT CGCTGT CGC

      14582 CGTCTCCTCC


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   6   25  1.00

ACGTcount: A:0.00, C:0.39, G:0.33, T:0.27


Consensus pattern (6 bp):   
CGCTGT

Found at i:14572 original size:18 final size:18

Alignment explanation


    Indices: 14549--14585  Score: 74
    Period size: 18  Copynumber: 2.1  Consensus size: 18

      14539 CACTCTCCTC

                              
      14549 CGCTGTCGCTGTCGCCGT
          1 CGCTGTCGCTGTCGCCGT

                              
      14567 CGCTGTCGCTGTCGCCGT
          1 CGCTGTCGCTGTCGCCGT

             
      14585 C
          1 C

      14586 TCCTCCCCTC


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   19  1.00

ACGTcount: A:0.00, C:0.41, G:0.32, T:0.27


Consensus pattern (18 bp):   
CGCTGTCGCTGTCGCCGT

Found at i:19504 original size:19 final size:20

Alignment explanation


    Indices: 19458--19505  Score: 62
    Period size: 22  Copynumber: 2.4  Consensus size: 20

      19448 TGTGGTACGC

                                 *
      19458 CACATGTACCAAAAAGTCGTGC
          1 CACATGTACCAAAAA--CGTGA

                                
      19480 CACATGTACCAAAAA-GTGA
          1 CACATGTACCAAAAACGTGA

                   
      19499 CACATGT
          1 CACATGT

      19506 CACGTCACGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  19   10  0.40
  22   15  0.60

ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19


Consensus pattern (20 bp):   
CACATGTACCAAAAACGTGA

Found at i:19519 original size:53 final size:53

Alignment explanation


    Indices: 19425--19525  Score: 141
    Period size: 53  Copynumber: 1.9  Consensus size: 53

      19415 GACGTGGCAC

                 *                 **                            
      19425 GCCACGTGTACCAAAAAGTGACATGTGGTACGCCACATGTACCAAAAAGTCGT
          1 GCCACATGTACCAAAAAGTGACACATGGTACGCCACATGTACCAAAAAGTCGT

                                             *   *           
      19478 GCCACATGTACCAAAAAGTGACACAT-GTCACGTCACGTGTACCAAAAA
          1 GCCACATGTACCAAAAAGTGACACATGGT-ACGCCACATGTACCAAAAA

      19526 TTGACACGTG


Statistics
Matches: 42,  Mismatches: 5, Indels: 2
        0.86            0.10        0.04

Matches are distributed among these distances:
  52    2  0.05
  53   40  0.95

ACGTcount: A:0.37, C:0.26, G:0.20, T:0.18


Consensus pattern (53 bp):   
GCCACATGTACCAAAAAGTGACACATGGTACGCCACATGTACCAAAAAGTCGT

Found at i:19544 original size:31 final size:30

Alignment explanation


    Indices: 19484--19585  Score: 107
    Period size: 31  Copynumber: 3.3  Consensus size: 30

      19474 TCGTGCCACA

                              *  *  *      
      19484 TGTACCAAAAAGTGACACATGTCACGTCACG
          1 TGTACCAAAAA-TGACACGTGGCATGTCACG

                                          *
      19515 TGTACCAAAAATTGACACGTGGCATGTCACA
          1 TGTACCAAAAA-TGACACGTGGCATGTCACG

              * *                     *    
      19546 TATTTCCAAAAATGACACGTGGCATGCCACG
          1 T-GTACCAAAAATGACACGTGGCATGTCACG

                      
      19577 TGTA-CAAAA
          1 TGTACCAAAA

      19586 GGATACATGC


Statistics
Matches: 59,  Mismatches: 11, Indels: 4
        0.80            0.15        0.05

Matches are distributed among these distances:
  29    5  0.08
  30    1  0.02
  31   45  0.76
  32    8  0.14

ACGTcount: A:0.36, C:0.24, G:0.19, T:0.22


Consensus pattern (30 bp):   
TGTACCAAAAATGACACGTGGCATGTCACG
Done.