Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004857.1 Corchorus capsularis cultivar CVL-1 contig04875, 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: 10039
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:766 original size:20 final size:21

Alignment explanation


    Indices: 741--800  Score: 63
    Period size: 20  Copynumber: 3.0  Consensus size: 21

        731 AAGGGAATCT

                                 
        741 TTCAATAATGCTATGCAAAG-
          1 TTCAATAATGCTATGCAAAGC

                       * *        
        761 TTCAATAATG-GAAG-ACAAGC
          1 TTCAATAATGCTATGCA-AAGC

                        *       
        781 TTCAATAATGCTCTGCAAAG
          1 TTCAATAATGCTATGCAAAG

        801 ATAGTTCAAA


Statistics
Matches: 31,  Mismatches: 5, Indels: 7
        0.72            0.12        0.16

Matches are distributed among these distances:
  18    1  0.03
  19    5  0.16
  20   20  0.65
  21    4  0.13
  22    1  0.03

ACGTcount: A:0.40, C:0.17, G:0.17, T:0.27


Consensus pattern (21 bp):   
TTCAATAATGCTATGCAAAGC

Found at i:940 original size:2 final size:2

Alignment explanation


    Indices: 933--960  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

        923 GACTGTAAAG

                                                     
        933 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

        961 TGGTATGATA


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

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:1522 original size:2 final size:2

Alignment explanation


    Indices: 1511--1539  Score: 51
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       1501 GAGAAAACCA

                                                        
       1511 AT AT -T 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

       1540 TTAGAATTAT


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   25  0.96

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
AT

Found at i:2635 original size:31 final size:31

Alignment explanation


    Indices: 2597--2659  Score: 90
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       2587 ATATATTAGA

                        *      *    *      
       2597 TAAATAAGGATATAATAGGTATTTTAAAAGT
          1 TAAATAAGGATACAATAGGCATTTCAAAAGT

                     *                     
       2628 TAAATAAGGGTACAATAGGCATTTCAAAAGT
          1 TAAATAAGGATACAATAGGCATTTCAAAAGT

             
       2659 T
          1 T

       2660 TTTCAAAACT


Statistics
Matches: 28,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  31   28  1.00

ACGTcount: A:0.46, C:0.05, G:0.17, T:0.32


Consensus pattern (31 bp):   
TAAATAAGGATACAATAGGCATTTCAAAAGT

Found at i:2884 original size:33 final size:28

Alignment explanation


    Indices: 2823--2880  Score: 116
    Period size: 28  Copynumber: 2.1  Consensus size: 28

       2813 AAACATTAGA

                                        
       2823 TTTCTAATAATATTTTATTCCATTTAAT
          1 TTTCTAATAATATTTTATTCCATTTAAT

                                        
       2851 TTTCTAATAATATTTTATTCCATTTAAT
          1 TTTCTAATAATATTTTATTCCATTTAAT

              
       2879 TT
          1 TT

       2881 AATTACGATT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   30  1.00

ACGTcount: A:0.31, C:0.10, G:0.00, T:0.59


Consensus pattern (28 bp):   
TTTCTAATAATATTTTATTCCATTTAAT

Found at i:6804 original size:54 final size:54

Alignment explanation


    Indices: 6718--6828  Score: 195
    Period size: 54  Copynumber: 2.1  Consensus size: 54

       6708 CATTGTTTGT

                                       *          *               
       6718 TTTGATAATTTTAGATGTGAAAATAATTTTAAGGGCACTTTGTAAGGCACCTAC
          1 TTTGATAATTTTAGATGTGAAAATAATCTTAAGGGCACCTTGTAAGGCACCTAC

                                                        *         
       6772 TTTGATAATTTTAGATGTGAAAATAATCTTAAGGGCACCTTGTAGGGCACCTAC
          1 TTTGATAATTTTAGATGTGAAAATAATCTTAAGGGCACCTTGTAAGGCACCTAC

               
       6826 TTT
          1 TTT

       6829 CCTTGCTAGA


Statistics
Matches: 54,  Mismatches: 3, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  54   54  1.00

ACGTcount: A:0.32, C:0.13, G:0.19, T:0.37


Consensus pattern (54 bp):   
TTTGATAATTTTAGATGTGAAAATAATCTTAAGGGCACCTTGTAAGGCACCTAC

Found at i:7613 original size:32 final size:32

Alignment explanation


    Indices: 7540--7628  Score: 117
    Period size: 32  Copynumber: 2.8  Consensus size: 32

       7530 GACGCTATTG

                                            
       7540 ACGTGGCATTGCCATGTCAGACC-AAAATGCC
          1 ACGTGGCATTGCCATGTCAGACCAAAAATGCC

              *  *        *   *           * 
       7571 ACATGACATTGCCACGTCGGACCAAAAATGTC
          1 ACGTGGCATTGCCATGTCAGACCAAAAATGCC

             *                        
       7603 ATGTGGCATTGCCATGTCAGACCAAA
          1 ACGTGGCATTGCCATGTCAGACCAAA

       7629 CCGTTGATAT


Statistics
Matches: 47,  Mismatches: 10, Indels: 1
        0.81            0.17        0.02

Matches are distributed among these distances:
  31   19  0.40
  32   28  0.60

ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20


Consensus pattern (32 bp):   
ACGTGGCATTGCCATGTCAGACCAAAAATGCC
Done.