Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009422.1 Corchorus capsularis cultivar CVL-1 contig09443, 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: 17012
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:532 original size:20 final size:20

Alignment explanation


    Indices: 491--532  Score: 57
    Period size: 20  Copynumber: 2.1  Consensus size: 20

        481 AAATCATAGT

                *         *  *  
        491 AAAATCAAGATAATCAATCA
          1 AAAACCAAGATAATAAACCA

                                
        511 AAAACCAAGATAATAAACCA
          1 AAAACCAAGATAATAAACCA

              
        531 AA
          1 AA

        533 CCAGTCAAAT


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.64, C:0.17, G:0.05, T:0.14


Consensus pattern (20 bp):   
AAAACCAAGATAATAAACCA

Found at i:5984 original size:2 final size:2

Alignment explanation


    Indices: 5977--6017  Score: 73
    Period size: 2  Copynumber: 20.0  Consensus size: 2

       5967 ATTGTTTTAA

                                                                        
       5977 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT

       6018 TAATTTAAAC


Statistics
Matches: 38,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   2   36  0.95
   3    2  0.05

ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:7609 original size:17 final size:16

Alignment explanation


    Indices: 7589--7637  Score: 53
    Period size: 17  Copynumber: 2.9  Consensus size: 16

       7579 CAGATCACTG

                             
       7589 GTGATCTAAGATTACCA
          1 GTGATC-AAGATTACCA

                        *   *
       7606 GTGATGCAAGATCACCG
          1 GTGAT-CAAGATTACCA

                           
       7623 GTGATCAAAGATTAC
          1 GTGATC-AAGATTAC

       7638 ATGGGTTTAT


Statistics
Matches: 27,  Mismatches: 3, Indels: 4
        0.79            0.09        0.12

Matches are distributed among these distances:
  16    1  0.04
  17   25  0.93
  18    1  0.04

ACGTcount: A:0.35, C:0.18, G:0.22, T:0.24


Consensus pattern (16 bp):   
GTGATCAAGATTACCA

Found at i:13650 original size:31 final size:31

Alignment explanation


    Indices: 13603--13681  Score: 106
    Period size: 31  Copynumber: 2.5  Consensus size: 31

      13593 ATTTTTAGCC

                *                          
      13603 ACCACTTTGAGTCTAAACCTTTCAAAAGTTG
          1 ACCAATTTGAGTCTAAACCTTTCAAAAGTTG

                        *     *             
      13634 -CTCAATTTGAGCCTAAAGCTTTCAAAAGTTG
          1 AC-CAATTTGAGTCTAAACCTTTCAAAAGTTG

                    *        
      13665 ACCAATTTAAGTCTAAA
          1 ACCAATTTGAGTCTAAA

      13682 AACAGAAAAC


Statistics
Matches: 41,  Mismatches: 5, Indels: 4
        0.82            0.10        0.08

Matches are distributed among these distances:
  30    1  0.02
  31   39  0.95
  32    1  0.02

ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32


Consensus pattern (31 bp):   
ACCAATTTGAGTCTAAACCTTTCAAAAGTTG

Found at i:16758 original size:2 final size:2

Alignment explanation


    Indices: 16747--16778  Score: 57
    Period size: 2  Copynumber: 16.5  Consensus size: 2

      16737 AGATATGTAT

                                                             
      16747 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      16779 TAAAATATAG


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

Matches are distributed among these distances:
   1    1  0.03
   2   28  0.97

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


Consensus pattern (2 bp):   
TA

Done.