Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011267.1 Corchorus capsularis cultivar CVL-1 contig11288, 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: 17906
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:5422 original size:99 final size:98

Alignment explanation


    Indices: 5233--5431  Score: 330
    Period size: 99  Copynumber: 2.0  Consensus size: 98

       5223 TATCAGAATG

                                                                             
       5233 TTCTAAATGTAGCTTAAATCACGGATCAAAATTGTCAATATTAACATATATGTTATGTAAATATT
          1 TTCTAAATGTAGCTTAAATCACGGATCAAAATTGTCAATATTAACATATATGTTATGTAAATATT

                                             
       5298 TGTAATTATCACCATTATTTACTTTCCATTTGT
         66 TGTAATTATCACCATTATTTACTTTCCATTTGT

                                                             *               
       5331 TTCTAAATGTAGCTTAAATCACGGATCAAAATTG-CAATATTAACAGATTTATGTTATGTAAATA
          1 TTCTAAATGTAGCTTAAATCACGGATCAAAATTGTCAATATTAAC--ATATATGTTATGTAAATA

                 *     *                        
       5395 TTTGTTATTATTACCAATT-TTTACTTTCCATTTGT
         64 TTTGTAATTATCACC-ATTATTTACTTTCCATTTGT

              
       5430 TT
          1 TT

       5432 AGCCTTGTTT


Statistics
Matches: 95,  Mismatches: 3, Indels: 5
        0.92            0.03        0.05

Matches are distributed among these distances:
  97   10  0.11
  98   34  0.36
  99   48  0.51
 100    3  0.03

ACGTcount: A:0.34, C:0.13, G:0.10, T:0.44


Consensus pattern (98 bp):   
TTCTAAATGTAGCTTAAATCACGGATCAAAATTGTCAATATTAACATATATGTTATGTAAATATT
TGTAATTATCACCATTATTTACTTTCCATTTGT

Found at i:7310 original size:17 final size:17

Alignment explanation


    Indices: 7288--7342  Score: 58
    Period size: 17  Copynumber: 3.2  Consensus size: 17

       7278 ATCACCCCCC

                             
       7288 AGATCACTAGTGATCAA
          1 AGATCACTAGTGATCAA

                   * * *      
       7305 AGATCACCAATTATGC-A
          1 AGATCACTAGTGAT-CAA

                    *        
       7322 AGATCACTGGTGATCAA
          1 AGATCACTAGTGATCAA

                
       7339 AGAT
          1 AGAT

       7343 TACATGGGTT


Statistics
Matches: 29,  Mismatches: 7, Indels: 4
        0.73            0.17        0.10

Matches are distributed among these distances:
  16    1  0.03
  17   27  0.93
  18    1  0.03

ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24


Consensus pattern (17 bp):   
AGATCACTAGTGATCAA

Found at i:7485 original size:20 final size:20

Alignment explanation


    Indices: 7460--7508  Score: 80
    Period size: 20  Copynumber: 2.5  Consensus size: 20

       7450 ATCACCTGCC

                           *    
       7460 AAGATCACCACAGGTGATCA
          1 AAGATCACCACAGGTAATCA

                  *             
       7480 AAGATCGCCACAGGTAATCA
          1 AAGATCACCACAGGTAATCA

                     
       7500 AAGATCACC
          1 AAGATCACC

       7509 CCCAACCAAA


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  20   26  1.00

ACGTcount: A:0.41, C:0.27, G:0.18, T:0.14


Consensus pattern (20 bp):   
AAGATCACCACAGGTAATCA
Done.