Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008222.1 Corchorus capsularis cultivar CVL-1 contig08243, 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: 27037
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34


Found at i:5778 original size:20 final size:20

Alignment explanation


    Indices: 5742--5781  Score: 55
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       5732 AAACTTCCTG

                        *       
       5742 GAAAAAAAAAACGAGAAAAA
          1 GAAAAAAAAAACAAGAAAAA

                                 
       5762 GAAAAAAAAGAA-AAGAAAAA
          1 GAAAAAAAA-AACAAGAAAAA

       5782 AGTGGGGGCT


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  20   16  0.89
  21    2  0.11

ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00


Consensus pattern (20 bp):   
GAAAAAAAAAACAAGAAAAA

Found at i:11050 original size:13 final size:13

Alignment explanation


    Indices: 11029--11064  Score: 54
    Period size: 13  Copynumber: 2.8  Consensus size: 13

      11019 CCCTTTTTTT

                     *   
      11029 TAAAAAAAAAAAA
          1 TAAAAAAAATAAA

                *        
      11042 TAAATAAAATAAA
          1 TAAAAAAAATAAA

                      
      11055 TAAAAAAAAT
          1 TAAAAAAAAT

      11065 TGCAACATAT


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  13   20  1.00

ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17


Consensus pattern (13 bp):   
TAAAAAAAATAAA

Found at i:23496 original size:156 final size:156

Alignment explanation


    Indices: 23212--23523  Score: 534
    Period size: 156  Copynumber: 2.0  Consensus size: 156

      23202 CCCTGTAAAG

                               *                              *              
      23212 GATCGTAATTCAAAGCCCCTTTCAATGATGGATAATTATCACTTCCAATTTAAATTTACATCTGT
          1 GATCGTAATTCAAAGCCCCATTCAATGATGGATAATTATCACTTCCAATTAAAATTTACATCTGT

                            *                     *                          
      23277 CAAGTGAGAATTTTAGTATAAAATACATGTGAAATCCAGTATACCATCCAAAAATAAAAGCAAAT
         66 CAAGTGAGAATTTTAGCATAAAATACATGTGAAATCCAATATACCATCCAAAAATAAAAGCAAAT

                                      
      23342 TTATGACAAACACATAAATAAAGTAA
        131 TTATGACAAACACATAAATAAAGTAA

                           * *             *            *                    
      23368 GATCGTAATTCAAAGTCTCATTCAATGATGGTTAATTATCACTTTCAATTAAAATTTACATCTGT
          1 GATCGTAATTCAAAGCCCCATTCAATGATGGATAATTATCACTTCCAATTAAAATTTACATCTGT

                                                                *            
      23433 CAAGTGAGAATTTTAGCATAAAATACATGTGAAATCCAATATACCATCCAAACATAAAAGCAAAT
         66 CAAGTGAGAATTTTAGCATAAAATACATGTGAAATCCAATATACCATCCAAAAATAAAAGCAAAT

                      *               
      23498 TTATGACAAAGACATAAATAAAGTAA
        131 TTATGACAAACACATAAATAAAGTAA

      23524 ATACTTTCAT


Statistics
Matches: 146,  Mismatches: 10, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
 156  146  1.00

ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30


Consensus pattern (156 bp):   
GATCGTAATTCAAAGCCCCATTCAATGATGGATAATTATCACTTCCAATTAAAATTTACATCTGT
CAAGTGAGAATTTTAGCATAAAATACATGTGAAATCCAATATACCATCCAAAAATAAAAGCAAAT
TTATGACAAACACATAAATAAAGTAA
Done.