Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001515.1 Corchorus capsularis cultivar CVL-1 contig01515, 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, 659

Length: 1099
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30


Found at i:54 original size:16 final size:16

Alignment explanation


    Indices: 23--57  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

         13 AAGAAAGAGC

                       *    
         23 AAATACGCTAATAAAT
          1 AAATACGCTAAGAAAT

                      *     
         39 AAATACGCTAGGAAAT
          1 AAATACGCTAAGAAAT

               
         55 AAA
          1 AAA

         58 ATACCCGATA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.57, C:0.11, G:0.11, T:0.20


Consensus pattern (16 bp):   
AAATACGCTAAGAAAT

Found at i:1063 original size:22 final size:22

Alignment explanation


    Indices: 1010--1054  Score: 81
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       1000 TTATTTTTAT

                   *              
       1010 TAAATTTTAAATTCTATTTAAA
          1 TAAATTTAAAATTCTATTTAAA

                                  
       1032 TAAATTTAAAATTCTATTTAAA
          1 TAAATTTAAAATTCTATTTAAA

             
       1054 T
          1 T

       1055 TCTATTAAAT


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49


Consensus pattern (22 bp):   
TAAATTTAAAATTCTATTTAAA

Found at i:1064 original size:10 final size:11

Alignment explanation


    Indices: 1015--1074  Score: 63
    Period size: 11  Copynumber: 5.6  Consensus size: 11

       1005 TTTATTAAAT

                       
       1015 TTTAAATTCTA
          1 TTTAAATTCTA

                    ** 
       1026 TTTAAA-TAAA
          1 TTTAAATTCTA

                        
       1036 TTTAAAATTCTA
          1 TTT-AAATTCTA

                       
       1048 TTTAAATTCTA
          1 TTTAAATTCTA

                     * 
       1059 -TTAAA-TCCA
          1 TTTAAATTCTA

                   
       1068 TTTAAAT
          1 TTTAAAT

       1075 ATTAAATCAA


Statistics
Matches: 40,  Mismatches: 5, Indels: 8
        0.75            0.09        0.15

Matches are distributed among these distances:
   9    3  0.08
  10   15  0.38
  11   17  0.43
  12    5  0.12

ACGTcount: A:0.43, C:0.08, G:0.00, T:0.48


Consensus pattern (11 bp):   
TTTAAATTCTA
Done.