Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011161.1 Corchorus capsularis cultivar CVL-1 contig11182, 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: 26470
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:14 original size:2 final size:2

Alignment explanation


    Indices: 8--42  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

          1 TGGAATG

                                                                
          8 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

         43 CACAATAAAA


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:4744 original size:8 final size:9

Alignment explanation


    Indices: 4713--4744  Score: 55
    Period size: 9  Copynumber: 3.6  Consensus size: 9

       4703 ACGAGGAAGG

                     
       4713 CGGGGGTGA
          1 CGGGGGTGA

                  *  
       4722 CGGGGGCGA
          1 CGGGGGTGA

                     
       4731 CGGGGGTGA
          1 CGGGGGTGA

                 
       4740 CGGGG
          1 CGGGG

       4745 AGGCGGAGGC


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   9   21  1.00

ACGTcount: A:0.09, C:0.16, G:0.69, T:0.06


Consensus pattern (9 bp):   
CGGGGGTGA

Found at i:5021 original size:24 final size:22

Alignment explanation


    Indices: 4990--5033  Score: 61
    Period size: 24  Copynumber: 1.9  Consensus size: 22

       4980 TTTTAATTTA

                     *             
       4990 ATTTATTTTTTTATAACAGTAGT
          1 ATTTATTTTATTATAA-AGTAGT

                                 
       5013 ATTTCATTTTATTATAAAGTA
          1 ATTT-ATTTTATTATAAAGTA

       5034 CTACTATATT


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  23    8  0.42
  24   11  0.58

ACGTcount: A:0.34, C:0.05, G:0.07, T:0.55


Consensus pattern (22 bp):   
ATTTATTTTATTATAAAGTAGT

Found at i:24258 original size:85 final size:84

Alignment explanation


    Indices: 24140--24310  Score: 315
    Period size: 85  Copynumber: 2.0  Consensus size: 84

      24130 TTGAAAATAA

                *                                                            
      24140 ACCATCAAGGATATATATAATAATTAATTTTTATTTATATCATTAAAAAAAACTAACAATTTAAA
          1 ACCACCAAGGATATATATAATAATTAATTTTTATTTATATCATTAAAAAAAACTAACAATTTAAA

                                
      24205 TGGACCAAAAAAAGAAAACT
         66 TGGACC-AAAAAAGAAAACT

                                                                             
      24225 ACCACCAAGGATATATATAATAATTAATTTTTATTTATATCATTAAAAAAAACTAACAATTTAAA
          1 ACCACCAAGGATATATATAATAATTAATTTTTATTTATATCATTAAAAAAAACTAACAATTTAAA

               *               
      24290 TGGGCCAAAAAAGAAAACT
         66 TGGACCAAAAAAGAAAACT

              
      24309 AC
          1 AC

      24311 TATAAACTAC


Statistics
Matches: 84,  Mismatches: 2, Indels: 1
        0.97            0.02        0.01

Matches are distributed among these distances:
  84   15  0.18
  85   69  0.82

ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30


Consensus pattern (84 bp):   
ACCACCAAGGATATATATAATAATTAATTTTTATTTATATCATTAAAAAAAACTAACAATTTAAA
TGGACCAAAAAAGAAAACT

Found at i:26447 original size:1 final size:1

Alignment explanation


    Indices: 26441--26470  Score: 60
    Period size: 1  Copynumber: 30.0  Consensus size: 1

      26431 AATGTTCATG

                                          
      26441 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   29  1.00

ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00


Consensus pattern (1 bp):   
T

Done.