Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009835.1 Corchorus capsularis cultivar CVL-1 contig09856, 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: 22943
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30


Found at i:145 original size:12 final size:12

Alignment explanation


    Indices: 128--152  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

        118 TCAATCAATT

                        
        128 TGCACACCAAAG
          1 TGCACACCAAAG

                        
        140 TGCACACCAAAG
          1 TGCACACCAAAG

             
        152 T
          1 T

        153 TCCAAGCAAG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.40, C:0.32, G:0.16, T:0.12


Consensus pattern (12 bp):   
TGCACACCAAAG

Found at i:1920 original size:13 final size:13

Alignment explanation


    Indices: 1900--1933  Score: 50
    Period size: 13  Copynumber: 2.6  Consensus size: 13

       1890 ATAGTCTTGG

                         
       1900 CCATTATTACACA
          1 CCATTATTACACA

             *       *   
       1913 CTATTATTATACA
          1 CCATTATTACACA

                    
       1926 CCATTATT
          1 CCATTATT

       1934 TTCTAATGAC


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  13   18  1.00

ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41


Consensus pattern (13 bp):   
CCATTATTACACA

Found at i:2033 original size:10 final size:11

Alignment explanation


    Indices: 1993--2036  Score: 56
    Period size: 10  Copynumber: 4.2  Consensus size: 11

       1983 AAGTCTACAT

                     * 
       1993 CACACTTAAAA
          1 CACACTTAATA

               *       
       2004 CACTCTTAA-A
          1 CACACTTAATA

                       
       2014 CACACTTAATA
          1 CACACTTAATA

                       
       2025 CACAC-TAATA
          1 CACACTTAATA

              
       2035 CA
          1 CA

       2037 TATAATTAAT


Statistics
Matches: 30,  Mismatches: 2, Indels: 3
        0.86            0.06        0.09

Matches are distributed among these distances:
  10   16  0.53
  11   14  0.47

ACGTcount: A:0.48, C:0.30, G:0.00, T:0.23


Consensus pattern (11 bp):   
CACACTTAATA

Found at i:8115 original size:77 final size:79

Alignment explanation


    Indices: 7986--8141  Score: 271
    Period size: 77  Copynumber: 2.0  Consensus size: 79

       7976 GACAGTCACA

                                         *              *                    
       7986 AGAAAACAAAATCCAATTGGTCTAATATATATCCCAAAATATCAGAATAATAGTCTCAACAGCTA
          1 AGAAAACAAAATCCAATTGGTCTAATATACATCCCAAAATATCACAATAATAGTCTCAACAGCTA

                          
       8051 GAGTCAGTGGGACT
         66 GAGTCAGTGGGACT

                *                                                            
       8065 AGAACACAAAATCCAATTGGTCT-A-ATACATCCCAAAATATCACAATAATAGTCTCAACAGCTA
          1 AGAAAACAAAATCCAATTGGTCTAATATACATCCCAAAATATCACAATAATAGTCTCAACAGCTA

                          
       8128 GAGTCAGTGGGACT
         66 GAGTCAGTGGGACT

       8142 CAAAACTTCA


Statistics
Matches: 74,  Mismatches: 3, Indels: 2
        0.94            0.04        0.03

Matches are distributed among these distances:
  77   51  0.69
  78    1  0.01
  79   22  0.30

ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23


Consensus pattern (79 bp):   
AGAAAACAAAATCCAATTGGTCTAATATACATCCCAAAATATCACAATAATAGTCTCAACAGCTA
GAGTCAGTGGGACT

Found at i:12091 original size:32 final size:32

Alignment explanation


    Indices: 12045--12106  Score: 106
    Period size: 32  Copynumber: 1.9  Consensus size: 32

      12035 TTCTAATTAG

                *                           
      12045 AGCTGATATTTTTCCAATTATAAGACAAAAGC
          1 AGCTCATATTTTTCCAATTATAAGACAAAAGC

                            *             
      12077 AGCTCATATTTTTCCAGTTATAAGACAAAA
          1 AGCTCATATTTTTCCAATTATAAGACAAAA

      12107 ACAATAAAAG


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  32   28  1.00

ACGTcount: A:0.40, C:0.16, G:0.11, T:0.32


Consensus pattern (32 bp):   
AGCTCATATTTTTCCAATTATAAGACAAAAGC

Found at i:12945 original size:2 final size:2

Alignment explanation


    Indices: 12938--12970  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

      12928 TCGTCCCACC

                                                             
      12938 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 A

      12971 GTAATAATAA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:22597 original size:18 final size:18

Alignment explanation


    Indices: 22576--22614  Score: 78
    Period size: 18  Copynumber: 2.2  Consensus size: 18

      22566 GGGAGATTGA

                              
      22576 TGAAAGTGGGGACTATGC
          1 TGAAAGTGGGGACTATGC

                              
      22594 TGAAAGTGGGGACTATGC
          1 TGAAAGTGGGGACTATGC

               
      22612 TGA
          1 TGA

      22615 GCGAAATATA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.28, C:0.10, G:0.38, T:0.23


Consensus pattern (18 bp):   
TGAAAGTGGGGACTATGC
Done.