Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018580.1 Corchorus olitorius cultivar O-4 contig18613, 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: 3224
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:2006 original size:34 final size:34

Alignment explanation


    Indices: 1967--2046  Score: 117
    Period size: 34  Copynumber: 2.3  Consensus size: 34

       1957 AAAACAAAAC

                                          *    
       1967 AAAAGAAAAAGGGCCTAGCCCATAA-GAAATAAGA
          1 AAAAGAAAAAGGGCCTAGCCCATAACG-AAGAAGA

                             *                
       2001 AAAAGAAAAAGGGCCTATCCCATAACGAAGAAGA
          1 AAAAGAAAAAGGGCCTAGCCCATAACGAAGAAGA

                        
       2035 AAGAAGAAAAAG
          1 AA-AAGAAAAAG

       2047 AATAAGGAAG


Statistics
Matches: 42,  Mismatches: 2, Indels: 3
        0.89            0.04        0.06

Matches are distributed among these distances:
  34   32  0.76
  35   10  0.24

ACGTcount: A:0.57, C:0.14, G:0.21, T:0.07


Consensus pattern (34 bp):   
AAAAGAAAAAGGGCCTAGCCCATAACGAAGAAGA

Found at i:2042 original size:10 final size:10

Alignment explanation


    Indices: 2027--2076  Score: 50
    Period size: 10  Copynumber: 5.0  Consensus size: 10

       2017 ATCCCATAAC

                      
       2027 GAAGAAGAAA
          1 GAAGAAGAAA

                      
       2037 GAAGAA-AAA
          1 GAAGAAGAAA

               *   *  
       2046 GAATAAGGAA
          1 GAAGAAGAAA

                        
       2056 GAAGAAAGAAAA
          1 GAAG-AAG-AAA

                      
       2068 GAA-AAGAAA
          1 GAAGAAGAAA

       2077 AGAAAATAAG


Statistics
Matches: 33,  Mismatches: 4, Indels: 7
        0.75            0.09        0.16

Matches are distributed among these distances:
   9   11  0.33
  10   14  0.42
  11    3  0.09
  12    5  0.15

ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02


Consensus pattern (10 bp):   
GAAGAAGAAA

Found at i:2051 original size:26 final size:27

Alignment explanation


    Indices: 2022--2075  Score: 83
    Period size: 26  Copynumber: 2.0  Consensus size: 27

       2012 GGCCTATCCC

                              *        
       2022 ATAACGAAGAAGAAAGAAGA-AAAAGA
          1 ATAACGAAGAAGAAAGAAAAGAAAAGA

                *                      
       2048 ATAAGGAAGAAGAAAGAAAAGAAAAGA
          1 ATAACGAAGAAGAAAGAAAAGAAAAGA

             
       2075 A
          1 A

       2076 AAGAAAATAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  26   18  0.72
  27    7  0.28

ACGTcount: A:0.70, C:0.02, G:0.24, T:0.04


Consensus pattern (27 bp):   
ATAACGAAGAAGAAAGAAAAGAAAAGA

Found at i:2059 original size:19 final size:19

Alignment explanation


    Indices: 2035--2089  Score: 57
    Period size: 17  Copynumber: 3.1  Consensus size: 19

       2025 ACGAAGAAGA

                               
       2035 AAGAAGAAAAAGAATAAGG
          1 AAGAAGAAAAAGAATAAGG

                               
       2054 AAGAAG--AAAGAA-AA-G
          1 AAGAAGAAAAAGAATAAGG

                        *       
       2069 AA-AAGAAAAGAAAATAAGG
          1 AAGAAGAAAA-AGAATAAGG

              
       2088 AA
          1 AA

       2090 ATTTGGAATA


Statistics
Matches: 30,  Mismatches: 1, Indels: 10
        0.73            0.02        0.24

Matches are distributed among these distances:
  14    3  0.10
  15    3  0.10
  16    4  0.13
  17    9  0.30
  18    2  0.07
  19    9  0.30

ACGTcount: A:0.73, C:0.00, G:0.24, T:0.04


Consensus pattern (19 bp):   
AAGAAGAAAAAGAATAAGG

Found at i:2067 original size:22 final size:19

Alignment explanation


    Indices: 2042--2081  Score: 53
    Period size: 22  Copynumber: 1.9  Consensus size: 19

       2032 AGAAAGAAGA

                                  
       2042 AAAAGAATAAGGAAGAAGAAAG
          1 AAAAGAA-AA-GAA-AAGAAAG

                              
       2064 AAAAGAAAAGAAAAGAAA
          1 AAAAGAAAAGAAAAGAAA

       2082 ATAAGGAAAT


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

Matches are distributed among these distances:
  19    6  0.33
  20    3  0.17
  21    2  0.11
  22    7  0.39

ACGTcount: A:0.75, C:0.00, G:0.23, T:0.03


Consensus pattern (19 bp):   
AAAAGAAAAGAAAAGAAAG
Done.