Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015796.1 Corchorus olitorius cultivar O-4 contig15829, 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: 31194
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.29


Found at i:21250 original size:6 final size:6

Alignment explanation


    Indices: 21241--21270  Score: 51
    Period size: 6  Copynumber: 5.0  Consensus size: 6

      21231 AGAAAAATGA

                                      *       
      21241 AAAAGC AAAAGC AAAAGC AAAAGT AAAAGC
          1 AAAAGC AAAAGC AAAAGC AAAAGC AAAAGC

      21271 GCAAAAATAT


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   6   22  1.00

ACGTcount: A:0.67, C:0.13, G:0.17, T:0.03


Consensus pattern (6 bp):   
AAAAGC

Found at i:29923 original size:14 final size:13

Alignment explanation


    Indices: 29894--29965  Score: 64
    Period size: 12  Copynumber: 5.7  Consensus size: 13

      29884 GTTTAATAAT

                         
      29894 TATATATT-ATTA
          1 TATATATTAATTA

                  *      
      29906 TATAT-GTAATTA
          1 TATATATTAATTA

                          
      29918 TATATATCTAA-TA
          1 TATATAT-TAATTA

                           
      29931 TTATATATATAA-TA
          1 -TATATAT-TAATTA

                         
      29945 TATAT-TTAATTA
          1 TATATATTAATTA

              *      
      29957 TAAATATTA
          1 TATATATTA

      29966 CTAAACGGTC


Statistics
Matches: 50,  Mismatches: 4, Indels: 11
        0.77            0.06        0.17

Matches are distributed among these distances:
  11    4  0.08
  12   21  0.42
  13   10  0.20
  14   15  0.30

ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51


Consensus pattern (13 bp):   
TATATATTAATTA

Found at i:29930 original size:39 final size:39

Alignment explanation


    Indices: 29887--29963  Score: 111
    Period size: 39  Copynumber: 2.0  Consensus size: 39

      29877 TTAAACCGTT

                             *                *     
      29887 TAATAATTATATAT-TATTATATATGTAATTATATATATC
          1 TAAT-ATTATATATATAATATATATGTAATTATAAATATC

                                    *             
      29926 TAATATTATATATATAATATATATTTAATTATAAATAT
          1 TAATATTATATATATAATATATATGTAATTATAAATAT

      29964 TACTAAACGG


Statistics
Matches: 34,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
  38    9  0.26
  39   25  0.74

ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51


Consensus pattern (39 bp):   
TAATATTATATATATAATATATATGTAATTATAAATATC

Found at i:29947 original size:16 final size:15

Alignment explanation


    Indices: 29894--29947  Score: 56
    Period size: 16  Copynumber: 3.5  Consensus size: 15

      29884 GTTTAATAAT

                           
      29894 TATATATTAT-TATA
          1 TATATATTATATATA

               *            
      29908 TATGTAATTATATATA
          1 TATAT-ATTATATATA

             *              
      29924 TCTAATATTATATATA
          1 TAT-ATATTATATATA

                    
      29940 TAATATAT
          1 T-ATATAT

      29948 ATTTAATTAT


Statistics
Matches: 32,  Mismatches: 4, Indels: 6
        0.76            0.10        0.14

Matches are distributed among these distances:
  14    4  0.12
  15    5  0.16
  16   21  0.66
  17    2  0.06

ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52


Consensus pattern (15 bp):   
TATATATTATATATA
Done.