Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012771.1 Corchorus olitorius cultivar O-4 contig12804, 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: 11177
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32


Found at i:531 original size:32 final size:31

Alignment explanation


    Indices: 482--544  Score: 92
    Period size: 32  Copynumber: 2.0  Consensus size: 31

        472 GAAACGTTTA

                                            
        482 TGGGAGACTTTTGGCTGTAATGAAGTTCCGAC
          1 TGGGAGACTTTTGGCTGTAATGAAG-TCCGAC

                         *                  
        514 TGGGAGA-TTCTTTGCTGTAATGAAGTCCGAC
          1 TGGGAGACTT-TTGGCTGTAATGAAGTCCGAC

        545 GAAGCTCTGG


Statistics
Matches: 29,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  31    8  0.28
  32   21  0.72

ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32


Consensus pattern (31 bp):   
TGGGAGACTTTTGGCTGTAATGAAGTCCGAC

Found at i:1468 original size:8 final size:8

Alignment explanation


    Indices: 1448--1489  Score: 68
    Period size: 8  Copynumber: 5.4  Consensus size: 8

       1438 AAGTTTATTG

                    
       1448 ATAATAT-
          1 ATAATATA

                    
       1455 ATAATATA
          1 ATAATATA

                    
       1463 ATAATATA
          1 ATAATATA

            *       
       1471 GTAATATA
          1 ATAATATA

                    
       1479 ATAATATA
          1 ATAATATA

               
       1487 ATA
          1 ATA

       1490 TAACATTATT


Statistics
Matches: 32,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
   7    7  0.22
   8   25  0.78

ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38


Consensus pattern (8 bp):   
ATAATATA

Found at i:2372 original size:16 final size:16

Alignment explanation


    Indices: 2330--2373  Score: 61
    Period size: 16  Copynumber: 2.8  Consensus size: 16

       2320 TCGGGTTGCC

                      *  *  
       2330 TCGGGTTCGGATATTT
          1 TCGGGTTCGGGTAATT

               *            
       2346 TCGAGTTCGGGTAATT
          1 TCGGGTTCGGGTAATT

                        
       2362 TCGGGTTCGGGT
          1 TCGGGTTCGGGT

       2374 TCGGGCGGGT


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  16   24  1.00

ACGTcount: A:0.11, C:0.14, G:0.36, T:0.39


Consensus pattern (16 bp):   
TCGGGTTCGGGTAATT

Found at i:5612 original size:2 final size:2

Alignment explanation


    Indices: 5605--5632  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

       5595 TACAAATTTG

                                                     
       5605 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       5633 AACAATACTA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:8602 original size:24 final size:23

Alignment explanation


    Indices: 8575--8626  Score: 59
    Period size: 23  Copynumber: 2.2  Consensus size: 23

       8565 AGGTTGCGCA

                      *             
       8575 AACTTCAGGGTTCAACCTGGCCCC
          1 AACTTCAGGGGT-AACCTGGCCCC

                 *        **       
       8599 AACTTGAGGGGTAAGTTGGCCCC
          1 AACTTCAGGGGTAACCTGGCCCC

                 
       8622 AACTT
          1 AACTT

       8627 GGTGTTCGTC


Statistics
Matches: 24,  Mismatches: 4, Indels: 1
        0.83            0.14        0.03

Matches are distributed among these distances:
  23   14  0.58
  24   10  0.42

ACGTcount: A:0.23, C:0.29, G:0.25, T:0.23


Consensus pattern (23 bp):   
AACTTCAGGGGTAACCTGGCCCC
Done.