Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024381.1 Corchorus olitorius cultivar O-4 contig24414, 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: 1777
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29


Found at i:513 original size:26 final size:25

Alignment explanation


    Indices: 484--593  Score: 86
    Period size: 25  Copynumber: 4.4  Consensus size: 25

        474 CAAAATTTTA

                *                    
        484 TTTTCTTTTTATGACGCAAAAACTC
          1 TTTTTTTTTTATGACGCAAAAACTC

                                          
        509 TTTTTTTTTTA-GAAAAAACGCAAAAA--C
          1 TTTTTTTTTTATG-----ACGCAAAAACTC

                              *      *
        536 --TTTTTTTTATGACGCAGAAACATA
          1 TTTTTTTTTTATGACGCAAAAAC-TC

                                  * *
        560 TTTTTTTTTTATGACGCAAAAAATA
          1 TTTTTTTTTTATGACGCAAAAACTC

                     
        585 TTTTTTTTT
          1 TTTTTTTTT

        594 CGACGCAAAA


Statistics
Matches: 69,  Mismatches: 5, Indels: 22
        0.72            0.05        0.23

Matches are distributed among these distances:
  21    8  0.12
  24    1  0.01
  25   30  0.43
  26   20  0.29
  27    1  0.01
  29    9  0.13

ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47


Consensus pattern (25 bp):   
TTTTTTTTTTATGACGCAAAAACTC

Found at i:563 original size:23 final size:23

Alignment explanation


    Indices: 536--605  Score: 88
    Period size: 23  Copynumber: 2.9  Consensus size: 23

        526 ACGCAAAAAC

                                    
        536 TTTTTTTTATGACGCAGAAACATA
          1 TTTTTTTTATGACGCA-AAACATA

                                 *   
        560 TTTTTTTTTTATGACGCAAAAAATA
          1 --TTTTTTTTATGACGCAAAACATA

                                  
        585 TTTTTTTT-TCGACGCAAAACA
          1 TTTTTTTTAT-GACGCAAAACA

        606 CAAAACAAAC


Statistics
Matches: 41,  Mismatches: 2, Indels: 5
        0.85            0.04        0.10

Matches are distributed among these distances:
  22    1  0.02
  23   18  0.44
  25    6  0.15
  26   16  0.39

ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44


Consensus pattern (23 bp):   
TTTTTTTTATGACGCAAAACATA

Found at i:636 original size:36 final size:37

Alignment explanation


    Indices: 596--676  Score: 98
    Period size: 34  Copynumber: 2.2  Consensus size: 37

        586 TTTTTTTTCG

                                                  
        596 ACGCAAAACACAAAACAAACT-TTGTTTTTT-TCAAAA
          1 ACGCAAAACACAAAACAAA-TATTGTTTTTTATCAAAA

                                   *         *    
        632 ACGC--AACACAAAACAAATATTTTTTTTTAATTAAAA
          1 ACGCAAAACACAAAACAAATATTGTTTTTT-ATCAAAA

                     
        668 ACGCAAAAC
          1 ACGCAAAAC

        677 TTTTTTTTTA


Statistics
Matches: 38,  Mismatches: 2, Indels: 8
        0.79            0.04        0.17

Matches are distributed among these distances:
  33    1  0.03
  34   21  0.55
  36   13  0.34
  38    3  0.08

ACGTcount: A:0.49, C:0.19, G:0.05, T:0.27


Consensus pattern (37 bp):   
ACGCAAAACACAAAACAAATATTGTTTTTTATCAAAA

Found at i:687 original size:22 final size:23

Alignment explanation


    Indices: 653--697  Score: 56
    Period size: 22  Copynumber: 2.0  Consensus size: 23

        643 AACAAATATT

                                    
        653 TTTTTTTAATTAAAAACGCAAAAC
          1 TTTTTTT-ATTAAAAACGCAAAAC

                        **        
        677 TTTTTTT-TTAATGACGCAAAA
          1 TTTTTTTATTAAAAACGCAAAA

        698 ACAAATAATT


Statistics
Matches: 19,  Mismatches: 2, Indels: 2
        0.83            0.09        0.09

Matches are distributed among these distances:
  22   12  0.63
  24    7  0.37

ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42


Consensus pattern (23 bp):   
TTTTTTTATTAAAAACGCAAAAC

Found at i:1019 original size:15 final size:16

Alignment explanation


    Indices: 995--1034  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

        985 AGAGGTTGAA

                 *          
        995 AGAAAGCAATTAAAC-
          1 AGAAAACAATTAAACT

                        *   
       1010 AGAAAACAATTATACT
          1 AGAAAACAATTAAACT

                     
       1026 AGAAAACAA
          1 AGAAAACAA

       1035 AGCAAAGTAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   13  0.59
  16    9  0.41

ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15


Consensus pattern (16 bp):   
AGAAAACAATTAAACT

Done.