Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017779.1 Corchorus olitorius cultivar O-4 contig17812, 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, 907

Length: 1513
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30


Found at i:453 original size:53 final size:52

Alignment explanation


    Indices: 336--457  Score: 124
    Period size: 53  Copynumber: 2.3  Consensus size: 52

        326 GACAGAAAAT

                           * *                              *      
        336 AAATAAATTTTTTTTAATAAAAACGCAAAAACAAGAAATTTTTTTTTTCTGACGC
          1 AAATAAATTTTTTTTTAGAAAAACGCAAAAAC---AAATTTTTTTTTTATGACGC

                  *                          **                 
        391 AAAT--TTTTTTTTTTAGAAAAACGCAAAAAC-CCTTTTTTTTTTATGACGC
          1 AAATAAATTTTTTTTTAGAAAAACGCAAAAACAAATTTTTTTTTTATGACGC

                              
        440 AGAAATAAATTTTTTTTT
          1 --AAATAAATTTTTTTTT

        458 TTATGACGCA


Statistics
Matches: 56,  Mismatches: 7, Indels: 10
        0.77            0.10        0.14

Matches are distributed among these distances:
  49   16  0.29
  51    4  0.07
  53   32  0.57
  55    4  0.07

ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43


Consensus pattern (52 bp):   
AAATAAATTTTTTTTTAGAAAAACGCAAAAACAAATTTTTTTTTTATGACGC

Found at i:470 original size:21 final size:22

Alignment explanation


    Indices: 446--491  Score: 76
    Period size: 21  Copynumber: 2.1  Consensus size: 22

        436 ACGCAGAAAT

                                  
        446 AAATTTTTTTTTTTAT-GACGC
          1 AAATTTTTTTTTTTATCGACGC

                          *       
        467 AAATTTTTTTTTTTTTCGACGC
          1 AAATTTTTTTTTTTATCGACGC

               
        489 AAA
          1 AAA

        492 ACACAAAATT


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  21   15  0.65
  22    8  0.35

ACGTcount: A:0.26, C:0.11, G:0.09, T:0.54


Consensus pattern (22 bp):   
AAATTTTTTTTTTTATCGACGC

Found at i:474 original size:22 final size:23

Alignment explanation


    Indices: 374--491  Score: 80
    Period size: 27  Copynumber: 4.9  Consensus size: 23

        364 AAACAAGAAA

                      *            
        374 TTTTTTTTTTCTGACGCAAAT-T
          1 TTTTTTTTTTATGACGCAAATAT

                       * **       *   *
        396 TTTTTTTTTAGAAAAACGCAAAAACCC
          1 TTTTTTTTT--TATGACGCAAATA--T

                                       
        423 TTTTTTTTTTATGACGCAGAAATAAAT
          1 TTTTTTTTTTATGACGC--AAAT--AT

                                   
        450 TTTTTTTTTTATGACGCAAAT-T
          1 TTTTTTTTTTATGACGCAAATAT

                                 
        472 TTTTTTTTTT-TCGACGCAAA
          1 TTTTTTTTTTAT-GACGCAAA

        492 ACACAAAATT


Statistics
Matches: 75,  Mismatches: 11, Indels: 20
        0.71            0.10        0.19

Matches are distributed among these distances:
  21    1  0.01
  22   28  0.37
  24    7  0.09
  25    9  0.12
  27   29  0.39
  29    1  0.01

ACGTcount: A:0.28, C:0.13, G:0.09, T:0.50


Consensus pattern (23 bp):   
TTTTTTTTTTATGACGCAAATAT

Found at i:879 original size:16 final size:15

Alignment explanation


    Indices: 839--880  Score: 57
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        829 ACAGAGGTTG

                    *      
        839 ACAGAAAATAATTAA
          1 ACAGAAAACAATTAA

               *           
        854 ACACAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
        869 ACTAGAAAACAA
          1 AC-AGAAAACAA

        881 AGCAAAGTAA


Statistics
Matches: 23,  Mismatches: 3, Indels: 1
        0.85            0.11        0.04

Matches are distributed among these distances:
  15   15  0.65
  16    8  0.35

ACGTcount: A:0.67, C:0.14, G:0.05, T:0.14


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.