Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000648.1 Corchorus olitorius cultivar O-4 contig00648, 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, 694

Length: 1158
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35


Found at i:665 original size:24 final size:23

Alignment explanation


    Indices: 638--719  Score: 59
    Period size: 20  Copynumber: 3.7  Consensus size: 23

        628 AACCGTTTAA

                                   
        638 TAATTTTATATATTATTATATAT
          1 TAATTTTATATATTATTATATAT

                                     
        661 GTAA--TTATATA--ATCTA-ATAT
          1 -TAATTTTATATATTAT-TATATAT

                            *        
        681 T-ATTTTATATATATAATATATATT
          1 TAATTTTATATAT-TATTATATA-T

                 *  *      
        705 TAATTATAAATATTA
          1 TAATTTTATATATTA

        720 CTAAACAGTC


Statistics
Matches: 46,  Mismatches: 3, Indels: 18
        0.69            0.04        0.27

Matches are distributed among these distances:
  18    1  0.02
  19    1  0.02
  20   13  0.28
  21    2  0.04
  22    9  0.20
  23    4  0.09
  24    7  0.15
  25    9  0.20

ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54


Consensus pattern (23 bp):   
TAATTTTATATATTATTATATAT

Found at i:688 original size:20 final size:20

Alignment explanation


    Indices: 640--717  Score: 65
    Period size: 19  Copynumber: 3.9  Consensus size: 20

        630 CCGTTTAATA

                          *     
        640 ATTTTATATAT-TATTATAT
          1 ATTTTATATATATAATATAT

                           *        
        659 ATGTAATTATATAATCTAATAT-T
          1 AT-T--TTATAT-ATATAATATAT

                                
        682 ATTTTATATATATAATATAT
          1 ATTTTATATATATAATATAT

                *             
        702 ATTTAAT-TATA-AATAT
          1 ATTTTATATATATAATAT

        718 TACTAAACAG


Statistics
Matches: 50,  Mismatches: 3, Indels: 13
        0.76            0.05        0.20

Matches are distributed among these distances:
  18    5  0.10
  19   14  0.28
  20   14  0.28
  22    7  0.14
  23    5  0.10
  24    5  0.10

ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54


Consensus pattern (20 bp):   
ATTTTATATATATAATATAT

Found at i:699 original size:19 final size:19

Alignment explanation


    Indices: 665--719  Score: 60
    Period size: 20  Copynumber: 2.9  Consensus size: 19

        655 ATATATGTAA

                     *          
        665 TTATATAATCTAATATTATT
          1 TTATAT-ATATAATATTATT

                                
        685 TTATATATATAATATATATT
          1 TTATATATATAATAT-TATT

             *               
        705 TAAT-TATA-AATATTA
          1 TTATATATATAATATTA

        720 CTAAACAGTC


Statistics
Matches: 32,  Mismatches: 2, Indels: 5
        0.82            0.05        0.13

Matches are distributed among these distances:
  17    2  0.06
  18    5  0.16
  19   12  0.38
  20   13  0.41

ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53


Consensus pattern (19 bp):   
TTATATATATAATATTATT
Done.