Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012660.1 Corchorus olitorius cultivar O-4 contig12693, 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: 21027
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31


Found at i:15614 original size:12 final size:11

Alignment explanation


    Indices: 15587--15660  Score: 59
    Period size: 12  Copynumber: 6.7  Consensus size: 11

      15577 AACCGTTTAA

                       
      15587 TAATTATATAT
          1 TAATTATATAT

                       
      15598 T-ATTATATAT
          1 TAATTATATAT

                        
      15608 GTAATTATATA-
          1 -TAATTATATAT

                        
      15619 T-ATCTA-ATAT
          1 TAAT-TATATAT

               *        
      15629 TATTTTATATAT
          1 TA-ATTATATAT

                         
      15641 ATAA-TATATATT
          1 -TAATTATATA-T

                    
      15653 TAATTATA
          1 TAATTATA

      15661 AATATTACTA


Statistics
Matches: 51,  Mismatches: 2, Indels: 19
        0.71            0.03        0.26

Matches are distributed among these distances:
   9    5  0.10
  10   13  0.25
  11   13  0.25
  12   18  0.35
  13    2  0.04

ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54


Consensus pattern (11 bp):   
TAATTATATAT

Found at i:15639 original size:19 final size:20

Alignment explanation


    Indices: 15586--15665  Score: 66
    Period size: 19  Copynumber: 4.3  Consensus size: 20

      15576 AAACCGTTTA

                       *        
      15586 ATAAT-TATATATTAT-TAT
          1 ATAATATATATTTTATATAT

                 *      *       
      15604 AT-ATGTA-ATTATATATAT
          1 ATAATATATATTTTATATAT

            *                   
      15622 CTAATAT-TATTTTATATAT
          1 ATAATATATATTTTATATAT

                         *      
      15641 ATAATATATATTTAAT-TAT
          1 ATAATATATATTTTATATAT

                   
      15660 A-AATAT
          1 ATAATAT

      15666 TACTAAACGG


Statistics
Matches: 50,  Mismatches: 7, Indels: 10
        0.75            0.10        0.15

Matches are distributed among these distances:
  17    7  0.14
  18   13  0.26
  19   23  0.46
  20    7  0.14

ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53


Consensus pattern (20 bp):   
ATAATATATATTTTATATAT

Found at i:15642 original size:14 final size:14

Alignment explanation


    Indices: 15591--15651  Score: 52
    Period size: 16  Copynumber: 4.2  Consensus size: 14

      15581 GTTTAATAAT

                          
      15591 TATATATTATTATA
          1 TATATATTATTATA

               *            
      15605 TATGTAATTATATATA
          1 TATAT-ATTAT-TATA

             *          *  
      15621 TCTAATATTATTTTA
          1 TAT-ATATTATTATA

                     *    
      15636 TATATA-TAATATA
          1 TATATATTATTATA

               
      15649 TAT
          1 TAT

      15652 TTAATTATAA


Statistics
Matches: 37,  Mismatches: 7, Indels: 7
        0.73            0.14        0.14

Matches are distributed among these distances:
  13    8  0.22
  14    7  0.19
  15   10  0.27
  16   11  0.30
  17    1  0.03

ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54


Consensus pattern (14 bp):   
TATATATTATTATA

Found at i:15649 original size:21 final size:21

Alignment explanation


    Indices: 15590--15665  Score: 54
    Period size: 21  Copynumber: 3.7  Consensus size: 21

      15580 CGTTTAATAA

                       *          *
      15590 TTATATATTATTATATATGTA-A
          1 TTATATA-TATAATATAT-TATT

                       *          
      15612 TTATATATAT-CTAATATTATT
          1 TTATATATATAAT-ATATTATT

                                 
      15633 TTATATATATAATATA-TATT
          1 TTATATATATAATATATTATT

             *             
      15653 TAAT-TATA-AATAT
          1 TTATATATATAATAT

      15666 TACTAAACGG


Statistics
Matches: 47,  Mismatches: 4, Indels: 10
        0.77            0.07        0.16

Matches are distributed among these distances:
  18    5  0.11
  19    4  0.09
  20   10  0.21
  21   20  0.43
  22    8  0.17

ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54


Consensus pattern (21 bp):   
TTATATATATAATATATTATT
Done.