Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022997.1 Corchorus olitorius cultivar O-4 contig23030, 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: 3876
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.38


Found at i:517 original size:15 final size:15

Alignment explanation


    Indices: 484--567  Score: 56
    Period size: 15  Copynumber: 5.8  Consensus size: 15

        474 TACATACCAC

                      *    
        484 TAATAATAATTATTA
          1 TAATAATAATAATTA

                            
        499 TAATAATAATAAGTT-
          1 TAATAATAATAA-TTA

                   *       
        514 TAATAATTATAA-TA
          1 TAATAATAATAATTA

             *                
        528 CCACA-AATAATAAGTT-
          1 -TA-ATAATAATAA-TTA

                           
        544 TAATAAT--T-ATTA
          1 TAATAATAATAATTA

                        
        556 TAATAATAATAA
          1 TAATAATAATAA

        568 GCCTAAATTA


Statistics
Matches: 53,  Mismatches: 5, Indels: 22
        0.66            0.06        0.28

Matches are distributed among these distances:
  11    2  0.04
  12    8  0.15
  13    2  0.04
  14    2  0.04
  15   35  0.66
  16    3  0.06
  17    1  0.02

ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39


Consensus pattern (15 bp):   
TAATAATAATAATTA

Found at i:518 original size:30 final size:30

Alignment explanation


    Indices: 484--567  Score: 100
    Period size: 30  Copynumber: 2.8  Consensus size: 30

        474 TACATACCAC

                   *                      
        484 TAATAATAATTATTATAATAATAATAAGTT
          1 TAATAATTATTATTATAATAATAATAAGTT

                        *   *               
        514 TAATAATTA-TAATACCACA-AATAATAAGTT
          1 TAATAATTATTATTA-TA-ATAATAATAAGTT

                         *          
        544 TAATAATTATTATAATAATAATAA
          1 TAATAATTATTATTATAATAATAA

        568 GCCTAAATTA


Statistics
Matches: 44,  Mismatches: 6, Indels: 8
        0.76            0.10        0.14

Matches are distributed among these distances:
  29    5  0.11
  30   35  0.80
  31    4  0.09

ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39


Consensus pattern (30 bp):   
TAATAATTATTATTATAATAATAATAAGTT

Found at i:906 original size:11 final size:11

Alignment explanation


    Indices: 863--900  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

        853 TTCCTATATA

                *      
        863 AAATAAATTAT
          1 AAATTAATTAT

                        
        874 CAAA-TAATTAT
          1 -AAATTAATTAT

                       
        885 AAATTAATTAT
          1 AAATTAATTAT

                 
        896 AAATT
          1 AAATT

        901 TGTTATGAAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  10    3  0.12
  11   18  0.75
  12    3  0.12

ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39


Consensus pattern (11 bp):   
AAATTAATTAT
Done.