Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024768.1 Corchorus olitorius cultivar O-4 contig24801, 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: 6896
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35


Found at i:2516 original size:15 final size:15

Alignment explanation


    Indices: 2491--2563  Score: 57
    Period size: 15  Copynumber: 5.1  Consensus size: 15

       2481 AAAGAATGTT

                  *        
       2491 TTTTTATAGGATTTA
          1 TTTTTAAAGGATTTA

                 *         
       2506 TTTTTGAAGGA--TA
          1 TTTTTAAAGGATTTA

                     *  *  
       2519 --TTT-AAGAATGTA
          1 TTTTTAAAGGATTTA

                            
       2531 TTTTTTAAAGGATTTA
          1 -TTTTTAAAGGATTTA

                        *  
       2547 TTTTTAAAGGATATA
          1 TTTTTAAAGGATTTA

              
       2562 TT
          1 TT

       2564 ATGATGATAT


Statistics
Matches: 46,  Mismatches: 6, Indels: 12
        0.72            0.09        0.19

Matches are distributed among these distances:
  10    4  0.09
  11    3  0.07
  12    2  0.04
  13    2  0.04
  15   28  0.61
  16    7  0.15

ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52


Consensus pattern (15 bp):   
TTTTTAAAGGATTTA

Found at i:2535 original size:41 final size:40

Alignment explanation


    Indices: 2469--2560  Score: 139
    Period size: 41  Copynumber: 2.3  Consensus size: 40

       2459 TACTCCATTG

                    *                   *           
       2469 TTGAAGGAAATTAAAGAATGTTTTTTTATAGGATTTATTT
          1 TTGAAGGATATTAAAGAATGTTTTTTTAAAGGATTTATTT

                        *                            
       2509 TTGAAGGATATTTAAGAATGTATTTTTTAAAGGATTTATTT
          1 TTGAAGGATATTAAAGAATGT-TTTTTTAAAGGATTTATTT

              *        
       2550 TTAAAGGATAT
          1 TTGAAGGATAT

       2561 ATTATGATGA


Statistics
Matches: 47,  Mismatches: 4, Indels: 1
        0.90            0.08        0.02

Matches are distributed among these distances:
  40   19  0.40
  41   28  0.60

ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47


Consensus pattern (40 bp):   
TTGAAGGATATTAAAGAATGTTTTTTTAAAGGATTTATTT

Done.