Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018209.1 Corchorus olitorius cultivar O-4 contig18242, 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: 3096
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29


Found at i:2348 original size:16 final size:15

Alignment explanation


    Indices: 2323--2363  Score: 64
    Period size: 16  Copynumber: 2.7  Consensus size: 15

       2313 AAGTCGACGT

                           
       2323 AGGATCAAGTCGATA
          1 AGGATCAAGTCGATA

                            
       2338 AGGATCAAAGTCGATA
          1 AGGATC-AAGTCGATA

                *     
       2354 AGGAGCAAGT
          1 AGGATCAAGT

       2364 TTCGACTAGG


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  15   10  0.42
  16   14  0.58

ACGTcount: A:0.41, C:0.12, G:0.29, T:0.17


Consensus pattern (15 bp):   
AGGATCAAGTCGATA

Found at i:2437 original size:22 final size:21

Alignment explanation


    Indices: 2411--2509  Score: 81
    Period size: 22  Copynumber: 4.5  Consensus size: 21

       2401 GTCGACTAAG

                                  
       2411 AATTGTCGACTTCAAGGAAAGA
          1 AATTGTCGAC-TCAAGGAAAGA

                                 *
       2433 AATTGTCGACTCTAAGGAAAGC
          1 AATTGTCGACTC-AAGGAAAGA

               **       *     *   
       2455 AATAATCGACTAAAAGGAGAGA
          1 AATTGTCGACT-CAAGGAAAGA

                *            *     
       2477 AATTTTCGACTCAAGAGGAAGCA
          1 AATTGTCGACTCAAG-GAAAG-A

               *      
       2500 AATCGTCGAC
          1 AATTGTCGAC

       2510 AAGAAGGCAA


Statistics
Matches: 60,  Mismatches: 13, Indels: 7
        0.75            0.16        0.09

Matches are distributed among these distances:
  21    5  0.08
  22   46  0.77
  23    9  0.15

ACGTcount: A:0.41, C:0.16, G:0.22, T:0.20


Consensus pattern (21 bp):   
AATTGTCGACTCAAGGAAAGA

Done.