Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001825.1 Corchorus capsularis cultivar CVL-1 contig01826, 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: 2974
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34


Found at i:873 original size:2 final size:2

Alignment explanation


    Indices: 862--902  Score: 59
    Period size: 2  Copynumber: 21.5  Consensus size: 2

        852 TAATTTACCC

                                                       *                  
        862 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA -A TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

             
        902 T
          1 T

        903 GGATGGATTT


Statistics
Matches: 35,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
   1    2  0.06
   2   33  0.94

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:2482 original size:19 final size:20

Alignment explanation


    Indices: 2458--2502  Score: 74
    Period size: 19  Copynumber: 2.3  Consensus size: 20

       2448 TCCAATTTTA

                            *   
       2458 ATATATGTTATTATA-TTAT
          1 ATATATGTTATTATAGATAT

                                
       2477 ATATATGTTATTATAGATAT
          1 ATATATGTTATTATAGATAT

                  
       2497 ATATAT
          1 ATATAT

       2503 ATATATATAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  19   15  0.62
  20    9  0.38

ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53


Consensus pattern (20 bp):   
ATATATGTTATTATAGATAT

Found at i:2490 original size:14 final size:13

Alignment explanation


    Indices: 2469--2511  Score: 52
    Period size: 12  Copynumber: 3.3  Consensus size: 13

       2459 TATATGTTAT

                         
       2469 TATATTATATATA
          1 TATATTATATATA

              *       *   
       2482 TGTTATTATAGATA
          1 T-ATATTATATATA

                         
       2496 TATA-TATATATA
          1 TATATTATATATA

                
       2508 TATA
          1 TATA

       2512 AAATATGGAT


Statistics
Matches: 25,  Mismatches: 4, Indels: 3
        0.78            0.12        0.09

Matches are distributed among these distances:
  12   11  0.44
  13    3  0.12
  14   11  0.44

ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51


Consensus pattern (13 bp):   
TATATTATATATA
Done.