Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002354.1 Corchorus olitorius cultivar O-4 contig02354, 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, 737

Length: 1229
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34


Found at i:654 original size:5 final size:5

Alignment explanation


    Indices: 644--688  Score: 63
    Period size: 5  Copynumber: 8.6  Consensus size: 5

        634 TATAATTATA

                                                           *     
        644 ATAAT ATAAT ATAAT ATAAT ATAAT ATATAT ATATAT ATATT ATA
          1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT ATA-AT ATAAT ATA

        689 TCTTTTTTCT


Statistics
Matches: 38,  Mismatches: 1, Indels: 2
        0.93            0.02        0.05

Matches are distributed among these distances:
   5   27  0.71
   6   11  0.29

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (5 bp):   
ATAAT

Found at i:674 original size:2 final size:2

Alignment explanation


    Indices: 647--689  Score: 51
    Period size: 2  Copynumber: 24.0  Consensus size: 2

        637 AATTATAATA

                                                                          
        647 AT AT A- AT AT A- AT AT A- AT AT A- AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                    
        685 -T AT AT
          1 AT AT AT

        690 CTTTTTTCTT


Statistics
Matches: 36,  Mismatches: 0, Indels: 10
        0.78            0.00        0.22

Matches are distributed among these distances:
   1    5  0.14
   2   31  0.86

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:689 original size:15 final size:15

Alignment explanation


    Indices: 625--689  Score: 52
    Period size: 12  Copynumber: 4.5  Consensus size: 15

        615 CATAGGTTAT

                           
        625 TATTAT-TAT-TATA
          1 TATTATATATATATA

                           
        638 -ATTATA-ATA-ATA
          1 TATTATATATATATA

              *             
        650 TAATATA-ATATAATA
          1 TATTATATATAT-ATA

                             
        665 TAATATATATATATATA
          1 T-AT-TATATATATATA

                    
        682 TATTATAT
          1 TATTATAT

        690 CTTTTTTCTT


Statistics
Matches: 42,  Mismatches: 2, Indels: 14
        0.72            0.03        0.24

Matches are distributed among these distances:
  12   10  0.24
  13    8  0.19
  15    9  0.21
  16    3  0.07
  17    8  0.19
  18    4  0.10

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


Consensus pattern (15 bp):   
TATTATATATATATA
Done.