Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023919.1 Corchorus olitorius cultivar O-4 contig23952, 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: 4825
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26


Found at i:750 original size:2 final size:2

Alignment explanation


    Indices: 743--781  Score: 57
    Period size: 2  Copynumber: 21.0  Consensus size: 2

        733 GTTTATTCTT

                                                                          
        743 TA TA TA TA TA TA -A TA TA TA TA TA TA -A TA TA TA -A TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

        782 ATTATAGTGG


Statistics
Matches: 34,  Mismatches: 0, Indels: 6
        0.85            0.00        0.15

Matches are distributed among these distances:
   1    3  0.09
   2   31  0.91

ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46


Consensus pattern (2 bp):   
TA

Found at i:758 original size:7 final size:7

Alignment explanation


    Indices: 743--787  Score: 69
    Period size: 7  Copynumber: 6.9  Consensus size: 7

        733 GTTTATTCTT

                   
        743 TATAT-A
          1 TATATAA

                   
        749 TATATAA
          1 TATATAA

                   
        756 TATAT-A
          1 TATATAA

                   
        762 TATATAA
          1 TATATAA

                   
        769 TATATAA
          1 TATATAA

                   
        776 TATATAA
          1 TATATAA

                  
        783 T-TATA
          1 TATATA

        788 GTGGTAAGGA


Statistics
Matches: 37,  Mismatches: 0, Indels: 4
        0.90            0.00        0.10

Matches are distributed among these distances:
   6   15  0.41
   7   22  0.59

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


Consensus pattern (7 bp):   
TATATAA

Found at i:760 original size:9 final size:9

Alignment explanation


    Indices: 746--781  Score: 54
    Period size: 9  Copynumber: 3.8  Consensus size: 9

        736 TATTCTTTAT

                     
        746 ATATATATA
          1 ATATATATA

                     
        755 ATATATATA
          1 ATATATATA

                       
        764 TATAATATATA
          1 -AT-ATATATA

                   
        775 ATATATA
          1 ATATATA

        782 ATTATAGTGG


Statistics
Matches: 25,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
   9   14  0.56
  10    4  0.16
  11    7  0.28

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


Consensus pattern (9 bp):   
ATATATATA

Found at i:760 original size:11 final size:11

Alignment explanation


    Indices: 744--781  Score: 62
    Period size: 11  Copynumber: 3.6  Consensus size: 11

        734 TTTATTCTTT

                       
        744 ATATATATATA
          1 ATATATATATA

                       
        755 ATATATATAT-
          1 ATATATATATA

                       
        765 ATA-ATATATA
          1 ATATATATATA

                   
        775 ATATATA
          1 ATATATA

        782 ATTATAGTGG


Statistics
Matches: 25,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
   9    6  0.24
  10    6  0.24
  11   13  0.52

ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45


Consensus pattern (11 bp):   
ATATATATATA

Found at i:761 original size:13 final size:13

Alignment explanation


    Indices: 743--787  Score: 74
    Period size: 13  Copynumber: 3.5  Consensus size: 13

        733 GTTTATTCTT

                         
        743 TATATATATATAA
          1 TATATATATATAA

                         
        756 TATATATATATAA
          1 TATATATATATAA

                          
        769 TATATAATATATAA
          1 TATAT-ATATATAA

                  
        783 T-TATA
          1 TATATA

        788 GTGGTAAGGA


Statistics
Matches: 31,  Mismatches: 0, Indels: 3
        0.91            0.00        0.09

Matches are distributed among these distances:
  12    1  0.03
  13   21  0.68
  14    9  0.29

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


Consensus pattern (13 bp):   
TATATATATATAA
Done.