Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000889.1 Corchorus olitorius cultivar O-4 contig00889, 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: 4307
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--39  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

                                                                      
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

         40 GGGACAAAAC


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:3045 original size:2 final size:2

Alignment explanation


    Indices: 3038--3070  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       3028 CTAGACCTTT

                                                             
       3038 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       3071 CACAAAGTTT


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:3601 original size:20 final size:20

Alignment explanation


    Indices: 3576--3618  Score: 61
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       3566 GTCATCATAA

                                 
       3576 TTGTTTTGA-TAACCTTTAAT
          1 TTGTTTTGAGTAACC-TTAAT

                   *            
       3596 TTGTTTTTAGTAACCTTAAT
          1 TTGTTTTGAGTAACCTTAAT

               
       3616 TTG
          1 TTG

       3619 ATAGGAGATT


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  20   16  0.76
  21    5  0.24

ACGTcount: A:0.23, C:0.09, G:0.12, T:0.56


Consensus pattern (20 bp):   
TTGTTTTGAGTAACCTTAAT

Done.