Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024524.1 Corchorus olitorius cultivar O-4 contig24557, 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: 24723
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32


Found at i:4639 original size:15 final size:15

Alignment explanation


    Indices: 4609--4650  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       4599 TTACTTTGCT

                            
       4609 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
       4625 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

               *       
       4640 TTGCTTTCTGT
          1 TTGTTTTCTGT

       4651 CAATCTATGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:11828 original size:15 final size:14

Alignment explanation


    Indices: 11804--11846  Score: 68
    Period size: 15  Copynumber: 2.9  Consensus size: 14

      11794 AATTACATAA

                          
      11804 TCTTTCTCTTCTAT
          1 TCTTTCTCTTCTAT

                           
      11818 TCTTCTCTCTTCTAT
          1 TCTT-TCTCTTCTAT

                          
      11833 TCTTTACTCTTCTA
          1 TCTTT-CTCTTCTA

      11847 CTTTTCTTGT


Statistics
Matches: 27,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  14    5  0.19
  15   22  0.81

ACGTcount: A:0.09, C:0.30, G:0.00, T:0.60


Consensus pattern (14 bp):   
TCTTTCTCTTCTAT

Found at i:12485 original size:25 final size:25

Alignment explanation


    Indices: 12435--12486  Score: 61
    Period size: 24  Copynumber: 2.1  Consensus size: 25

      12425 ATTGAAGTAT

                           *         
      12435 TTATTTATCTTGTTGCTTAATTTTA
          1 TTATTTATCTTGTTGATTAATTTTA

                          *   *       
      12460 TTATTT-TCTTGTTTATTTATTATTA
          1 TTATTTATCTTGTTGATTAATT-TTA

              
      12485 TT
          1 TT

      12487 GTTACTTTAA


Statistics
Matches: 23,  Mismatches: 3, Indels: 2
        0.82            0.11        0.07

Matches are distributed among these distances:
  24   12  0.52
  25   11  0.48

ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69


Consensus pattern (25 bp):   
TTATTTATCTTGTTGATTAATTTTA
Done.