Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013729.1 Corchorus olitorius cultivar O-4 contig13762, 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: 14840
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34


Found at i:7708 original size:3 final size:3

Alignment explanation


    Indices: 7700--7739  Score: 80
    Period size: 3  Copynumber: 13.3  Consensus size: 3

       7690 TTTTTCTTAT

                                                                 
       7700 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
          1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A

       7740 ATTATATGAT


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

Matches are distributed among these distances:
   3   37  1.00

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
ATA

Found at i:10044 original size:2 final size:2

Alignment explanation


    Indices: 10037--10068  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

      10027 AAAGATGATT

                                                           
      10037 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      10069 CACTCCAAAA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:12257 original size:25 final size:25

Alignment explanation


    Indices: 12210--12257  Score: 71
    Period size: 25  Copynumber: 1.9  Consensus size: 25

      12200 AACTTGACTT

                              *      
      12210 TAAATTATATACTATATTTGAAATC
          1 TAAATTATATACTATATTGGAAATC

                                    
      12235 TAAATTATATACTAT-TTAGGAAA
          1 TAAATTATATACTATATT-GGAAA

      12258 CCTAGAAAGT


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

Matches are distributed among these distances:
  24    2  0.10
  25   19  0.90

ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42


Consensus pattern (25 bp):   
TAAATTATATACTATATTGGAAATC
Done.