Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012069.1 Corchorus olitorius cultivar O-4 contig12102, 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: 28247
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30


Found at i:13683 original size:3 final size:3

Alignment explanation


    Indices: 13675--13699  Score: 50
    Period size: 3  Copynumber: 8.3  Consensus size: 3

      13665 CATTATATGT

                                             
      13675 TCA TCA TCA TCA TCA TCA TCA TCA T
          1 TCA TCA TCA TCA TCA TCA TCA TCA T

      13700 ATATGTCAAG


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   22  1.00

ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36


Consensus pattern (3 bp):   
TCA

Found at i:27888 original size:26 final size:25

Alignment explanation


    Indices: 27852--27907  Score: 94
    Period size: 26  Copynumber: 2.2  Consensus size: 25

      27842 TTACCAGTTC

                             *       
      27852 ATGTTGTTCAAGTTAAATAATATTG
          1 ATGTTGTTCAAGTTAAAGAATATTG

                                      
      27877 AATGTTGTTCAAGTTAAAGAATATTG
          1 -ATGTTGTTCAAGTTAAAGAATATTG

                 
      27903 ATGTT
          1 ATGTT

      27908 CCATAAACAA


Statistics
Matches: 29,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  25    5  0.17
  26   24  0.83

ACGTcount: A:0.36, C:0.04, G:0.18, T:0.43


Consensus pattern (25 bp):   
ATGTTGTTCAAGTTAAAGAATATTG

Found at i:28221 original size:2 final size:2

Alignment explanation


    Indices: 28214--28247  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

      28204 CAATTTCTTT

                                                              
      28214 TA 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 TA


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

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


Consensus pattern (2 bp):   
TA

Done.