Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01007059.1 Corchorus olitorius cultivar O-4 contig07084, 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, 851

Length: 1419
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33


Found at i:569 original size:20 final size:19

Alignment explanation


    Indices: 544--607  Score: 67
    Period size: 20  Copynumber: 3.2  Consensus size: 19

        534 GTAAAATCCC

                                
        544 AAAAGAAGATTTTGGAAAAT
          1 AAAAGAAG-TTTTGGAAAAT

                              * 
        564 AAAAGAAGTTTT-GATAATT
          1 AAAAGAAGTTTTGGA-AAAT

                                  
        583 CCAAAAGAAGGTTTTGGAAAAT
          1 --AAAAGAA-GTTTTGGAAAAT

               
        605 AAA
          1 AAA

        608 GGTTCCCAAA


Statistics
Matches: 37,  Mismatches: 2, Indels: 10
        0.76            0.04        0.20

Matches are distributed among these distances:
  18    2  0.05
  19    7  0.19
  20   11  0.30
  21    7  0.19
  22    8  0.22
  23    2  0.05

ACGTcount: A:0.52, C:0.03, G:0.19, T:0.27


Consensus pattern (19 bp):   
AAAAGAAGTTTTGGAAAAT

Found at i:618 original size:29 final size:29

Alignment explanation


    Indices: 581--636  Score: 78
    Period size: 29  Copynumber: 1.9  Consensus size: 29

        571 GTTTTGATAA

                         *                
        581 TTCCAAAA-GAAGGTTTTGGAAAATAAAGG
          1 TTCCAAAAGGAAGATTTTGG-AAATAAAGG

                *                      
        610 TTCCCAAAGGAAGATTTTGGAAATAAA
          1 TTCCAAAAGGAAGATTTTGGAAATAAA

        637 TAAAATTGGT


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  29   14  0.58
  30   10  0.42

ACGTcount: A:0.45, C:0.09, G:0.21, T:0.25


Consensus pattern (29 bp):   
TTCCAAAAGGAAGATTTTGGAAATAAAGG
Done.