Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010108.1 Corchorus olitorius cultivar O-4 contig10140, 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: 5625
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34


Found at i:437 original size:21 final size:19

Alignment explanation


    Indices: 412--469  Score: 80
    Period size: 19  Copynumber: 2.9  Consensus size: 19

        402 GCTGCTCTAA

                                 
        412 TAATCTCATCTGTACAGTACC
          1 TAATCTCATCTGTACAGT--C

                  *           *
        433 TAATCTAATCTGTACAGTG
          1 TAATCTCATCTGTACAGTC

                              
        452 TAATCTCATCTGTACAGT
          1 TAATCTCATCTGTACAGT

        470 TGCTAAACAG


Statistics
Matches: 34,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
  19   17  0.50
  21   17  0.50

ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36


Consensus pattern (19 bp):   
TAATCTCATCTGTACAGTC

Found at i:4142 original size:39 final size:40

Alignment explanation


    Indices: 4063--4144  Score: 148
    Period size: 40  Copynumber: 2.1  Consensus size: 40

       4053 CTTGATACCA

                                               *    
       4063 GTTGTTGGATGAAGCATGCATAAAGGGATAGGAAACTTTT
          1 GTTGTTGGATGAAGCATGCATAAAGGGATAGGAAAATTTT

                                                    
       4103 GTTGTTGGATGAAGCATGCATAAA-GGATAGGAAAATTTT
          1 GTTGTTGGATGAAGCATGCATAAAGGGATAGGAAAATTTT

               
       4142 GTT
          1 GTT

       4145 TTTTGTTTTT


Statistics
Matches: 41,  Mismatches: 1, Indels: 1
        0.95            0.02        0.02

Matches are distributed among these distances:
  39   17  0.41
  40   24  0.59

ACGTcount: A:0.33, C:0.06, G:0.29, T:0.32


Consensus pattern (40 bp):   
GTTGTTGGATGAAGCATGCATAAAGGGATAGGAAAATTTT
Done.