Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012078.1 Corchorus olitorius cultivar O-4 contig12111, 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: 5482
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30


Found at i:1636 original size:19 final size:19

Alignment explanation


    Indices: 1614--1665  Score: 54
    Period size: 19  Copynumber: 2.8  Consensus size: 19

       1604 GGGCTGAAAT

                               
       1614 TAATTAATTATTAAATAAA
          1 TAATTAATTATTAAATAAA

                         * * *  
       1633 TAA-TAATTATTTTATTGAA
          1 TAATTAATTA-TTAAATAAA

                           
       1652 TAATT-ATTATTAAA
          1 TAATTAATTATTAAA

       1666 AATCCCACAT


Statistics
Matches: 26,  Mismatches: 5, Indels: 5
        0.72            0.14        0.14

Matches are distributed among these distances:
  18    9  0.35
  19   16  0.62
  20    1  0.04

ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48


Consensus pattern (19 bp):   
TAATTAATTATTAAATAAA

Found at i:3105 original size:51 final size:50

Alignment explanation


    Indices: 3004--3105  Score: 111
    Period size: 51  Copynumber: 2.0  Consensus size: 50

       2994 GTTCTTCATA

                                                     * **     
       3004 TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
          1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGT

                                      *                           
       3054 TTTTCTCTTGTTTCAG-TCTTGTCTCCGGAC-ATACAAACACT-GTACACGTGT
          1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACAAT-CAAACACTCGTACA-GTGT

             
       3105 T
          1 T

       3106 CTTCATTCAG


Statistics
Matches: 44,  Mismatches: 4, Indels: 7
        0.80            0.07        0.13

Matches are distributed among these distances:
  50    9  0.20
  51   33  0.75
  52    2  0.05

ACGTcount: A:0.21, C:0.23, G:0.15, T:0.42


Consensus pattern (50 bp):   
TTTTCCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCGTACAGTGT
Done.