Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016835.1 Corchorus olitorius cultivar O-4 contig16868, 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: 16200
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:621 original size:47 final size:47

Alignment explanation


    Indices: 568--661  Score: 188
    Period size: 47  Copynumber: 2.0  Consensus size: 47

        558 TCCATCAAAC

                                                           
        568 AGAAACTCTTACAATGAAAAAGAATAAAGAAACCCCAATTTATCTCA
          1 AGAAACTCTTACAATGAAAAAGAATAAAGAAACCCCAATTTATCTCA

                                                           
        615 AGAAACTCTTACAATGAAAAAGAATAAAGAAACCCCAATTTATCTCA
          1 AGAAACTCTTACAATGAAAAAGAATAAAGAAACCCCAATTTATCTCA

        662 CAACAACTAA


Statistics
Matches: 47,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  47   47  1.00

ACGTcount: A:0.51, C:0.19, G:0.09, T:0.21


Consensus pattern (47 bp):   
AGAAACTCTTACAATGAAAAAGAATAAAGAAACCCCAATTTATCTCA

Found at i:1835 original size:15 final size:14

Alignment explanation


    Indices: 1812--1841  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

       1802 ATAAAAATTA

                          
       1812 AATATTTTTATTTT
          1 AATATTTTTATTTT

                           
       1826 AATATATTTTATTTT
          1 AATAT-TTTTATTTT

             
       1841 A
          1 A

       1842 TTGAAATTTA


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    5  0.33
  15   10  0.67

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (14 bp):   
AATATTTTTATTTT

Found at i:3168 original size:15 final size:15

Alignment explanation


    Indices: 3136--3165  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       3126 TAAATTTAGA

                           
       3136 TAAAATAAAATATAT
          1 TAAAATAAAATATAT

                           
       3151 TAAAATAAAA-ATAT
          1 TAAAATAAAATATAT

             
       3165 T
          1 T

       3166 TAATTTTTAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    5  0.33
  15   10  0.67

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (15 bp):   
TAAAATAAAATATAT

Found at i:4370 original size:7 final size:7

Alignment explanation


    Indices: 4358--4382  Score: 50
    Period size: 7  Copynumber: 3.6  Consensus size: 7

       4348 AAAATCCTTT

                   
       4358 TTTGACA
          1 TTTGACA

                   
       4365 TTTGACA
          1 TTTGACA

                   
       4372 TTTGACA
          1 TTTGACA

                
       4379 TTTG
          1 TTTG

       4383 CACAGTTTAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   18  1.00

ACGTcount: A:0.24, C:0.12, G:0.16, T:0.48


Consensus pattern (7 bp):   
TTTGACA
Done.