Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006944.1 Corchorus olitorius cultivar O-4 contig06969, 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, 763

Length: 1273
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.36


Found at i:621 original size:49 final size:50

Alignment explanation


    Indices: 559--660  Score: 170
    Period size: 50  Copynumber: 2.1  Consensus size: 50

        549 TTAATATATT

                                              **              
        559 TAATTTAATTGATAAAT-AAAATTACATATGAAATTTTAAAAGTTAAAGA
          1 TAATTTAATTGATAAATAAAAATTACATATGAAACCTTAAAAGTTAAAGA

                                          *                   
        608 TAATTTAATTGATAAATAAAAATTACATATTAAACCTTAAAAGTTAAAGA
          1 TAATTTAATTGATAAATAAAAATTACATATGAAACCTTAAAAGTTAAAGA

               
        658 TAA
          1 TAA

        661 AGAAGGATAT


Statistics
Matches: 49,  Mismatches: 3, Indels: 1
        0.92            0.06        0.02

Matches are distributed among these distances:
  49   17  0.35
  50   32  0.65

ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35


Consensus pattern (50 bp):   
TAATTTAATTGATAAATAAAAATTACATATGAAACCTTAAAAGTTAAAGA

Found at i:1060 original size:17 final size:18

Alignment explanation


    Indices: 1038--1071  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       1028 CAAACGTGAT

                              
       1038 AAACGC-GACGCGACCGA
          1 AAACGCGGACGCGACCGA

                    *        
       1055 AAACGCGGCCGCGACCG
          1 AAACGCGGACGCGACCG

       1072 CAATTTAAAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    6  0.40
  18    9  0.60

ACGTcount: A:0.29, C:0.38, G:0.32, T:0.00


Consensus pattern (18 bp):   
AAACGCGGACGCGACCGA
Done.