Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010240.1 Corchorus olitorius cultivar O-4 contig10272, 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: 4505
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.36


Found at i:56 original size:39 final size:40

Alignment explanation


    Indices: 2--82  Score: 137
    Period size: 39  Copynumber: 2.0  Consensus size: 40

          1 A

                                             *      
          2 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

                                 *                  
         41 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
          1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

              
         81 AT
          1 AT

         83 AGAAATTAAA


Statistics
Matches: 39,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  39   31  0.79
  40    8  0.21

ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51


Consensus pattern (40 bp):   
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC

Found at i:1347 original size:11 final size:11

Alignment explanation


    Indices: 1331--1358  Score: 56
    Period size: 11  Copynumber: 2.5  Consensus size: 11

       1321 TTTTTACCTC

                       
       1331 ATCCGGTACTA
          1 ATCCGGTACTA

                       
       1342 ATCCGGTACTA
          1 ATCCGGTACTA

                  
       1353 ATCCGG
          1 ATCCGG

       1359 ATTCGACCCA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   17  1.00

ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25


Consensus pattern (11 bp):   
ATCCGGTACTA

Found at i:2902 original size:3 final size:3

Alignment explanation


    Indices: 2881--2915  Score: 52
    Period size: 3  Copynumber: 11.7  Consensus size: 3

       2871 TCTCTGATGC

                    *         *                           
       2881 AAG AAG GAG AAG AAA AAG AAG AAG AAG AAG AAG AA
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA

       2916 AGAATTTACT


Statistics
Matches: 28,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   3   28  1.00

ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00


Consensus pattern (3 bp):   
AAG
Done.