Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010921.1 Corchorus olitorius cultivar O-4 contig10953, 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: 5790
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Found at i:1434 original size:10 final size:10

Alignment explanation


    Indices: 1416--1445  Score: 51
    Period size: 10  Copynumber: 3.0  Consensus size: 10

       1406 GGGAATTAAT

                      
       1416 GGAAGGGAAA
          1 GGAAGGGAAA

                *     
       1426 GGAAAGGAAA
          1 GGAAGGGAAA

                      
       1436 GGAAGGGAAA
          1 GGAAGGGAAA

       1446 TAAAGGGCCA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  10   18  1.00

ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00


Consensus pattern (10 bp):   
GGAAGGGAAA

Found at i:3258 original size:5 final size:5

Alignment explanation


    Indices: 3228--3257  Score: 53
    Period size: 5  Copynumber: 6.2  Consensus size: 5

       3218 AGTACTTCAC

                                                 
       3228 TCTTT TCTTT TCTTT TCTTT TCTTT T-TTT T
          1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T

       3258 TGGGTGAAAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
   4    4  0.16
   5   21  0.84

ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83


Consensus pattern (5 bp):   
TCTTT

Found at i:3725 original size:6 final size:6

Alignment explanation


    Indices: 3714--3745  Score: 64
    Period size: 6  Copynumber: 5.3  Consensus size: 6

       3704 AAAATGGCCC

                                                 
       3714 CCAAGG CCAAGG CCAAGG CCAAGG CCAAGG CC
          1 CCAAGG CCAAGG CCAAGG CCAAGG CCAAGG CC

       3746 CCCCCCCTTT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   26  1.00

ACGTcount: A:0.31, C:0.38, G:0.31, T:0.00


Consensus pattern (6 bp):   
CCAAGG

Done.