Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009829.1 Corchorus olitorius cultivar O-4 contig09861, 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: 2665
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39


Found at i:2214 original size:25 final size:24

Alignment explanation


    Indices: 2181--2258  Score: 71
    Period size: 25  Copynumber: 3.5  Consensus size: 24

       2171 TAAAATTGTT

                                    
       2181 TAAATTTTACAATTTTTTTAGAAA
          1 TAAATTTTACAATTTTTTTAGAAA

                          *  *       
       2205 TAAACTTTTA-AA-ATTGTT-----
          1 TAAA-TTTTACAATTTTTTTAGAAA

                                    
       2223 TAAATTTTACAATTTTTTTAGAAA
          1 TAAATTTTACAATTTTTTTAGAAA

                        
       2247 TAAACTTTTACA
          1 TAAA-TTTTACA

       2259 GTTATTCTAC


Statistics
Matches: 41,  Mismatches: 4, Indels: 17
        0.66            0.06        0.27

Matches are distributed among these distances:
  17    5  0.12
  18    6  0.15
  19    4  0.10
  23    4  0.10
  24   10  0.24
  25   12  0.29

ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49


Consensus pattern (24 bp):   
TAAATTTTACAATTTTTTTAGAAA

Found at i:2223 original size:42 final size:42

Alignment explanation


    Indices: 2171--2256  Score: 172
    Period size: 42  Copynumber: 2.0  Consensus size: 42

       2161 ATTCCTGAAA

                                                      
       2171 TAAAATTGTTTAAATTTTACAATTTTTTTAGAAATAAACTTT
          1 TAAAATTGTTTAAATTTTACAATTTTTTTAGAAATAAACTTT

                                                      
       2213 TAAAATTGTTTAAATTTTACAATTTTTTTAGAAATAAACTTT
          1 TAAAATTGTTTAAATTTTACAATTTTTTTAGAAATAAACTTT

              
       2255 TA
          1 TA

       2257 CAGTTATTCT


Statistics
Matches: 44,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  42   44  1.00

ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50


Consensus pattern (42 bp):   
TAAAATTGTTTAAATTTTACAATTTTTTTAGAAATAAACTTT
Done.