Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008564.1 Corchorus olitorius cultivar O-4 contig08591, 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, 723

Length: 1206
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34


Found at i:479 original size:15 final size:15

Alignment explanation


    Indices: 461--495  Score: 52
    Period size: 15  Copynumber: 2.3  Consensus size: 15

        451 AAATTGAGGC

                      *    
        461 TAATTAAATTGGATT
          1 TAATTAAATTAGATT

                        *  
        476 TAATTAAATTAGTTT
          1 TAATTAAATTAGATT

                 
        491 TAATT
          1 TAATT

        496 TTTGGGCTAG


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

Matches are distributed among these distances:
  15   18  1.00

ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51


Consensus pattern (15 bp):   
TAATTAAATTAGATT

Found at i:1102 original size:2 final size:2

Alignment explanation


    Indices: 1095--1166  Score: 144
    Period size: 2  Copynumber: 36.0  Consensus size: 2

       1085 ATATTGCTAT

                                                                          
       1095 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
          1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA

                                                        
       1137 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
          1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA

       1167 TATATATATA


Statistics
Matches: 70,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   70  1.00

ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00


Consensus pattern (2 bp):   
CA

Found at i:1171 original size:2 final size:2

Alignment explanation


    Indices: 1166--1206  Score: 82
    Period size: 2  Copynumber: 20.5  Consensus size: 2

       1156 ACACACACAC

                                                                         
       1166 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   39  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.