Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005878.1 Corchorus capsularis cultivar CVL-1 contig05896, 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: 5203
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36


Found at i:2716 original size:2 final size:2

Alignment explanation


    Indices: 2711--2737  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       2701 ATAACTAACC

                                                    
       2711 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

       2738 CTAAATTTGA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:3955 original size:17 final size:18

Alignment explanation


    Indices: 3928--3963  Score: 56
    Period size: 17  Copynumber: 2.1  Consensus size: 18

       3918 TAAATTGCGT

                       *      
       3928 AATTATATATAGTAATTA
          1 AATTATATATAATAATTA

                              
       3946 AATTAT-TATAATAATTA
          1 AATTATATATAATAATTA

             
       3963 A
          1 A

       3964 CTCAATTTTC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  17   11  0.65
  18    6  0.35

ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44


Consensus pattern (18 bp):   
AATTATATATAATAATTA

Found at i:5140 original size:2 final size:2

Alignment explanation


    Indices: 5133--5164  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

       5123 CTAAGCAAAG

                                                           
       5133 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       5165 CAAATTTTGA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
AT

Done.