Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005478.1 Corchorus capsularis cultivar CVL-1 contig05496, 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: 10339
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31


Found at i:631 original size:2 final size:2

Alignment explanation


    Indices: 624--649  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

        614 CTATGGCATC

                                                  
        624 TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA

        650 ATAGTGAATA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:6052 original size:12 final size:12

Alignment explanation


    Indices: 6027--6077  Score: 52
    Period size: 12  Copynumber: 4.2  Consensus size: 12

       6017 ATATATTTCG

                         
       6027 ATTATA-ATTGAT
          1 ATTATATATT-AT

                         
       6039 ATTATAT-TATAT
          1 ATTATATAT-TAT

                        
       6051 ATTATATATTAT
          1 ATTATATATTAT

              *          
       6063 ATAATATAATTAT
          1 ATTATAT-ATTAT

              
       6076 AT
          1 AT

       6078 GGGGACCACT


Statistics
Matches: 34,  Mismatches: 1, Indels: 7
        0.81            0.02        0.17

Matches are distributed among these distances:
  12   25  0.74
  13    9  0.26

ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53


Consensus pattern (12 bp):   
ATTATATATTAT

Found at i:6053 original size:7 final size:7

Alignment explanation


    Indices: 6041--6077  Score: 58
    Period size: 7  Copynumber: 5.4  Consensus size: 7

       6031 TAATTGATAT

                   
       6041 TATATTA
          1 TATATTA

                   
       6048 TATATTA
          1 TATATTA

                   
       6055 TATATTA
          1 TATATTA

                *  
       6062 TATAATA
          1 TATATTA

                   
       6069 TA-ATTA
          1 TATATTA

               
       6075 TAT
          1 TAT

       6078 GGGGACCACT


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
   6    5  0.19
   7   22  0.81

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (7 bp):   
TATATTA
Done.