Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005533.1 Corchorus capsularis cultivar CVL-1 contig05551, 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: 9876
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:2185 original size:11 final size:11

Alignment explanation


    Indices: 2142--2179  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

       2132 TTTCTATCTA

                *      
       2142 AAATAAATTAT
          1 AAATTAATTAT

                        
       2153 CAAA-TAATTAT
          1 -AAATTAATTAT

                       
       2164 AAATTAATTAT
          1 AAATTAATTAT

                 
       2175 AAATT
          1 AAATT

       2180 TGTTATGAAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  10    3  0.12
  11   18  0.75
  12    3  0.12

ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39


Consensus pattern (11 bp):   
AAATTAATTAT

Found at i:2419 original size:16 final size:16

Alignment explanation


    Indices: 2394--2428  Score: 52
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       2384 ATTTTCTTCT

                            
       2394 TCTCTATATTCTATTG
          1 TCTCTATATTCTATTG

                 *      *   
       2410 TCTCTCTATTCTCTTG
          1 TCTCTATATTCTATTG

               
       2426 TCT
          1 TCT

       2429 TTTACATACT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   17  1.00

ACGTcount: A:0.11, C:0.26, G:0.06, T:0.57


Consensus pattern (16 bp):   
TCTCTATATTCTATTG

Found at i:4637 original size:2 final size:2

Alignment explanation


    Indices: 4624--4673  Score: 82
    Period size: 2  Copynumber: 25.0  Consensus size: 2

       4614 TCTTAGGAGG

                   *              *                                       
       4624 AT AT AC AT AT AT AT AC 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 AT AT AT AT AT

                       
       4666 AT AT AT AT
          1 AT AT AT AT

       4674 GTGTGTGTGT


Statistics
Matches: 44,  Mismatches: 4, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   2   44  1.00

ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46


Consensus pattern (2 bp):   
AT

Done.