Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010998.1 Corchorus capsularis cultivar CVL-1 contig11019, 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: 6179
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:292 original size:10 final size:10

Alignment explanation


    Indices: 279--314  Score: 63
    Period size: 10  Copynumber: 3.6  Consensus size: 10

        269 AAATCTCGAT

                      
        279 ATATCCGTAA
          1 ATATCCGTAA

                      
        289 ATATCCGTAA
          1 ATATCCGTAA

                  *   
        299 ATATCCATAA
          1 ATATCCGTAA

                  
        309 ATATCC
          1 ATATCC

        315 ATATTAAATT


Statistics
Matches: 25,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  10   25  1.00

ACGTcount: A:0.42, C:0.22, G:0.06, T:0.31


Consensus pattern (10 bp):   
ATATCCGTAA

Found at i:2353 original size:12 final size:12

Alignment explanation


    Indices: 2336--2378  Score: 68
    Period size: 12  Copynumber: 3.5  Consensus size: 12

       2326 CATCGATACC

                        
       2336 TCGATATATCCG
          1 TCGATATATCCG

                       *
       2348 TCGATATATCCA
          1 TCGATATATCCG

                         
       2360 TCCGATATATCCG
          1 T-CGATATATCCG

                  
       2373 TCGATA
          1 TCGATA

       2379 CCTGTATTAA


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  12   17  0.61
  13   11  0.39

ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33


Consensus pattern (12 bp):   
TCGATATATCCG

Found at i:2496 original size:2 final size:2

Alignment explanation


    Indices: 2489--2513  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       2479 TAAACCAAAC

                                                 
       2489 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 A

       2514 ATAGTAATAG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:3453 original size:2 final size:2

Alignment explanation


    Indices: 3446--3471  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       3436 GTATAAATTA

                                                  
       3446 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

       3472 CTTAAATAAA


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):   
AT

Done.