Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010138.1 Corchorus capsularis cultivar CVL-1 contig10159, 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: 13419
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34


Found at i:9 original size:2 final size:2

Alignment explanation


    Indices: 3--33  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

          1 AG

                                                          
          3 TA TA 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 TA TA T

         34 TTACATTAGT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:2373 original size:14 final size:14

Alignment explanation


    Indices: 2354--2383  Score: 60
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       2344 ATCATTATGA

                          
       2354 ATATGGAGTATAGG
          1 ATATGGAGTATAGG

                          
       2368 ATATGGAGTATAGG
          1 ATATGGAGTATAGG

              
       2382 AT
          1 AT

       2384 GCAATATATA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.37, C:0.00, G:0.33, T:0.30


Consensus pattern (14 bp):   
ATATGGAGTATAGG

Found at i:6581 original size:2 final size:2

Alignment explanation


    Indices: 6574--6599  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       6564 GAGGTGTTGC

                                                  
       6574 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

       6600 TTGTCGCTTT


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

Found at i:6646 original size:74 final size:74

Alignment explanation


    Indices: 6525--6668  Score: 279
    Period size: 74  Copynumber: 1.9  Consensus size: 74

       6515 ACTCACATTT

                                   *                                         
       6525 TTTGTCGCTTTTAAAGTATTCTGTAGAAACCAGAGCGAGGAGGTGTTGCATATATATATATATAT
          1 TTTGTCGCTTTTAAAGTATTCTGCAGAAACCAGAGCGAGGAGGTGTTGCATATATATATATATAT

                     
       6590 ATATATATA
         66 ATATATATA

                                                                             
       6599 TTTGTCGCTTTTAAAGTATTCTGCAGAAACCAGAGCGAGGAGGTGTTGCATATATATATATATAT
          1 TTTGTCGCTTTTAAAGTATTCTGCAGAAACCAGAGCGAGGAGGTGTTGCATATATATATATATAT

                 
       6664 ATATA
         66 ATATA

       6669 CAAGTGGTGG


Statistics
Matches: 69,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  74   69  1.00

ACGTcount: A:0.33, C:0.10, G:0.19, T:0.37


Consensus pattern (74 bp):   
TTTGTCGCTTTTAAAGTATTCTGCAGAAACCAGAGCGAGGAGGTGTTGCATATATATATATATAT
ATATATATA

Found at i:6746 original size:2 final size:2

Alignment explanation


    Indices: 6739--6772  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       6729 TAGCTCTTCC

                                                              
       6739 AT 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 AT

       6773 TCTACCTCTG


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:13350 original size:33 final size:33

Alignment explanation


    Indices: 13308--13384  Score: 120
    Period size: 33  Copynumber: 2.3  Consensus size: 33

      13298 CTTTTACACT

                                     *        
      13308 GAGCCTCCCCACTA-GGACGGCTCAGCCACGGCG
          1 GAGCCTCCCCACTAGGGA-GGCTCAACCACGGCG

                                             
      13341 GAGCCTCCCCACTAGGGAGGCTCAACCACGGCG
          1 GAGCCTCCCCACTAGGGAGGCTCAACCACGGCG

            *          
      13374 AAGCCTCCCCA
          1 GAGCCTCCCCA

      13385 TTCGGGCGGC


Statistics
Matches: 41,  Mismatches: 2, Indels: 2
        0.91            0.04        0.04

Matches are distributed among these distances:
  33   38  0.93
  34    3  0.07

ACGTcount: A:0.21, C:0.43, G:0.27, T:0.09


Consensus pattern (33 bp):   
GAGCCTCCCCACTAGGGAGGCTCAACCACGGCG
Done.