Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004930.1 Corchorus capsularis cultivar CVL-1 contig04948, 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: 13803
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34


Found at i:12 original size:2 final size:2

Alignment explanation


    Indices: 1--66  Score: 123
    Period size: 2  Copynumber: 32.5  Consensus size: 2

                                                                           
          1 TC TC ATC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
          1 TC TC -TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC

                                              
         44 TC TC TC TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC T

         67 TTTATACCAC


Statistics
Matches: 63,  Mismatches: 0, Indels: 2
        0.97            0.00        0.03

Matches are distributed among these distances:
   2   61  0.97
   3    2  0.03

ACGTcount: A:0.02, C:0.48, G:0.00, T:0.50


Consensus pattern (2 bp):   
TC

Found at i:4877 original size:17 final size:17

Alignment explanation


    Indices: 4855--4895  Score: 55
    Period size: 18  Copynumber: 2.4  Consensus size: 17

       4845 ACCACCTCGT

                      *      
       4855 AGAAAAGGGATTAGAGA
          1 AGAAAAGGGACTAGAGA

                    *         
       4872 AGAAAAAGTGACTAGAGA
          1 AG-AAAAGGGACTAGAGA

                  
       4890 AGAAAA
          1 AGAAAA

       4896 ACCAGAGAAG


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  17    6  0.29
  18   15  0.71

ACGTcount: A:0.59, C:0.02, G:0.29, T:0.10


Consensus pattern (17 bp):   
AGAAAAGGGACTAGAGA

Found at i:6143 original size:14 final size:14

Alignment explanation


    Indices: 6124--6153  Score: 51
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       6114 GGGCAAATAG

                       *  
       6124 TTCTTTTTTTCTCT
          1 TTCTTTTTTTCACT

                          
       6138 TTCTTTTTTTCACT
          1 TTCTTTTTTTCACT

              
       6152 TT
          1 TT

       6154 ACATTGTTCA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77


Consensus pattern (14 bp):   
TTCTTTTTTTCACT

Found at i:6312 original size:20 final size:20

Alignment explanation


    Indices: 6287--6328  Score: 84
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       6277 TGTCCGTCAT

                                
       6287 CAATCTAACGATCCAGTTAA
          1 CAATCTAACGATCCAGTTAA

                                
       6307 CAATCTAACGATCCAGTTAA
          1 CAATCTAACGATCCAGTTAA

              
       6327 CA
          1 CA

       6329 GTATGACTTT


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   22  1.00

ACGTcount: A:0.40, C:0.26, G:0.10, T:0.24


Consensus pattern (20 bp):   
CAATCTAACGATCCAGTTAA

Found at i:11365 original size:16 final size:15

Alignment explanation


    Indices: 11344--11385  Score: 66
    Period size: 16  Copynumber: 2.7  Consensus size: 15

      11334 TCACCTGACA

                           
      11344 AATACTCACCTGGTG
          1 AATACTCACCTGGTG

                            
      11359 TAATACTCACCTGGTG
          1 -AATACTCACCTGGTG

                       
      11375 AGATACTCACC
          1 A-ATACTCACC

      11386 CACACTCTCC


Statistics
Matches: 25,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    1  0.04
  16   24  0.96

ACGTcount: A:0.29, C:0.29, G:0.17, T:0.26


Consensus pattern (15 bp):   
AATACTCACCTGGTG

Found at i:13664 original size:2 final size:2

Alignment explanation


    Indices: 13657--13688  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

      13647 ATCAGAATGA

                                                           
      13657 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

      13689 GGCTCAGTTA


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.