Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011439.1 Corchorus capsularis cultivar CVL-1 contig11460, 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: 23361
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33


Found at i:9515 original size:17 final size:17

Alignment explanation


    Indices: 9495--9534  Score: 55
    Period size: 17  Copynumber: 2.4  Consensus size: 17

       9485 ATGTGTCAAA

                       *      
       9495 TTTGTTA-ATTTGATAAT
          1 TTTGTTATATTCGA-AAT

                             
       9512 TTTGTTATATTCGAAAT
          1 TTTGTTATATTCGAAAT

                  
       9529 TTTGTT
          1 TTTGTT

       9535 GCAATTGGGA


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  17   16  0.76
  18    5  0.24

ACGTcount: A:0.25, C:0.03, G:0.12, T:0.60


Consensus pattern (17 bp):   
TTTGTTATATTCGAAAT

Found at i:12857 original size:5 final size:5

Alignment explanation


    Indices: 12849--12898  Score: 84
    Period size: 5  Copynumber: 10.2  Consensus size: 5

      12839 ACGGTTGTTG

                *                                                      
      12849 TTATG TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA -TATA
          1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA

             
      12898 T
          1 T

      12899 GAAATGAGTG


Statistics
Matches: 43,  Mismatches: 1, Indels: 2
        0.93            0.02        0.04

Matches are distributed among these distances:
   4    4  0.09
   5   39  0.91

ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60


Consensus pattern (5 bp):   
TTATA

Found at i:19476 original size:22 final size:22

Alignment explanation


    Indices: 19442--19483  Score: 66
    Period size: 22  Copynumber: 1.9  Consensus size: 22

      19432 AAAAAAACCT

                  * *             
      19442 GAAATTTATTTTTTATTTTTTA
          1 GAAATTCAATTTTTATTTTTTA

                                
      19464 GAAATTCAATTTTTATTTTT
          1 GAAATTCAATTTTTATTTTT

      19484 AATTCATTTA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   18  1.00

ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64


Consensus pattern (22 bp):   
GAAATTCAATTTTTATTTTTTA

Found at i:22004 original size:4 final size:4

Alignment explanation


    Indices: 21995--22019  Score: 50
    Period size: 4  Copynumber: 6.2  Consensus size: 4

      21985 TAACAGATAA

                                           
      21995 AAAG AAAG AAAG AAAG AAAG AAAG A
          1 AAAG AAAG AAAG AAAG AAAG AAAG A

      22020 GAAACGAAGA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   21  1.00

ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00


Consensus pattern (4 bp):   
AAAG

Found at i:22963 original size:15 final size:15

Alignment explanation


    Indices: 22943--22974  Score: 64
    Period size: 15  Copynumber: 2.1  Consensus size: 15

      22933 AGATGGTTTC

                           
      22943 TTTTGCATATTAATA
          1 TTTTGCATATTAATA

                           
      22958 TTTTGCATATTAATA
          1 TTTTGCATATTAATA

              
      22973 TT
          1 TT

      22975 GAAGAAAAGA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56


Consensus pattern (15 bp):   
TTTTGCATATTAATA

Found at i:23338 original size:2 final size:2

Alignment explanation


    Indices: 23333--23360  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      23323 TCTATATGTG

                                                     
      23333 TA 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 TA

      23361 A


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

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


Consensus pattern (2 bp):   
TA

Done.