Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007644.1 Corchorus capsularis cultivar CVL-1 contig07665, 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: 20711
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:514 original size:2 final size:2

Alignment explanation


    Indices: 507--545  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

        497 ACTATATGTG

                                                                      
        507 TA TA TA TA 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 TA TA TA TA T

        546 CACATATGTC


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:880 original size:15 final size:15

Alignment explanation


    Indices: 860--889  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

        850 TTGTTCTTCA

                           
        860 AAAAGAAAAGAGAAG
          1 AAAAGAAAAGAGAAG

                   *       
        875 AAAAGAAGAGAGAAG
          1 AAAAGAAAAGAGAAG

        890 CTCTATTTGA


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00


Consensus pattern (15 bp):   
AAAAGAAAAGAGAAG

Found at i:9132 original size:12 final size:12

Alignment explanation


    Indices: 9094--9136  Score: 50
    Period size: 12  Copynumber: 3.5  Consensus size: 12

       9084 CATAATATTA

                       *
       9094 TATTATATATAG
          1 TATTATATATAT

               * *       
       9106 TATAACATATGAT
          1 TATTATATAT-AT

                        
       9119 TATTATATATAT
          1 TATTATATATAT

                  
       9131 TATTAT
          1 TATTAT

       9137 TATTTGAAGG


Statistics
Matches: 25,  Mismatches: 5, Indels: 2
        0.78            0.16        0.06

Matches are distributed among these distances:
  12   16  0.64
  13    9  0.36

ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51


Consensus pattern (12 bp):   
TATTATATATAT

Found at i:17217 original size:2 final size:2

Alignment explanation


    Indices: 17210--17238  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      17200 TCCCTTTTTC

                                                       
      17210 AT AT 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 AT AT A

      17239 GATTTTGTAA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:18077 original size:2 final size:2

Alignment explanation


    Indices: 18070--18109  Score: 80
    Period size: 2  Copynumber: 20.0  Consensus size: 2

      18060 CCATAGGTGC

                                                                       
      18070 TA TA TA TA TA TA 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 TA TA TA TA TA TA

      18110 ATTAAATTAA


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   38  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:19774 original size:27 final size:27

Alignment explanation


    Indices: 19745--19798  Score: 90
    Period size: 27  Copynumber: 2.0  Consensus size: 27

      19735 ATTAATTACT

                                        
      19745 CCCTCTGTTCCTTTTTAATTGTCCCTTC
          1 CCCT-TGTTCCTTTTTAATTGTCCCTTC

                    *                 
      19773 CCCTTGTTTCTTTTTAATTGTCCCTT
          1 CCCTTGTTCCTTTTTAATTGTCCCTT

      19799 ATATTTCTTT


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  27   21  0.84
  28    4  0.16

ACGTcount: A:0.07, C:0.31, G:0.07, T:0.54


Consensus pattern (27 bp):   
CCCTTGTTCCTTTTTAATTGTCCCTTC
Done.