Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015047.1 Corchorus capsularis cultivar CVL-1 contig15068, 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: 35518
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35


Found at i:12554 original size:41 final size:42

Alignment explanation


    Indices: 12482--12565  Score: 143
    Period size: 41  Copynumber: 2.0  Consensus size: 42

      12472 CATATATATA

                                                      
      12482 TATATATATATATATTTCTAATCACAAACTCGAACCTAAAAC
          1 TATATATATATATATTTCTAATCACAAACTCGAACCTAAAAC

                         *            *               
      12524 TATATATATAT-TTTTTCTAATCACAGACTCGAACCTAAAAC
          1 TATATATATATATATTTCTAATCACAAACTCGAACCTAAAAC

             
      12565 T
          1 T

      12566 TTAAGAGGGA


Statistics
Matches: 40,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  41   29  0.73
  42   11  0.28

ACGTcount: A:0.42, C:0.19, G:0.04, T:0.36


Consensus pattern (42 bp):   
TATATATATATATATTTCTAATCACAAACTCGAACCTAAAAC

Found at i:25151 original size:2 final size:2

Alignment explanation


    Indices: 25144--25171  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      25134 CCTCTAATCT

                                                     
      25144 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

      25172 AAAGGAAATT


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:0.00, C:0.50, G:0.00, T:0.50


Consensus pattern (2 bp):   
TC

Found at i:25260 original size:11 final size:12

Alignment explanation


    Indices: 25230--25260  Score: 53
    Period size: 12  Copynumber: 2.6  Consensus size: 12

      25220 ATCTAGTAGT

                        
      25230 AACAAAAAAGGG
          1 AACAAAAAAGGG

                     *  
      25242 AACAAAAAATGG
          1 AACAAAAAAGGG

                   
      25254 AACAAAA
          1 AACAAAA

      25261 TCTACCAGTG


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  12   18  1.00

ACGTcount: A:0.71, C:0.10, G:0.16, T:0.03


Consensus pattern (12 bp):   
AACAAAAAAGGG

Found at i:34565 original size:2 final size:2

Alignment explanation


    Indices: 34558--34587  Score: 60
    Period size: 2  Copynumber: 15.0  Consensus size: 2

      34548 TATTATCAGA

                                                        
      34558 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

      34588 TAGTAATTTA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   28  1.00

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


Consensus pattern (2 bp):   
AT

Done.