Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014653.1 Corchorus capsularis cultivar CVL-1 contig14674, 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: 28130
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:10187 original size:29 final size:28

Alignment explanation


    Indices: 10153--10234  Score: 119
    Period size: 29  Copynumber: 2.8  Consensus size: 28

      10143 TTACACAAAA

                                         
      10153 CAGTCAAATAAGCCCATGAACTCTAATTG
          1 CAGTCAAATAAGCCC-TGAACTCTAATTG

            *                            
      10182 TAGTCAAATAAGCCTCTGAACTCTAATTG
          1 CAGTCAAATAAGCC-CTGAACTCTAATTG

               *                    
      10211 CAGCCAAATAAGCCCCTGAACTCT
          1 CAGTCAAATAAG-CCCTGAACTCT

      10235 TTAAAAAGCC


Statistics
Matches: 48,  Mismatches: 3, Indels: 4
        0.87            0.05        0.07

Matches are distributed among these distances:
  29   45  0.94
  30    3  0.06

ACGTcount: A:0.35, C:0.27, G:0.13, T:0.24


Consensus pattern (28 bp):   
CAGTCAAATAAGCCCTGAACTCTAATTG

Found at i:11817 original size:19 final size:19

Alignment explanation


    Indices: 11793--11829  Score: 65
    Period size: 19  Copynumber: 1.9  Consensus size: 19

      11783 TGTTTAGTAC

                               
      11793 ACCGTTTCACCACCGTTTG
          1 ACCGTTTCACCACCGTTTG

                     *        
      11812 ACCGTTTCATCACCGTTT
          1 ACCGTTTCACCACCGTTT

      11830 TGGATCCAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  19   17  1.00

ACGTcount: A:0.16, C:0.35, G:0.14, T:0.35


Consensus pattern (19 bp):   
ACCGTTTCACCACCGTTTG

Found at i:11904 original size:21 final size:19

Alignment explanation


    Indices: 11880--11937  Score: 71
    Period size: 19  Copynumber: 2.9  Consensus size: 19

      11870 GCTGCTCTAA

                *                
      11880 TAATTTCATCTGTACAGTACC
          1 TAATCTCATCTGTACAGT--C

                  *           *
      11901 TAATCTAATCTGTACAGTG
          1 TAATCTCATCTGTACAGTC

                              
      11920 TAATCTCATCTGTACAGT
          1 TAATCTCATCTGTACAGT

      11938 TGCTAAACAG


Statistics
Matches: 33,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  19   17  0.52
  21   16  0.48

ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38


Consensus pattern (19 bp):   
TAATCTCATCTGTACAGTC

Found at i:13220 original size:16 final size:16

Alignment explanation


    Indices: 13196--13226  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

      13186 GAAGTATGGA

                *           
      13196 AAAGGCAAGAGAATAG
          1 AAAGACAAGAGAATAG

                           
      13212 AAAGACAAGAGAATA
          1 AAAGACAAGAGAATA

      13227 TAGAGAAGAA


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

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.61, C:0.06, G:0.26, T:0.06


Consensus pattern (16 bp):   
AAAGACAAGAGAATAG

Found at i:14426 original size:15 final size:16

Alignment explanation


    Indices: 14392--14429  Score: 51
    Period size: 15  Copynumber: 2.4  Consensus size: 16

      14382 ATGGAATAAA

                     *   *  
      14392 AAATTTAATTACAGTG
          1 AAATTTAATCACAATG

                            
      14408 AAATTTAATCA-AATG
          1 AAATTTAATCACAATG

                   
      14423 AAATTTA
          1 AAATTTA

      14430 TTAAATAAAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  15   10  0.50
  16   10  0.50

ACGTcount: A:0.50, C:0.05, G:0.08, T:0.37


Consensus pattern (16 bp):   
AAATTTAATCACAATG

Found at i:22698 original size:5 final size:5

Alignment explanation


    Indices: 22682--22711  Score: 53
    Period size: 5  Copynumber: 6.2  Consensus size: 5

      22672 AATATATATA

                                                 
      22682 TCTTT T-TTT TCTTT TCTTT TCTTT TCTTT T
          1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T

      22712 TTCACCATGC


Statistics
Matches: 24,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
   4    4  0.17
   5   20  0.83

ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83


Consensus pattern (5 bp):   
TCTTT

Found at i:26676 original size:21 final size:21

Alignment explanation


    Indices: 26652--26692  Score: 66
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      26642 TTCATGATAA

                                  
      26652 CTTTGCAGACC-TTCATTTTTT
          1 CTTTGCAGACCATT-ATTTTTT

                                
      26673 CTTTGCAGACCATTATTTTT
          1 CTTTGCAGACCATTATTTTT

      26693 ACTCTTTTTT


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  21   17  0.89
  22    2  0.11

ACGTcount: A:0.17, C:0.22, G:0.10, T:0.51


Consensus pattern (21 bp):   
CTTTGCAGACCATTATTTTTT
Done.