Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015151.1 Corchorus capsularis cultivar CVL-1 contig15172, 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: 19979
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33


Found at i:15060 original size:16 final size:15

Alignment explanation


    Indices: 15039--15084  Score: 51
    Period size: 16  Copynumber: 3.1  Consensus size: 15

      15029 ATATATGTCG

                           
      15039 TATTAAAATTAATAT
          1 TATTAAAATTAATAT

                            
      15054 ATATT--AATTAATAT
          1 -TATTAAAATTAATAT

                *           
      15068 TATAAAAAATTAATAT
          1 TAT-TAAAATTAATAT

             
      15084 T
          1 T

      15085 GATAACGTAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 6
        0.79            0.03        0.18

Matches are distributed among these distances:
  13    3  0.12
  14    9  0.35
  16   14  0.54

ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46


Consensus pattern (15 bp):   
TATTAAAATTAATAT

Found at i:16865 original size:12 final size:12

Alignment explanation


    Indices: 16848--16878  Score: 62
    Period size: 12  Copynumber: 2.6  Consensus size: 12

      16838 CCTGACAATC

                        
      16848 CGTGTTTCGTGT
          1 CGTGTTTCGTGT

                        
      16860 CGTGTTTCGTGT
          1 CGTGTTTCGTGT

                   
      16872 CGTGTTT
          1 CGTGTTT

      16879 ACATAGGGTA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   19  1.00

ACGTcount: A:0.00, C:0.16, G:0.32, T:0.52


Consensus pattern (12 bp):   
CGTGTTTCGTGT

Found at i:17267 original size:20 final size:20

Alignment explanation


    Indices: 17230--17269  Score: 53
    Period size: 20  Copynumber: 2.0  Consensus size: 20

      17220 CCGTTAATTA

                      *  *      
      17230 AAACGTGTCACTCGTGTCTT
          1 AAACGTGTCAATCATGTCTT

                    *           
      17250 AAACGTGTTAATCATGTCTT
          1 AAACGTGTCAATCATGTCTT

      17270 GACACGATTA


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  20   17  1.00

ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38


Consensus pattern (20 bp):   
AAACGTGTCAATCATGTCTT

Found at i:17871 original size:20 final size:20

Alignment explanation


    Indices: 17846--17888  Score: 86
    Period size: 20  Copynumber: 2.1  Consensus size: 20

      17836 CACGCCATCT

                                
      17846 AATTTATAACTTGATTATCA
          1 AATTTATAACTTGATTATCA

                                
      17866 AATTTATAACTTGATTATCA
          1 AATTTATAACTTGATTATCA

               
      17886 AAT
          1 AAT

      17889 ATTTTGCAGG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   23  1.00

ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44


Consensus pattern (20 bp):   
AATTTATAACTTGATTATCA
Done.