Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011447.1 Corchorus capsularis cultivar CVL-1 contig11468, 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: 6072
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:3860 original size:12 final size:13

Alignment explanation


    Indices: 3819--3863  Score: 74
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       3809 AATTATTGTT

                         
       3819 TGCTTTATTAATC
          1 TGCTTTATTAATC

                        *
       3832 TGCTTTATTAATT
          1 TGCTTTATTAATC

                         
       3845 TGCTTTA-TAATC
          1 TGCTTTATTAATC

                   
       3857 TGCTTTA
          1 TGCTTTA

       3864 GATTTAGATT


Statistics
Matches: 30,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  12   11  0.37
  13   19  0.63

ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56


Consensus pattern (13 bp):   
TGCTTTATTAATC

Found at i:3871 original size:6 final size:6

Alignment explanation


    Indices: 3860--3893  Score: 59
    Period size: 6  Copynumber: 5.5  Consensus size: 6

       3850 TATAATCTGC

                                                   
       3860 TTTAGA TTTAGA TTTAAGA TTTAGA TTTAGA TTT
          1 TTTAGA TTTAGA TTT-AGA TTTAGA TTTAGA TTT

       3894 GCTTTGCTTT


Statistics
Matches: 27,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   6   21  0.78
   7    6  0.22

ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53


Consensus pattern (6 bp):   
TTTAGA

Found at i:3881 original size:13 final size:12

Alignment explanation


    Indices: 3860--3893  Score: 59
    Period size: 13  Copynumber: 2.8  Consensus size: 12

       3850 TATAATCTGC

                        
       3860 TTTAGATTTAGA
          1 TTTAGATTTAGA

                         
       3872 TTTAAGATTTAGA
          1 TTT-AGATTTAGA

                     
       3885 TTTAGATTT
          1 TTTAGATTT

       3894 GCTTTGCTTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  12    9  0.43
  13   12  0.57

ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53


Consensus pattern (12 bp):   
TTTAGATTTAGA

Found at i:3942 original size:14 final size:15

Alignment explanation


    Indices: 3914--3946  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       3904 ATTTTTAGTT

                    *      
       3914 TAATTGTTTTCTTCA
          1 TAATTGTTATCTTCA

                           
       3929 TAATTGTTAT-TTCA
          1 TAATTGTTATCTTCA

                
       3943 TAAT
          1 TAAT

       3947 CCTTGTTTTC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  14    8  0.47
  15    9  0.53

ACGTcount: A:0.27, C:0.09, G:0.06, T:0.58


Consensus pattern (15 bp):   
TAATTGTTATCTTCA

Found at i:6042 original size:16 final size:16

Alignment explanation


    Indices: 6021--6072  Score: 50
    Period size: 16  Copynumber: 3.2  Consensus size: 16

       6011 TTATTAAAAT

                  *    *    
       6021 ATATATTAATTCATAA
          1 ATATATAAATTAATAA

                             
       6037 ATATATAAATTAATAAA
          1 ATATATAAATTAAT-AA

             *   *        * 
       6054 AAATAAAAATTAATTA
          1 ATATATAAATTAATAA

               
       6070 ATA
          1 ATA


Statistics
Matches: 29,  Mismatches: 6, Indels: 2
        0.78            0.16        0.05

Matches are distributed among these distances:
  16   15  0.52
  17   14  0.48

ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37


Consensus pattern (16 bp):   
ATATATAAATTAATAA
Done.