Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019037.1 Corchorus olitorius cultivar O-4 contig19070, 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: 17923
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32


Found at i:13837 original size:17 final size:17

Alignment explanation


    Indices: 13793--13866  Score: 75
    Period size: 16  Copynumber: 4.6  Consensus size: 17

      13783 GTCGGGTTGA

                             
      13793 TCGGGTTCGGGTCATTT
          1 TCGGGTTCGGGTCATTT

                   *         
      13810 T-GGGTTTGGGTCATTT
          1 TCGGGTTCGGGTCATTT

                  *       *  
      13826 TCGGGTCCGGGTC-GTT
          1 TCGGGTTCGGGTCATTT

                *         *  
      13842 T-GGATTCGGGT-AATT
          1 TCGGGTTCGGGTCATTT

                      
      13857 TCGGGTTCGG
          1 TCGGGTTCGG

      13867 ATATCCAAAA


Statistics
Matches: 46,  Mismatches: 8, Indels: 7
        0.75            0.13        0.11

Matches are distributed among these distances:
  15   11  0.24
  16   25  0.54
  17   10  0.22

ACGTcount: A:0.07, C:0.15, G:0.39, T:0.39


Consensus pattern (17 bp):   
TCGGGTTCGGGTCATTT

Found at i:17357 original size:21 final size:21

Alignment explanation


    Indices: 17331--17378  Score: 69
    Period size: 21  Copynumber: 2.2  Consensus size: 21

      17321 ATTTTTTCGC

                  *               
      17331 TAAAAAAAATATTAAAAAAATA
          1 TAAAAAGAATATT-AAAAAATA

                         *       
      17353 TAAAAAGAATATTTAAAAATA
          1 TAAAAAGAATATTAAAAAATA

                 
      17374 TAAAA
          1 TAAAA

      17379 TGCCACGTAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  21   12  0.50
  22   12  0.50

ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25


Consensus pattern (21 bp):   
TAAAAAGAATATTAAAAAATA

Found at i:17369 original size:13 final size:11

Alignment explanation


    Indices: 17333--17371  Score: 53
    Period size: 11  Copynumber: 3.5  Consensus size: 11

      17323 TTTTTCGCTA

                       
      17333 AAAAAAATATT
          1 AAAAAAATATT

                       
      17344 AAAAAAATA-T
          1 AAAAAAATATT

                         
      17354 AAAAAGAATATTT
          1 AAAAA-AATA-TT

                 
      17367 AAAAA
          1 AAAAA

      17372 TATAAAATGC


Statistics
Matches: 25,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
  10    6  0.24
  11   13  0.52
  13    6  0.24

ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23


Consensus pattern (11 bp):   
AAAAAAATATT
Done.