Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021051.1 Corchorus olitorius cultivar O-4 contig21084, 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: 13782
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31


Found at i:4989 original size:27 final size:26

Alignment explanation


    Indices: 4959--5009  Score: 75
    Period size: 27  Copynumber: 1.9  Consensus size: 26

       4949 TCTCATATAT

                                       
       4959 TTTTATTTAAAATATATATTTATTTTA
          1 TTTTATTTAAAATAT-TATTTATTTTA

                     * *            
       4986 TTTTATTTATATTATTATTTATTT
          1 TTTTATTTAAAATATTATTTATTT

       5010 AGGCAACTCA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  26    9  0.41
  27   13  0.59

ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69


Consensus pattern (26 bp):   
TTTTATTTAAAATATTATTTATTTTA

Found at i:8601 original size:9 final size:9

Alignment explanation


    Indices: 8589--8624  Score: 54
    Period size: 9  Copynumber: 3.9  Consensus size: 9

       8579 CATATTTCAT

                     
       8589 TCATCAATA
          1 TCATCAATA

                      
       8598 TCATCAATCA
          1 TCATCAAT-A

            *        
       8608 CCATCAATA
          1 TCATCAATA

                    
       8617 TCATCAAT
          1 TCATCAAT

       8625 CATTTACTTA


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
   9   16  0.67
  10    8  0.33

ACGTcount: A:0.42, C:0.28, G:0.00, T:0.31


Consensus pattern (9 bp):   
TCATCAATA

Found at i:8614 original size:19 final size:19

Alignment explanation


    Indices: 8590--8626  Score: 74
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       8580 ATATTTCATT

                               
       8590 CATCAATATCATCAATCAC
          1 CATCAATATCATCAATCAC

                              
       8609 CATCAATATCATCAATCA
          1 CATCAATATCATCAATCA

       8627 TTTACTTAGC


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   18  1.00

ACGTcount: A:0.43, C:0.30, G:0.00, T:0.27


Consensus pattern (19 bp):   
CATCAATATCATCAATCAC

Found at i:8655 original size:20 final size:20

Alignment explanation


    Indices: 8619--8659  Score: 57
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       8609 CATCAATATC

                     *          
       8619 ATCAATCATTTACTTAGCAA
          1 ATCAATCATATACTTAGCAA

                                 
       8639 ATCAATCATCATA-TTAGCAA
          1 ATCAATCAT-ATACTTAGCAA

             
       8659 A
          1 A

       8660 AAATGAAAAT


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  20   17  0.89
  21    2  0.11

ACGTcount: A:0.44, C:0.20, G:0.05, T:0.32


Consensus pattern (20 bp):   
ATCAATCATATACTTAGCAA

Found at i:12396 original size:25 final size:25

Alignment explanation


    Indices: 12368--12416  Score: 98
    Period size: 25  Copynumber: 2.0  Consensus size: 25

      12358 TTATTAGAAG

                                     
      12368 GGACAATCCCATCACATTAACCATA
          1 GGACAATCCCATCACATTAACCATA

                                    
      12393 GGACAATCCCATCACATTAACCAT
          1 GGACAATCCCATCACATTAACCAT

      12417 GGTGAAGGGA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   24  1.00

ACGTcount: A:0.39, C:0.33, G:0.08, T:0.20


Consensus pattern (25 bp):   
GGACAATCCCATCACATTAACCATA
Done.