Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008098.1 Corchorus olitorius cultivar O-4 contig08125, 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, 726

Length: 1210
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25


Found at i:663 original size:31 final size:31

Alignment explanation


    Indices: 623--949  Score: 461
    Period size: 31  Copynumber: 11.0  Consensus size: 31

        613 GGAGAAACCA

                             *              
        623 AAAAGTGAACTATATGCTATAACGATAGACCT
          1 AAAA-TGAACTATATGCAATAACGATAGACCT

                           **              
        655 AAAATGAACTATATGTTATAACGATAGACCT
          1 AAAATGAACTATATGCAATAACGATAGACCT

                                           
        686 --AA--AACTATATGCAATAACGATAGACCT
          1 AAAATGAACTATATGCAATAACGATAGACCT

                                           
        713 --AA--AACTATATGCAATAACGATAGACCT
          1 AAAATGAACTATATGCAATAACGATAGACCT

                                           
        740 AAAATGAACTATATGCAATAACGATAGACCT
          1 AAAATGAACTATATGCAATAACGATAGACCT

                                     *     
        771 --AA--AACTATATGCAATAACGATGGACCT
          1 AAAATGAACTATATGCAATAACGATAGACCT

                                     *     
        798 AAAATGAACTATATGCAATAACGATGGACCT
          1 AAAATGAACTATATGCAATAACGATAGACCT

                                     *     
        829 AAAATGAACTATATGCAATAACGATGGACCT
          1 AAAATGAACTATATGCAATAACGATAGACCT

                                     *     
        860 AAAATGAACTATATGCAATAACGATGGACCT
          1 AAAATGAACTATATGCAATAACGATAGACCT

                           *               
        891 AAAATGAACTATATGTAATAACGATAGACCT
          1 AAAATGAACTATATGCAATAACGATAGACCT

                                           
        922 ---A-GAACTATATGCAATAACGATAGACCT
          1 AAAATGAACTATATGCAATAACGATAGACCT

             
        949 A
          1 A

        950 GAACTATATG


Statistics
Matches: 279,  Mismatches: 7, Indels: 22
        0.91            0.02        0.07

Matches are distributed among these distances:
  27   99  0.35
  28    1  0.00
  29    8  0.03
  31  167  0.60
  32    4  0.01

ACGTcount: A:0.46, C:0.16, G:0.14, T:0.24


Consensus pattern (31 bp):   
AAAATGAACTATATGCAATAACGATAGACCT

Found at i:703 original size:58 final size:60

Alignment explanation


    Indices: 629--949  Score: 432
    Period size: 58  Copynumber: 5.5  Consensus size: 60

        619 ACCAAAAAGT

                       *                             **                 
        629 GAACTATATGCTATAACGATAGACCTAAAATGAACTATATGTTATAACGATAGACCT-AA
          1 GAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAAA

                                                                         
        688 -AACTATATGCAATAACGATAGACCT--AA--AACTATATGCAATAACGATAGACCTAAAA
          1 GAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCT-AAA

                                                                *         
        744 TGAACTATATGCAATAACGATAGACCT--AA--AACTATATGCAATAACGATGGACCTAAAA
          1 -GAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCT-AAA

                                 *                              *         
        802 TGAACTATATGCAATAACGATGGACCTAAAATGAACTATATGCAATAACGATGGACCTAAAA
          1 -GAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCT-AAA

                                 *                    *                  
        864 TGAACTATATGCAATAACGATGGACCTAAAATGAACTATATGTAATAACGATAGACCT--A
          1 -GAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAAA

                                       
        923 GAACTATATGCAATAACGATAGACCTA
          1 GAACTATATGCAATAACGATAGACCTA

        950 GAACTATATG


Statistics
Matches: 246,  Mismatches: 8, Indels: 17
        0.91            0.03        0.06

Matches are distributed among these distances:
  54   23  0.09
  56    4  0.02
  58  131  0.53
  59    1  0.00
  60    2  0.01
  62   85  0.35

ACGTcount: A:0.46, C:0.17, G:0.14, T:0.24


Consensus pattern (60 bp):   
GAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAAA

Found at i:963 original size:21 final size:22

Alignment explanation


    Indices: 911--964  Score: 56
    Period size: 27  Copynumber: 2.3  Consensus size: 22

        901 ATATGTAATA

                                  
        911 ACGATAGACCTAGAACTATATG
          1 ACGATAGACCTAGAACTATATG

                                       
        933 CAATAACGATAGACCTAGAACTATATG
          1 -----ACGATAGACCTAGAACTATATG

                  
        960 -CGATA
          1 ACGATA

        965 ATGATAACTC


Statistics
Matches: 27,  Mismatches: 0, Indels: 6
        0.82            0.00        0.18

Matches are distributed among these distances:
  21    5  0.19
  27   22  0.81

ACGTcount: A:0.43, C:0.19, G:0.17, T:0.22


Consensus pattern (22 bp):   
ACGATAGACCTAGAACTATATG
Done.