Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019707.1 Corchorus olitorius cultivar O-4 contig19740, 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: 28514
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31


Found at i:883 original size:21 final size:21

Alignment explanation


    Indices: 859--902  Score: 56
    Period size: 21  Copynumber: 2.1  Consensus size: 21

        849 GCAGACTTTA

                                   
        859 AGAAGAA-TG-GAAGCTAAAAGG
          1 AGAAGAAGTGAGAAGC--AAAGG

                                 
        880 AGAAGAAGTGAGAAGCAAAGG
          1 AGAAGAAGTGAGAAGCAAAGG

              
        901 AG
          1 AG

        903 TTCAAGAGAG


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  21   14  0.67
  22    2  0.10
  23    5  0.24

ACGTcount: A:0.52, C:0.05, G:0.36, T:0.07


Consensus pattern (21 bp):   
AGAAGAAGTGAGAAGCAAAGG

Found at i:15629 original size:48 final size:48

Alignment explanation


    Indices: 15559--15664  Score: 117
    Period size: 48  Copynumber: 2.2  Consensus size: 48

      15549 TACTACTTCC

                                        **             *      
      15559 ACTGCTTGT-AATTTCAAAATCAA-ATGGTAGATGTCTTATTGGATACTT
          1 ACTGCTT-TCAATTTCAAAATCAAGAT-CAAGATGTCTTATTGAATACTT

                            **                   *          
      15607 ACTGCTTTCAATTTCATCATCAAGATCAAGATGTCTTCTTGAATACTT
          1 ACTGCTTTCAATTTCAAAATCAAGATCAAGATGTCTTATTGAATACTT

             *        
      15655 AATGCTTTCA
          1 ACTGCTTTCA

      15665 CTCTCCTCAC


Statistics
Matches: 49,  Mismatches: 7, Indels: 4
        0.82            0.12        0.07

Matches are distributed among these distances:
  47    1  0.02
  48   46  0.94
  49    2  0.04

ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40


Consensus pattern (48 bp):   
ACTGCTTTCAATTTCAAAATCAAGATCAAGATGTCTTATTGAATACTT

Found at i:17976 original size:33 final size:33

Alignment explanation


    Indices: 17914--17975  Score: 90
    Period size: 33  Copynumber: 1.9  Consensus size: 33

      17904 CTAATTCTAA

                          *     * *          
      17914 ATAGAATAGATAATTTATACTATAAAAAAATAC
          1 ATAGAATAGATAATATATACAAAAAAAAAATAC

                                          
      17947 ATAGAATAGATAATATAT-CAAAAAAAAAA
          1 ATAGAATAGATAATATATACAAAAAAAAAA

      17976 AAATATCTCC


Statistics
Matches: 26,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  32    9  0.35
  33   17  0.65

ACGTcount: A:0.63, C:0.05, G:0.06, T:0.26


Consensus pattern (33 bp):   
ATAGAATAGATAATATATACAAAAAAAAAATAC

Found at i:27289 original size:60 final size:60

Alignment explanation


    Indices: 27192--27339  Score: 176
    Period size: 60  Copynumber: 2.5  Consensus size: 60

      27182 TTATTTGAGC

                        *       *       *               *                
      27192 ATTTTGGCAAACGTTAGGCCTTTATTTGTCCAAATTAAAAGATCGGGTCCTT-TTTTGAAT
          1 ATTTTGGCAAACATTAGGCCCTTATTTGACCAAATTAAAAGATCAGGTCCTTATTTT-AAT

                             *               *       *                 * 
      27252 ATTTTGGCAAACATTAGCCCCTTATATT-ACCAGATTAAAATATCAGGTCCTTATTTTAGT
          1 ATTTTGGCAAACATTAGGCCCTTAT-TTGACCAAATTAAAAGATCAGGTCCTTATTTTAAT

                  *                      
      27312 A-TTTGACAAACATTAGGCCCTTATTTGA
          1 ATTTTGGCAAACATTAGGCCCTTATTTGA

      27340 GCAATTAGCC


Statistics
Matches: 75,  Mismatches: 10, Indels: 7
        0.82            0.11        0.08

Matches are distributed among these distances:
  58    2  0.03
  59   22  0.29
  60   45  0.60
  61    6  0.08

ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39


Consensus pattern (60 bp):   
ATTTTGGCAAACATTAGGCCCTTATTTGACCAAATTAAAAGATCAGGTCCTTATTTTAAT
Done.