Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008071.1 Corchorus olitorius cultivar O-4 contig08098, 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, 905

Length: 1509
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32


Found at i:504 original size:20 final size:20

Alignment explanation


    Indices: 471--509  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 20

        461 AATAGACGAA

                          *     
        471 ATTTTCAGAAATTATTATTT
          1 ATTTTCAGAAATTAGTATTT

                                
        491 ATTTTCA-AATATTAGTATT
          1 ATTTTCAGAA-ATTAGTATT

        510 GAATTTGGGT


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  19    2  0.12
  20   15  0.88

ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54


Consensus pattern (20 bp):   
ATTTTCAGAAATTAGTATTT

Found at i:604 original size:16 final size:16

Alignment explanation


    Indices: 543--609  Score: 75
    Period size: 16  Copynumber: 4.2  Consensus size: 16

        533 GGTTCAGTTA

                         *  
        543 TTTCGGGTTCG-GGTT
          1 TTTCGGGTTCGAGCTT

                           *  
        558 TTATCGGGTTTC-AGATT
          1 TT-TCGGG-TTCGAGCTT

                     *      
        575 TTTCGGGTTTGAGCTT
          1 TTTCGGGTTCGAGCTT

                            
        591 TTTCGGGTTCGAGCTT
          1 TTTCGGGTTCGAGCTT

               
        607 TTT
          1 TTT

        610 TAGGTCTAGT


Statistics
Matches: 44,  Mismatches: 4, Indels: 7
        0.80            0.07        0.13

Matches are distributed among these distances:
  15    4  0.09
  16   32  0.73
  17    8  0.18

ACGTcount: A:0.07, C:0.13, G:0.30, T:0.49


Consensus pattern (16 bp):   
TTTCGGGTTCGAGCTT

Found at i:609 original size:32 final size:32

Alignment explanation


    Indices: 535--599  Score: 80
    Period size: 32  Copynumber: 2.0  Consensus size: 32

        525 CAGGTTTGGG

                                 *           
        535 TTCAG-TTATTTCGGGTTCGGGTTTTATCGGGT
          1 TTCAGATT-TTTCGGGTTCGGCTTTTATCGGGT

                             *               
        567 TTCAGATTTTTCGGGTTTGAGCTTTT-TCGGGT
          1 TTCAGATTTTTCGGGTTCG-GCTTTTATCGGGT

             
        599 T
          1 T

        600 CGAGCTTTTT


Statistics
Matches: 29,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
  32   22  0.76
  33    7  0.24

ACGTcount: A:0.09, C:0.12, G:0.29, T:0.49


Consensus pattern (32 bp):   
TTCAGATTTTTCGGGTTCGGCTTTTATCGGGT
Done.