Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019547.1 Corchorus olitorius cultivar O-4 contig19580, 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: 5644
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.31


Found at i:419 original size:16 final size:16

Alignment explanation


    Indices: 398--457  Score: 57
    Period size: 16  Copynumber: 3.5  Consensus size: 16

        388 TTCCATTCCC

                            
        398 TTTTCTTTTTCTTTTT
          1 TTTTCTTTTTCTTTTT

                    *        
        414 TTTTCTTTCTCTTTTCT
          1 TTTTCTTTTTCTTTT-T

                *       *      
        431 TTTTTTTATTTATTTATTT
          1 TTTTCTT-TTT-CTT-TTT

                    
        450 TTTTCTTT
          1 TTTTCTTT

        458 CTAGCTTGGG


Statistics
Matches: 35,  Mismatches: 5, Indels: 6
        0.76            0.11        0.13

Matches are distributed among these distances:
  16   14  0.40
  17    7  0.20
  18    3  0.09
  19    9  0.26
  20    2  0.06

ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83


Consensus pattern (16 bp):   
TTTTCTTTTTCTTTTT

Found at i:428 original size:21 final size:20

Alignment explanation


    Indices: 399--437  Score: 69
    Period size: 21  Copynumber: 1.9  Consensus size: 20

        389 TCCATTCCCT

                                
        399 TTTCTTTTTCTTTTTTTTTC
          1 TTTCTTTTTCTTTTTTTTTC

                               
        419 TTTCTCTTTTCTTTTTTTT
          1 TTTCT-TTTTCTTTTTTTT

        438 ATTTATTTAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  20    5  0.28
  21   13  0.72

ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85


Consensus pattern (20 bp):   
TTTCTTTTTCTTTTTTTTTC

Found at i:537 original size:13 final size:13

Alignment explanation


    Indices: 506--558  Score: 70
    Period size: 13  Copynumber: 4.1  Consensus size: 13

        496 TACGCACAGA

                 *       
        506 GCCGCGCGCCTGG
          1 GCCGCACGCCTGG

             *       *   
        519 GTCGCACGCTTGG
          1 GCCGCACGCCTGG

                         
        532 GCCGCACGCCTGG
          1 GCCGCACGCCTGG

                  *      
        545 GCCGCATGCCTGG
          1 GCCGCACGCCTGG

             
        558 G
          1 G

        559 TCGCGCTAGG


Statistics
Matches: 34,  Mismatches: 6, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  13   34  1.00

ACGTcount: A:0.06, C:0.40, G:0.42, T:0.13


Consensus pattern (13 bp):   
GCCGCACGCCTGG

Done.