Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015853.1 Corchorus capsularis cultivar CVL-1 contig15874, 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: 3642
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39


Found at i:436 original size:7 final size:6

Alignment explanation


    Indices: 393--453  Score: 56
    Period size: 6  Copynumber: 10.2  Consensus size: 6

        383 TTTCCTTTAG

                        *           *                                
        393 TTTTGT TTTT-A TTTT-T TTTCGT ATTTTGT TTTTGT TTTTCGT TTTT-T
          1 TTTTGT TTTTGT TTTTGT TTTTGT -TTTTGT TTTTGT TTTT-GT TTTTGT

                            
        440 TTTGTGT TTTTGT T
          1 TTT-TGT TTTTGT T

        454 AATTTTGCAG


Statistics
Matches: 46,  Mismatches: 4, Indels: 10
        0.77            0.07        0.17

Matches are distributed among these distances:
   5   11  0.24
   6   20  0.43
   7   15  0.33

ACGTcount: A:0.03, C:0.03, G:0.13, T:0.80


Consensus pattern (6 bp):   
TTTTGT

Found at i:438 original size:19 final size:20

Alignment explanation


    Indices: 407--450  Score: 65
    Period size: 19  Copynumber: 2.2  Consensus size: 20

        397 GTTTTTATTT

                                 
        407 TTTTTCGTATTTTGTTTT-TG
          1 TTTTTCGTATTTT-TTTTGTG

                                
        427 TTTTTCGT-TTTTTTTTGTG
          1 TTTTTCGTATTTTTTTTGTG

                 
        446 TTTTT
          1 TTTTT

        451 GTTAATTTTG


Statistics
Matches: 23,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  18    4  0.17
  19   11  0.48
  20    8  0.35

ACGTcount: A:0.02, C:0.05, G:0.14, T:0.80


Consensus pattern (20 bp):   
TTTTTCGTATTTTTTTTGTG

Found at i:3600 original size:18 final size:19

Alignment explanation


    Indices: 3572--3612  Score: 57
    Period size: 18  Copynumber: 2.2  Consensus size: 19

       3562 TTCTCAAACG

                               
       3572 ATTTTTAAATTTGACAAAA
          1 ATTTTTAAATTTGACAAAA

                        **     
       3591 ATTTTT-AATTTTTCAAAA
          1 ATTTTTAAATTTGACAAAA

                
       3609 ATTT
          1 ATTT

       3613 GCTTCTCTGG


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  18   14  0.70
  19    6  0.30

ACGTcount: A:0.41, C:0.05, G:0.02, T:0.51


Consensus pattern (19 bp):   
ATTTTTAAATTTGACAAAA
Done.