Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006530.1 Corchorus capsularis cultivar CVL-1 contig06551, 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: 17398
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32


Found at i:1802 original size:2 final size:2

Alignment explanation


    Indices: 1797--1822  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       1787 TATAGGTAAG

                                                  
       1797 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

       1823 TTTCTAAATT


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:4400 original size:15 final size:14

Alignment explanation


    Indices: 4376--4406  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 14

       4366 ATTTGCACTC

                          
       4376 AAACAACTCTGACG
          1 AAACAACTCTGACG

                           
       4390 AAACGAACTCTGACG
          1 AAAC-AACTCTGACG

              
       4405 AA
          1 AA

       4407 GTTGAAAATT


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    4  0.25
  15   12  0.75

ACGTcount: A:0.45, C:0.26, G:0.16, T:0.13


Consensus pattern (14 bp):   
AAACAACTCTGACG

Found at i:5306 original size:13 final size:13

Alignment explanation


    Indices: 5288--5319  Score: 64
    Period size: 13  Copynumber: 2.5  Consensus size: 13

       5278 AATAATTTCC

                         
       5288 ATAATAGTTAAAA
          1 ATAATAGTTAAAA

                         
       5301 ATAATAGTTAAAA
          1 ATAATAGTTAAAA

                  
       5314 ATAATA
          1 ATAATA

       5320 TATAGTATAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   19  1.00

ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31


Consensus pattern (13 bp):   
ATAATAGTTAAAA

Found at i:12967 original size:2 final size:2

Alignment explanation


    Indices: 12960--12984  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      12950 CTATCAATAC

                                                 
      12960 AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A

      12985 AGTACGAATA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.