Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01002805.1 Corchorus capsularis cultivar CVL-1 contig02813, 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: 3130
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38


Found at i:1123 original size:2 final size:2

Alignment explanation


    Indices: 1118--1150  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       1108 TATAATTTGC

                                                             
       1118 AT AT AT AT 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 AT AT AT AT A

       1151 CACACACACA


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:1465 original size:34 final size:35

Alignment explanation


    Indices: 1403--1474  Score: 119
    Period size: 34  Copynumber: 2.1  Consensus size: 35

       1393 CCTATTGGTT

                            *                  
       1403 TGAAGAAGAAGGAAGGTACAAGACAAGAACCTTCC
          1 TGAAGAAGAAGGAAGGAACAAGACAAGAACCTTCC

                              *                
       1438 TGAAGAAGAAGGAA-GAAGAAGACAAGAACCTTCC
          1 TGAAGAAGAAGGAAGGAACAAGACAAGAACCTTCC

               
       1472 TGA
          1 TGA

       1475 TTGATGCTAG


Statistics
Matches: 35,  Mismatches: 2, Indels: 1
        0.92            0.05        0.03

Matches are distributed among these distances:
  34   21  0.60
  35   14  0.40

ACGTcount: A:0.47, C:0.15, G:0.26, T:0.11


Consensus pattern (35 bp):   
TGAAGAAGAAGGAAGGAACAAGACAAGAACCTTCC

Found at i:2308 original size:2 final size:2

Alignment explanation


    Indices: 2301--2347  Score: 80
    Period size: 2  Copynumber: 24.5  Consensus size: 2

       2291 CAACATGTGC

                                                                          
       2301 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT A- AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                      
       2341 AT AT AT A
          1 AT AT AT A

       2348 AAGGGAGGGG


Statistics
Matches: 43,  Mismatches: 0, Indels: 4
        0.91            0.00        0.09

Matches are distributed among these distances:
   1    2  0.05
   2   41  0.95

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:2992 original size:13 final size:14

Alignment explanation


    Indices: 2974--3004  Score: 55
    Period size: 14  Copynumber: 2.3  Consensus size: 14

       2964 TTGGATTTAA

                          
       2974 ATTTTT-ATAAATT
          1 ATTTTTAATAAATT

                          
       2987 ATTTTTAATAAATT
          1 ATTTTTAATAAATT

                
       3001 ATTT
          1 ATTT

       3005 AATTCAACAT


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13    6  0.35
  14   11  0.65

ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61


Consensus pattern (14 bp):   
ATTTTTAATAAATT

Done.