Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015877.1 Corchorus capsularis cultivar CVL-1 contig15898, 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: 6249
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30


Found at i:459 original size:17 final size:18

Alignment explanation


    Indices: 439--478  Score: 55
    Period size: 20  Copynumber: 2.2  Consensus size: 18

        429 AGTTTAGTTA

                              
        439 ATTTTTCC-TTACTTTTT
          1 ATTTTTCCATTACTTTTT

                                
        456 ATTTTTCCAAGTTACTTTTT
          1 ATTTTTCC-A-TTACTTTTT

               
        476 ATT
          1 ATT

        479 GTTGGATTCT


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  17    8  0.40
  20   12  0.60

ACGTcount: A:0.17, C:0.15, G:0.03, T:0.65


Consensus pattern (18 bp):   
ATTTTTCCATTACTTTTT

Found at i:3915 original size:13 final size:13

Alignment explanation


    Indices: 3897--3921  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       3887 GCCGCTGACA

                         
       3897 GCACCCATGCCAC
          1 GCACCCATGCCAC

                        
       3910 GCACCCATGCCA
          1 GCACCCATGCCA

       3922 TGCTGATGTC


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.24, C:0.52, G:0.16, T:0.08


Consensus pattern (13 bp):   
GCACCCATGCCAC

Found at i:5271 original size:33 final size:32

Alignment explanation


    Indices: 5199--5274  Score: 109
    Period size: 33  Copynumber: 2.3  Consensus size: 32

       5189 AAGCCGCGCA

                                     *      
       5199 ACACCGGCCACGCGACATGGACATGTCCGGTC
          1 ACACCGGCCACGCGACATGGACATGGCCGGTC

                                             
       5231 ATCACCGGCCACGCGACATGGACATGGCCGG-C
          1 A-CACCGGCCACGCGACATGGACATGGCCGGTC

                        
       5263 TACAACCGGCCA
          1 -AC-ACCGGCCA

       5275 AACGAGTCGG


Statistics
Matches: 40,  Mismatches: 1, Indels: 5
        0.87            0.02        0.11

Matches are distributed among these distances:
  32    3  0.08
  33   37  0.93

ACGTcount: A:0.24, C:0.38, G:0.28, T:0.11


Consensus pattern (32 bp):   
ACACCGGCCACGCGACATGGACATGGCCGGTC

Found at i:6229 original size:8 final size:8

Alignment explanation


    Indices: 6216--6249  Score: 50
    Period size: 8  Copynumber: 4.1  Consensus size: 8

       6206 CACCTTCTTG

                    
       6216 AAAAATTC
          1 AAAAATTC

                    
       6224 AAAAATTC
          1 AAAAATTC

                 *   
       6232 AGAAACTTC
          1 A-AAAATTC

                    
       6241 AAAAATTC
          1 AAAAATTC

             
       6249 A
          1 A


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
   8   16  0.70
   9    7  0.30

ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24


Consensus pattern (8 bp):   
AAAAATTC
Done.