Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011197.1 Corchorus capsularis cultivar CVL-1 contig11218, 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: 6343
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31


Found at i:2629 original size:33 final size:33

Alignment explanation


    Indices: 2592--2698  Score: 126
    Period size: 33  Copynumber: 3.2  Consensus size: 33

       2582 AGCACTAGTG

                    *            *           
       2592 ACCGGCCATGCGACTTGGAGAAGTCCGGCCAAC
          1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC

                      *    *       *         
       2625 ACCGGCCACGTGACTCGGAGATGCCCGGCCAAC
          1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC

                          *    *    *        
       2658 ACCGGCCACGCGACATGGACATGTTCGGCC-AC
          1 ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC

                     
       2690 AACCGGCCA
          1 -ACCGGCCA

       2699 TCGCTAGGCG


Statistics
Matches: 62,  Mismatches: 11, Indels: 2
        0.83            0.15        0.03

Matches are distributed among these distances:
  32    2  0.03
  33   60  0.97

ACGTcount: A:0.23, C:0.37, G:0.29, T:0.10


Consensus pattern (33 bp):   
ACCGGCCACGCGACTTGGAGATGTCCGGCCAAC

Found at i:5402 original size:17 final size:17

Alignment explanation


    Indices: 5380--5413  Score: 52
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       5370 TTCTGGTCGA

                              
       5380 ATTTTTTATTT-TATTTT
          1 ATTTTTT-TTTATATTTT

                             
       5397 ATTTTTTTTTATATTTT
          1 ATTTTTTTTTATATTTT

       5414 TCGATATAAC


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  16    3  0.19
  17   13  0.81

ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82


Consensus pattern (17 bp):   
ATTTTTTTTTATATTTT

Found at i:5524 original size:9 final size:8

Alignment explanation


    Indices: 5487--5520  Score: 50
    Period size: 8  Copynumber: 4.1  Consensus size: 8

       5477 GAATTGGCTA

                    
       5487 TGAATTTT
          1 TGAATTTT

                    *
       5495 TGAAGTTTC
          1 TGAA-TTTT

                    
       5504 TGAATTTT
          1 TGAATTTT

                    
       5512 TGAATTTT
          1 TGAATTTT

             
       5520 T
          1 T

       5521 TGAAGAAGGT


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


Consensus pattern (8 bp):   
TGAATTTT
Done.