Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015594.1 Corchorus capsularis cultivar CVL-1 contig15615, 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: 18245
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:310 original size:17 final size:17

Alignment explanation


    Indices: 285--317  Score: 57
    Period size: 17  Copynumber: 1.9  Consensus size: 17

        275 GATTCTATCC

                *            
        285 GATCTATTAAGACCCGT
          1 GATCCATTAAGACCCGT

                            
        302 GATCCATTAAGACCCG
          1 GATCCATTAAGACCCG

        318 GAACTTGTTA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.30, C:0.27, G:0.18, T:0.24


Consensus pattern (17 bp):   
GATCCATTAAGACCCGT

Found at i:3287 original size:33 final size:33

Alignment explanation


    Indices: 3217--3329  Score: 140
    Period size: 33  Copynumber: 3.4  Consensus size: 33

       3207 CAGCCACAAG

                                     *        
       3217 ACCGGCCACGCGACATGGACATGTCGGGCCATC-
          1 ACCGGCCACGCGACATGGACATGTCCGGCCA-CA

                                         *   
       3250 ACCGGCCACGCGACATGGACATGTCCGGCTACA
          1 ACCGGCCACGCGACATGGACATGTCCGGCCACA

                    **         *    *         
       3283 ACCGGCCAAACGAC-TCGGCCATGCCCGGCCACA
          1 ACCGGCCACGCGACAT-GGACATGTCCGGCCACA

                          
       3316 ACCGGCCACGCGAC
          1 ACCGGCCACGCGAC

       3330 CCTTTGTCTA


Statistics
Matches: 69,  Mismatches: 9, Indels: 4
        0.84            0.11        0.05

Matches are distributed among these distances:
  32    2  0.03
  33   67  0.97

ACGTcount: A:0.23, C:0.41, G:0.27, T:0.09


Consensus pattern (33 bp):   
ACCGGCCACGCGACATGGACATGTCCGGCCACA

Found at i:4995 original size:19 final size:18

Alignment explanation


    Indices: 4971--5007  Score: 56
    Period size: 19  Copynumber: 2.0  Consensus size: 18

       4961 TTGAAGATTT

                               
       4971 CTTGAAGATAATTTGAAGA
          1 CTTGAAGATAA-TTGAAGA

                     *        
       4990 CTTGAAGATCATTGAAGA
          1 CTTGAAGATAATTGAAGA

       5008 ATTATTTCAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  18    7  0.41
  19   10  0.59

ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30


Consensus pattern (18 bp):   
CTTGAAGATAATTGAAGA
Done.