Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007378.1 Corchorus capsularis cultivar CVL-1 contig07399, 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: 26264
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30


Found at i:6 original size:1 final size:1

Alignment explanation


    Indices: 1--28  Score: 56
    Period size: 1  Copynumber: 28.0  Consensus size: 1

                                        
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA

         29 CTATTTTCAG


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   27  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Found at i:965 original size:38 final size:38

Alignment explanation


    Indices: 868--966  Score: 171
    Period size: 40  Copynumber: 2.6  Consensus size: 38

        858 GAGCTTCACT

                                               *  
        868 CCGAATTAGTCAGGGTTCAATAGGGCACTCGACTCTGA
          1 CCGAATTAGTCAGGGTTCAATAGGGCACTCGACTCCGA

                                                    
        906 CCGAATACTAGTCAGGGTTCAATAGGGCACTCGACTCCGA
          1 CCGAAT--TAGTCAGGGTTCAATAGGGCACTCGACTCCGA

                                 
        946 CCGAATTAGTCAGGGTTCAAT
          1 CCGAATTAGTCAGGGTTCAAT

        967 TATGCCTATC


Statistics
Matches: 58,  Mismatches: 1, Indels: 4
        0.92            0.02        0.06

Matches are distributed among these distances:
  38   21  0.36
  40   37  0.64

ACGTcount: A:0.27, C:0.24, G:0.25, T:0.23


Consensus pattern (38 bp):   
CCGAATTAGTCAGGGTTCAATAGGGCACTCGACTCCGA

Found at i:14865 original size:21 final size:21

Alignment explanation


    Indices: 14839--14883  Score: 63
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      14829 CAGATGAGAG

                              *  
      14839 TGATGAAAAAGGCGACGAGGT
          1 TGATGAAAAAGGCGACGAAGT

                     *  *        
      14860 TGATGAAAATGGTGACGAAGT
          1 TGATGAAAAAGGCGACGAAGT

               
      14881 TGA
          1 TGA

      14884 CAAACCGGTG


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   21  1.00

ACGTcount: A:0.38, C:0.07, G:0.36, T:0.20


Consensus pattern (21 bp):   
TGATGAAAAAGGCGACGAAGT

Found at i:21156 original size:12 final size:12

Alignment explanation


    Indices: 21139--21178  Score: 62
    Period size: 12  Copynumber: 3.3  Consensus size: 12

      21129 ACCAGCATTA

                       *
      21139 GCTGCCGCTGCC
          1 GCTGCCGCTGCT

                        
      21151 GCTGCCGCTGCT
          1 GCTGCCGCTGCT

                 *      
      21163 GCTGCTGCTGCT
          1 GCTGCCGCTGCT

                
      21175 GCTG
          1 GCTG

      21179 TAGGTGGGAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  12   26  1.00

ACGTcount: A:0.00, C:0.40, G:0.35, T:0.25


Consensus pattern (12 bp):   
GCTGCCGCTGCT

Found at i:21165 original size:3 final size:3

Alignment explanation


    Indices: 21139--21178  Score: 53
    Period size: 3  Copynumber: 13.3  Consensus size: 3

      21129 ACCAGCATTA

                  *       *       *                              
      21139 GCT GCC GCT GCC GCT GCC GCT GCT GCT GCT GCT GCT GCT G
          1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT G

      21179 TAGGTGGGAA


Statistics
Matches: 31,  Mismatches: 6, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
   3   31  1.00

ACGTcount: A:0.00, C:0.40, G:0.35, T:0.25


Consensus pattern (3 bp):   
GCT

Found at i:24452 original size:2 final size:2

Alignment explanation


    Indices: 24445--24470  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

      24435 TATTTTATGC

                                                  
      24445 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

      24471 TCTTGAAGTT


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

Done.