Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007086.1 Corchorus capsularis cultivar CVL-1 contig07107, 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: 3048
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.26


Found at i:258 original size:14 final size:14

Alignment explanation


    Indices: 241--277  Score: 65
    Period size: 14  Copynumber: 2.6  Consensus size: 14

        231 TAGGTTTTAC

                        * 
        241 AAATTAGGGACATG
          1 AAATTAGGGACAGG

                          
        255 AAATTAGGGACAGG
          1 AAATTAGGGACAGG

                     
        269 AAATTAGGG
          1 AAATTAGGG

        278 TTACACCCAA


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  14   22  1.00

ACGTcount: A:0.43, C:0.05, G:0.32, T:0.19


Consensus pattern (14 bp):   
AAATTAGGGACAGG

Found at i:353 original size:12 final size:12

Alignment explanation


    Indices: 336--390  Score: 67
    Period size: 12  Copynumber: 4.7  Consensus size: 12

        326 GAACTCACGG

                    *   
        336 AAGGAAAAAGAA
          1 AAGGAAAATGAA

                        
        348 AAGG-AAATGAA
          1 AAGGAAAATGAA

               *        
        359 AAGTAAAATGAA
          1 AAGGAAAATGAA

               *    *   
        371 AAGTAAAAGGAA
          1 AAGGAAAATGAA

                    
        383 AAGGAAAA
          1 AAGGAAAA

        391 GAACTTACTG


Statistics
Matches: 38,  Mismatches: 4, Indels: 2
        0.86            0.09        0.05

Matches are distributed among these distances:
  11    9  0.24
  12   29  0.76

ACGTcount: A:0.69, C:0.00, G:0.24, T:0.07


Consensus pattern (12 bp):   
AAGGAAAATGAA

Found at i:354 original size:6 final size:6

Alignment explanation


    Indices: 336--391  Score: 60
    Period size: 6  Copynumber: 9.5  Consensus size: 6

        326 GAACTCACGG

                     *             *       *     *       *         
        336 AAGGAA AAAGAA AAGG-A AATGAA AAGTAA AATGAA AAGTAA AAGGAA
          1 AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA AAGGAA

                      
        383 AAGGAA AAG
          1 AAGGAA AAG

        392 AACTTACTGT


Statistics
Matches: 39,  Mismatches: 10, Indels: 2
        0.76            0.20        0.04

Matches are distributed among these distances:
   5    4  0.10
   6   35  0.90

ACGTcount: A:0.68, C:0.00, G:0.25, T:0.07


Consensus pattern (6 bp):   
AAGGAA

Found at i:550 original size:17 final size:18

Alignment explanation


    Indices: 515--552  Score: 60
    Period size: 17  Copynumber: 2.2  Consensus size: 18

        505 TCGAAAAACA

                          *   
        515 CTTAGGAAATTTTTGTGC
          1 CTTAGGAAATTTTTATGC

                              
        533 CTTAGGAAA-TTTTATGC
          1 CTTAGGAAATTTTTATGC

               
        550 CTT
          1 CTT

        553 CAATGGTTTA


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  17   10  0.53
  18    9  0.47

ACGTcount: A:0.24, C:0.13, G:0.18, T:0.45


Consensus pattern (18 bp):   
CTTAGGAAATTTTTATGC

Found at i:2407 original size:33 final size:34

Alignment explanation


    Indices: 2370--2443  Score: 98
    Period size: 33  Copynumber: 2.2  Consensus size: 34

       2360 CCGAGTCGTT

                              *            *  
       2370 TGGCCGGTTG-TAGCCAGCCATGTCCATGTCTCG
          1 TGGCCGGTTGATAGCCAGACATGTCCATGTCGCG

                        *   *                 
       2403 TGGCCGG-TGATGGCCGGACATGTCCATGTCGCG
          1 TGGCCGGTTGATAGCCAGACATGTCCATGTCGCG

                    
       2436 TGGCCGGT
          1 TGGCCGGT

       2444 CTTGTGGCCG


Statistics
Matches: 35,  Mismatches: 4, Indels: 3
        0.83            0.10        0.07

Matches are distributed among these distances:
  32    2  0.06
  33   33  0.94

ACGTcount: A:0.11, C:0.28, G:0.36, T:0.24


Consensus pattern (34 bp):   
TGGCCGGTTGATAGCCAGACATGTCCATGTCGCG
Done.