Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003942.1 Corchorus capsularis cultivar CVL-1 contig03950, 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: 2882
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30


Found at i:421 original size:7 final size:7

Alignment explanation


    Indices: 409--472  Score: 56
    Period size: 7  Copynumber: 8.3  Consensus size: 7

        399 TTCTCGGGTT

                   
        409 TTTCGGG
          1 TTTCGGG

                   
        416 TTTCGGG
          1 TTTCGGG

                *    
        423 TCATACGGG
          1 T--TTCGGG

             *     
        432 TCTCGGG
          1 TTTCGGG

                     
        439 TCATTCGGG
          1 T--TTCGGG

                   
        448 TTTCGGG
          1 TTTCGGG

                     
        455 TTATCTGGG
          1 TT-TC-GGG

                   
        464 TTTCGGG
          1 TTTCGGG

              
        471 TT
          1 TT

        473 ATTCAGGTCT


Statistics
Matches: 47,  Mismatches: 4, Indels: 12
        0.75            0.06        0.19

Matches are distributed among these distances:
   7   26  0.55
   8    4  0.09
   9   17  0.36

ACGTcount: A:0.06, C:0.17, G:0.38, T:0.39


Consensus pattern (7 bp):   
TTTCGGG

Found at i:423 original size:16 final size:16

Alignment explanation


    Indices: 400--519  Score: 111
    Period size: 16  Copynumber: 7.5  Consensus size: 16

        390 CGGGTTAACT

                     *      
        400 TCTCGGGTTTTTCGGG
          1 TCTCGGGTTATTCGGG

             *      *  *    
        416 TTTCGGGTCATACGGG
          1 TCTCGGGTTATTCGGG

                    *       
        432 TCTCGGGTCATTCGGG
          1 TCTCGGGTTATTCGGG

             *               
        448 TTTCGGGTTA-TCTGGG
          1 TCTCGGGTTATTC-GGG

             *           *  
        464 TTTCGGGTTATTCAGG
          1 TCTCGGGTTATTCGGG

                    *       
        480 TCTCGGGTCATTCGGG
          1 TCTCGGGTTATTCGGG

                              
        496 TCAT-GGGTT-TGTCGGG
          1 TC-TCGGGTTAT-TCGGG

                    
        512 TCTCGGGT
          1 TCTCGGGT

        520 CGGGCGGGTT


Statistics
Matches: 86,  Mismatches: 13, Indels: 10
        0.79            0.12        0.09

Matches are distributed among these distances:
  15    4  0.05
  16   79  0.92
  17    3  0.03

ACGTcount: A:0.07, C:0.18, G:0.38, T:0.38


Consensus pattern (16 bp):   
TCTCGGGTTATTCGGG

Found at i:455 original size:48 final size:49

Alignment explanation


    Indices: 402--520  Score: 145
    Period size: 48  Copynumber: 2.5  Consensus size: 49

        392 GGTTAACTTC

                    *                  *                    *
        402 TCGGGTTTTTCGGGTTTCGGGTCATACGGGTCTCGGGTCATTCGGGT-T
          1 TCGGGTTTATCGGGTTTCGGGTCATACAGGTCTCGGGTCATTCGGGTCA

                                   *  *                       
        450 TCGGG-TTATCTGGGTTTCGGGTTATTCAGGTCTCGGGTCATTCGGGTCA
          1 TCGGGTTTATC-GGGTTTCGGGTCATACAGGTCTCGGGTCATTCGGGTCA

                    *      *       
        499 T-GGGTTTGTCGGGTCTCGGGTC
          1 TCGGGTTTATCGGGTTTCGGGTC

        521 GGGCGGGTTC


Statistics
Matches: 60,  Mismatches: 8, Indels: 6
        0.81            0.11        0.08

Matches are distributed among these distances:
  47    4  0.07
  48   51  0.85
  49    5  0.08

ACGTcount: A:0.07, C:0.18, G:0.38, T:0.37


Consensus pattern (49 bp):   
TCGGGTTTATCGGGTTTCGGGTCATACAGGTCTCGGGTCATTCGGGTCA

Found at i:586 original size:17 final size:18

Alignment explanation


    Indices: 558--601  Score: 74
    Period size: 18  Copynumber: 2.6  Consensus size: 18

        548 TTTGTCAAAA

                              
        558 CGGGTT-GGGCGGGTT-T
          1 CGGGTTCGGGCGGGTTCT

                              
        574 CGGGTTCGGGCGGGTTCT
          1 CGGGTTCGGGCGGGTTCT

                      
        592 CGGGTTCGGG
          1 CGGGTTCGGG

        602 TCAGGTTTTG


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

Matches are distributed among these distances:
  16    6  0.23
  17    9  0.35
  18   11  0.42

ACGTcount: A:0.00, C:0.18, G:0.55, T:0.27


Consensus pattern (18 bp):   
CGGGTTCGGGCGGGTTCT

Done.