Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012888.1 Corchorus capsularis cultivar CVL-1 contig12909, 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: 6366
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33


Found at i:406 original size:2 final size:2

Alignment explanation


    Indices: 395--445  Score: 77
    Period size: 2  Copynumber: 26.0  Consensus size: 2

        385 AGTTTAGACT

                                                            *        *    
        395 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA CA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                          
        436 TA TA TA TA TA
          1 TA TA TA TA TA

        446 AACAGAAAAA


Statistics
Matches: 44,  Mismatches: 4, Indels: 2
        0.88            0.08        0.04

Matches are distributed among these distances:
   1    1  0.02
   2   43  0.98

ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45


Consensus pattern (2 bp):   
TA

Found at i:2251 original size:2 final size:2

Alignment explanation


    Indices: 2244--2279  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       2234 TAATATGTAG

                                                                 
       2244 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       2280 ATTCCTAACA


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:6278 original size:18 final size:18

Alignment explanation


    Indices: 6255--6291  Score: 74
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       6245 CGTGACCCAC

                              
       6255 CATGGCACGGGTCGCGTG
          1 CATGGCACGGGTCGCGTG

                              
       6273 CATGGCACGGGTCGCGTG
          1 CATGGCACGGGTCGCGTG

             
       6291 C
          1 C

       6292 GGATCGCGAC


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   19  1.00

ACGTcount: A:0.11, C:0.30, G:0.43, T:0.16


Consensus pattern (18 bp):   
CATGGCACGGGTCGCGTG
Done.