Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008398.1 Corchorus capsularis cultivar CVL-1 contig08419, 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: 28832
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31

Warning! 2 characters in sequence are not A, C, G, or T


Found at i:2258 original size:27 final size:26

Alignment explanation


    Indices: 2228--2307  Score: 97
    Period size: 27  Copynumber: 3.0  Consensus size: 26

       2218 GGATAGGAAT

                *             *        
       2228 AAAGAATCAATAGAATATTAGACAAGA
          1 AAAGGATCAAT-GAATATGAGACAAGA

                         *             
       2255 AAAGGATCGAATGGATATGAGACAAGA
          1 AAAGGATC-AATGAATATGAGACAAGA

                         *            
       2282 AAAGGATCAAATGGATATGAGACAAG
          1 AAAGGATC-AATGAATATGAGACAAG

       2308 GACGTGGGCC


Statistics
Matches: 48,  Mismatches: 4, Indels: 2
        0.89            0.07        0.04

Matches are distributed among these distances:
  27   45  0.94
  28    3  0.06

ACGTcount: A:0.53, C:0.07, G:0.24, T:0.16


Consensus pattern (26 bp):   
AAAGGATCAATGAATATGAGACAAGA

Found at i:25219 original size:21 final size:21

Alignment explanation


    Indices: 25193--25234  Score: 66
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      25183 GCACAAGTGA

                   *       *     
      25193 CCGGCCATGCGACTTGGAGAT
          1 CCGGCCACGCGACTTAGAGAT

                                 
      25214 CCGGCCACGCGACTTAGAGAT
          1 CCGGCCACGCGACTTAGAGAT

      25235 GCCCGCGCAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.21, C:0.31, G:0.31, T:0.17


Consensus pattern (21 bp):   
CCGGCCACGCGACTTAGAGAT

Found at i:25317 original size:33 final size:32

Alignment explanation


    Indices: 25214--25352  Score: 118
    Period size: 33  Copynumber: 4.2  Consensus size: 32

      25204 ACTTGGAGAT

                         * *  *          *   
      25214 CCGGCCACGCGACTTAGAGATGCCCGCGCAACA
          1 CCGGCCACGCGACATGGACATGCCCG-GCCACA

               *   *          *              
      25247 CCGACCATGCGACATGGAGATGCCCGGCCATCA
          1 CCGGCCACGCGACATGGACATGCCCGGCCA-CA

                             *              
      25280 CCGGCCACGCGACATGGCCATGCCCGGCCACA
          1 CCGGCCACGCGACATGGACATGCCCGGCCACA

                     **        *       *       
      25312 CCCGGCCACATGAC-TCGGTCATGCCCAGCCACAA
          1 -CCGGCCACGCGACAT-GGACATGCCCGGCCAC-A

                   
      25346 CCGGCCA
          1 CCGGCCA

      25353 TATGATCCTT


Statistics
Matches: 89,  Mismatches: 13, Indels: 8
        0.81            0.12        0.07

Matches are distributed among these distances:
  32    6  0.07
  33   82  0.92
  34    1  0.01

ACGTcount: A:0.22, C:0.42, G:0.26, T:0.09


Consensus pattern (32 bp):   
CCGGCCACGCGACATGGACATGCCCGGCCACA
Done.