Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008089.1 Corchorus capsularis cultivar CVL-1 contig08110, 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: 26111
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:2469 original size:1 final size:1

Alignment explanation


    Indices: 2463--2502  Score: 80
    Period size: 1  Copynumber: 40.0  Consensus size: 1

       2453 AAGCAGTGAG

                                                    
       2463 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
          1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

       2503 CTCTCTTTAT


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   39  1.00

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


Consensus pattern (1 bp):   
T

Found at i:7238 original size:109 final size:109

Alignment explanation


    Indices: 7042--7259  Score: 391
    Period size: 109  Copynumber: 2.0  Consensus size: 109

       7032 TAGTCATTTT

                                         *                  *             *  
       7042 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTCTTGTTTGGTATATGTGTTT
          1 GGTGCTTGTATTTTTCTTTAAATCCAATAATTCATTGCACTTTGTCTTATTTGGTATATGTGCTT

                                                        
       7107 ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
         66 ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA

                                                                     *       
       7151 GGTGCTTGTATTTTTCTTTAAATCCAATAATTCATTGCACTTTGTCTTATTTGGTATGTGTGCTT
          1 GGTGCTTGTATTTTTCTTTAAATCCAATAATTCATTGCACTTTGTCTTATTTGGTATATGTGCTT

                             *                          
       7216 ATTTAATAGGTTCAATTTAATAAACAACACAATTAATAATAATA
         66 ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA

       7260 TATATAATAG


Statistics
Matches: 104,  Mismatches: 5, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
 109  104  1.00

ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44


Consensus pattern (109 bp):   
GGTGCTTGTATTTTTCTTTAAATCCAATAATTCATTGCACTTTGTCTTATTTGGTATATGTGCTT
ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA

Found at i:12359 original size:21 final size:21

Alignment explanation


    Indices: 12311--12351  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      12301 ATTTATGAGT

                                 
      12311 AACAAATATAAAAAATTTTCA
          1 AACAAATATAAAAAATTTTCA

              *       **        
      12332 AATAAATATACTAAATTTTC
          1 AACAAATATAAAAAATTTTC

      12352 TTACAAATTA


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34


Consensus pattern (21 bp):   
AACAAATATAAAAAATTTTCA

Found at i:12965 original size:26 final size:26

Alignment explanation


    Indices: 12936--12989  Score: 99
    Period size: 26  Copynumber: 2.1  Consensus size: 26

      12926 AAGAATATTC

                                      
      12936 AACATTAAGACCTATCTTTTCAAAAA
          1 AACATTAAGACCTATCTTTTCAAAAA

                                *     
      12962 AACATTAAGACCTATCTTTTGAAAAA
          1 AACATTAAGACCTATCTTTTCAAAAA

              
      12988 AA
          1 AA

      12990 ACATGGTATT


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  26   27  1.00

ACGTcount: A:0.48, C:0.17, G:0.06, T:0.30


Consensus pattern (26 bp):   
AACATTAAGACCTATCTTTTCAAAAA

Found at i:17890 original size:2 final size:2

Alignment explanation


    Indices: 17883--17917  Score: 70
    Period size: 2  Copynumber: 17.5  Consensus size: 2

      17873 TTCAAAGTCC

                                                                
      17883 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      17918 CAATAAATCG


Statistics
Matches: 33,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.