Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010260.1 Corchorus capsularis cultivar CVL-1 contig10281, 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: 24665
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31


Found at i:12812 original size:22 final size:20

Alignment explanation


    Indices: 12784--12825  Score: 57
    Period size: 22  Copynumber: 2.0  Consensus size: 20

      12774 AAAAAAAAAG

                    *             
      12784 TGGGTTTTTTTTAGTTTTGTTT
          1 TGGGTTTTGTTTA--TTTGTTT

                                
      12806 TGGGTTTTGTTTATTTGTTT
          1 TGGGTTTTGTTTATTTGTTT

      12826 GTTTCAAAGC


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  20    7  0.37
  22   12  0.63

ACGTcount: A:0.05, C:0.00, G:0.24, T:0.71


Consensus pattern (20 bp):   
TGGGTTTTGTTTATTTGTTT

Found at i:14254 original size:35 final size:35

Alignment explanation


    Indices: 14208--14281  Score: 148
    Period size: 35  Copynumber: 2.1  Consensus size: 35

      14198 AATGCTCAGA

                                               
      14208 TGCAATAATAGTGAAGATTATTAGTAATAATAAGT
          1 TGCAATAATAGTGAAGATTATTAGTAATAATAAGT

                                               
      14243 TGCAATAATAGTGAAGATTATTAGTAATAATAAGT
          1 TGCAATAATAGTGAAGATTATTAGTAATAATAAGT

                
      14278 TGCA
          1 TGCA

      14282 CACGAAAATG


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

Matches are distributed among these distances:
  35   39  1.00

ACGTcount: A:0.45, C:0.04, G:0.18, T:0.34


Consensus pattern (35 bp):   
TGCAATAATAGTGAAGATTATTAGTAATAATAAGT

Found at i:14409 original size:8 final size:8

Alignment explanation


    Indices: 14391--14430  Score: 62
    Period size: 8  Copynumber: 5.0  Consensus size: 8

      14381 TTTTCATGAT

                  * 
      14391 TATAAATA
          1 TATAAAAA

                *   
      14399 TATATAAA
          1 TATAAAAA

                    
      14407 TATAAAAA
          1 TATAAAAA

                    
      14415 TATAAAAA
          1 TATAAAAA

                    
      14423 TATAAAAA
          1 TATAAAAA

      14431 GATATTTTGT


Statistics
Matches: 29,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   8   29  1.00

ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30


Consensus pattern (8 bp):   
TATAAAAA

Found at i:18106 original size:16 final size:17

Alignment explanation


    Indices: 18077--18108  Score: 57
    Period size: 16  Copynumber: 1.9  Consensus size: 17

      18067 CTCACTCTCA

                             
      18077 TAATCCTGGTCAGAAAT
          1 TAATCCTGGTCAGAAAT

                            
      18094 TAATCCT-GTCAGAAA
          1 TAATCCTGGTCAGAAA

      18109 GCTGCATCTC


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16    8  0.53
  17    7  0.47

ACGTcount: A:0.38, C:0.19, G:0.16, T:0.28


Consensus pattern (17 bp):   
TAATCCTGGTCAGAAAT
Done.