Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021007.1 Corchorus olitorius cultivar O-4 contig21040, 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: 3886
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.34


Found at i:331 original size:21 final size:21

Alignment explanation


    Indices: 297--337  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        287 AAATACAAGA

                     *     *     
        297 CAACTTCGGTCCAGATGTTGT
          1 CAACTTCGGCCCAGAAGTTGT

                   *            
        318 CAACTTCTGCCCAGAAGTTG
          1 CAACTTCGGCCCAGAAGTTG

        338 GCCTGTCGAA


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:0.22, C:0.27, G:0.22, T:0.29


Consensus pattern (21 bp):   
CAACTTCGGCCCAGAAGTTGT

Found at i:405 original size:22 final size:22

Alignment explanation


    Indices: 369--412  Score: 61
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        359 TTGCGCAGGA

                      *           
        369 CAACTTCGGCCCAGAACTTGTT
          1 CAACTTCGGCACAGAACTTGTT

                     *      *     
        391 CAACTTCGGGACAGAAGTTGTT
          1 CAACTTCGGCACAGAACTTGTT

        413 GCGCAGGACA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27


Consensus pattern (22 bp):   
CAACTTCGGCACAGAACTTGTT

Found at i:417 original size:52 final size:52

Alignment explanation


    Indices: 351--467  Score: 234
    Period size: 52  Copynumber: 2.2  Consensus size: 52

        341 TGTCGAAAAG

                                                                
        351 AGAAGTTGTTGCGCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGAC
          1 AGAAGTTGTTGCGCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGAC

                                                                
        403 AGAAGTTGTTGCGCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGAC
          1 AGAAGTTGTTGCGCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGAC

                         
        455 AGAAGTTGTTGCG
          1 AGAAGTTGTTGCG

        468 GAAAGAAAAA


Statistics
Matches: 65,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  52   65  1.00

ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24


Consensus pattern (52 bp):   
AGAAGTTGTTGCGCAGGACAACTTCGGCCCAGAACTTGTTCAACTTCGGGAC

Found at i:457 original size:22 final size:22

Alignment explanation


    Indices: 421--464  Score: 61
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        411 TTGCGCAGGA

                      *           
        421 CAACTTCGGCCCAGAACTTGTT
          1 CAACTTCGGCACAGAACTTGTT

                     *      *     
        443 CAACTTCGGGACAGAAGTTGTT
          1 CAACTTCGGCACAGAACTTGTT

        465 GCGGAAAGAA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27


Consensus pattern (22 bp):   
CAACTTCGGCACAGAACTTGTT

Found at i:2647 original size:33 final size:33

Alignment explanation


    Indices: 2602--2682  Score: 92
    Period size: 33  Copynumber: 2.5  Consensus size: 33

       2592 GTGTTTTAGA

                   *      **                  
       2602 TGTTGTTAGTGATGTTACTAAAACTAATTTGA-G
          1 TGTTGTTTGTGATGACACTAAAACT-ATTTGAGG

                                  *  *   *   
       2635 TGTTGTTTGTGATGACACTAAATCTGTTTTAGG
          1 TGTTGTTTGTGATGACACTAAAACTATTTGAGG

                           
       2668 TGTTGTTTGTGATGA
          1 TGTTGTTTGTGATGA

       2683 AACAAATTCT


Statistics
Matches: 41,  Mismatches: 6, Indels: 2
        0.84            0.12        0.04

Matches are distributed among these distances:
  32    4  0.10
  33   37  0.90

ACGTcount: A:0.23, C:0.06, G:0.25, T:0.46


Consensus pattern (33 bp):   
TGTTGTTTGTGATGACACTAAAACTATTTGAGG
Done.