Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018297.1 Corchorus olitorius cultivar O-4 contig18330, 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: 4389
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:398 original size:16 final size:16

Alignment explanation


    Indices: 377--410  Score: 52
    Period size: 16  Copynumber: 2.1  Consensus size: 16

        367 AACACTTAAA

                             
        377 TTTCTAT-TTTTAATTT
          1 TTTCTATCTTTT-ATTT

                            
        393 TTTCTATCTTTTATTT
          1 TTTCTATCTTTTATTT

              
        409 TT
          1 TT

        411 ATTTCGTTTA


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  16   13  0.76
  17    4  0.24

ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76


Consensus pattern (16 bp):   
TTTCTATCTTTTATTT

Found at i:1960 original size:30 final size:31

Alignment explanation


    Indices: 1918--2009  Score: 95
    Period size: 30  Copynumber: 3.1  Consensus size: 31

       1908 TTGAGAAGTT

                                           
       1918 TGGTAAGG-TTGTGAAAGTTGAGAAAAAAAA
          1 TGGTAAGGTTTGTGAAAGTTGAGAAAAAAAA

                                    *  * ** 
       1948 TGGT-AGGTTTGTGAGAA-TTGAGGAAGATGA
          1 TGGTAAGGTTTGTGA-AAGTTGAGAAAAAAAA

                                            
       1978 TGGTAAGGTTTG-GAAAGTTGA-AAAGAAAAA
          1 TGGTAAGGTTTGTGAAAGTTGAGAAA-AAAAA

              
       2008 TG
          1 TG

       2010 AGAAAAAGAT


Statistics
Matches: 49,  Mismatches: 8, Indels: 10
        0.73            0.12        0.15

Matches are distributed among these distances:
  29    7  0.14
  30   33  0.67
  31    9  0.18

ACGTcount: A:0.40, C:0.00, G:0.34, T:0.26


Consensus pattern (31 bp):   
TGGTAAGGTTTGTGAAAGTTGAGAAAAAAAA

Found at i:3597 original size:26 final size:26

Alignment explanation


    Indices: 3552--3611  Score: 68
    Period size: 26  Copynumber: 2.3  Consensus size: 26

       3542 TAAAAAAAAA

                                *     
       3552 ATTTGCATTTTTGCATTTTTGTTTAT
          1 ATTTGCATTTTTGCATTTTTCTTTAT

                         *           * 
       3578 ATTTGCATATTTTTCA-TTTTCTTTTT
          1 ATTTGCAT-TTTTGCATTTTTCTTTAT

            *       
       3604 GTTTGCAT
          1 ATTTGCAT

       3612 GCATTGCATT


Statistics
Matches: 29,  Mismatches: 4, Indels: 2
        0.83            0.11        0.06

Matches are distributed among these distances:
  26   23  0.79
  27    6  0.21

ACGTcount: A:0.15, C:0.10, G:0.10, T:0.65


Consensus pattern (26 bp):   
ATTTGCATTTTTGCATTTTTCTTTAT
Done.