Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016841.1 Corchorus olitorius cultivar O-4 contig16874, 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: 28264
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31


Found at i:392 original size:28 final size:29

Alignment explanation


    Indices: 356--419  Score: 80
    Period size: 28  Copynumber: 2.2  Consensus size: 29

        346 AAATTCTTCT

                                   *       
        356 TTTTACTTTTT-TACTCTTTAATTA-CCAAA
          1 TTTTACTTTTTAT-CT-TTTAATAACCCAAA

                                         
        385 TTTT-CTTTTTATCTTTTAATAACCCAAA
          1 TTTTACTTTTTATCTTTTAATAACCCAAA

                   
        413 TTTTACT
          1 TTTTACT

        420 CTTTGACTAT


Statistics
Matches: 31,  Mismatches: 1, Indels: 6
        0.82            0.03        0.16

Matches are distributed among these distances:
  27    7  0.23
  28   17  0.55
  29    7  0.23

ACGTcount: A:0.27, C:0.17, G:0.00, T:0.56


Consensus pattern (29 bp):   
TTTTACTTTTTATCTTTTAATAACCCAAA

Found at i:402 original size:27 final size:28

Alignment explanation


    Indices: 363--416  Score: 76
    Period size: 27  Copynumber: 2.0  Consensus size: 28

        353 TCTTTTTACT

                           *            
        363 TTTTTACTCTTTAATTA-CCAAATTTTC
          1 TTTTTACTCTTTAATAACCCAAATTTTC

                                        
        390 TTTTTA-TCTTTTAATAACCCAAATTTT
          1 TTTTTACTC-TTTAATAACCCAAATTTT

        417 ACTCTTTGAC


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  26    2  0.08
  27   13  0.54
  28    9  0.38

ACGTcount: A:0.28, C:0.17, G:0.00, T:0.56


Consensus pattern (28 bp):   
TTTTTACTCTTTAATAACCCAAATTTTC

Found at i:540 original size:41 final size:41

Alignment explanation


    Indices: 434--609  Score: 185
    Period size: 41  Copynumber: 4.2  Consensus size: 41

        424 GACTATCAAA

                          *      *         *   *   * * 
        434 TTACTCTTTACTGATTACTATGAC-CATTTTGTTGTTTATTGT
          1 TTACTCTTTACTGACTACTATTACTC--TTTCTTGATTACTCT

                           *                        * 
        476 TTACTCTTTTACTGATTACTATTACTCTTTCTTGATTACTGT
          1 TTACTC-TTTACTGACTACTATTACTCTTTCTTGATTACTCT

                             *                       
        518 TTACTCTTTACTGACTATTATTACTCTTTCTTGATTACTCT
          1 TTACTCTTTACTGACTACTATTACTCTTTCTTGATTACTCT

                 *      *                          *   
        559 TTACTTTTTACTTACTACTATTACTCTTT-TACTGATTATTCT
          1 TTACTCTTTACTGACTACTATTACTCTTTCT--TGATTACTCT

                     
        601 TTACTCTTT
          1 TTACTCTTT

        610 TATTGATTAC


Statistics
Matches: 118,  Mismatches: 12, Indels: 8
        0.86            0.09        0.06

Matches are distributed among these distances:
  40    1  0.01
  41   58  0.49
  42   41  0.35
  43   17  0.14
  44    1  0.01

ACGTcount: A:0.19, C:0.19, G:0.06, T:0.56


Consensus pattern (41 bp):   
TTACTCTTTACTGACTACTATTACTCTTTCTTGATTACTCT

Found at i:11622 original size:15 final size:16

Alignment explanation


    Indices: 11598--11637  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

      11588 AGAGATTGAA

                 *          
      11598 AGAAAGCAATTAAAC-
          1 AGAAAACAATTAAACT

                            
      11613 AGAAAACAATTAAACT
          1 AGAAAACAATTAAACT

              *      
      11629 AGGAAACAA
          1 AGAAAACAA

      11638 AGCAAAGCAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   14  0.64
  16    8  0.36

ACGTcount: A:0.62, C:0.12, G:0.12, T:0.12


Consensus pattern (16 bp):   
AGAAAACAATTAAACT

Found at i:11637 original size:16 final size:15

Alignment explanation


    Indices: 11599--11637  Score: 51
    Period size: 16  Copynumber: 2.5  Consensus size: 15

      11589 GAGATTGAAA

                            
      11599 GAAAGCAATTAAACAG
          1 GAAA-CAATTAAACAG

            *               
      11615 AAAACAATTAAACTAG
          1 GAAACAATTAAAC-AG

                   
      11631 GAAACAA
          1 GAAACAA

      11638 AGCAAAGCAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  15    9  0.45
  16   11  0.55

ACGTcount: A:0.62, C:0.13, G:0.13, T:0.13


Consensus pattern (15 bp):   
GAAACAATTAAACAG
Done.