Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015108.1 Corchorus olitorius cultivar O-4 contig15141, 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: 11836
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:428 original size:28 final size:28

Alignment explanation


    Indices: 360--436  Score: 93
    Period size: 28  Copynumber: 2.7  Consensus size: 28

        350 ACGTGAACTT

                          *    *       *
        360 AAAATGACCAAAATACCCCCGAATGTGC
          1 AAAATGACCAAAATGCCCCTGAATGTGA

                                        
        388 AAAATGACCAAAATGCCCCTGAATGT-A
          1 AAAATGACCAAAATGCCCCTGAATGTGA

                      *           
        415 AAAATGACTGAAAAATGCCCCT
          1 AAAATGAC--CAAAATGCCCCT

        437 ATGTGACTCT


Statistics
Matches: 43,  Mismatches: 4, Indels: 3
        0.86            0.08        0.06

Matches are distributed among these distances:
  27    8  0.19
  28   24  0.56
  29   11  0.26

ACGTcount: A:0.44, C:0.25, G:0.14, T:0.17


Consensus pattern (28 bp):   
AAAATGACCAAAATGCCCCTGAATGTGA

Found at i:6573 original size:27 final size:27

Alignment explanation


    Indices: 6543--6619  Score: 136
    Period size: 27  Copynumber: 2.9  Consensus size: 27

       6533 AGTGAACTTA

                                       
       6543 AAATGACCAAAATGCCCCTGAATATGC
          1 AAATGACCAAAATGCCCCTGAATATGC

                                  *    
       6570 AAATGACCAAAATGCCCCTGAACATGC
          1 AAATGACCAAAATGCCCCTGAATATGC

                   *               
       6597 AAATGACTAAAATGCCCCTGAAT
          1 AAATGACCAAAATGCCCCTGAAT

       6620 GACCCTAATG


Statistics
Matches: 47,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  27   47  1.00

ACGTcount: A:0.42, C:0.26, G:0.14, T:0.18


Consensus pattern (27 bp):   
AAATGACCAAAATGCCCCTGAATATGC

Found at i:11092 original size:25 final size:25

Alignment explanation


    Indices: 11064--11124  Score: 79
    Period size: 25  Copynumber: 2.4  Consensus size: 25

      11054 AGTTATCTAG

                                      
      11064 GTTTGGGCTTTTAGTTGGC-TTTTAT
          1 GTTTGGGCTTTTAGTT-GCATTTTAT

                    *       *         
      11089 GTTTGGGCCTTTAGTTTCAATTTTAT
          1 GTTTGGGCTTTTAGTTGC-ATTTTAT

                      
      11115 GTTTGGGCTT
          1 GTTTGGGCTT

      11125 ATAATATTTC


Statistics
Matches: 31,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
  24    1  0.03
  25   15  0.48
  26   15  0.48

ACGTcount: A:0.10, C:0.10, G:0.26, T:0.54


Consensus pattern (25 bp):   
GTTTGGGCTTTTAGTTGCATTTTAT

Found at i:11105 original size:13 final size:13

Alignment explanation


    Indices: 11064--11105  Score: 52
    Period size: 11  Copynumber: 3.3  Consensus size: 13

      11054 AGTTATCTAG

                         
      11064 GTTTGGGCTTTTA
          1 GTTTGGGCTTTTA

                         
      11077 G-TT-GGCTTTTA
          1 GTTTGGGCTTTTA

                     *    
      11088 TGTTTGGGCCTTTA
          1 -GTTTGGGCTTTTA

                
      11102 GTTT
          1 GTTT

      11106 CAATTTTATG


Statistics
Matches: 25,  Mismatches: 1, Indels: 6
        0.78            0.03        0.19

Matches are distributed among these distances:
  11    8  0.32
  12    3  0.12
  13    7  0.28
  14    7  0.28

ACGTcount: A:0.07, C:0.10, G:0.29, T:0.55


Consensus pattern (13 bp):   
GTTTGGGCTTTTA
Done.