Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010773.1 Corchorus olitorius cultivar O-4 contig10805, 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: 27512
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31


Found at i:12195 original size:29 final size:29

Alignment explanation


    Indices: 12163--12233  Score: 81
    Period size: 29  Copynumber: 2.4  Consensus size: 29

      12153 AAAATATCCC

                                  *       
      12163 TTTTTTTATTTTTCCTTTAGACTA-TTACA
          1 TTTTTTTATTTTT-CTTTAGACAAGTTACA

                    *        *  *        
      12192 TTTTTTTAATTTTCTTTGGAGAAGTTACA
          1 TTTTTTTATTTTTCTTTAGACAAGTTACA

                  *      
      12221 TTTTTTAATTTTT
          1 TTTTTTTATTTTT

      12234 ATTATCTTAA


Statistics
Matches: 35,  Mismatches: 6, Indels: 2
        0.81            0.14        0.05

Matches are distributed among these distances:
  28    7  0.20
  29   28  0.80

ACGTcount: A:0.21, C:0.08, G:0.07, T:0.63


Consensus pattern (29 bp):   
TTTTTTTATTTTTCTTTAGACAAGTTACA

Found at i:12208 original size:28 final size:30

Alignment explanation


    Indices: 12163--12232  Score: 83
    Period size: 28  Copynumber: 2.4  Consensus size: 30

      12153 AAAATATCCC

                    *             *       
      12163 TTTTTTTATTTTTCCTTTAGACTA-TTACA
          1 TTTTTTTAATTTTCCTTTAGACAAGTTACA

                              *  *        
      12192 TTTTTTTAATTTT-CTTTGGAGAAGTTACA
          1 TTTTTTTAATTTTCCTTTAGACAAGTTACA

                         
      12221 -TTTTTTAATTTT
          1 TTTTTTTAATTTT

      12233 TATTATCTTA


Statistics
Matches: 36,  Mismatches: 4, Indels: 3
        0.84            0.09        0.07

Matches are distributed among these distances:
  28   19  0.53
  29   17  0.47

ACGTcount: A:0.21, C:0.09, G:0.07, T:0.63


Consensus pattern (30 bp):   
TTTTTTTAATTTTCCTTTAGACAAGTTACA

Found at i:13644 original size:25 final size:24

Alignment explanation


    Indices: 13623--13669  Score: 62
    Period size: 25  Copynumber: 2.0  Consensus size: 24

      13613 TTACATTTAC

                                    
      13623 ATTT-ACATTTGTAAAAGACA-TT
          1 ATTTAACATTTGTAAAAGACATTT

                                     
      13645 ATTTCAAACATTTGTAAAAGACATT
          1 ATTT--AACATTTGTAAAAGACATT

      13670 AAAGTTGGGC


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  22    4  0.19
  25   16  0.76
  26    1  0.05

ACGTcount: A:0.43, C:0.11, G:0.09, T:0.38


Consensus pattern (24 bp):   
ATTTAACATTTGTAAAAGACATTT

Found at i:23863 original size:6 final size:6

Alignment explanation


    Indices: 23854--23880  Score: 54
    Period size: 6  Copynumber: 4.5  Consensus size: 6

      23844 CAGTATGTTT

                                           
      23854 TCTTTC TCTTTC TCTTTC TCTTTC TCT
          1 TCTTTC TCTTTC TCTTTC TCTTTC TCT

      23881 ATTTTGCTTC


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   21  1.00

ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67


Consensus pattern (6 bp):   
TCTTTC

Done.