Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020580.1 Corchorus olitorius cultivar O-4 contig20613, 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: 12359
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35


Found at i:9663 original size:31 final size:31

Alignment explanation


    Indices: 9625--9689  Score: 121
    Period size: 31  Copynumber: 2.1  Consensus size: 31

       9615 TAAAGTGATA

                         *                 
       9625 TTTTTTTTTGGCATCAAAAGTGATATTTTAG
          1 TTTTTTTTTGGCACCAAAAGTGATATTTTAG

                                           
       9656 TTTTTTTTTGGCACCAAAAGTGATATTTTAG
          1 TTTTTTTTTGGCACCAAAAGTGATATTTTAG

               
       9687 TTT
          1 TTT

       9690 AGTTGGTAAG


Statistics
Matches: 33,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  31   33  1.00

ACGTcount: A:0.25, C:0.08, G:0.15, T:0.52


Consensus pattern (31 bp):   
TTTTTTTTTGGCACCAAAAGTGATATTTTAG

Found at i:10631 original size:124 final size:125

Alignment explanation


    Indices: 10410--10657  Score: 435
    Period size: 124  Copynumber: 2.0  Consensus size: 125

      10400 TACTCCCTCC

                                            *                                
      10410 CATTTAAAATAAGTGAAACATTTTAATTTTTGTAGTCTTTCAGTATAAGTGAAAAAATTACAACA
          1 CATTTAAAATAAGTGAAACATTTTAATTTTTGCAGTCTTTCAGTATAAGTGAAAAAATTACAACA

                                                                  *     
      10475 CCAATGCAATTTTACTCTTTTTTCCATATATACCCCCAAGTGTTAATTAAAGTGGTTGAA
         66 CCAATGCAATTTTACTCTTTTTTCCATATATACCCCCAAGTGTTAATTAAAGTGATTGAA

                                                                  *        * 
      10535 CATTTAAAATAAGTGAAACATTTTAATTTTTGCAGTCTTTC-GTATAAGTGAAACAATTACAAGA
          1 CATTTAAAATAAGTGAAACATTTTAATTTTTGCAGTCTTTCAGTATAAGTGAAAAAATTACAACA

                                                *           *          
      10599 CCAATGCAATTTTACTCTTTTTTCCATATATACCCCTAAGTGTTAATTGAAGTGATTGA
         66 CCAATGCAATTTTACTCTTTTTTCCATATATACCCCCAAGTGTTAATTAAAGTGATTGA

      10658 GCTTTTAGGT


Statistics
Matches: 117,  Mismatches: 6, Indels: 1
        0.94            0.05        0.01

Matches are distributed among these distances:
 124   77  0.66
 125   40  0.34

ACGTcount: A:0.36, C:0.15, G:0.12, T:0.38


Consensus pattern (125 bp):   
CATTTAAAATAAGTGAAACATTTTAATTTTTGCAGTCTTTCAGTATAAGTGAAAAAATTACAACA
CCAATGCAATTTTACTCTTTTTTCCATATATACCCCCAAGTGTTAATTAAAGTGATTGAA

Found at i:12047 original size:96 final size:96

Alignment explanation


    Indices: 11883--12075  Score: 368
    Period size: 96  Copynumber: 2.0  Consensus size: 96

      11873 GTATTGGCAT

                                                                             
      11883 AGTAGATAATAATTTGACATCTTGGCATGAAATAAAAGTGCCAAGCTAATTTCATTACTAATAAA
          1 AGTAGATAATAATTTGACATCTTGGCATGAAATAAAAGTGCCAAGCTAATTTCATTACTAATAAA

                                           
      11948 AGTGCCAAGCTCCTGTGGAGACAAAAATGGC
         66 AGTGCCAAGCTCCTGTGGAGACAAAAATGGC

                                                       *                     
      11979 AGTAGATAATAATTTGACATCTTGGCATGAAATAAAAGTGCCAGGCTAATTTCATTACTAATAAA
          1 AGTAGATAATAATTTGACATCTTGGCATGAAATAAAAGTGCCAAGCTAATTTCATTACTAATAAA

                        *                  
      12044 AGTGCCAAGCTCTTGTGGAGACAAAAATGGC
         66 AGTGCCAAGCTCCTGTGGAGACAAAAATGGC

             
      12075 A
          1 A

      12076 AAGTTTTGTC


Statistics
Matches: 95,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  96   95  1.00

ACGTcount: A:0.39, C:0.15, G:0.19, T:0.26


Consensus pattern (96 bp):   
AGTAGATAATAATTTGACATCTTGGCATGAAATAAAAGTGCCAAGCTAATTTCATTACTAATAAA
AGTGCCAAGCTCCTGTGGAGACAAAAATGGC

Found at i:12351 original size:30 final size:31

Alignment explanation


    Indices: 12297--12356  Score: 113
    Period size: 31  Copynumber: 2.0  Consensus size: 31

      12287 TAATATATAT

                                           
      12297 TGACACCAGAAGTTGTCAATGGCCTTGCAAA
          1 TGACACCAGAAGTTGTCAATGGCCTTGCAAA

                                          
      12328 TGACACCAGAAGTTGTC-ATGGCCTTGCAA
          1 TGACACCAGAAGTTGTCAATGGCCTTGCAA

      12357 TTG


Statistics
Matches: 29,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  30   12  0.41
  31   17  0.59

ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23


Consensus pattern (31 bp):   
TGACACCAGAAGTTGTCAATGGCCTTGCAAA
Done.