Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024745.1 Corchorus olitorius cultivar O-4 contig24778, 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: 26194
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33


Found at i:634 original size:26 final size:27

Alignment explanation


    Indices: 575--637  Score: 78
    Period size: 26  Copynumber: 2.3  Consensus size: 27

        565 CTAAATTTTC

                                        
        575 ATTATTTTAATAATGGAATAATTAAAAT
          1 ATTA-TTTAATAATGGAATAATTAAAAT

                                        
        603 ATTATTTAATAAT-G-ATAATTTAAAA-
          1 ATTATTTAATAATGGAATAA-TTAAAAT

                      
        628 ATATATTTAA
          1 AT-TATTTAA

        638 AAAAAAAGAT


Statistics
Matches: 33,  Mismatches: 0, Indels: 6
        0.85            0.00        0.15

Matches are distributed among these distances:
  25    6  0.18
  26   14  0.42
  27    9  0.27
  28    4  0.12

ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44


Consensus pattern (27 bp):   
ATTATTTAATAATGGAATAATTAAAAT

Found at i:2446 original size:7 final size:7

Alignment explanation


    Indices: 2434--2460  Score: 54
    Period size: 7  Copynumber: 3.9  Consensus size: 7

       2424 ATTCAATTTA

                   
       2434 CTATAGT
          1 CTATAGT

                   
       2441 CTATAGT
          1 CTATAGT

                   
       2448 CTATAGT
          1 CTATAGT

                  
       2455 CTATAG
          1 CTATAG

       2461 GTAGAGAGAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   20  1.00

ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41


Consensus pattern (7 bp):   
CTATAGT

Found at i:2737 original size:130 final size:131

Alignment explanation


    Indices: 2590--2853  Score: 422
    Period size: 130  Copynumber: 2.0  Consensus size: 131

       2580 TTGTTTAAAC

                   *          *                       *                      
       2590 TTTTATAGTTTTACTCAATTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
          1 TTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATCAAATCTAATATCCTTATAACTA

                                  *                               *  **      
       2655 TTTTATTTTTACCATTTTACTATTTTAATTAAAAAAACTT-ATATATTAGAATTTTTTTAATATA
         66 TTTTATTTTTACCATTTTACTAATTTAATTAAAAAAACTTAATATATTAGAATTGTTAGAATATA

             
       2719 T
        131 T

                                                                   *     *   
       2720 TTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATCAAATCTAATATCTTTATACCTA
          1 TTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATCAAATCTAATATCCTTATAACTA

                        *                                                    
       2785 TTTTATTTTTACTATTTTACTAATTTAATTAAAAAAACTTAGATATATTAGAATTGTTAGAATAT
         66 TTTTATTTTTACCATTTTACTAATTTAATTAAAAAAACTTA-ATATATTAGAATTGTTAGAATAT

              
       2850 AT
        130 AT

              
       2852 TT
          1 TT

       2854 CTTAAATAAC


Statistics
Matches: 122,  Mismatches: 10, Indels: 2
        0.91            0.07        0.01

Matches are distributed among these distances:
 130   98  0.80
 132   24  0.20

ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51


Consensus pattern (131 bp):   
TTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATCAAATCTAATATCCTTATAACTA
TTTTATTTTTACCATTTTACTAATTTAATTAAAAAAACTTAATATATTAGAATTGTTAGAATATA
T

Found at i:13575 original size:48 final size:47

Alignment explanation


    Indices: 13513--13633  Score: 145
    Period size: 48  Copynumber: 2.5  Consensus size: 47

      13503 AATTTTGTCC

                     *      *          *    *            ** 
      13513 AAAAATTGATAAAAAGAGCAAGGAAAATTAAATATTCAATTCTGTCTT
          1 AAAAATTGAGAAAAAGTGC-AGGAAAAATAAAGATTCAATTCTGTAGT

                                                      *      
      13561 AAAAATTGAGAAAAAGGTGC-GAGAAAAATAAAGATTCAATTTTGTAGT
          1 AAAAATTGAGAAAAA-GTGCAG-GAAAAATAAAGATTCAATTCTGTAGT

                                     
      13609 AAAAATTGAGAAAAAGTGCAGGAAA
          1 AAAAATTGAGAAAAAGTGCAGGAAA

      13634 TGTAATAGAT


Statistics
Matches: 63,  Mismatches: 7, Indels: 7
        0.82            0.09        0.09

Matches are distributed among these distances:
  47    9  0.14
  48   51  0.81
  49    3  0.05

ACGTcount: A:0.52, C:0.06, G:0.18, T:0.24


Consensus pattern (47 bp):   
AAAAATTGAGAAAAAGTGCAGGAAAAATAAAGATTCAATTCTGTAGT

Done.