Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019935.1 Corchorus olitorius cultivar O-4 contig19968, 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: 3824
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35


Found at i:23 original size:2 final size:2

Alignment explanation


    Indices: 18--56  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

          8 CTACTACTCA

                                                                      
         18 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T

         57 ATATATATAT


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51


Consensus pattern (2 bp):   
TC

Found at i:61 original size:2 final size:2

Alignment explanation


    Indices: 56--86  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

         46 TCTCTCTCTC

                                                          
         56 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

         87 CTTGCAAAAC


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:2672 original size:55 final size:55

Alignment explanation


    Indices: 2583--2692  Score: 184
    Period size: 55  Copynumber: 2.0  Consensus size: 55

       2573 TGATAAACAT

                *                        *                         
       2583 GTAAGTATTAATATGGTAGATATTGATGGGAGGGAAATAACTAACAAAATTTTGA
          1 GTAACTATTAATATGGTAGATATTGATGGAAGGGAAATAACTAACAAAATTTTGA

                        *        *                                 
       2638 GTAACTATTAATTTGGTAGATTTTGATGGAAGGGAAATAACTAACAAAATTTTGA
          1 GTAACTATTAATATGGTAGATATTGATGGAAGGGAAATAACTAACAAAATTTTGA

       2693 ATAAGTTGAC


Statistics
Matches: 51,  Mismatches: 4, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  55   51  1.00

ACGTcount: A:0.41, C:0.05, G:0.22, T:0.33


Consensus pattern (55 bp):   
GTAACTATTAATATGGTAGATATTGATGGAAGGGAAATAACTAACAAAATTTTGA

Found at i:3541 original size:2 final size:2

Alignment explanation


    Indices: 3534--3568  Score: 56
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       3524 ATTATTTTGC

                                                                   
       3534 TA TA TA TA TA TA TA T- TA TA T- TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       3569 GATACATCAG


Statistics
Matches: 31,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
   1    2  0.06
   2   29  0.94

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (2 bp):   
TA

Found at i:3757 original size:2 final size:2

Alignment explanation


    Indices: 3750--3789  Score: 80
    Period size: 2  Copynumber: 20.0  Consensus size: 2

       3740 ATAACTATCC

                                                                       
       3750 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       3790 TAGAGAGAGA


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   38  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:3796 original size:2 final size:2

Alignment explanation


    Indices: 3791--3824  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       3781 TATATATATT

                                                              
       3791 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00


Consensus pattern (2 bp):   
AG

Done.