Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010726.1 Corchorus capsularis cultivar CVL-1 contig10747, 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: 19538
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30


Found at i:6318 original size:27 final size:27

Alignment explanation


    Indices: 6278--6334  Score: 105
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       6268 GCATCGCTGA

                                       
       6278 AGAAAAGTACAAAAAGCCATTTTAATC
          1 AGAAAAGTACAAAAAGCCATTTTAATC

                     *                 
       6305 AGAAAAGTAGAAAAAGCCATTTTAATC
          1 AGAAAAGTACAAAAAGCCATTTTAATC

               
       6332 AGA
          1 AGA

       6335 GAGCTCACAA


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

Matches are distributed among these distances:
  27   29  1.00

ACGTcount: A:0.53, C:0.12, G:0.14, T:0.21


Consensus pattern (27 bp):   
AGAAAAGTACAAAAAGCCATTTTAATC

Found at i:10615 original size:28 final size:27

Alignment explanation


    Indices: 10542--10599  Score: 80
    Period size: 28  Copynumber: 2.0  Consensus size: 27

      10532 TTTTTTTGAA

                      *                  
      10542 AAAAAAAGAAAAGAAGAAAATGTTTTTTT
          1 AAAAAAA-AACAGAA-AAAATGTTTTTTT

                                        
      10571 AAAAAAAAACAGGAAAAAATGTTTTTTT
          1 AAAAAAAAACA-GAAAAAATGTTTTTTT

             
      10599 A
          1 A

      10600 TTAGAAAAAC


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  28   17  0.63
  29   10  0.37

ACGTcount: A:0.59, C:0.02, G:0.12, T:0.28


Consensus pattern (27 bp):   
AAAAAAAAACAGAAAAAATGTTTTTTT

Found at i:16538 original size:14 final size:14

Alignment explanation


    Indices: 16519--16545  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

      16509 AGTAATCAGT

                          
      16519 AAAAGTAAAAGAAC
          1 AAAAGTAAAAGAAC

                         
      16533 AAAAGTAAAAGAA
          1 AAAAGTAAAAGAA

      16546 GTGAAGAAGT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.74, C:0.04, G:0.15, T:0.07


Consensus pattern (14 bp):   
AAAAGTAAAAGAAC

Found at i:16822 original size:21 final size:21

Alignment explanation


    Indices: 16797--16854  Score: 71
    Period size: 21  Copynumber: 2.7  Consensus size: 21

      16787 AGTAACAGGT

                                 
      16797 AATCAGTAAGAGTAAAATAGC
          1 AATCAGTAAGAGTAAAATAGC

                        *     * *
      16818 AATCAGTAAGAGCAAAATGGT
          1 AATCAGTAAGAGTAAAATAGC

               *            
      16839 AATTAGTAAGGAGTAA
          1 AATCAGTAA-GAGTAA

      16855 TCAGTAAAGA


Statistics
Matches: 31,  Mismatches: 5, Indels: 1
        0.84            0.14        0.03

Matches are distributed among these distances:
  21   26  0.84
  22    5  0.16

ACGTcount: A:0.50, C:0.07, G:0.22, T:0.21


Consensus pattern (21 bp):   
AATCAGTAAGAGTAAAATAGC

Found at i:16965 original size:28 final size:27

Alignment explanation


    Indices: 16934--16993  Score: 66
    Period size: 27  Copynumber: 2.2  Consensus size: 27

      16924 GGTAACAAGT

                                   *    
      16934 GGTAATCAATAAAAGAGAGTAAGGAAAG
          1 GGTAATCAATAAAA-AGAGTAAGAAAAG

                  * *       *          
      16962 GGTAATTAGTAAAAAGCGTAAGAAAAG
          1 GGTAATCAATAAAAAGAGTAAGAAAAG

            *    
      16989 AGTAA
          1 GGTAA

      16994 AAATGATAAA


Statistics
Matches: 27,  Mismatches: 5, Indels: 1
        0.82            0.15        0.03

Matches are distributed among these distances:
  27   15  0.56
  28   12  0.44

ACGTcount: A:0.53, C:0.03, G:0.27, T:0.17


Consensus pattern (27 bp):   
GGTAATCAATAAAAAGAGTAAGAAAAG

Found at i:18268 original size:17 final size:19

Alignment explanation


    Indices: 18241--18278  Score: 53
    Period size: 17  Copynumber: 2.1  Consensus size: 19

      18231 TACTAACTAA

                       *       
      18241 TTTCTTTTGTTGTTT-GCT
          1 TTTCTTTTGTTCTTTCGCT

                               
      18259 TTTC-TTTGTTCTTTCGCT
          1 TTTCTTTTGTTCTTTCGCT

              
      18277 TT
          1 TT

      18279 GCATTTTGCA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  17    9  0.50
  18    9  0.50

ACGTcount: A:0.00, C:0.16, G:0.13, T:0.71


Consensus pattern (19 bp):   
TTTCTTTTGTTCTTTCGCT
Done.