Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023631.1 Corchorus olitorius cultivar O-4 contig23664, 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: 14973
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:4632 original size:10 final size:10

Alignment explanation


    Indices: 4617--4656  Score: 64
    Period size: 10  Copynumber: 4.1  Consensus size: 10

       4607 TAGATGAAGA

                      
       4617 TCATCTTCAC
          1 TCATCTTCAC

                      
       4627 TCATCTTCAC
          1 TCATCTTCAC

                      
       4637 TCATCTTCAC
          1 TCATCTTCAC

                  *   
       4647 T-ATCTGCAC
          1 TCATCTTCAC

             
       4656 T
          1 T

       4657 AAAACATTCT


Statistics
Matches: 29,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
   9    8  0.28
  10   21  0.72

ACGTcount: A:0.20, C:0.38, G:0.03, T:0.40


Consensus pattern (10 bp):   
TCATCTTCAC

Found at i:8832 original size:2 final size:2

Alignment explanation


    Indices: 8825--8849  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       8815 CTCACAAATA

                                                 
       8825 GT GT GT GT GT GT GT GT GT GT GT GT G
          1 GT GT GT GT GT GT GT GT GT GT GT GT G

       8850 ATTACCAACA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

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


Consensus pattern (2 bp):   
GT

Found at i:10499 original size:41 final size:41

Alignment explanation


    Indices: 10454--10591  Score: 170
    Period size: 41  Copynumber: 3.4  Consensus size: 41

      10444 TTCTAAGTCC

                                                     
      10454 GGGACAAAATTGAATCAATGAATAAATAACAGCCTAAATTA
          1 GGGACAAAATTGAATCAATGAATAAATAACAGCCTAAATTA

                          *    *  *   * **       *  * 
      10495 GGGACAAAATTGAAGCAATTAACAAACATTA-CCTTAGATCA
          1 GGGACAAAATTGAATCAATGAATAAATAACAGCC-TAAATTA

                                                     
      10536 GGGACAAAATTGAATCAATGAATAAATAACAGCCTAAATTA
          1 GGGACAAAATTGAATCAATGAATAAATAACAGCCTAAATTA

                 **        
      10577 GGGACCCAATTGAAT
          1 GGGACAAAATTGAAT

      10592 GGAATCAAAC


Statistics
Matches: 77,  Mismatches: 18, Indels: 4
        0.78            0.18        0.04

Matches are distributed among these distances:
  40    2  0.03
  41   73  0.95
  42    2  0.03

ACGTcount: A:0.48, C:0.14, G:0.16, T:0.22


Consensus pattern (41 bp):   
GGGACAAAATTGAATCAATGAATAAATAACAGCCTAAATTA

Found at i:13061 original size:58 final size:61

Alignment explanation


    Indices: 12996--13114  Score: 217
    Period size: 61  Copynumber: 2.0  Consensus size: 61

      12986 CATACTTATA

                                                                         
      12996 TTCTAAATGCAACT-A-AAAAACATTTTTGCAAATGAC-AACTAATGTTAAATTGATGGAG
          1 TTCTAAATGCAACTAATAAAAACATTTTTGCAAATGACAAACTAATGTTAAATTGATGGAG

                                                                         
      13054 TTCTAAATGCAACTAATAAAAACATTTTTGCAAATGACAAACTAATGTTAAATTGATGGAG
          1 TTCTAAATGCAACTAATAAAAACATTTTTGCAAATGACAAACTAATGTTAAATTGATGGAG

      13115 GATTGCTAAA


Statistics
Matches: 58,  Mismatches: 0, Indels: 3
        0.95            0.00        0.05

Matches are distributed among these distances:
  58   14  0.24
  59    1  0.02
  60   21  0.36
  61   22  0.38

ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31


Consensus pattern (61 bp):   
TTCTAAATGCAACTAATAAAAACATTTTTGCAAATGACAAACTAATGTTAAATTGATGGAG

Found at i:14164 original size:16 final size:16

Alignment explanation


    Indices: 14143--14173  Score: 62
    Period size: 16  Copynumber: 1.9  Consensus size: 16

      14133 TGAATTTTTG

                            
      14143 AAACTTGATGAATGAA
          1 AAACTTGATGAATGAA

                           
      14159 AAACTTGATGAATGA
          1 AAACTTGATGAATGA

      14174 TGAATAAAAG


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.48, C:0.06, G:0.19, T:0.26


Consensus pattern (16 bp):   
AAACTTGATGAATGAA
Done.