Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013543.1 Corchorus olitorius cultivar O-4 contig13576, 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: 17045
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:7729 original size:21 final size:22

Alignment explanation


    Indices: 7689--7729  Score: 57
    Period size: 21  Copynumber: 1.9  Consensus size: 22

       7679 GACAAACTCG

                           *      
       7689 TAACCCGAATAACCCGAGAAGA
          1 TAACCCGAATAACCCAAGAAGA

                      *         
       7711 TAACCCG-ATGACCCAAGAA
          1 TAACCCGAATAACCCAAGAA

       7730 TATTATGAAC


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  21   10  0.59
  22    7  0.41

ACGTcount: A:0.44, C:0.29, G:0.17, T:0.10


Consensus pattern (22 bp):   
TAACCCGAATAACCCAAGAAGA

Found at i:9583 original size:2 final size:2

Alignment explanation


    Indices: 9576--9631  Score: 94
    Period size: 2  Copynumber: 27.5  Consensus size: 2

       9566 ACTTTAGTAA

                                                                       *   
       9576 AT AT AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT
          1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                               
       9619 AT AT AT AT AT AT A
          1 AT AT AT AT AT AT A

       9632 AAACTTTTTA


Statistics
Matches: 51,  Mismatches: 2, Indels: 2
        0.93            0.04        0.04

Matches are distributed among these distances:
   2   49  0.96
   3    2  0.04

ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46


Consensus pattern (2 bp):   
AT

Found at i:11412 original size:14 final size:14

Alignment explanation


    Indices: 11393--11423  Score: 62
    Period size: 14  Copynumber: 2.2  Consensus size: 14

      11383 TAAAGTATTG

                          
      11393 ATATTATTAAATAA
          1 ATATTATTAAATAA

                          
      11407 ATATTATTAAATAA
          1 ATATTATTAAATAA

               
      11421 ATA
          1 ATA

      11424 AATAAAAATA


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   17  1.00

ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42


Consensus pattern (14 bp):   
ATATTATTAAATAA

Found at i:11432 original size:10 final size:10

Alignment explanation


    Indices: 11419--11460  Score: 66
    Period size: 10  Copynumber: 4.0  Consensus size: 10

      11409 ATTATTAAAT

                      
      11419 AAATAAATAA
          1 AAATAAATAA

                      
      11429 AAATAAATAA
          1 AAATAAATAA

                       
      11439 AAATAAATAAA
          1 AAATAAAT-AA

                       
      11450 TAAATAAATAA
          1 -AAATAAATAA

      11461 TTTTTTATAA


Statistics
Matches: 30,  Mismatches: 0, Indels: 3
        0.91            0.00        0.09

Matches are distributed among these distances:
  10   18  0.60
  11    4  0.13
  12    8  0.27

ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21


Consensus pattern (10 bp):   
AAATAAATAA

Found at i:11432 original size:14 final size:14

Alignment explanation


    Indices: 11415--11457  Score: 70
    Period size: 14  Copynumber: 3.1  Consensus size: 14

      11405 AAATATTATT

                          
      11415 AAATAAATAAATAA
          1 AAATAAATAAATAA

                          
      11429 AAATAAATAAA-AA
          1 AAATAAATAAATAA

                           
      11442 TAAATAAATAAATAA
          1 -AAATAAATAAATAA

             
      11457 A
          1 A

      11458 TAATTTTTTA


Statistics
Matches: 27,  Mismatches: 0, Indels: 4
        0.87            0.00        0.13

Matches are distributed among these distances:
  13    2  0.07
  14   23  0.85
  15    2  0.07

ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21


Consensus pattern (14 bp):   
AAATAAATAAATAA

Found at i:11450 original size:32 final size:32

Alignment explanation


    Indices: 11400--11460  Score: 95
    Period size: 32  Copynumber: 1.9  Consensus size: 32

      11390 TTGATATTAT

                    *  * *                  
      11400 TAAATAAATATTATTAAATAAATAAATAAAAA
          1 TAAATAAAAATAAATAAATAAATAAATAAAAA

                                         
      11432 TAAATAAAAATAAATAAATAAATAAATAA
          1 TAAATAAAAATAAATAAATAAATAAATAA

      11461 TTTTTTATAA


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  32   26  1.00

ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28


Consensus pattern (32 bp):   
TAAATAAAAATAAATAAATAAATAAATAAAAA

Found at i:11474 original size:4 final size:4

Alignment explanation


    Indices: 11400--11460  Score: 67
    Period size: 4  Copynumber: 15.8  Consensus size: 4

      11390 TTGATATTAT

                           *                                             
      11400 TAAA TAAA TATTAT TAAA TAAA TAAA T-AA -AAA TAAA T-AA -AAA TAAA
          1 TAAA TAAA TA--AA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA

                              
      11446 TAAA TAAA TAAA TAA
          1 TAAA TAAA TAAA TAA

      11461 TTTTTTATAA


Statistics
Matches: 49,  Mismatches: 2, Indels: 12
        0.78            0.03        0.19

Matches are distributed among these distances:
   3    8  0.16
   4   38  0.78
   6    3  0.06

ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28


Consensus pattern (4 bp):   
TAAA
Done.