Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020087.1 Corchorus olitorius cultivar O-4 contig20120, 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: 15107
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:307 original size:29 final size:31

Alignment explanation


    Indices: 233--299  Score: 111
    Period size: 31  Copynumber: 2.2  Consensus size: 31

        223 CCTAACGGAC

                                           
        233 TATATCCTTAATTGCTCGCTTTTCGTAACGT
          1 TATATCCTTAATTGCTCGCTTTTCGTAACGT

                            *              
        264 TATATCCTTAATTGCTTG-TTTT-GTAACGT
          1 TATATCCTTAATTGCTCGCTTTTCGTAACGT

                   
        293 TATATCC
          1 TATATCC

        300 CAAATTGCAT


Statistics
Matches: 35,  Mismatches: 1, Indels: 2
        0.92            0.03        0.05

Matches are distributed among these distances:
  29   14  0.40
  30    4  0.11
  31   17  0.49

ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48


Consensus pattern (31 bp):   
TATATCCTTAATTGCTCGCTTTTCGTAACGT

Found at i:554 original size:2 final size:2

Alignment explanation


    Indices: 547--608  Score: 51
    Period size: 2  Copynumber: 32.5  Consensus size: 2

        537 CGACCAACTT

                                  *                                       *
        547 TA TA TA TA TA TA TA TG TA TA TA TA T- TA TA TA TA -A TA GT- TT
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA

             *        *                       
        587 TT TA TA TT TA TA TA T- TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA T

        609 TAATCAATAA


Statistics
Matches: 50,  Mismatches: 5, Indels: 10
        0.77            0.08        0.15

Matches are distributed among these distances:
   1    4  0.08
   2   45  0.90
   3    1  0.02

ACGTcount: A:0.40, C:0.00, G:0.03, T:0.56


Consensus pattern (2 bp):   
TA

Found at i:2428 original size:21 final size:21

Alignment explanation


    Indices: 2404--2443  Score: 71
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       2394 TGGAATATGG

                                 
       2404 ATTCTGAAATATGGATTCTGA
          1 ATTCTGAAATATGGATTCTGA

                          *    
       2425 ATTCTGAAATATGGGTTCT
          1 ATTCTGAAATATGGATTCT

       2444 CTATGTATAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40


Consensus pattern (21 bp):   
ATTCTGAAATATGGATTCTGA

Found at i:2443 original size:14 final size:14

Alignment explanation


    Indices: 2397--2425  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       2387 ACTGTTTTGG

                          
       2397 AATATGGATTCTGA
          1 AATATGGATTCTGA

                          
       2411 AATATGGATTCTGA
          1 AATATGGATTCTGA

             
       2425 A
          1 A

       2426 TTCTGAAATA


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

Matches are distributed among these distances:
  14   15  1.00

ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34


Consensus pattern (14 bp):   
AATATGGATTCTGA

Found at i:6463 original size:12 final size:12

Alignment explanation


    Indices: 6446--6471  Score: 52
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       6436 ACTTATCAAT

                        
       6446 AATTTTGCTAGA
          1 AATTTTGCTAGA

                        
       6458 AATTTTGCTAGA
          1 AATTTTGCTAGA

              
       6470 AA
          1 AA

       6472 AACAATTAAT


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   14  1.00

ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38


Consensus pattern (12 bp):   
AATTTTGCTAGA

Found at i:9718 original size:102 final size:101

Alignment explanation


    Indices: 9542--9745  Score: 390
    Period size: 102  Copynumber: 2.0  Consensus size: 101

       9532 GGGAAATAAT

                                                                             
       9542 AAACGTTAGACCAGATTCTGGCAAAAAAAAAACATTAAACCAGATTCAACCAAGATGAAGAAACC
          1 AAACGTTAGACCAGATTCTGGCAAAAAAAAAACATTAAACCAGATTCAACCAAGATGAAGAAACC

                                                 
       9607 AAGCAGATCAAGCAAGAATAAACACCTTCAGACCAAA
         66 AAGCAGATCAAGCAAGAATAAACACCTTCAGA-CAAA

                                                 *                           
       9644 AAACGTTAGACCAGATTCTGGCAAAAAAAAAACATTAGACCAGATTCAACCAAGATGAAGAAACC
          1 AAACGTTAGACCAGATTCTGGCAAAAAAAAAACATTAAACCAGATTCAACCAAGATGAAGAAACC

                                                
       9709 AAGCAGATCAAGCAAGAATAAACACCTTCAGACAAA
         66 AAGCAGATCAAGCAAGAATAAACACCTTCAGACAAA

             
       9745 A
          1 A

       9746 GACCAAACAG


Statistics
Matches: 101,  Mismatches: 1, Indels: 1
        0.98            0.01        0.01

Matches are distributed among these distances:
 101    5  0.05
 102   96  0.95

ACGTcount: A:0.51, C:0.21, G:0.14, T:0.14


Consensus pattern (101 bp):   
AAACGTTAGACCAGATTCTGGCAAAAAAAAAACATTAAACCAGATTCAACCAAGATGAAGAAACC
AAGCAGATCAAGCAAGAATAAACACCTTCAGACAAA
Done.