Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012299.1 Corchorus capsularis cultivar CVL-1 contig12320, 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: 1932
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30


Found at i:372 original size:14 final size:14

Alignment explanation


    Indices: 351--392  Score: 61
    Period size: 14  Copynumber: 3.1  Consensus size: 14

        341 AATGTGTGGT

                          
        351 GAAAAAAAGAA-AA
          1 GAAAAAAAGAAGAA

                           
        364 GAGAAAAAA-AAGAA
          1 GA-AAAAAAGAAGAA

                          
        378 GAAAAAAAGAAGAA
          1 GAAAAAAAGAAGAA

             
        392 G
          1 G

        393 GAAATGATAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 5
        0.84            0.00        0.16

Matches are distributed among these distances:
  13   10  0.38
  14   16  0.62

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


Consensus pattern (14 bp):   
GAAAAAAAGAAGAA

Found at i:380 original size:12 final size:12

Alignment explanation


    Indices: 355--391  Score: 51
    Period size: 11  Copynumber: 3.2  Consensus size: 12

        345 TGTGGTGAAA

                         
        355 AAAAGAAAAG-AG
          1 AAAA-AAAAGAAG

                        
        367 AAAAAAAAGAAG
          1 AAAAAAAAGAAG

                        
        379 -AAAAAAAGAAG
          1 AAAAAAAAGAAG

              
        390 AA
          1 AA

        392 GGAAATGATA


Statistics
Matches: 23,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  11   16  0.70
  12    7  0.30

ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00


Consensus pattern (12 bp):   
AAAAAAAAGAAG

Found at i:1557 original size:35 final size:35

Alignment explanation


    Indices: 1470--1930  Score: 657
    Period size: 35  Copynumber: 13.2  Consensus size: 35

       1460 CTGTGCGGTC

                       *                         
       1470 TTTCATAGAAGCTTTCAGAGGTCAGAGTTGATC-CAA
          1 TTTCA-AGAAGTTTTCAGAGGTCAGAGTTGATCTC-A

                                               
       1506 TTTC-A-AAGTTTTCAGAGGTCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

                                               
       1539 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

                                *               
       1574 -TTCTAAGAAGTTTTCAGAGTTCAGAGTTGATCTCA
          1 TTTC-AAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

                                                
       1609 TTTCAAGAAG-TTTCAAGAGGTCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTC-AGAGGTCAGAGTTGATCTCA

                                                
       1644 TTTCAAGAAG-TTTCAAGAGGTCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTC-AGAGGTCAGAGTTGATCTCA

                           *                    
       1679 TATT-AAGAAGTTTTAAGAGGTCAGAGTTGATCTCA
          1 T-TTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

              *                  *          *  
       1714 TTCCAAGAAGTTTTCAGAGGTTAGAGTTGATCACA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

              *    *                           
       1749 TTCCAAGGAGTTTTCAGAGGTCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

              *    *                           
       1784 TTCCAAGGAGTTTTCAGAGGTCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

              *    *                           
       1819 TTCCAAGGAGTTTTCAGAGGTCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

              *    *                           
       1854 TTCCAAGGAGTTTTCAGAGGTCAGAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

              *    *               *           
       1889 TTCCAAGCAGTTTTCAGAGGTCAAAGTTGATCTCA
          1 TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

              *    
       1924 TTGCAAG
          1 TTTCAAG

       1931 GA


Statistics
Matches: 402,  Mismatches: 14, Indels: 19
        0.92            0.03        0.04

Matches are distributed among these distances:
  33   29  0.07
  34   11  0.03
  35  350  0.87
  36   12  0.03

ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33


Consensus pattern (35 bp):   
TTTCAAGAAGTTTTCAGAGGTCAGAGTTGATCTCA

Done.