Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004758.1 Corchorus capsularis cultivar CVL-1 contig04776, 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: 8080
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35


Found at i:3270 original size:11 final size:12

Alignment explanation


    Indices: 3238--3309  Score: 54
    Period size: 13  Copynumber: 5.4  Consensus size: 12

       3228 GATTAAAGCT

                        *
       3238 TATTATTACTATT
          1 TATTATTA-TATA

                          
       3251 TATTATTATTATTA
          1 TATTATTA-TA-TA

                        
       3265 TATTATTATATA
          1 TATTATTATATA

                  *     * 
       3277 TATATACTATACAA
          1 TAT-TATTATA-TA

                          
       3291 TATATATATATATA
          1 TAT-TAT-TATATA

                 
       3305 TATTA
          1 TATTA

       3310 CATATTATTT


Statistics
Matches: 49,  Mismatches: 6, Indels: 8
        0.78            0.10        0.13

Matches are distributed among these distances:
  12    5  0.10
  13   20  0.41
  14   20  0.41
  15    4  0.08

ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54


Consensus pattern (12 bp):   
TATTATTATATA

Found at i:3278 original size:2 final size:2

Alignment explanation


    Indices: 3263--3307  Score: 51
    Period size: 2  Copynumber: 23.5  Consensus size: 2

       3253 TTATTATTAT

                                                    *                      
       3263 TA TA T- TA T- TA TA TA TA TA TA CTA TA CA -A TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA

                   
       3303 TA TA T
          1 TA TA T

       3308 TACATATTAT


Statistics
Matches: 38,  Mismatches: 1, Indels: 8
        0.81            0.02        0.17

Matches are distributed among these distances:
   1    3  0.08
   2   33  0.87
   3    2  0.05

ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:4576 original size:27 final size:27

Alignment explanation


    Indices: 4525--4576  Score: 68
    Period size: 27  Copynumber: 1.9  Consensus size: 27

       4515 TACTCAACTT

                        *   **         
       4525 TTCCTACTCCTTTACATTACCAAACGA
          1 TTCCTACTCCTTAACAACACCAAACGA

                                *    
       4552 TTCCTACTCCTTAACAACACTAAAC
          1 TTCCTACTCCTTAACAACACCAAAC

       4577 TACACCAAAA


Statistics
Matches: 21,  Mismatches: 4, Indels: 0
        0.84            0.16        0.00

Matches are distributed among these distances:
  27   21  1.00

ACGTcount: A:0.33, C:0.35, G:0.02, T:0.31


Consensus pattern (27 bp):   
TTCCTACTCCTTAACAACACCAAACGA

Found at i:7476 original size:22 final size:22

Alignment explanation


    Indices: 7429--7476  Score: 78
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       7419 TTTTTTAATT

                              *  *
       7429 ACCATAAATAAACTACCTGCAG
          1 ACCATAAATAAACTACCTACAA

                                  
       7451 ACCATAAATAAACTACCTACAA
          1 ACCATAAATAAACTACCTACAA

                
       7473 ACCA
          1 ACCA

       7477 AATACACAAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  22   24  1.00

ACGTcount: A:0.50, C:0.29, G:0.04, T:0.17


Consensus pattern (22 bp):   
ACCATAAATAAACTACCTACAA
Done.