Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004863.1 Corchorus capsularis cultivar CVL-1 contig04881, 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: 8583
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--50  Score: 100
    Period size: 2  Copynumber: 25.0  Consensus size: 2

                                                                          
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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

                       
         43 TA TA TA TA
          1 TA TA TA TA

         51 GACACACACA


Statistics
Matches: 48,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   48  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:1492 original size:13 final size:12

Alignment explanation


    Indices: 1445--1492  Score: 51
    Period size: 13  Copynumber: 3.8  Consensus size: 12

       1435 GTCAAACCCA

                         
       1445 TTTTTCTTTTTTC
          1 TTTTT-TTTTTTC

                    *    
       1458 TTTTTGTTGTTTC
          1 TTTTT-TTTTTTC

                         
       1471 TCTTTTTTTTTTC
          1 T-TTTTTTTTTTC

                *    
       1484 TTTTCTTTT
          1 TTTTTTTTT

       1493 CCTTATGCAA


Statistics
Matches: 30,  Mismatches: 4, Indels: 3
        0.81            0.11        0.08

Matches are distributed among these distances:
  12    7  0.23
  13   19  0.63
  14    4  0.13

ACGTcount: A:0.00, C:0.12, G:0.04, T:0.83


Consensus pattern (12 bp):   
TTTTTTTTTTTC

Found at i:6713 original size:23 final size:23

Alignment explanation


    Indices: 6667--6713  Score: 60
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       6657 TTATATATCT

                         *     *   
       6667 ATACTTAAGATTTTTTTCACTGA
          1 ATACTTAAGATTTATTTCAATGA

                                    
       6690 ATACTTAAGATTATATTT-AATGA
          1 ATACTTAAGATT-TATTTCAATGA

             
       6713 A
          1 A

       6714 ACATTCATTT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  23   17  0.81
  24    4  0.19

ACGTcount: A:0.38, C:0.09, G:0.09, T:0.45


Consensus pattern (23 bp):   
ATACTTAAGATTTATTTCAATGA

Found at i:7406 original size:14 final size:14

Alignment explanation


    Indices: 7387--7415  Score: 58
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       7377 GATTGAACAG

                          
       7387 ATCTATTCACGTGT
          1 ATCTATTCACGTGT

                          
       7401 ATCTATTCACGTGT
          1 ATCTATTCACGTGT

             
       7415 A
          1 A

       7416 AATCCATGTT


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:0.24, C:0.21, G:0.14, T:0.41


Consensus pattern (14 bp):   
ATCTATTCACGTGT
Done.