Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007061.1 Corchorus capsularis cultivar CVL-1 contig07082, 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: 14696
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:5599 original size:18 final size:19

Alignment explanation


    Indices: 5564--5603  Score: 64
    Period size: 18  Copynumber: 2.2  Consensus size: 19

       5554 TAGAAGATTT

                               
       5564 ATTGAAGATAATTTGAAGA
          1 ATTGAAGATAATTTGAAGA

                     *         
       5583 ATTGAAGATCA-TTGAAGA
          1 ATTGAAGATAATTTGAAGA

               
       5601 ATT
          1 ATT

       5604 ATTTCAAGAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  18   10  0.50
  19   10  0.50

ACGTcount: A:0.45, C:0.03, G:0.20, T:0.33


Consensus pattern (19 bp):   
ATTGAAGATAATTTGAAGA

Found at i:6651 original size:14 final size:13

Alignment explanation


    Indices: 6628--6670  Score: 52
    Period size: 13  Copynumber: 3.2  Consensus size: 13

       6618 TAATGCACCC

                         
       6628 AAAACATTTAATA
          1 AAAACATTTAATA

                          
       6641 AAAATCATTT-ATA
          1 AAAA-CATTTAATA

                       *  
       6654 AAAACAATTTATTA
          1 AAAAC-ATTTAATA

               
       6668 AAA
          1 AAA

       6671 GTAGTAATAA


Statistics
Matches: 26,  Mismatches: 1, Indels: 5
        0.81            0.03        0.16

Matches are distributed among these distances:
  12    1  0.04
  13   15  0.58
  14   10  0.38

ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33


Consensus pattern (13 bp):   
AAAACATTTAATA

Found at i:8873 original size:21 final size:21

Alignment explanation


    Indices: 8825--8873  Score: 53
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       8815 GGCGCTGGTG

                      ** *      *
       8825 ACATGGGTGCTGAGGCCAACG
          1 ACATGGGTGCACAAGCCAACC

              *                  
       8846 ACCTGGGTGCACAAGCCAACC
          1 ACATGGGTGCACAAGCCAACC

                   
       8867 ACATGGG
          1 ACATGGG

       8874 CACCCAGGGG


Statistics
Matches: 22,  Mismatches: 6, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.27, C:0.29, G:0.33, T:0.12


Consensus pattern (21 bp):   
ACATGGGTGCACAAGCCAACC

Found at i:11649 original size:21 final size:21

Alignment explanation


    Indices: 11610--11658  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

      11600 TCAATGCTTT

                         **       
      11610 AGGAATGCAAGAGGGATTTCAA
          1 AGGAA-GCAAGAGCCATTTCAA

                               * 
      11632 AGGAAGCAAGAGCCATTTCCA
          1 AGGAAGCAAGAGCCATTTCAA

                   
      11653 A-GAAGC
          1 AGGAAGC

      11659 TACAATTCTT


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  20    5  0.21
  21   14  0.58
  22    5  0.21

ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14


Consensus pattern (21 bp):   
AGGAAGCAAGAGCCATTTCAA
Done.