Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001360.1 Corchorus capsularis cultivar CVL-1 contig01360, 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: 3923
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35


Found at i:253 original size:20 final size:21

Alignment explanation


    Indices: 228--268  Score: 75
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        218 CGGCTCAGCC

                                 
        228 CCTAGATCT-ATTTTTTTACA
          1 CCTAGATCTAATTTTTTTACA

                                 
        248 CCTAGATCTAATTTTTTTACA
          1 CCTAGATCTAATTTTTTTACA

        269 TCCATTCCTC


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  20    9  0.45
  21   11  0.55

ACGTcount: A:0.27, C:0.20, G:0.05, T:0.49


Consensus pattern (21 bp):   
CCTAGATCTAATTTTTTTACA

Found at i:1550 original size:16 final size:16

Alignment explanation


    Indices: 1526--1564  Score: 51
    Period size: 16  Copynumber: 2.4  Consensus size: 16

       1516 ATTTTTGGGT

                *     *     
       1526 ACCCGAACCCGAAATG
          1 ACCCAAACCCAAAATG

             *              
       1542 ATCCAAACCCAAAATG
          1 ACCCAAACCCAAAATG

                   
       1558 ACCCAAA
          1 ACCCAAA

       1565 TCTGATCAAC


Statistics
Matches: 19,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  16   19  1.00

ACGTcount: A:0.46, C:0.36, G:0.10, T:0.08


Consensus pattern (16 bp):   
ACCCAAACCCAAAATG

Found at i:3229 original size:20 final size:20

Alignment explanation


    Indices: 3204--3243  Score: 62
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       3194 ATTAAATATT

                  *      *      
       3204 ATTAATCTTTGGGTGAATTA
          1 ATTAATATTTGGGGGAATTA

                                
       3224 ATTAATATTTGGGGGAATTA
          1 ATTAATATTTGGGGGAATTA

       3244 TCTTTGAATG


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.33, C:0.03, G:0.23, T:0.42


Consensus pattern (20 bp):   
ATTAATATTTGGGGGAATTA

Found at i:3753 original size:30 final size:32

Alignment explanation


    Indices: 3699--3764  Score: 109
    Period size: 31  Copynumber: 2.1  Consensus size: 32

       3689 AACTTTATGT

                 *                          
       3699 TTTCCGATTGTACCCTTATTTTTAAAAA-ATA
          1 TTTCCAATTGTACCCTTATTTTTAAAAACATA

                                            
       3730 TTTCCAATTGTACCCTT-TTTTTAAAAACATA
          1 TTTCCAATTGTACCCTTATTTTTAAAAACATA

                
       3761 TTTC
          1 TTTC

       3765 TAAATTGCCA


Statistics
Matches: 33,  Mismatches: 1, Indels: 2
        0.92            0.03        0.06

Matches are distributed among these distances:
  30   10  0.30
  31   23  0.70

ACGTcount: A:0.30, C:0.18, G:0.05, T:0.47


Consensus pattern (32 bp):   
TTTCCAATTGTACCCTTATTTTTAAAAACATA
Done.