Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011027.1 Corchorus capsularis cultivar CVL-1 contig11048, 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: 18473
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34


Found at i:1825 original size:2 final size:2

Alignment explanation


    Indices: 1818--1844  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       1808 TGTATGAAAG

                                                    
       1818 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

       1845 TTGAGAGTGA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:2022 original size:21 final size:21

Alignment explanation


    Indices: 1990--2040  Score: 95
    Period size: 21  Copynumber: 2.5  Consensus size: 21

       1980 TCGAATTGAA

                                 
       1990 AAATTG-AAAATGTAAGGACC
          1 AAATTGAAAAATGTAAGGACC

                                 
       2010 AAATTGAAAAATGTAAGGACC
          1 AAATTGAAAAATGTAAGGACC

                      
       2031 AAATTGAAAA
          1 AAATTGAAAA

       2041 CATTATTTGT


Statistics
Matches: 30,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  20    6  0.20
  21   24  0.80

ACGTcount: A:0.55, C:0.08, G:0.18, T:0.20


Consensus pattern (21 bp):   
AAATTGAAAAATGTAAGGACC

Found at i:12564 original size:40 final size:40

Alignment explanation


    Indices: 12508--12587  Score: 126
    Period size: 40  Copynumber: 2.0  Consensus size: 40

      12498 TTTCTAGATG

                                                     
      12508 TATGCTTTCCTCTTTTCATTGCT-AGATGTTCACAACTTAT
          1 TATGCTTTCCTCTTTTCATTG-TAAGATGTTCACAACTTAT

                       *     *                      
      12548 TATGCTTTCCTTTTTTCGTTGTAAGATGTTCACAACTTAT
          1 TATGCTTTCCTCTTTTCATTGTAAGATGTTCACAACTTAT

      12588 AATACAATGT


Statistics
Matches: 37,  Mismatches: 2, Indels: 2
        0.90            0.05        0.05

Matches are distributed among these distances:
  39    1  0.03
  40   36  0.97

ACGTcount: A:0.20, C:0.20, G:0.11, T:0.49


Consensus pattern (40 bp):   
TATGCTTTCCTCTTTTCATTGTAAGATGTTCACAACTTAT
Done.