Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008896.1 Corchorus capsularis cultivar CVL-1 contig08917, 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: 10962
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:1621 original size:12 final size:13

Alignment explanation


    Indices: 1606--1639  Score: 52
    Period size: 12  Copynumber: 2.7  Consensus size: 13

       1596 AATCTAAATC

                   *     
       1606 TAAAGCAGATT-A
          1 TAAAGCAAATTAA

                         
       1618 TAAAGCAAATTAA
          1 TAAAGCAAATTAA

                     
       1631 TAAAGCAAA
          1 TAAAGCAAA

       1640 CAATAATTAA


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

Matches are distributed among these distances:
  12   10  0.50
  13   10  0.50

ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21


Consensus pattern (13 bp):   
TAAAGCAAATTAA

Found at i:6944 original size:8 final size:9

Alignment explanation


    Indices: 6933--6980  Score: 64
    Period size: 10  Copynumber: 5.3  Consensus size: 9

       6923 AGTCAACCAT

                     
       6933 TATTATAT-
          1 TATTATATA

                      
       6941 TATTACTATA
          1 TATTA-TATA

                     
       6951 TATTATATA
          1 TATTATATA

                     
       6960 TA-TATATA
          1 TATTATATA

                      
       6968 TATATATATA
          1 TAT-TATATA

               
       6978 TAT
          1 TAT

       6981 CCAACTATCT


Statistics
Matches: 36,  Mismatches: 0, Indels: 6
        0.86            0.00        0.14

Matches are distributed among these distances:
   8   13  0.36
   9    9  0.25
  10   14  0.39

ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54


Consensus pattern (9 bp):   
TATTATATA

Found at i:6959 original size:2 final size:2

Alignment explanation


    Indices: 6947--6980  Score: 61
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       6937 ATATTATTAC

                                                                
       6947 TA TA TA T- 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 TA TA TA TA T

       6981 CCAACTATCT


Statistics
Matches: 31,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   1    1  0.03
   2   30  0.97

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
TA

Found at i:7014 original size:17 final size:18

Alignment explanation


    Indices: 6992--7030  Score: 53
    Period size: 17  Copynumber: 2.2  Consensus size: 18

       6982 CAACTATCTC

                       *      
       6992 AAAAAAAAAAGTAAA-AA
          1 AAAAAAAAAAGGAAAGAA

                  *           
       7009 AAAAAACAAAGGAAAGAA
          1 AAAAAAAAAAGGAAAGAA

                
       7027 AAAA
          1 AAAA

       7031 GTGCAAAATT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  17   13  0.68
  18    6  0.32

ACGTcount: A:0.85, C:0.03, G:0.10, T:0.03


Consensus pattern (18 bp):   
AAAAAAAAAAGGAAAGAA
Done.