Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009425.1 Corchorus capsularis cultivar CVL-1 contig09446, 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: 4540
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33


Found at i:786 original size:12 final size:12

Alignment explanation


    Indices: 766--797  Score: 55
    Period size: 12  Copynumber: 2.7  Consensus size: 12

        756 TTGCTTTTTT

                *       
        766 TATACATACATA
          1 TATATATACATA

                        
        778 TATATATACATA
          1 TATATATACATA

                    
        790 TATATATA
          1 TATATATA

        798 TTTTCTACTG


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  12   19  1.00

ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41


Consensus pattern (12 bp):   
TATATATACATA

Found at i:787 original size:16 final size:16

Alignment explanation


    Indices: 766--798  Score: 57
    Period size: 16  Copynumber: 2.1  Consensus size: 16

        756 TTGCTTTTTT

                            
        766 TATACATACATATATA
          1 TATACATACATATATA

                    *       
        782 TATACATATATATATA
          1 TATACATACATATATA

             
        798 T
          1 T

        799 TTTCTACTGT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42


Consensus pattern (16 bp):   
TATACATACATATATA

Found at i:1182 original size:22 final size:22

Alignment explanation


    Indices: 1140--1182  Score: 59
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       1130 AAGGGATAAG

                     *            
       1140 TGGAAAAAATGAAAAAAAATGA
          1 TGGAAAAAAAGAAAAAAAATGA

                        *   *    
       1162 TGGAAAAAAAGAGAAAGAATG
          1 TGGAAAAAAAGAAAAAAAATG

       1183 CTTAGAATGC


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  22   18  1.00

ACGTcount: A:0.65, C:0.00, G:0.23, T:0.12


Consensus pattern (22 bp):   
TGGAAAAAAAGAAAAAAAATGA

Found at i:1217 original size:19 final size:20

Alignment explanation


    Indices: 1179--1223  Score: 65
    Period size: 19  Copynumber: 2.2  Consensus size: 20

       1169 AAAGAGAAAG

                                  
       1179 AATGCTTAGAATGCTTTTTAAC
          1 AATGCTTAGAA--CTTTTTAAC

                                
       1201 AATGCTTAGAA-TTTTTAAC
          1 AATGCTTAGAACTTTTTAAC

                
       1220 AATG
          1 AATG

       1224 TTTTATTCAT


Statistics
Matches: 23,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  19   12  0.52
  22   11  0.48

ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40


Consensus pattern (20 bp):   
AATGCTTAGAACTTTTTAAC
Done.