Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009040.1 Corchorus capsularis cultivar CVL-1 contig09061, 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, 637

Length: 1063
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32


Found at i:844 original size:12 final size:11

Alignment explanation


    Indices: 827--868  Score: 52
    Period size: 12  Copynumber: 3.9  Consensus size: 11

        817 AGTTGCCCAA

                        
        827 AAAAAAAAAGTG
          1 AAAAAAAAAG-G

                       
        839 AAAAAAAAAGG
          1 AAAAAAAAAGG

                      *
        850 --AAAAAAAGA
          1 AAAAAAAAAGG

                      
        859 AAAAAAAAAG
          1 AAAAAAAAAG

        869 AATTGTGACA


Statistics
Matches: 27,  Mismatches: 1, Indels: 5
        0.82            0.03        0.15

Matches are distributed among these distances:
   9    8  0.30
  11    9  0.33
  12   10  0.37

ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02


Consensus pattern (11 bp):   
AAAAAAAAAGG

Found at i:855 original size:21 final size:20

Alignment explanation


    Indices: 829--868  Score: 62
    Period size: 20  Copynumber: 1.9  Consensus size: 20

        819 TTGCCCAAAA

                     *           
        829 AAAAAAAGTGAAAAAAAAAGG
          1 AAAAAAAG-AAAAAAAAAAGG

                               
        850 AAAAAAAGAAAAAAAAAAG
          1 AAAAAAAGAAAAAAAAAAG

        869 AATTGTGACA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  20   10  0.56
  21    8  0.44

ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03


Consensus pattern (20 bp):   
AAAAAAAGAAAAAAAAAAGG

Found at i:953 original size:14 final size:15

Alignment explanation


    Indices: 936--973  Score: 60
    Period size: 14  Copynumber: 2.6  Consensus size: 15

        926 TCGAAAAAAA

                  *        
        936 TTTCAAGAAAATG-C
          1 TTTCAAAAAAATGAC

                           
        950 TTTCAAAAAAATGAC
          1 TTTCAAAAAAATGAC

                     
        965 TTTCAAAAA
          1 TTTCAAAAA

        974 TGAGTTTTCA


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  14   12  0.55
  15   10  0.45

ACGTcount: A:0.50, C:0.13, G:0.08, T:0.29


Consensus pattern (15 bp):   
TTTCAAAAAAATGAC

Found at i:987 original size:15 final size:14

Alignment explanation


    Indices: 936--987  Score: 54
    Period size: 14  Copynumber: 3.6  Consensus size: 14

        926 TCGAAAAAAA

                           
        936 TTTCAAGAAAATG-C
          1 TTTCAA-AAAATGAC

                           
        950 TTTCAAAAAAATGAC
          1 TTTC-AAAAAATGAC

                          *
        965 TTTC-AAAAATGAGT
          1 TTTCAAAAAATGA-C

                     
        979 TTTCAAAAA
          1 TTTCAAAAA

        988 GGTTTTCAGT


Statistics
Matches: 33,  Mismatches: 1, Indels: 7
        0.80            0.02        0.17

Matches are distributed among these distances:
  13    8  0.24
  14   14  0.42
  15   11  0.33

ACGTcount: A:0.48, C:0.12, G:0.10, T:0.31


Consensus pattern (14 bp):   
TTTCAAAAAATGAC

Found at i:994 original size:12 final size:14

Alignment explanation


    Indices: 956--995  Score: 50
    Period size: 13  Copynumber: 3.1  Consensus size: 14

        946 ATGCTTTCAA

                     *    
        956 AAAAATGA-CTTTC
          1 AAAAATGAGTTTTC

                          
        969 AAAAATGAGTTTTC
          1 AAAAATGAGTTTTC

                          
        983 AAAAA-G-GTTTTC
          1 AAAAATGAGTTTTC

             
        995 A
          1 A

        996 GTTTTCAAAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  12    7  0.28
  13    9  0.36
  14    9  0.36

ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33


Consensus pattern (14 bp):   
AAAAATGAGTTTTC
Done.