Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004516.1 Corchorus capsularis cultivar CVL-1 contig04527, 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, 623

Length: 1039
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37


Found at i:645 original size:13 final size:13

Alignment explanation


    Indices: 627--651  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

        617 ATTCTTAATT

                         
        627 TTATTTATTATTC
          1 TTATTTATTATTC

                        
        640 TTATTTATTATT
          1 TTATTTATTATT

        652 GCTGCTATAG


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72


Consensus pattern (13 bp):   
TTATTTATTATTC

Found at i:868 original size:20 final size:21

Alignment explanation


    Indices: 843--884  Score: 77
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        833 ACATTATGAT

                                 
        843 AAAAT-AACATATAAAAAATA
          1 AAAATAAACATATAAAAAATA

                                 
        863 AAAATAAACATATAAAAAATA
          1 AAAATAAACATATAAAAAATA

             
        884 A
          1 A

        885 GAAAAATAGT


Statistics
Matches: 21,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  20    5  0.24
  21   16  0.76

ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19


Consensus pattern (21 bp):   
AAAATAAACATATAAAAAATA

Found at i:967 original size:13 final size:12

Alignment explanation


    Indices: 951--991  Score: 50
    Period size: 13  Copynumber: 3.4  Consensus size: 12

        941 TTTTTGTATT

                         
        951 TTTTTTAATAGTC
          1 TTTTTTAATA-TC

                        
        964 TTTTTTAATA--
          1 TTTTTTAATATC

                         
        974 TTTTTTAATATTC
          1 TTTTTTAATA-TC

                 
        987 TTTTT
          1 TTTTT

        992 CTAAAACATT


Statistics
Matches: 25,  Mismatches: 0, Indels: 6
        0.81            0.00        0.19

Matches are distributed among these distances:
  10   10  0.40
  13   15  0.60

ACGTcount: A:0.22, C:0.05, G:0.02, T:0.71


Consensus pattern (12 bp):   
TTTTTTAATATC
Done.