Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012828.1 Corchorus olitorius cultivar O-4 contig12861, 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: 31827
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:24909 original size:12 final size:12

Alignment explanation


    Indices: 24892--24925  Score: 52
    Period size: 12  Copynumber: 2.8  Consensus size: 12

      24882 ATCCATCTAA

                        
      24892 ATCTACTTCACC
          1 ATCTACTTCACC

                         
      24904 ATCTACTTCAACC
          1 ATCTACTTC-ACC

                      
      24917 -TCTACTTCA
          1 ATCTACTTCA

      24926 GCAGCATGAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  11    1  0.05
  12   17  0.81
  13    3  0.14

ACGTcount: A:0.26, C:0.38, G:0.00, T:0.35


Consensus pattern (12 bp):   
ATCTACTTCACC

Found at i:24987 original size:21 final size:21

Alignment explanation


    Indices: 24962--25011  Score: 64
    Period size: 21  Copynumber: 2.4  Consensus size: 21

      24952 GTGGCCATTT

                                 
      24962 TCACCATCATTAACTCCCTGA
          1 TCACCATCATTAACTCCCTGA

                    *   **      *
      24983 TCACCATCCTTATTTCCCTGT
          1 TCACCATCATTAACTCCCTGA

                    
      25004 TCACCATC
          1 TCACCATC

      25012 TTGGCCATTC


Statistics
Matches: 25,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   25  1.00

ACGTcount: A:0.22, C:0.40, G:0.04, T:0.34


Consensus pattern (21 bp):   
TCACCATCATTAACTCCCTGA

Found at i:25543 original size:16 final size:16

Alignment explanation


    Indices: 25522--25558  Score: 74
    Period size: 16  Copynumber: 2.3  Consensus size: 16

      25512 AAAGCCATGA

                            
      25522 ATACCCATCAAAGGGT
          1 ATACCCATCAAAGGGT

                            
      25538 ATACCCATCAAAGGGT
          1 ATACCCATCAAAGGGT

                 
      25554 ATACC
          1 ATACC

      25559 GTAAACACCC


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   21  1.00

ACGTcount: A:0.38, C:0.27, G:0.16, T:0.19


Consensus pattern (16 bp):   
ATACCCATCAAAGGGT

Found at i:25587 original size:24 final size:25

Alignment explanation


    Indices: 25540--25590  Score: 86
    Period size: 24  Copynumber: 2.1  Consensus size: 25

      25530 CAAAGGGTAT

                               *     
      25540 ACCCATCAAAGGGTATACCGTAAAC
          1 ACCCATCAAAGGGTATACCATAAAC

                                     
      25565 ACCCATCAAA-GGTATACCATAAAC
          1 ACCCATCAAAGGGTATACCATAAAC

              
      25589 AC
          1 AC

      25591 ACCAACCAAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  24   15  0.60
  25   10  0.40

ACGTcount: A:0.43, C:0.29, G:0.12, T:0.16


Consensus pattern (25 bp):   
ACCCATCAAAGGGTATACCATAAAC

Found at i:25600 original size:26 final size:25

Alignment explanation


    Indices: 25540--25600  Score: 70
    Period size: 24  Copynumber: 2.4  Consensus size: 25

      25530 CAAAGGGTAT

                 *             *     
      25540 ACCCATCAAAGGGTATACCGTAAAC
          1 ACCCACCAAAGGGTATACCATAAAC

                 *                   
      25565 ACCCATCAAA-GGTATACCATAAAC
          1 ACCCACCAAAGGGTATACCATAAAC

                        
      25589 ACACCAACCAAA
          1 AC-CC-ACCAAA

      25601 TATTATACCC


Statistics
Matches: 32,  Mismatches: 2, Indels: 3
        0.86            0.05        0.08

Matches are distributed among these distances:
  24   15  0.47
  25   12  0.38
  26    5  0.16

ACGTcount: A:0.46, C:0.31, G:0.10, T:0.13


Consensus pattern (25 bp):   
ACCCACCAAAGGGTATACCATAAAC
Done.