Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01004594.1 Corchorus olitorius cultivar O-4 contig04610, 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, 757

Length: 1262
ACGTcount: A:0.15, C:0.37, G:0.35, T:0.13


Found at i:201 original size:10 final size:10

Alignment explanation


    Indices: 188--213  Score: 52
    Period size: 10  Copynumber: 2.6  Consensus size: 10

        178 CCCGGCAGGC

                      
        188 CGGGGCAGCG
          1 CGGGGCAGCG

                      
        198 CGGGGCAGCG
          1 CGGGGCAGCG

                  
        208 CGGGGC
          1 CGGGGC

        214 CGATAGCCGA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   16  1.00

ACGTcount: A:0.08, C:0.31, G:0.62, T:0.00


Consensus pattern (10 bp):   
CGGGGCAGCG

Found at i:515 original size:18 final size:18

Alignment explanation


    Indices: 477--515  Score: 51
    Period size: 18  Copynumber: 2.2  Consensus size: 18

        467 CCGCAATGAC

                         *  * 
        477 CGCAATGAACGCGGCGGG
          1 CGCAATGAACGCGACGAG

                        *     
        495 CGCAATGAACGCTACGAG
          1 CGCAATGAACGCGACGAG

               
        513 CGC
          1 CGC

        516 TCCGACCGCC


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

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.26, C:0.31, G:0.36, T:0.08


Consensus pattern (18 bp):   
CGCAATGAACGCGACGAG

Found at i:570 original size:27 final size:27

Alignment explanation


    Indices: 524--592  Score: 88
    Period size: 27  Copynumber: 2.6  Consensus size: 27

        514 GCTCCGACCG

                           *        *  
        524 CCGTGATGCAGGCCCTCGCGGCGATGC
          1 CCGTGATGCAGGCCCCCGCGGCGACGC

                                        
        551 CCGTGATGC-GGCACCCCGCGGCGACGC
          1 CCGTGATGCAGGC-CCCCGCGGCGACGC

                            
        578 CCGTGAT-CAGCGCCC
          1 CCGTGATGCAG-GCCC

        593 GCGCAGCAGC


Statistics
Matches: 37,  Mismatches: 2, Indels: 6
        0.82            0.04        0.13

Matches are distributed among these distances:
  26    4  0.11
  27   31  0.84
  28    2  0.05

ACGTcount: A:0.12, C:0.42, G:0.35, T:0.12


Consensus pattern (27 bp):   
CCGTGATGCAGGCCCCCGCGGCGACGC

Found at i:918 original size:24 final size:24

Alignment explanation


    Indices: 869--928  Score: 70
    Period size: 24  Copynumber: 2.5  Consensus size: 24

        859 GTGATCGCCC

                  *        *        
        869 CCGTGACGACGCCCGGGGTCCCCG
          1 CCGTGATGACGCCCGCGGTCCCCG

                                     
        893 CCGTGATGACGCCCGCGG-CCCGCG
          1 CCGTGATGACGCCCGCGGTCCC-CG

               *         
        917 CCGCGATG-CGCC
          1 CCGTGATGACGCC

        929 GGCCCAGGCC


Statistics
Matches: 32,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
  23    7  0.22
  24   25  0.78

ACGTcount: A:0.08, C:0.47, G:0.37, T:0.08


Consensus pattern (24 bp):   
CCGTGATGACGCCCGCGGTCCCCG
Done.