Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008068.1 Corchorus olitorius cultivar O-4 contig08095, 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, 674

Length: 1124
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30


Found at i:477 original size:25 final size:24

Alignment explanation


    Indices: 440--486  Score: 69
    Period size: 26  Copynumber: 1.9  Consensus size: 24

        430 TTAGAAAATT

                                      
        440 TGAAAAACTTTGATGGATGAGATGGA
          1 TGAAAAACTTTGAT-GAT-AGATGGA

                                  
        466 TGAAAAAC-TTGATGATAGATG
          1 TGAAAAACTTTGATGATAGATG

        487 AATAGAAGAA


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

Matches are distributed among these distances:
  23    5  0.24
  24    3  0.14
  25    5  0.24
  26    8  0.38

ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28


Consensus pattern (24 bp):   
TGAAAAACTTTGATGATAGATGGA

Found at i:942 original size:11 final size:11

Alignment explanation


    Indices: 911--963  Score: 81
    Period size: 11  Copynumber: 4.9  Consensus size: 11

        901 CTCCAATGGG

                       
        911 CTTCAAATGAT
          1 CTTCAAATGAT

                *      
        922 C-TCCAATGAT
          1 CTTCAAATGAT

                       
        932 CTTCAAATGAT
          1 CTTCAAATGAT

                       
        943 CTTCAAATGAT
          1 CTTCAAATGAT

                 *    
        954 CTTCAGATGA
          1 CTTCAAATGA

        964 ACTCGTCAAG


Statistics
Matches: 38,  Mismatches: 3, Indels: 2
        0.88            0.07        0.05

Matches are distributed among these distances:
  10    9  0.24
  11   29  0.76

ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34


Consensus pattern (11 bp):   
CTTCAAATGAT

Found at i:954 original size:22 final size:21

Alignment explanation


    Indices: 896--963  Score: 82
    Period size: 21  Copynumber: 3.2  Consensus size: 21

        886 TCCTTTGGTG

                    *    **      
        896 ATGATCTCCAATGGGCTTCAA
          1 ATGATCTCAAATGATCTTCAA

                    *            
        917 ATGATCTCCAATGATCTTCAA
          1 ATGATCTCAAATGATCTTCAA

                                 *
        938 ATGATCTTCAAATGATCTTCAG
          1 ATGATC-TCAAATGATCTTCAA

                
        960 ATGA
          1 ATGA

        964 ACTCGTCAAG


Statistics
Matches: 42,  Mismatches: 4, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  21   25  0.60
  22   17  0.40

ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32


Consensus pattern (21 bp):   
ATGATCTCAAATGATCTTCAA

Found at i:1104 original size:21 final size:21

Alignment explanation


    Indices: 1080--1124  Score: 81
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       1070 CTTAGGCAAT

                                 
       1080 TCCAATGAGCTTGAAACCTTC
          1 TCCAATGAGCTTGAAACCTTC

                         *       
       1101 TCCAATGAGCTTGGAACCTTC
          1 TCCAATGAGCTTGAAACCTTC

               
       1122 TCC
          1 TCC


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29


Consensus pattern (21 bp):   
TCCAATGAGCTTGAAACCTTC
Done.