Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020121.1 Corchorus olitorius cultivar O-4 contig20154, 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: 8941
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32


Found at i:4100 original size:66 final size:66

Alignment explanation


    Indices: 4017--4151  Score: 252
    Period size: 66  Copynumber: 2.0  Consensus size: 66

       4007 AACAGGTGTC

                                  *                                          
       4017 ACTAAATCTATATGGTTAATGAGCAAAGGAAAATAAAAAGAAAATAAATATAAGCATGCCTAATG
          1 ACTAAATCTATATGGTTAATGAACAAAGGAAAATAAAAAGAAAATAAATATAAGCATGCCTAATG

             
       4082 A
         66 A

                   *                                                         
       4083 ACTAAATGTATATGGTTAATGAACAAAGGAAAATAAAAAGAAAATAAATATAAGCATGCCTAATG
          1 ACTAAATCTATATGGTTAATGAACAAAGGAAAATAAAAAGAAAATAAATATAAGCATGCCTAATG

             
       4148 A
         66 A

               
       4149 ACT
          1 ACT

       4152 CGAATATGCT


Statistics
Matches: 67,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  66   67  1.00

ACGTcount: A:0.53, C:0.09, G:0.15, T:0.23


Consensus pattern (66 bp):   
ACTAAATCTATATGGTTAATGAACAAAGGAAAATAAAAAGAAAATAAATATAAGCATGCCTAATG
A

Found at i:6780 original size:23 final size:23

Alignment explanation


    Indices: 6754--6815  Score: 79
    Period size: 23  Copynumber: 2.7  Consensus size: 23

       6744 AGGCATTTGG

                                   
       6754 TTGGGCCATTTTATTTCCTTTAC
          1 TTGGGCCATTTTATTTCCTTTAC

                   *   *    *      
       6777 TTGGGCCGTTTAATTTTCTTTAC
          1 TTGGGCCATTTTATTTCCTTTAC

            *   *           
       6800 CTGGTCCATTTTATTT
          1 TTGGGCCATTTTATTT

       6816 ACTTGGTCCA


Statistics
Matches: 32,  Mismatches: 7, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  23   32  1.00

ACGTcount: A:0.13, C:0.19, G:0.15, T:0.53


Consensus pattern (23 bp):   
TTGGGCCATTTTATTTCCTTTAC

Found at i:6816 original size:18 final size:18

Alignment explanation


    Indices: 6789--6826  Score: 58
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       6779 GGGCCGTTTA

                 *            
       6789 ATTTTCTTTACCTGGTCC
          1 ATTTTATTTACCTGGTCC

                       *      
       6807 ATTTTATTTACTTGGTCC
          1 ATTTTATTTACCTGGTCC

              
       6825 AT
          1 AT

       6827 CTCTTTATTT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.16, C:0.21, G:0.11, T:0.53


Consensus pattern (18 bp):   
ATTTTATTTACCTGGTCC
Done.