Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011238.1 Corchorus olitorius cultivar O-4 contig11271, 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: 11254
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:730 original size:2 final size:2

Alignment explanation


    Indices: 723--747  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

        713 GAGCAATAGA

                                                 
        723 AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A

        748 CATAATGGAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:3017 original size:16 final size:16

Alignment explanation


    Indices: 2992--3022  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       2982 TAGATACTTA

                            
       2992 TGATGATTTGCATGAC
          1 TGATGATTTGCATGAC

                 *         
       3008 TGATGCTTTGCATGA
          1 TGATGATTTGCATGA

       3023 ATGCACTTTG


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.23, C:0.13, G:0.26, T:0.39


Consensus pattern (16 bp):   
TGATGATTTGCATGAC

Found at i:8103 original size:25 final size:25

Alignment explanation


    Indices: 8065--8115  Score: 75
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       8055 ACTATGGACC

                 *          *        
       8065 AACATTGGACTTCCCACAATGACTT
          1 AACATCGGACTTCCCAAAATGACTT

                     *               
       8090 AACATCGGATTTCCCAAAATGACTT
          1 AACATCGGACTTCCCAAAATGACTT

             
       8115 A
          1 A

       8116 GTATTGAGAA


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  25   23  1.00

ACGTcount: A:0.35, C:0.25, G:0.12, T:0.27


Consensus pattern (25 bp):   
AACATCGGACTTCCCAAAATGACTT

Found at i:8482 original size:26 final size:27

Alignment explanation


    Indices: 8453--8536  Score: 91
    Period size: 27  Copynumber: 3.1  Consensus size: 27

       8443 AAATCAAAAG

                 *                     
       8453 TGAACCTA-AAATGACCAAAATGCCCC
          1 TGAACATACAAATGACCAAAATGCCCC

                                       
       8479 TGAACATACAAATGACCAAAATG-CCC
          1 TGAACATACAAATGACCAAAATGCCCC

             *  ***  *                  
       8505 TTAGGTGTATAAATGACCAAAATGCCCC
          1 TGA-ACATACAAATGACCAAAATGCCCC

                
       8533 TGAA
          1 TGAA

       8537 TTTTTGAAAA


Statistics
Matches: 47,  Mismatches: 8, Indels: 5
        0.78            0.13        0.08

Matches are distributed among these distances:
  26   12  0.26
  27   30  0.64
  28    5  0.11

ACGTcount: A:0.42, C:0.25, G:0.14, T:0.19


Consensus pattern (27 bp):   
TGAACATACAAATGACCAAAATGCCCC

Found at i:8847 original size:15 final size:15

Alignment explanation


    Indices: 8817--8850  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       8807 CATGGTAAAT

                      *    
       8817 TTTTTTCTAACCATA
          1 TTTTTTCTAAACATA

                       *   
       8832 TTTTTTCTAAATATA
          1 TTTTTTCTAAACATA

                
       8847 TTTT
          1 TTTT

       8851 ATATAATATA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.26, C:0.12, G:0.00, T:0.62


Consensus pattern (15 bp):   
TTTTTTCTAAACATA
Done.