Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021039.1 Corchorus olitorius cultivar O-4 contig21072, 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: 3541
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33


Found at i:2731 original size:15 final size:15

Alignment explanation


    Indices: 2711--2753  Score: 50
    Period size: 16  Copynumber: 2.8  Consensus size: 15

       2701 CCAGAAAAAT

                           
       2711 GAAAATGAAAATGAA
          1 GAAAATGAAAATGAA

                   *        
       2726 GAAAATAAAAAATGAA
          1 GAAAAT-GAAAATGAA

            *    *      
       2742 AAAAAGGAAAAT
          1 GAAAATGAAAAT

       2754 AAAGGCACTT


Statistics
Matches: 23,  Mismatches: 4, Indels: 2
        0.79            0.14        0.07

Matches are distributed among these distances:
  15   11  0.48
  16   12  0.52

ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12


Consensus pattern (15 bp):   
GAAAATGAAAATGAA

Found at i:2736 original size:21 final size:21

Alignment explanation


    Indices: 2706--2756  Score: 59
    Period size: 22  Copynumber: 2.4  Consensus size: 21

       2696 ATTTCCCAGA

                 *           *    
       2706 AAAATGAAAATGAAAATGAA-G
          1 AAAATAAAAATGAAAA-AAAGG

                                  
       2727 AAAATAAAAAATGAAAAAAAGG
          1 AAAAT-AAAAATGAAAAAAAGG

                    
       2749 AAAATAAA
          1 AAAATAAA

       2757 GGCACTTGGA


Statistics
Matches: 26,  Mismatches: 2, Indels: 4
        0.81            0.06        0.12

Matches are distributed among these distances:
  21   10  0.38
  22   16  0.62

ACGTcount: A:0.75, C:0.00, G:0.14, T:0.12


Consensus pattern (21 bp):   
AAAATAAAAATGAAAAAAAGG

Found at i:2751 original size:22 final size:22

Alignment explanation


    Indices: 2712--2756  Score: 65
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       2702 CAGAAAAATG

                       *          
       2712 AAAATGAAAATGAAGAAAATAA
          1 AAAATGAAAATAAAGAAAATAA

                                   
       2734 AAAATGAAAA-AAAGGAAAATAA
          1 AAAATGAAAATAAA-GAAAATAA

             
       2756 A
          1 A

       2757 GGCACTTGGA


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  21    2  0.10
  22   19  0.90

ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11


Consensus pattern (22 bp):   
AAAATGAAAATAAAGAAAATAA

Found at i:3166 original size:15 final size:15

Alignment explanation


    Indices: 3146--3175  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       3136 TCAAATCAAT

                    *      
       3146 TAAAAAAAGTAAAAA
          1 TAAAAAAAATAAAAA

                           
       3161 TAAAAAAAATAAAAA
          1 TAAAAAAAATAAAAA

       3176 AAATCAAATC


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

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13


Consensus pattern (15 bp):   
TAAAAAAAATAAAAA
Done.