Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021513.1 Corchorus olitorius cultivar O-4 contig21546, 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: 17078
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31


Found at i:2519 original size:10 final size:10

Alignment explanation


    Indices: 2504--2532  Score: 58
    Period size: 10  Copynumber: 2.9  Consensus size: 10

       2494 CGGCAAGGAG

                      
       2504 GCTTGAAGAA
          1 GCTTGAAGAA

                      
       2514 GCTTGAAGAA
          1 GCTTGAAGAA

                     
       2524 GCTTGAAGA
          1 GCTTGAAGA

       2533 TGCTAGGAGT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   19  1.00

ACGTcount: A:0.38, C:0.10, G:0.31, T:0.21


Consensus pattern (10 bp):   
GCTTGAAGAA

Found at i:2569 original size:21 final size:21

Alignment explanation


    Indices: 2543--2636  Score: 136
    Period size: 21  Copynumber: 4.5  Consensus size: 21

       2533 TGCTAGGAGT

                     *           
       2543 TCATTGGAGCAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                                  
       2564 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                  *              
       2585 TCATTGAAGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                *                
       2606 TCATGGGAGAAGGTTCCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

              *       
       2627 TCGTTGGAGA
          1 TCATTGGAGA

       2637 TCATTTGAAG


Statistics
Matches: 65,  Mismatches: 6, Indels: 4
        0.87            0.08        0.05

Matches are distributed among these distances:
  20    2  0.03
  21   62  0.95
  22    1  0.02

ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Found at i:3518 original size:20 final size:20

Alignment explanation


    Indices: 3478--3518  Score: 64
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       3468 CGCCAACTCA

                            *   
       3478 GCTTTTTGGTATTTTCCTAT
          1 GCTTTTTGGTATTTTCATAT

                           *    
       3498 GCTTTTTGGTATTTTTATAT
          1 GCTTTTTGGTATTTTCATAT

             
       3518 G
          1 G

       3519 TGATTTAACC


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.12, C:0.10, G:0.17, T:0.61


Consensus pattern (20 bp):   
GCTTTTTGGTATTTTCATAT

Found at i:3746 original size:29 final size:28

Alignment explanation


    Indices: 3690--3754  Score: 73
    Period size: 29  Copynumber: 2.3  Consensus size: 28

       3680 ATTGAAGATT

                                        
       3690 AATTGAAG-ATAATTTCAAGACATGAAG
          1 AATTGAAGAATAATTTCAAGACATGAAG

                         *                 
       3717 ACCATTGAAGAATTATTTCAAGA-A-GCAAG
          1 A--ATTGAAGAATAATTTCAAGACATG-AAG

                     
       3746 AATTGAAGA
          1 AATTGAAGA

       3755 TTGAGCTTAA


Statistics
Matches: 33,  Mismatches: 1, Indels: 8
        0.79            0.02        0.19

Matches are distributed among these distances:
  27    9  0.27
  28    1  0.03
  29   12  0.36
  30   11  0.33

ACGTcount: A:0.48, C:0.09, G:0.18, T:0.25


Consensus pattern (28 bp):   
AATTGAAGAATAATTTCAAGACATGAAG

Found at i:7259 original size:21 final size:21

Alignment explanation


    Indices: 7235--7282  Score: 96
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       7225 AAGATCCTAA

                                 
       7235 AAACTATCCAAATAAAGGTCC
          1 AAACTATCCAAATAAAGGTCC

                                 
       7256 AAACTATCCAAATAAAGGTCC
          1 AAACTATCCAAATAAAGGTCC

                  
       7277 AAACTA
          1 AAACTA

       7283 ATTAAAGAGC


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   27  1.00

ACGTcount: A:0.50, C:0.23, G:0.08, T:0.19


Consensus pattern (21 bp):   
AAACTATCCAAATAAAGGTCC

Found at i:7597 original size:17 final size:17

Alignment explanation


    Indices: 7575--7607  Score: 66
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       7565 ACTATCCAAA

                             
       7575 TAAAGGTCCAAACTAAT
          1 TAAAGGTCCAAACTAAT

                            
       7592 TAAAGGTCCAAACTAA
          1 TAAAGGTCCAAACTAA

       7608 GATAGAATAA


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

Matches are distributed among these distances:
  17   16  1.00

ACGTcount: A:0.48, C:0.18, G:0.12, T:0.21


Consensus pattern (17 bp):   
TAAAGGTCCAAACTAAT

Found at i:16524 original size:12 final size:13

Alignment explanation


    Indices: 16502--16531  Score: 53
    Period size: 12  Copynumber: 2.4  Consensus size: 13

      16492 ACTAGCAATT

                         
      16502 AAAATCAATCAAG
          1 AAAATCAATCAAG

                         
      16515 AAAA-CAATCAAG
          1 AAAATCAATCAAG

                 
      16527 AAAAT
          1 AAAAT

      16532 TAAAGAAAAC


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  12   12  0.75
  13    4  0.25

ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13


Consensus pattern (13 bp):   
AAAATCAATCAAG
Done.