Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01003547.1 Corchorus capsularis cultivar CVL-1 contig03555, 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: 2564
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30


Found at i:79 original size:13 final size:14

Alignment explanation


    Indices: 12--88  Score: 52
    Period size: 16  Copynumber: 5.3  Consensus size: 14

          2 ACATGTTAAC

                 *        
         12 AATTATAATTAATT
          1 AATTAAAATTAATT

              *             
         26 AAATAGAAATATAATT
          1 AATTA-AAAT-TAATT

                              
         42 AATCGT-AAA-TAACTCT
          1 AAT--TAAAATTAA-T-T

                *         
         58 AATTTAAATTAA-T
          1 AATTAAAATTAATT

                          
         71 AATTAAAATTAATT
          1 AATTAAAATTAATT

                
         85 AATT
          1 AATT

         89 TCAATATTCA


Statistics
Matches: 50,  Mismatches: 4, Indels: 18
        0.69            0.06        0.25

Matches are distributed among these distances:
  13   12  0.24
  14   13  0.26
  15    7  0.14
  16   17  0.34
  18    1  0.02

ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40


Consensus pattern (14 bp):   
AATTAAAATTAATT

Found at i:255 original size:32 final size:32

Alignment explanation


    Indices: 219--284  Score: 89
    Period size: 32  Copynumber: 2.1  Consensus size: 32

        209 CTCAGCCATT

                         **            *     
        219 GCAAGGCCGCACCTTAGGG-GCGGCCTGCCGTG
          1 GCAAGGCCG-ACCCCAGGGTGCGGCCTACCGTG

                                            
        251 GCAAGGCCGACCCCAGGGTGCGGCCTACCGTG
          1 GCAAGGCCGACCCCAGGGTGCGGCCTACCGTG

              
        283 GC
          1 GC

        285 GCGGCCGCCC


Statistics
Matches: 30,  Mismatches: 3, Indels: 2
        0.86            0.09        0.06

Matches are distributed among these distances:
  31    7  0.23
  32   23  0.77

ACGTcount: A:0.14, C:0.36, G:0.39, T:0.11


Consensus pattern (32 bp):   
GCAAGGCCGACCCCAGGGTGCGGCCTACCGTG

Found at i:531 original size:20 final size:20

Alignment explanation


    Indices: 506--545  Score: 71
    Period size: 20  Copynumber: 2.0  Consensus size: 20

        496 CGGCTCAGCC

                      *         
        506 CCTAGATCTATTTTTTTACA
          1 CCTAGATCTAATTTTTTACA

                                
        526 CCTAGATCTAATTTTTTACA
          1 CCTAGATCTAATTTTTTACA

        546 TCCATTCCTC


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.28, C:0.20, G:0.05, T:0.47


Consensus pattern (20 bp):   
CCTAGATCTAATTTTTTACA

Found at i:922 original size:32 final size:32

Alignment explanation


    Indices: 863--930  Score: 91
    Period size: 32  Copynumber: 2.1  Consensus size: 32

        853 TTGAGTTAAG

                *                           
        863 TCGGGTTAAATTTAGGTAAGATCGATTCAGGT
          1 TCGGATTAAATTTAGGTAAGATCGATTCAGGT

                         *   *  * *         
        895 TCGGATTAAATTTGGGTCAGGTTGATTCAGGT
          1 TCGGATTAAATTTAGGTAAGATCGATTCAGGT

                
        927 TCGG
          1 TCGG

        931 GTCGATTTTA


Statistics
Matches: 31,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  32   31  1.00

ACGTcount: A:0.24, C:0.10, G:0.31, T:0.35


Consensus pattern (32 bp):   
TCGGATTAAATTTAGGTAAGATCGATTCAGGT

Found at i:949 original size:32 final size:32

Alignment explanation


    Indices: 870--949  Score: 79
    Period size: 32  Copynumber: 2.5  Consensus size: 32

        860 AAGTCGGGTT

                      *  * *               *
        870 AAATTTAGGTAAGATCGATTCAGGTTCGGATT
          1 AAATTTAGGTCAGGTTGATTCAGGTTCGGATC

                  *                      *  
        902 AAATTTGGGTCAGGTTGATTCAGGTTCGGGTC
          1 AAATTTAGGTCAGGTTGATTCAGGTTCGGATC

            * *       *     
        934 GATTTTAGGTTAGGTT
          1 AAATTTAGGTCAGGTT

        950 AATTTGGGTT


Statistics
Matches: 38,  Mismatches: 10, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  32   38  1.00

ACGTcount: A:0.24, C:0.09, G:0.30, T:0.38


Consensus pattern (32 bp):   
AAATTTAGGTCAGGTTGATTCAGGTTCGGATC

Found at i:2392 original size:27 final size:27

Alignment explanation


    Indices: 2359--2419  Score: 104
    Period size: 27  Copynumber: 2.2  Consensus size: 27

       2349 TCTGGAAAAT

                    *                  
       2359 AAGGGAAATGGACAATTAAAAAGGAAC
          1 AAGGGAAAGGGACAATTAAAAAGGAAC

                                       
       2386 AAGGGAAAGGGACAATTAAAAAGGAAC
          1 AAGGGAAAGGGACAATTAAAAAGGAAC

                   
       2413 AGAGGGA
          1 A-AGGGA

       2420 GTATTTTATA


Statistics
Matches: 32,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  27   27  0.84
  28    5  0.16

ACGTcount: A:0.54, C:0.07, G:0.31, T:0.08


Consensus pattern (27 bp):   
AAGGGAAAGGGACAATTAAAAAGGAAC
Done.