Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004949.1 Corchorus capsularis cultivar CVL-1 contig04967, 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: 14828
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30


Found at i:387 original size:15 final size:14

Alignment explanation


    Indices: 336--428  Score: 58
    Period size: 11  Copynumber: 7.1  Consensus size: 14

        326 TTATGATTAG

                        * 
        336 TTTTAATTAGTTAA
          1 TTTTAATTAGTTTA

              **      *   
        350 TTAAAATTA-CTTA
          1 TTTTAATTAGTTTA

            *             
        363 GTTT-ATTAGTTTA
          1 TTTTAATTAGTTTA

                           
        376 TGTTTAATTAG--TA
          1 T-TTTAATTAGTTTA

              *           
        389 -TCTAATTAGTTTA
          1 TTTTAATTAGTTTA

                           
        402 TTATTAATTAG--TA
          1 TT-TTAATTAGTTTA

                          
        415 -TTTAATTAGTTTA
          1 TTTTAATTAGTTTA

             
        428 T
          1 T

        429 GATTAAAATG


Statistics
Matches: 58,  Mismatches: 11, Indels: 20
        0.65            0.12        0.22

Matches are distributed among these distances:
  11   16  0.28
  12    5  0.09
  13   14  0.24
  14   11  0.19
  15   12  0.21

ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56


Consensus pattern (14 bp):   
TTTTAATTAGTTTA

Found at i:396 original size:26 final size:26

Alignment explanation


    Indices: 367--434  Score: 102
    Period size: 26  Copynumber: 2.6  Consensus size: 26

        357 TACTTAGTTT

                                      
        367 ATTAGTTTATGTTTAATTAGTATCTA
          1 ATTAGTTTATGTTTAATTAGTATCTA

                                    *  
        393 ATTAGTTTAT-TATTAATTAGTATTTA
          1 ATTAGTTTATGT-TTAATTAGTATCTA

                       *    
        419 ATTAGTTTATGATTAA
          1 ATTAGTTTATGTTTAA

        435 AATGAAGGAA


Statistics
Matches: 38,  Mismatches: 2, Indels: 4
        0.86            0.05        0.09

Matches are distributed among these distances:
  25    1  0.03
  26   37  0.97

ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54


Consensus pattern (26 bp):   
ATTAGTTTATGTTTAATTAGTATCTA

Found at i:482 original size:24 final size:25

Alignment explanation


    Indices: 443--502  Score: 79
    Period size: 25  Copynumber: 2.5  Consensus size: 25

        433 AAAATGAAGG

                              *      
        443 AAAATGAA-TTTGAAG-ATTTGTTA
          1 AAAATGAAGTTTGAAGAAGTTGTTA

                                     
        466 AAAATGAAGTTTGAAGAAGTTGTTA
          1 AAAATGAAGTTTGAAGAAGTTGTTA

            *    *      
        491 GAAATTAAGTTT
          1 AAAATGAAGTTT

        503 AGGGTTTGAA


Statistics
Matches: 32,  Mismatches: 3, Indels: 2
        0.86            0.08        0.05

Matches are distributed among these distances:
  23    8  0.25
  24    7  0.22
  25   17  0.53

ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37


Consensus pattern (25 bp):   
AAAATGAAGTTTGAAGAAGTTGTTA

Found at i:2892 original size:33 final size:33

Alignment explanation


    Indices: 2828--2892  Score: 78
    Period size: 33  Copynumber: 2.0  Consensus size: 33

       2818 AGCAAAGAGA

                    *          *      *      
       2828 GAAGGTGGCAAAAAGGAGGGAAAAGGTGAGAAG
          1 GAAGGTGGAAAAAAGGAGGCAAAAGGAGAGAAG

                  *                          
       2861 GAAGGTTGAAAAAAGGA-GCAAAAGAGAGAGAA
          1 GAAGGTGGAAAAAAGGAGGCAAAAG-GAGAGAA

       2893 TTGTTTTTGG


Statistics
Matches: 27,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  32    6  0.22
  33   21  0.78

ACGTcount: A:0.51, C:0.03, G:0.40, T:0.06


Consensus pattern (33 bp):   
GAAGGTGGAAAAAAGGAGGCAAAAGGAGAGAAG

Found at i:5771 original size:42 final size:43

Alignment explanation


    Indices: 5724--5806  Score: 125
    Period size: 42  Copynumber: 2.0  Consensus size: 43

       5714 CGTGTTTGGC

                                          *             
       5724 TTATCGTGTCTCGTGTC-TGAATCGTGTC-GGACACGATTAAGA
          1 TTATCGTGTCTCGTGTCGT-AATCGTGTCAAGACACGATTAAGA

                     *                               
       5766 TTATCGTGTTTCGTGTCGTAATCGTGTCAAGACACGATTAA
          1 TTATCGTGTCTCGTGTCGTAATCGTGTCAAGACACGATTAA

       5807 CACGTTTAAG


Statistics
Matches: 37,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  42   25  0.68
  43   12  0.32

ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35


Consensus pattern (43 bp):   
TTATCGTGTCTCGTGTCGTAATCGTGTCAAGACACGATTAAGA

Found at i:5819 original size:20 final size:21

Alignment explanation


    Indices: 5794--5836  Score: 61
    Period size: 20  Copynumber: 2.1  Consensus size: 21

       5784 TAATCGTGTC

                     *           
       5794 AAGACACGATTAACACG-TTT
          1 AAGACACGAGTAACACGCTTT

                       *         
       5814 AAGACACGAGTGACACGCTTT
          1 AAGACACGAGTAACACGCTTT

              
       5835 AA
          1 AA

       5837 TTAACGGGTT


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  20   15  0.75
  21    5  0.25

ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21


Consensus pattern (21 bp):   
AAGACACGAGTAACACGCTTT
Done.