Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007979.1 Corchorus capsularis cultivar CVL-1 contig08000, 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: 13380
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Found at i:909 original size:16 final size:16

Alignment explanation


    Indices: 888--944  Score: 62
    Period size: 16  Copynumber: 3.6  Consensus size: 16

        878 GTTGGGTTGA

                    *   *   
        888 TCGGGTTCAGGTCATT
          1 TCGGGTTCGGGTAATT

                        **  
        904 TCGGGTTCGGGTTGTT
          1 TCGGGTTCGGGTAATT

                *           
        920 T-GGATTCGGGTAATT
          1 TCGGGTTCGGGTAATT

                      
        935 TCGGGTTCGG
          1 TCGGGTTCGG

        945 ACACCAAAAA


Statistics
Matches: 33,  Mismatches: 7, Indels: 2
        0.79            0.17        0.05

Matches are distributed among these distances:
  15   12  0.36
  16   21  0.64

ACGTcount: A:0.09, C:0.14, G:0.39, T:0.39


Consensus pattern (16 bp):   
TCGGGTTCGGGTAATT

Found at i:3268 original size:26 final size:27

Alignment explanation


    Indices: 3239--3290  Score: 79
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       3229 AATATATAAG

                                       
       3239 CGGCAATGATA-AAATGGTTTTAATCA
          1 CGGCAATGATATAAATGGTTTTAATCA

                    *     *           
       3265 CGGCAATGGTATAATTGGTTTTAATC
          1 CGGCAATGATATAAATGGTTTTAATC

       3291 GAATTAAACA


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  26   10  0.43
  27   13  0.57

ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35


Consensus pattern (27 bp):   
CGGCAATGATATAAATGGTTTTAATCA

Found at i:5187 original size:2 final size:2

Alignment explanation


    Indices: 5180--5210  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       5170 TGTTACTTCT

                                                          
       5180 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       5211 GATTTAAAGA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:6541 original size:2 final size:2

Alignment explanation


    Indices: 6534--6560  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       6524 CAGAGTCTAG

                                                    
       6534 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

       6561 TATTGGTCAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:11610 original size:19 final size:17

Alignment explanation


    Indices: 11588--11634  Score: 53
    Period size: 15  Copynumber: 2.8  Consensus size: 17

      11578 AAATGGGGTT

                               
      11588 GAAGGAAAGAGAAGAAGAA
          1 GAAGGAAA-AGAA-AAGAA

                             
      11607 GAAGGAAAAGAAAAG-A
          1 GAAGGAAAAGAAAAGAA

             *           
      11623 -CAGGAAAAGAAA
          1 GAAGGAAAAGAAA

      11635 GGAAAGCAAA


Statistics
Matches: 27,  Mismatches: 1, Indels: 4
        0.84            0.03        0.12

Matches are distributed among these distances:
  15   11  0.41
  16    1  0.04
  17    3  0.11
  18    4  0.15
  19    8  0.30

ACGTcount: A:0.66, C:0.02, G:0.32, T:0.00


Consensus pattern (17 bp):   
GAAGGAAAAGAAAAGAA

Found at i:11627 original size:15 final size:14

Alignment explanation


    Indices: 11599--11634  Score: 54
    Period size: 15  Copynumber: 2.4  Consensus size: 14

      11589 AAGGAAAGAG

                           
      11599 AAGAAGAAGAAGGAA
          1 AAGAA-AAGAAGGAA

                           
      11614 AAGAAAAGACAGGAA
          1 AAGAAAAGA-AGGAA

                  
      11629 AAGAAA
          1 AAGAAA

      11635 GGAAAGCAAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  14    4  0.20
  15   16  0.80

ACGTcount: A:0.69, C:0.03, G:0.28, T:0.00


Consensus pattern (14 bp):   
AAGAAAAGAAGGAA
Done.