Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006257.1 Corchorus capsularis cultivar CVL-1 contig06276, 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: 21764
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.29


Found at i:4466 original size:19 final size:18

Alignment explanation


    Indices: 4433--4468  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       4423 TTGAAATAAT

                              
       4433 TCTTCAATGATCTTCAAA
          1 TCTTCAATGATCTTCAAA

                     *        
       4451 TCTTCAAATTATCTTCAA
          1 TCTTC-AATGATCTTCAA

       4469 GAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGATCTTCAAA

Found at i:5919 original size:15 final size:15

Alignment explanation


    Indices: 5895--5938  Score: 70
    Period size: 15  Copynumber: 2.9  Consensus size: 15

       5885 TGCTAGGGTG

                 *         
       5895 AATGGCGCAAACAAC
          1 AATGGTGCAAACAAC

                           
       5910 AATGGTGCAAACAAC
          1 AATGGTGCAAACAAC

                    *     
       5925 AATGGTGCGAACAA
          1 AATGGTGCAAACAA

       5939 TCATGTTGTG


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   27  1.00

ACGTcount: A:0.45, C:0.20, G:0.23, T:0.11


Consensus pattern (15 bp):   
AATGGTGCAAACAAC

Found at i:12358 original size:28 final size:28

Alignment explanation


    Indices: 12310--12363  Score: 74
    Period size: 28  Copynumber: 1.9  Consensus size: 28

      12300 AATAAAATCG

                      *  *              
      12310 ATGAGCAATCTATTAACTATTTTAAACA
          1 ATGAGCAATCCATCAACTATTTTAAACA

                                       
      12338 ATGAGCAATCCATCCAA-TATTTTAAA
          1 ATGAGCAATCCAT-CAACTATTTTAAA

      12364 GTATAAGTTA


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  28   21  0.91
  29    2  0.09

ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33


Consensus pattern (28 bp):   
ATGAGCAATCCATCAACTATTTTAAACA
Done.