Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014694.1 Corchorus capsularis cultivar CVL-1 contig14715, 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: 19492
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:2618 original size:60 final size:59

Alignment explanation


    Indices: 2523--2709  Score: 268
    Period size: 60  Copynumber: 3.1  Consensus size: 59

       2513 AAGATGAAAG

                                                                         
       2523 TGATTCTGATATTT-CAGCTGATGAAAAAGTAGAAAAGAGTAGGAGAAGAGGTAGAAGACA
          1 TGATTCTGATATTTCCAG-TGATGAAAAAGTAGAAAAGAGTAGG-GAAGAGGTAGAAGACA

             *                            *                             
       2583 TAATTCTGATATTTCCAGTGATGAAAAAGTGGAAAAGAGTAGTGGAAGAGGTAGAAGACA
          1 TGATTCTGATATTTCCAGTGATGAAAAAGTAGAAAAGAGTAG-GGAAGAGGTAGAAGACA

                     *     *             *               **             
       2643 TGATTCTGACATTTCAAGTGATGAAAAAGAAGAAAAGAGTAGGGGTCGAGGTAGAAGACA
          1 TGATTCTGATATTTCCAGTGATGAAAAAGTAGAAAAGAGTA-GGGAAGAGGTAGAAGACA

                   
       2703 TGATTCT
          1 TGATTCT

       2710 AGTGATGATG


Statistics
Matches: 115,  Mismatches: 9, Indels: 6
        0.88            0.07        0.05

Matches are distributed among these distances:
  60  110  0.96
  61    5  0.04

ACGTcount: A:0.41, C:0.07, G:0.28, T:0.23


Consensus pattern (59 bp):   
TGATTCTGATATTTCCAGTGATGAAAAAGTAGAAAAGAGTAGGGAAGAGGTAGAAGACA

Found at i:4872 original size:2 final size:2

Alignment explanation


    Indices: 4859--4890  Score: 50
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       4849 AATACAACCA

                                                              
       4859 AT AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       4891 CAACATTTCA


Statistics
Matches: 28,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
   1    2  0.07
   2   26  0.93

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:18476 original size:25 final size:23

Alignment explanation


    Indices: 18411--18476  Score: 62
    Period size: 25  Copynumber: 2.7  Consensus size: 23

      18401 GTTTTTTCTA

                                   
      18411 AAAAAAAAAAAAG-TTTGCGTCG
          1 AAAAAAAAAAAAGTTTTGCGTCG

                       **            
      18433 AAAAAAAAAATTTGTTTTTGCGTCG
          1 AAAAAAAAAA-AAG-TTTTGCGTCG

                        *      
      18458 ATTAAAAAAAAAGAGTTTT
          1 A--AAAAAAAAAAAGTTTT

      18477 TTCCGTTTTT


Statistics
Matches: 35,  Mismatches: 4, Indels: 7
        0.76            0.09        0.15

Matches are distributed among these distances:
  22   10  0.29
  23    1  0.03
  25   14  0.40
  26    1  0.03
  27    9  0.26

ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29


Consensus pattern (23 bp):   
AAAAAAAAAAAAGTTTTGCGTCG
Done.