Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01015934.1 Corchorus capsularis cultivar CVL-1 contig15955, 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: 27820
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30


Found at i:14220 original size:5 final size:5

Alignment explanation


    Indices: 14210--14252  Score: 52
    Period size: 5  Copynumber: 8.4  Consensus size: 5

      14200 AAAAACGGAA

                                         *                      
      14210 AAAAG AAAAG AGAAA- AAAAG AAAAA AAAAG AAAAG AAAGAG AA
          1 AAAAG AAAAG A-AAAG AAAAG AAAAG AAAAG AAAAG AAA-AG AA

      14253 GTTTATAATT


Statistics
Matches: 33,  Mismatches: 2, Indels: 5
        0.82            0.05        0.12

Matches are distributed among these distances:
   4    3  0.09
   5   23  0.70
   6    7  0.21

ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00


Consensus pattern (5 bp):   
AAAAG

Found at i:14226 original size:15 final size:15

Alignment explanation


    Indices: 14208--14252  Score: 58
    Period size: 15  Copynumber: 3.1  Consensus size: 15

      14198 GAAAAAACGG

                           
      14208 AAAAAAGAAAAGAGA
          1 AAAAAAGAAAAGAGA

                         * 
      14223 AAAAAAGAAAA-AAA
          1 AAAAAAGAAAAGAGA

                            
      14237 AAGAAAAG-AAAGAGA
          1 AA-AAAAGAAAAGAGA

             
      14252 A
          1 A

      14253 GTTTATAATT


Statistics
Matches: 26,  Mismatches: 2, Indels: 4
        0.81            0.06        0.12

Matches are distributed among these distances:
  14    7  0.27
  15   19  0.73

ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00


Consensus pattern (15 bp):   
AAAAAAGAAAAGAGA

Found at i:14228 original size:10 final size:10

Alignment explanation


    Indices: 14215--14252  Score: 53
    Period size: 9  Copynumber: 3.9  Consensus size: 10

      14205 CGGAAAAAAG

                      
      14215 AAAAGAGAAA
          1 AAAAGAGAAA

                      
      14225 AAAAGA-AAA
          1 AAAAGAGAAA

                      
      14234 AAAA-AGAAA
          1 AAAAGAGAAA

                      
      14243 AGAAAGAGAA
          1 A-AAAGAGAA

      14253 GTTTATAATT


Statistics
Matches: 25,  Mismatches: 0, Indels: 5
        0.83            0.00        0.17

Matches are distributed among these distances:
   8    1  0.04
   9   11  0.44
  10    9  0.36
  11    4  0.16

ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00


Consensus pattern (10 bp):   
AAAAGAGAAA

Found at i:17155 original size:37 final size:37

Alignment explanation


    Indices: 17106--17302  Score: 340
    Period size: 37  Copynumber: 5.3  Consensus size: 37

      17096 TAAGAAAAGC

                *             *               *  
      17106 AAAGTACTTAATTCAGGGAAATTAAGTAAAAGCAATT
          1 AAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTT

                *              *                *
      17143 AAAGGACTTAATTCAGGGTGATTAAGTAAAAGCAGTA
          1 AAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTT

                                                 
      17180 AAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTT
          1 AAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTT

                                                 
      17217 AAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTT
          1 AAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTT

                                                 
      17254 AAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTT
          1 AAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTT

                        
      17291 AAAGAACTTAAT
          1 AAAGAACTTAAT

      17303 CCTAGTGTGA


Statistics
Matches: 152,  Mismatches: 8, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  37  152  1.00

ACGTcount: A:0.47, C:0.08, G:0.19, T:0.26


Consensus pattern (37 bp):   
AAAGAACTTAATTCAGGGTAATTAAGTAAAAGCAGTT

Found at i:27504 original size:17 final size:18

Alignment explanation


    Indices: 27476--27513  Score: 60
    Period size: 17  Copynumber: 2.2  Consensus size: 18

      27466 CCTCCCCATA

                        *     
      27476 GTACCTAGGTAGTATGAG
          1 GTACCTAGGTAGAATGAG

                              
      27494 GTACC-AGGTAGAATGAG
          1 GTACCTAGGTAGAATGAG

               
      27511 GTA
          1 GTA

      27514 ATAGGCTGCA


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  17   14  0.74
  18    5  0.26

ACGTcount: A:0.32, C:0.11, G:0.34, T:0.24


Consensus pattern (18 bp):   
GTACCTAGGTAGAATGAG
Done.