Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017647.1 Corchorus olitorius cultivar O-4 contig17680, 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: 22851
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30


Found at i:1908 original size:21 final size:21

Alignment explanation


    Indices: 1867--1908  Score: 57
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       1857 TTTGTTTAAT

                          ***    
       1867 TAACAATTGTCCCTTTTCAAG
          1 TAACAATTGTCCCTCAACAAG

                                 
       1888 TAACAATTGTCCCTCAACAAG
          1 TAACAATTGTCCCTCAACAAG

       1909 CTTTTCCATG


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.33, C:0.26, G:0.10, T:0.31


Consensus pattern (21 bp):   
TAACAATTGTCCCTCAACAAG

Found at i:2532 original size:21 final size:21

Alignment explanation


    Indices: 2484--2532  Score: 57
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       2474 AGTAACAATA

                           *     
       2484 AAATAAA-TAAGCAAGAAAAT
          1 AAATAAATTAAGCAACAAAAT

                               *  
       2504 -AATAAAATTAAGCAACAAGAT
          1 AAAT-AAATTAAGCAACAAAAT

                    
       2525 AAATAAAT
          1 AAATAAAT

       2533 ACTCCAATCC


Statistics
Matches: 24,  Mismatches: 2, Indels: 5
        0.77            0.06        0.16

Matches are distributed among these distances:
  19    3  0.12
  20    3  0.12
  21   15  0.62
  22    3  0.12

ACGTcount: A:0.67, C:0.06, G:0.08, T:0.18


Consensus pattern (21 bp):   
AAATAAATTAAGCAACAAAAT

Found at i:8517 original size:13 final size:13

Alignment explanation


    Indices: 8499--8539  Score: 57
    Period size: 13  Copynumber: 3.1  Consensus size: 13

       8489 TGCATATTTA

                         
       8499 ATTTTAATTTTTT
          1 ATTTTAATTTTTT

                          
       8512 ATTTT-ATTTTATT
          1 ATTTTAATTTT-TT

                          
       8525 ATTTTTAATTTTTT
          1 A-TTTTAATTTTTT

             
       8539 A
          1 A

       8540 CACTAATTTT


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

Matches are distributed among these distances:
  12    5  0.20
  13    8  0.32
  14    7  0.28
  15    5  0.20

ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76


Consensus pattern (13 bp):   
ATTTTAATTTTTT

Found at i:9227 original size:22 final size:22

Alignment explanation


    Indices: 9199--9298  Score: 98
    Period size: 22  Copynumber: 4.5  Consensus size: 22

       9189 AGAGGCAAAA

                              *   
       9199 AAAATTGTCGACTTAAAGGAGC
          1 AAAATTGTCGACTTAAAGAAGC

                             *    
       9221 AAAATTGTCGACTTAAAAAAGC
          1 AAAATTGTCGACTTAAAGAAGC

               * *       *         
       9243 AAAGTAGTCGACTAAGAAGAAGC
          1 AAAATTGTCGACTTA-AAGAAGC

                  *                 
       9266 -AAATTATCGAC-TAAAGGGAAGC
          1 AAAATTGTCGACTTAAA--GAAGC

                        
       9288 -AAATTGTCGAC
          1 AAAATTGTCGAC

       9299 AAGAAATCAA


Statistics
Matches: 64,  Mismatches: 11, Indels: 6
        0.79            0.14        0.07

Matches are distributed among these distances:
  20    2  0.03
  21    1  0.02
  22   55  0.86
  23    6  0.09

ACGTcount: A:0.45, C:0.14, G:0.21, T:0.20


Consensus pattern (22 bp):   
AAAATTGTCGACTTAAAGAAGC

Found at i:9297 original size:44 final size:44

Alignment explanation


    Indices: 9200--9303  Score: 108
    Period size: 44  Copynumber: 2.4  Consensus size: 44

       9190 GAGGCAAAAA

                        *     *         *               
       9200 AAATTGTCGACTTA-AAGGAGCAAAATTGTCGACTTAAAAAAGC
          1 AAATTGTCGACTAAGAAGAAGCAAAATTATCGACTTAAAAAAGC

                 *                                    *    
       9243 AAAGTAGTCGACTAAGAAGAAGC-AAATTATCGAC-TAAAGGGAAGC
          1 AAA-TTGTCGACTAAGAAGAAGCAAAATTATCGACTTAAA--AAAGC

                             
       9288 AAATTGTCGAC-AAGAA
          1 AAATTGTCGACTAAGAA

       9304 ATCAAGCAAA


Statistics
Matches: 51,  Mismatches: 6, Indels: 8
        0.78            0.09        0.12

Matches are distributed among these distances:
  43   12  0.24
  44   26  0.51
  45   13  0.25

ACGTcount: A:0.46, C:0.13, G:0.21, T:0.19


Consensus pattern (44 bp):   
AAATTGTCGACTAAGAAGAAGCAAAATTATCGACTTAAAAAAGC

Found at i:15720 original size:18 final size:18

Alignment explanation


    Indices: 15697--15732  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

      15687 ACCGTTTGTG

                              
      15697 CATGTTGTTGTTGTTGCA
          1 CATGTTGTTGTTGTTGCA

                              
      15715 CATGTTGTTGTTGTTGCA
          1 CATGTTGTTGTTGTTGCA

      15733 ATAAGTTAGC


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.11, C:0.11, G:0.28, T:0.50


Consensus pattern (18 bp):   
CATGTTGTTGTTGTTGCA
Done.