Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023520.1 Corchorus olitorius cultivar O-4 contig23553, 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: 5647
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31


Found at i:529 original size:12 final size:12

Alignment explanation


    Indices: 492--570  Score: 113
    Period size: 12  Copynumber: 6.5  Consensus size: 12

        482 TTAATACAGG

                *       
        492 TATCCATGGATA
          1 TATCGATGGATA

                   *     
        504 TATCGAAGGGATA
          1 TATCG-ATGGATA

                        
        517 TATCGATGGATA
          1 TATCGATGGATA

                  *     
        529 TATCGACGGATA
          1 TATCGATGGATA

                        
        541 TATCGATGGATA
          1 TATCGATGGATA

                  *     
        553 TATCGACGGATA
          1 TATCGATGGATA

                  
        565 TATCGA
          1 TATCGA

        571 GGTATCGATG


Statistics
Matches: 60,  Mismatches: 6, Indels: 2
        0.88            0.09        0.03

Matches are distributed among these distances:
  12   49  0.82
  13   11  0.18

ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29


Consensus pattern (12 bp):   
TATCGATGGATA

Found at i:544 original size:24 final size:24

Alignment explanation


    Indices: 492--570  Score: 131
    Period size: 24  Copynumber: 3.2  Consensus size: 24

        482 TTAATACAGG

                *              *     
        492 TATCCATGGATATATCGAAGGGATA
          1 TATCGATGGATATATCG-ACGGATA

                                    
        517 TATCGATGGATATATCGACGGATA
          1 TATCGATGGATATATCGACGGATA

                                    
        541 TATCGATGGATATATCGACGGATA
          1 TATCGATGGATATATCGACGGATA

                  
        565 TATCGA
          1 TATCGA

        571 GGTATCGATG


Statistics
Matches: 52,  Mismatches: 2, Indels: 1
        0.95            0.04        0.02

Matches are distributed among these distances:
  24   36  0.69
  25   16  0.31

ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29


Consensus pattern (24 bp):   
TATCGATGGATATATCGACGGATA

Found at i:2199 original size:13 final size:13

Alignment explanation


    Indices: 2175--2214  Score: 53
    Period size: 13  Copynumber: 2.9  Consensus size: 13

       2165 ATATTCCACA

                          
       2175 TACTACTTAATTAT
          1 TACTA-TTAATTAT

                         
       2189 TACTATTAATTAT
          1 TACTATTAATTAT

              *          
       2202 TATTATTACATTA
          1 TACTATTA-ATTA

       2215 AATGTCATAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  13   15  0.62
  14    9  0.38

ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53


Consensus pattern (13 bp):   
TACTATTAATTAT

Found at i:2571 original size:10 final size:10

Alignment explanation


    Indices: 2543--2579  Score: 67
    Period size: 10  Copynumber: 3.8  Consensus size: 10

       2533 TGAGCTCGAC

                      
       2543 AGGTATATAT
          1 AGGTATATAT

                      
       2553 AGGTA-ATAT
          1 AGGTATATAT

                      
       2562 AGGTATATAT
          1 AGGTATATAT

                    
       2572 AGGTATAT
          1 AGGTATAT

       2580 CGAGTAGCTC


Statistics
Matches: 26,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   9    9  0.35
  10   17  0.65

ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38


Consensus pattern (10 bp):   
AGGTATATAT

Found at i:3138 original size:19 final size:20

Alignment explanation


    Indices: 3114--3152  Score: 62
    Period size: 19  Copynumber: 2.0  Consensus size: 20

       3104 CATTCTCAAC

                         *      
       3114 ACAAAAAAA-AAATCAAAAA
          1 ACAAAAAAACAAAACAAAAA

                                
       3133 ACAAAAAAACAAAACAAAAA
          1 ACAAAAAAACAAAACAAAAA

       3153 GGATTGCAAG


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  19    9  0.50
  20    9  0.50

ACGTcount: A:0.85, C:0.13, G:0.00, T:0.03


Consensus pattern (20 bp):   
ACAAAAAAACAAAACAAAAA

Found at i:3140 original size:21 final size:20

Alignment explanation


    Indices: 3111--3152  Score: 57
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       3101 GGTCATTCTC

                           *     
       3111 AACACAAAAAAAAAATCAAAA
          1 AACA-AAAAAAAAAAACAAAA

                      *         
       3132 AACAAAAAAACAAAACAAAA
          1 AACAAAAAAAAAAAACAAAA

             
       3152 A
          1 A

       3153 GGATTGCAAG


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  20   15  0.79
  21    4  0.21

ACGTcount: A:0.83, C:0.14, G:0.00, T:0.02


Consensus pattern (20 bp):   
AACAAAAAAAAAAAACAAAA
Done.