Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005762.1 Corchorus capsularis cultivar CVL-1 contig05780, 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: 11255
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36


Found at i:3272 original size:20 final size:19

Alignment explanation


    Indices: 3238--3275  Score: 58
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       3228 TGATTACTAA

                      *        
       3238 AAAACAATTAGAGGTTATC
          1 AAAACAATTAAAGGTTATC

                               
       3257 AAAACAATTATAAGGTTAT
          1 AAAACAATTA-AAGGTTAT

       3276 TAATAAATTC


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  19   10  0.59
  20    7  0.41

ACGTcount: A:0.50, C:0.08, G:0.13, T:0.29


Consensus pattern (19 bp):   
AAAACAATTAAAGGTTATC

Found at i:5041 original size:12 final size:12

Alignment explanation


    Indices: 5009--5047  Score: 50
    Period size: 12  Copynumber: 3.6  Consensus size: 12

       4999 ATGGAATTAA

                        
       5009 ATATCCGTCG--
          1 ATATCCGTCGAT

                        
       5019 ATA-CC-TCGAT
          1 ATATCCGTCGAT

                        
       5029 ATATCCGTCGAT
          1 ATATCCGTCGAT

                   
       5041 ATATCCG
          1 ATATCCG

       5048 ATATCTGTAC


Statistics
Matches: 25,  Mismatches: 0, Indels: 6
        0.81            0.00        0.19

Matches are distributed among these distances:
   8    3  0.12
   9    2  0.08
  10    6  0.24
  11    2  0.08
  12   12  0.48

ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31


Consensus pattern (12 bp):   
ATATCCGTCGAT

Found at i:6871 original size:13 final size:12

Alignment explanation


    Indices: 6853--6883  Score: 53
    Period size: 13  Copynumber: 2.5  Consensus size: 12

       6843 CATCGATACC

                        
       6853 TCGATATATCCG
          1 TCGATATATCCG

                         
       6865 TTCGATATATCCG
          1 -TCGATATATCCG

                  
       6878 TCGATA
          1 TCGATA

       6884 GTTGTATTAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  12    6  0.33
  13   12  0.67

ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35


Consensus pattern (12 bp):   
TCGATATATCCG

Found at i:8009 original size:16 final size:16

Alignment explanation


    Indices: 7988--8024  Score: 74
    Period size: 16  Copynumber: 2.3  Consensus size: 16

       7978 TATTTGTCAT

                            
       7988 TCATTTATTTATAATA
          1 TCATTTATTTATAATA

                            
       8004 TCATTTATTTATAATA
          1 TCATTTATTTATAATA

                 
       8020 TCATT
          1 TCATT

       8025 AGTGTAGACA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   21  1.00

ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57


Consensus pattern (16 bp):   
TCATTTATTTATAATA

Found at i:8155 original size:33 final size:34

Alignment explanation


    Indices: 8118--8190  Score: 89
    Period size: 33  Copynumber: 2.2  Consensus size: 34

       8108 TTGATTATAA

                               *               
       8118 AATATGTTTGTCTTGGGT-TA-ATGCCTTTGTCTT
          1 AATATGTTT-TCTTGGGTACATATGCCTTTGTCTT

                      *  *                    
       8151 AATAT-TTTTTTTTGGTACATATGCCTTTGTCTT
          1 AATATGTTTTCTTGGGTACATATGCCTTTGTCTT

                   
       8184 AATATGT
          1 AATATGT

       8191 AAGAACAATT


Statistics
Matches: 34,  Mismatches: 3, Indels: 5
        0.81            0.07        0.12

Matches are distributed among these distances:
  31    6  0.18
  32    4  0.12
  33   23  0.68
  34    1  0.03

ACGTcount: A:0.19, C:0.11, G:0.16, T:0.53


Consensus pattern (34 bp):   
AATATGTTTTCTTGGGTACATATGCCTTTGTCTT
Done.