Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011220.1 Corchorus capsularis cultivar CVL-1 contig11241, 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: 16393
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36


Found at i:2267 original size:16 final size:17

Alignment explanation


    Indices: 2248--2280  Score: 50
    Period size: 16  Copynumber: 2.0  Consensus size: 17

       2238 TTCGGACGGG

                             
       2248 TTCGGATTCGGG-TATT
          1 TTCGGATTCGGGATATT

                 *           
       2264 TTCGGGTTCGGGATATT
          1 TTCGGATTCGGGATATT

       2281 GACTTTTCTA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  16   11  0.73
  17    4  0.27

ACGTcount: A:0.12, C:0.12, G:0.33, T:0.42


Consensus pattern (17 bp):   
TTCGGATTCGGGATATT

Found at i:3628 original size:12 final size:13

Alignment explanation


    Indices: 3606--3631  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

       3596 GACTAGAAAA

                         
       3606 TTTGTTTTTTTTT
          1 TTTGTTTTTTTTT

                         
       3619 TTTGTTTTTTTTT
          1 TTTGTTTTTTTTT

       3632 CTCTGAGGAT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92


Consensus pattern (13 bp):   
TTTGTTTTTTTTT

Found at i:8764 original size:15 final size:17

Alignment explanation


    Indices: 8744--8776  Score: 52
    Period size: 15  Copynumber: 2.1  Consensus size: 17

       8734 CGATCAAATG

                             
       8744 TCGGGTC-ATT-TGGGT
          1 TCGGGTCAATTCTGGGT

                             
       8759 TCGGGTCAATTCTGGGT
          1 TCGGGTCAATTCTGGGT

             
       8776 T
          1 T

       8777 GGACCGTTTT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  15    7  0.44
  16    3  0.19
  17    6  0.38

ACGTcount: A:0.09, C:0.15, G:0.36, T:0.39


Consensus pattern (17 bp):   
TCGGGTCAATTCTGGGT

Found at i:11318 original size:2 final size:2

Alignment explanation


    Indices: 11313--11339  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      11303 TATATACTGC

                                                    
      11313 TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA T

      11340 TAAACTTGCC


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:12282 original size:86 final size:86

Alignment explanation


    Indices: 12127--12285  Score: 284
    Period size: 86  Copynumber: 1.8  Consensus size: 86

      12117 ATGAAAAGAC

                                                                             
      12127 TAAACAGATGAATATGGAAATTGGAATGTTAGGTAGTGAAAGAATTTGGGATGTAGCGTTAAAGC
          1 TAAACAGATGAATATGGAAATTGGAATGTTAGGTAGTGAAAGAATTTGGGATGTAGCGTTAAAGC

                                 
      12192 ATTTCCATTCTTTTAGACTAT
         66 ATTTCCATTCTTTTAGACTAT

                *                                                            
      12213 TAAAGAGATGAATATGGAAATTGGAATGTTAGGTAGT-ATAAGAATTTGGGATGTAGCGTTAAAG
          1 TAAACAGATGAATATGGAAATTGGAATGTTAGGTAGTGA-AAGAATTTGGGATGTAGCGTTAAAG

            *        
      12277 TATTTCCAT
         65 CATTTCCAT

      12286 ATTCACTGAC


Statistics
Matches: 70,  Mismatches: 2, Indels: 2
        0.95            0.03        0.03

Matches are distributed among these distances:
  85    1  0.01
  86   69  0.99

ACGTcount: A:0.36, C:0.06, G:0.25, T:0.33


Consensus pattern (86 bp):   
TAAACAGATGAATATGGAAATTGGAATGTTAGGTAGTGAAAGAATTTGGGATGTAGCGTTAAAGC
ATTTCCATTCTTTTAGACTAT

Found at i:15647 original size:2 final size:2

Alignment explanation


    Indices: 15640--15666  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

      15630 ATGACGAGAC

                                                    
      15640 AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT A

      15667 GCTATTTTCT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.