Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009956.1 Corchorus capsularis cultivar CVL-1 contig09977, 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: 20848
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:878 original size:24 final size:24

Alignment explanation


    Indices: 842--889  Score: 78
    Period size: 24  Copynumber: 2.0  Consensus size: 24

        832 AAGGTCTGGA

                  * *               
        842 CCAATCTAGAGTCAAGTCACGCTT
          1 CCAATCCAAAGTCAAGTCACGCTT

                                    
        866 CCAATCCAAAGTCAAGTCACGCTT
          1 CCAATCCAAAGTCAAGTCACGCTT

        890 ATAACGTTCA


Statistics
Matches: 22,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  24   22  1.00

ACGTcount: A:0.31, C:0.31, G:0.15, T:0.23


Consensus pattern (24 bp):   
CCAATCCAAAGTCAAGTCACGCTT

Found at i:4198 original size:2 final size:2

Alignment explanation


    Indices: 4193--4218  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       4183 TATTCATCAG

                                                  
       4193 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

       4219 GCTTTTACAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:10519 original size:5 final size:5

Alignment explanation


    Indices: 10511--10535  Score: 50
    Period size: 5  Copynumber: 5.0  Consensus size: 5

      10501 ATGAGAGATG

                                         
      10511 GAGAA GAGAA GAGAA GAGAA GAGAA
          1 GAGAA GAGAA GAGAA GAGAA GAGAA

      10536 ATTGAAGAGA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   20  1.00

ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00


Consensus pattern (5 bp):   
GAGAA

Found at i:19163 original size:29 final size:30

Alignment explanation


    Indices: 19130--19191  Score: 90
    Period size: 29  Copynumber: 2.1  Consensus size: 30

      19120 TATGTTCCTC

                   *                      
      19130 AGTATTCGGTAATCACATTGGA-CCGAATT
          1 AGTATTCAGTAATCACATTGGACCCGAATT

                  *   *                   
      19159 AGTATTTAGTTATCACATTGGACCCGAATT
          1 AGTATTCAGTAATCACATTGGACCCGAATT

               
      19189 AGT
          1 AGT

      19192 CACATTGGAC


Statistics
Matches: 29,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  29   19  0.66
  30   10  0.34

ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34


Consensus pattern (30 bp):   
AGTATTCAGTAATCACATTGGACCCGAATT

Found at i:19206 original size:19 final size:20

Alignment explanation


    Indices: 19171--19210  Score: 73
    Period size: 19  Copynumber: 2.0  Consensus size: 20

      19161 TATTTAGTTA

                                
      19171 TCACATTGGACCCGAATTAG
          1 TCACATTGGACCCGAATTAG

                                
      19191 TCACATTGGA-CCGAATTAG
          1 TCACATTGGACCCGAATTAG

             
      19210 T
          1 T

      19211 ATTTAGTTAT


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  19   10  0.50
  20   10  0.50

ACGTcount: A:0.30, C:0.23, G:0.20, T:0.28


Consensus pattern (20 bp):   
TCACATTGGACCCGAATTAG

Found at i:19214 original size:49 final size:49

Alignment explanation


    Indices: 19142--19241  Score: 200
    Period size: 49  Copynumber: 2.0  Consensus size: 49

      19132 TATTCGGTAA

                                                             
      19142 TCACATTGGACCGAATTAGTATTTAGTTATCACATTGGACCCGAATTAG
          1 TCACATTGGACCGAATTAGTATTTAGTTATCACATTGGACCCGAATTAG

                                                             
      19191 TCACATTGGACCGAATTAGTATTTAGTTATCACATTGGACCCGAATTAG
          1 TCACATTGGACCGAATTAGTATTTAGTTATCACATTGGACCCGAATTAG

              
      19240 TC
          1 TC

      19242 CGCCGGTTCT


Statistics
Matches: 51,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  49   51  1.00

ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33


Consensus pattern (49 bp):   
TCACATTGGACCGAATTAGTATTTAGTTATCACATTGGACCCGAATTAG

Found at i:19290 original size:32 final size:32

Alignment explanation


    Indices: 19249--19312  Score: 128
    Period size: 32  Copynumber: 2.0  Consensus size: 32

      19239 GTCCGCCGGT

                                            
      19249 TCTCGTATTCTAATAGTTATCAAGAGATCATA
          1 TCTCGTATTCTAATAGTTATCAAGAGATCATA

                                            
      19281 TCTCGTATTCTAATAGTTATCAAGAGATCATA
          1 TCTCGTATTCTAATAGTTATCAAGAGATCATA

      19313 AGCATCAAGA


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  32   32  1.00

ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38


Consensus pattern (32 bp):   
TCTCGTATTCTAATAGTTATCAAGAGATCATA
Done.