Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014461.1 Corchorus capsularis cultivar CVL-1 contig14482, 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: 39212
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:213 original size:40 final size:40

Alignment explanation


    Indices: 151--227  Score: 111
    Period size: 40  Copynumber: 1.9  Consensus size: 40

        141 CTTCGATCCT

                        *                  *        
        151 CCTAATAATTAATGAAGTAAATTAAATTCAGGTTTAGCCC
          1 CCTAATAATTAAGGAAGTAAATTAAATTCAGATTTAGCCC

                                     *            
        191 CCTAATAATTAAGGTAAG-AAATTACATTCAGATTTAG
          1 CCTAATAATTAAGG-AAGTAAATTAAATTCAGATTTAG

        228 TCCTAGTTAT


Statistics
Matches: 33,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
  40   30  0.91
  41    3  0.09

ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32


Consensus pattern (40 bp):   
CCTAATAATTAAGGAAGTAAATTAAATTCAGATTTAGCCC

Found at i:17138 original size:11 final size:11

Alignment explanation


    Indices: 17122--17151  Score: 51
    Period size: 11  Copynumber: 2.7  Consensus size: 11

      17112 TAGAAATTTT

                  *    
      17122 ATTAGAGGTTA
          1 ATTAGAAGTTA

                       
      17133 ATTAGAAGTTA
          1 ATTAGAAGTTA

                    
      17144 ATTAGAAG
          1 ATTAGAAG

      17152 GGAGGGGCAA


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

Matches are distributed among these distances:
  11   18  1.00

ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33


Consensus pattern (11 bp):   
ATTAGAAGTTA

Found at i:25981 original size:23 final size:23

Alignment explanation


    Indices: 25954--26003  Score: 100
    Period size: 23  Copynumber: 2.2  Consensus size: 23

      25944 GATTAGTCAG

                                   
      25954 GACCAATATGACTACCAAATACC
          1 GACCAATATGACTACCAAATACC

                                   
      25977 GACCAATATGACTACCAAATACC
          1 GACCAATATGACTACCAAATACC

                
      26000 GACC
          1 GACC

      26004 GTACAGAAGA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   27  1.00

ACGTcount: A:0.42, C:0.32, G:0.10, T:0.16


Consensus pattern (23 bp):   
GACCAATATGACTACCAAATACC

Found at i:30225 original size:14 final size:14

Alignment explanation


    Indices: 30206--30240  Score: 61
    Period size: 14  Copynumber: 2.5  Consensus size: 14

      30196 AAAAAGCTGG

                  *       
      30206 CAGAATTGGATTAT
          1 CAGAATCGGATTAT

                          
      30220 CAGAATCGGATTAT
          1 CAGAATCGGATTAT

                   
      30234 CAGAATC
          1 CAGAATC

      30241 TATCTCACAC


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

Matches are distributed among these distances:
  14   20  1.00

ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29


Consensus pattern (14 bp):   
CAGAATCGGATTAT

Found at i:35762 original size:21 final size:21

Alignment explanation


    Indices: 35736--35779  Score: 88
    Period size: 21  Copynumber: 2.1  Consensus size: 21

      35726 ATTTCAATTG

                                 
      35736 TAATTGTCATGGGGAAAGGGT
          1 TAATTGTCATGGGGAAAGGGT

                                 
      35757 TAATTGTCATGGGGAAAGGGT
          1 TAATTGTCATGGGGAAAGGGT

              
      35778 TA
          1 TA

      35780 GATTCAAGAG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.30, C:0.05, G:0.36, T:0.30


Consensus pattern (21 bp):   
TAATTGTCATGGGGAAAGGGT
Done.