Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012723.1 Corchorus capsularis cultivar CVL-1 contig12744, 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: 14748
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:3114 original size:9 final size:10

Alignment explanation


    Indices: 3092--3124  Score: 66
    Period size: 10  Copynumber: 3.3  Consensus size: 10

       3082 AGTTATATCG

                      
       3092 AAAAATAACA
          1 AAAAATAACA

                      
       3102 AAAAATAACA
          1 AAAAATAACA

                      
       3112 AAAAATAACA
          1 AAAAATAACA

               
       3122 AAA
          1 AAA

       3125 TTTCTCGACC


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

Matches are distributed among these distances:
  10   23  1.00

ACGTcount: A:0.82, C:0.09, G:0.00, T:0.09


Consensus pattern (10 bp):   
AAAAATAACA

Found at i:6435 original size:11 final size:10

Alignment explanation


    Indices: 6417--6450  Score: 50
    Period size: 11  Copynumber: 3.2  Consensus size: 10

       6407 GAAGTTCGTG

                      
       6417 TTTTGAAGAT
          1 TTTTGAAGAT

                       
       6427 TTCTTGAAGAT
          1 TT-TTGAAGAT

                       
       6438 ATTTTGAAGAT
          1 -TTTTGAAGAT

              
       6449 TT
          1 TT

       6451 GAAGACAATT


Statistics
Matches: 22,  Mismatches: 0, Indels: 4
        0.85            0.00        0.15

Matches are distributed among these distances:
  10    4  0.18
  11   16  0.73
  12    2  0.09

ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50


Consensus pattern (10 bp):   
TTTTGAAGAT

Found at i:14097 original size:27 final size:28

Alignment explanation


    Indices: 14060--14131  Score: 101
    Period size: 27  Copynumber: 2.6  Consensus size: 28

      14050 GGTCATCTAG

                *                       
      14060 GGGGCATTTTGGTCATTTTCACA-TTCA
          1 GGGGTATTTTGGTCATTTTCACATTTCA

                               **     * 
      14087 GGGGTATTTTGGTCATTTTTGCATTTTA
          1 GGGGTATTTTGGTCATTTTCACATTTCA

                             
      14115 GGGGTATTTTGGTCATT
          1 GGGGTATTTTGGTCATT

      14132 CTTAATCTAC


Statistics
Matches: 40,  Mismatches: 4, Indels: 1
        0.89            0.09        0.02

Matches are distributed among these distances:
  27   20  0.50
  28   20  0.50

ACGTcount: A:0.15, C:0.11, G:0.26, T:0.47


Consensus pattern (28 bp):   
GGGGTATTTTGGTCATTTTCACATTTCA

Found at i:14724 original size:20 final size:20

Alignment explanation


    Indices: 14685--14725  Score: 55
    Period size: 20  Copynumber: 2.0  Consensus size: 20

      14675 ATGAATACAA

                          **    
      14685 GGCATTTGATTTACGGATTG
          1 GGCATTTGATTTACAAATTG

                        *       
      14705 GGCATTTGATTTGCAAATTG
          1 GGCATTTGATTTACAAATTG

             
      14725 G
          1 G

      14726 CGCTTTTCTT


Statistics
Matches: 18,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.22, C:0.10, G:0.29, T:0.39


Consensus pattern (20 bp):   
GGCATTTGATTTACAAATTG
Done.