Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01013887.1 Corchorus capsularis cultivar CVL-1 contig13908, 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: 11953
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:2643 original size:2 final size:2

Alignment explanation


    Indices: 2636--2672  Score: 65
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       2626 GGAATTCGTT

                                              *                    
       2636 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       2673 TATTTAAAGA


Statistics
Matches: 33,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (2 bp):   
TA

Found at i:3930 original size:32 final size:31

Alignment explanation


    Indices: 3805--3945  Score: 167
    Period size: 31  Copynumber: 4.5  Consensus size: 31

       3795 TCCTTTAGTG

                    *                   ** 
       3805 CACGTGGCATGCCACGTGTCA-TTTTTGAAA
          1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA

              *     *                 *    
       3835 CATGTGGCATGCCACGTGTCACTTTTCGGTA
          1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA

                       *  *                
       3866 CACGTGGCGTGACATGTGTCACTTTTTGGTA
          1 CACGTGGCGTGCCACGTGTCACTTTTTGGTA

              *            *            *   
       3897 CATGTGGCGTGCCACATGTCACTTTTTTTGTA
          1 CACGTGGCGTGCCACGTGTCAC-TTTTTGGTA

                             
       3929 CACGTGGCGTGCCACGT
          1 CACGTGGCGTGCCACGT

       3946 CGGACACCGT


Statistics
Matches: 93,  Mismatches: 16, Indels: 2
        0.84            0.14        0.02

Matches are distributed among these distances:
  30   20  0.22
  31   50  0.54
  32   23  0.25

ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33


Consensus pattern (31 bp):   
CACGTGGCGTGCCACGTGTCACTTTTTGGTA

Found at i:5542 original size:29 final size:29

Alignment explanation


    Indices: 5468--5544  Score: 109
    Period size: 29  Copynumber: 2.6  Consensus size: 29

       5458 GTTAGGTTGA

                                           
       5468 GGGAGCAAAACATCTCAAAATTGAAGTTCAT
          1 GGGA-CAAAACATC-CAAAATTGAAGTTCAT

                     **                  
       5499 GGGACAAAATGTCCAAAATTGAAGTTCAT
          1 GGGACAAAACATCCAAAATTGAAGTTCAT

                *            
       5528 GGGATAAAACATCCAAA
          1 GGGACAAAACATCCAAA

       5545 CACTAAAAAT


Statistics
Matches: 41,  Mismatches: 5, Indels: 2
        0.85            0.10        0.04

Matches are distributed among these distances:
  29   30  0.73
  30    7  0.17
  31    4  0.10

ACGTcount: A:0.44, C:0.16, G:0.19, T:0.21


Consensus pattern (29 bp):   
GGGACAAAACATCCAAAATTGAAGTTCAT

Found at i:8541 original size:16 final size:17

Alignment explanation


    Indices: 8510--8542  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       8500 AAGATAGTGA

                             
       8510 AATTTTTATGGAATAAT
          1 AATTTTTATGGAATAAT

                   *         
       8527 AATTTTTTTGG-ATAAT
          1 AATTTTTATGGAATAAT

       8543 TAAATCATAT


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

Matches are distributed among these distances:
  16    5  0.33
  17   10  0.67

ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52


Consensus pattern (17 bp):   
AATTTTTATGGAATAAT

Found at i:11867 original size:19 final size:19

Alignment explanation


    Indices: 11821--11873  Score: 52
    Period size: 19  Copynumber: 2.7  Consensus size: 19

      11811 AAAATATATT

                            *   
      11821 GAGAGAGAGAGAGAGATAGG
          1 GAGA-AGAGAGAGAGAAAGG

              **             * 
      11841 GACTAGAGAGAGAGAAATG
          1 GAGAAGAGAGAGAGAAAGG

                    *     
      11860 GAGAAGAGGGAGAG
          1 GAGAAGAGAGAGAG

      11874 CACTTTATTA


Statistics
Matches: 26,  Mismatches: 7, Indels: 1
        0.76            0.21        0.03

Matches are distributed among these distances:
  19   24  0.92
  20    2  0.08

ACGTcount: A:0.45, C:0.02, G:0.47, T:0.06


Consensus pattern (19 bp):   
GAGAAGAGAGAGAGAAAGG
Done.