Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014789.1 Corchorus capsularis cultivar CVL-1 contig14810, 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: 27019
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32


Found at i:2248 original size:2 final size:2

Alignment explanation


    Indices: 2241--2295  Score: 64
    Period size: 2  Copynumber: 29.5  Consensus size: 2

       2231 TTTTAGACCC

                                    *  *                                  
       2241 AT AT AT AT AT AT AT AT TT TT AT -T AT -T AT AT -T AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                                     
       2280 AT AT AT AT AT -T AT AT A
          1 AT AT AT AT AT AT AT AT A

       2296 AAGCTAAACT


Statistics
Matches: 47,  Mismatches: 2, Indels: 8
        0.82            0.04        0.14

Matches are distributed among these distances:
   1    4  0.09
   2   43  0.91

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (2 bp):   
AT

Found at i:8348 original size:28 final size:29

Alignment explanation


    Indices: 8303--8358  Score: 78
    Period size: 28  Copynumber: 2.0  Consensus size: 29

       8293 GAGCATTACC

                                         
       8303 TAAAAGTTAGGGCCCTTATTTGACATTTT
          1 TAAAAGTTAGGGCCCTTATTTGACATTTT

                    *    *         *    
       8332 TAAAA-TTTGGGCTCTTATTTGAGATTT
          1 TAAAAGTTAGGGCCCTTATTTGACATTT

       8359 ATGGCAAAGT


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  28   19  0.79
  29    5  0.21

ACGTcount: A:0.27, C:0.11, G:0.18, T:0.45


Consensus pattern (29 bp):   
TAAAAGTTAGGGCCCTTATTTGACATTTT

Found at i:16443 original size:12 final size:14

Alignment explanation


    Indices: 16412--16444  Score: 52
    Period size: 14  Copynumber: 2.5  Consensus size: 14

      16402 TTAACCTTTA

                          
      16412 TTATTGATAAAAGT
          1 TTATTGATAAAAGT

                          
      16426 TTATTGAT-AAAG-
          1 TTATTGATAAAAGT

                   
      16438 TTATTGA
          1 TTATTGA

      16445 ATTTGTGGAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  12    7  0.37
  13    4  0.21
  14    8  0.42

ACGTcount: A:0.39, C:0.00, G:0.15, T:0.45


Consensus pattern (14 bp):   
TTATTGATAAAAGT

Found at i:17138 original size:23 final size:23

Alignment explanation


    Indices: 17095--17138  Score: 54
    Period size: 23  Copynumber: 1.9  Consensus size: 23

      17085 ATGTCATTTA

                        *   *      
      17095 TTATATTTATATTATTTTTATTC
          1 TTATATTTATATAATTATTATTC

                                  
      17118 TTATATTT-TATAAATTATTAT
          1 TTATATTTATAT-AATTATTAT

      17139 CACACGTGCA


Statistics
Matches: 18,  Mismatches: 2, Indels: 2
        0.82            0.09        0.09

Matches are distributed among these distances:
  22    3  0.17
  23   15  0.83

ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66


Consensus pattern (23 bp):   
TTATATTTATATAATTATTATTC
Done.