Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016153.1 Corchorus capsularis cultivar CVL-1 contig16174, 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: 22813
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32


Found at i:3305 original size:19 final size:18

Alignment explanation


    Indices: 3281--3317  Score: 56
    Period size: 19  Copynumber: 2.0  Consensus size: 18

       3271 TTGAAGATTT

                               
       3281 CTTGAAGATAATTTGAAGA
          1 CTTGAAGATAA-TTGAAGA

                     *        
       3300 CTTGAAGATCATTGAAGA
          1 CTTGAAGATAATTGAAGA

       3318 ATTATTTCAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  18    7  0.41
  19   10  0.59

ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30


Consensus pattern (18 bp):   
CTTGAAGATAATTGAAGA

Found at i:13309 original size:116 final size:116

Alignment explanation


    Indices: 13105--13331  Score: 409
    Period size: 116  Copynumber: 2.0  Consensus size: 116

      13095 TGTGGGAGAG

                                                     *                       
      13105 TTTGTAAATGAGAAATTCCATGAGGTTGTAAAAATTGCTTGGGCTTTTCATACTCACCACCCCCA
          1 TTTGTAAATGAGAAATTCCATGAGGTTGTAAAAATTGCTTGAGCTTTTCATACTCACCACCCCCA

                          *                                    
      13170 TCAGAATATATTGAGATAATAGTGGCACCAAAAAATTACTCCACTACAACC
         66 TCAGAATATATTGAAATAATAGTGGCACCAAAAAATTACTCCACTACAACC

                                                                       *     
      13221 TTTGTAAATGAGAAATTCCATGAGGTTGTAAAAATTGCTTGAGCTTTTCATACTCACCATCCCCA
          1 TTTGTAAATGAGAAATTCCATGAGGTTGTAAAAATTGCTTGAGCTTTTCATACTCACCACCCCCA

                                             *   *        
      13286 TCAGAATATATTGAAATAATAGTGGCACCAAAACATTTCTCCACTA
         66 TCAGAATATATTGAAATAATAGTGGCACCAAAAAATTACTCCACTA

      13332 TAGTGCCTTG


Statistics
Matches: 106,  Mismatches: 5, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
 116  106  1.00

ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30


Consensus pattern (116 bp):   
TTTGTAAATGAGAAATTCCATGAGGTTGTAAAAATTGCTTGAGCTTTTCATACTCACCACCCCCA
TCAGAATATATTGAAATAATAGTGGCACCAAAAAATTACTCCACTACAACC

Found at i:17085 original size:18 final size:18

Alignment explanation


    Indices: 17062--17098  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

      17052 GAGTCAATCC

                              
      17062 TAGGGAACTAACTGTGAA
          1 TAGGGAACTAACTGTGAA

                     *   *    
      17080 TAGGGAACTGACTTTGAA
          1 TAGGGAACTAACTGTGAA

             
      17098 T
          1 T

      17099 GAGTCAATCT


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.35, C:0.11, G:0.27, T:0.27


Consensus pattern (18 bp):   
TAGGGAACTAACTGTGAA

Found at i:20919 original size:19 final size:18

Alignment explanation


    Indices: 20895--20930  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      20885 TGAAGATTTC

                               
      20895 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAA-TTGAAGAT

                    *        
      20914 TTGAAGATCATTGAAGA
          1 TTGAAGATAATTGAAGA

      20931 ATAATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33


Consensus pattern (18 bp):   
TTGAAGATAATTGAAGAT
Done.