Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023763.1 Corchorus olitorius cultivar O-4 contig23796, 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: 31253
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:12839 original size:16 final size:16

Alignment explanation


    Indices: 12818--12848  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

      12808 GTAATCATTT

                            
      12818 CTCTCTCTCTCTTTCA
          1 CTCTCTCTCTCTTTCA

                    *      
      12834 CTCTCTCTTTCTTTC
          1 CTCTCTCTCTCTTTC

      12849 TCTTTCTTTC


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.03, C:0.42, G:0.00, T:0.55


Consensus pattern (16 bp):   
CTCTCTCTCTCTTTCA

Found at i:12851 original size:14 final size:14

Alignment explanation


    Indices: 12815--12863  Score: 62
    Period size: 14  Copynumber: 3.4  Consensus size: 14

      12805 CAAGTAATCA

                       *  
      12815 TTTCTCTCTCTCTC
          1 TTTCTCTCTCTTTC

                            
      12829 TTTCACTCTCTCTTTC
          1 TTT--CTCTCTCTTTC

                   *      
      12845 TTTCTCTTTCTTTC
          1 TTTCTCTCTCTTTC

                 
      12859 TTTCT
          1 TTTCT

      12864 TGTTTTAGGT


Statistics
Matches: 31,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
  14   18  0.58
  16   13  0.42

ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63


Consensus pattern (14 bp):   
TTTCTCTCTCTTTC

Found at i:14270 original size:6 final size:6

Alignment explanation


    Indices: 14259--14310  Score: 95
    Period size: 6  Copynumber: 8.7  Consensus size: 6

      14249 CATTATCTTC

                                                                 * 
      14259 TCTCTG TCTCTG TCTCTG TCTCTG TCTCTG TCTCTG TCTCTG TCTCGG
          1 TCTCTG TCTCTG TCTCTG TCTCTG TCTCTG TCTCTG TCTCTG TCTCTG

                
      14307 TCTC
          1 TCTC

      14311 ATCTCACCCT


Statistics
Matches: 45,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
   6   45  1.00

ACGTcount: A:0.00, C:0.35, G:0.17, T:0.48


Consensus pattern (6 bp):   
TCTCTG

Found at i:22561 original size:31 final size:32

Alignment explanation


    Indices: 22526--22587  Score: 81
    Period size: 31  Copynumber: 2.0  Consensus size: 32

      22516 TCTTGGTCTG

                   *          *             
      22526 ACGTGGCCTCGCCACATGGCA-TTTTGGTCCA
          1 ACGTGGCATCGCCACATGACATTTTTGGTCCA

                     *     *               
      22557 ACGTGGCATTGCCACGTGACATTTTTGGTCC
          1 ACGTGGCATCGCCACATGACATTTTTGGTCC

      22588 GACATGGGAT


Statistics
Matches: 26,  Mismatches: 4, Indels: 1
        0.84            0.13        0.03

Matches are distributed among these distances:
  31   17  0.65
  32    9  0.35

ACGTcount: A:0.16, C:0.29, G:0.26, T:0.29


Consensus pattern (32 bp):   
ACGTGGCATCGCCACATGACATTTTTGGTCCA

Found at i:24906 original size:61 final size:61

Alignment explanation


    Indices: 24815--24931  Score: 216
    Period size: 61  Copynumber: 1.9  Consensus size: 61

      24805 TTTGTGAACA

                                     *                                   
      24815 AGTTAGCAATAACATTTAATCTTAATAAATGTTTCAACAAAGTTGGGCATTTATGTGATCG
          1 AGTTAGCAATAACATTTAATCTTAAAAAATGTTTCAACAAAGTTGGGCATTTATGTGATCG

                                              *                     
      24876 AGTTAGCAATAACATTTAATCTTAAAAAATGTTTTAACAAAGTTGGGCATTTATGT
          1 AGTTAGCAATAACATTTAATCTTAAAAAATGTTTCAACAAAGTTGGGCATTTATGT

      24932 TTGAGTTCTA


Statistics
Matches: 54,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  61   54  1.00

ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37


Consensus pattern (61 bp):   
AGTTAGCAATAACATTTAATCTTAAAAAATGTTTCAACAAAGTTGGGCATTTATGTGATCG
Done.