Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023005.1 Corchorus olitorius cultivar O-4 contig23038, 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: 22975
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32


Found at i:5377 original size:107 final size:104

Alignment explanation


    Indices: 5247--5512  Score: 417
    Period size: 107  Copynumber: 2.5  Consensus size: 104

       5237 TAATTATAGA

                                                                             
       5247 GTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCTCCAAATTAAAATTTTATTTTTA
          1 GTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAG-TCCAAATTAAAATTTTATTTTTA

                                              *       
       5312 TTTTAAGGGTAAATTCCAAAATTAATAATTTATTGTTACAGG
         65 TTTTAAGGGTAAATTCCAAAATTAATAA--TATTATTACAGG

                             *            *                                  
       5354 GTTTTAGAAATAAAATACAAAACTAATTTCGCTAAGTTTAGTCCCAAATTAAAATTTTATTTTTA
          1 GTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGT-CCAAATTAAAATTTTATTTTTA

                  *          **                 *   
       5419 TTTTAATGGTAAATTCCGTAATTAATAATATTATTATAGG
         65 TTTTAAGGGTAAATTCCAAAATTAATAATATTATTACAGG

                               *                                   
       5459 GTTTTAGAAATAAAATATATAACTAA-TTCACTAAGTTTAGTCCAAATTAAAATT
          1 GTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGTCCAAATTAAAATT

       5513 AAAATTTCAT


Statistics
Matches: 148,  Mismatches: 10, Indels: 6
        0.90            0.06        0.04

Matches are distributed among these distances:
 103   13  0.09
 104   14  0.09
 105   34  0.23
 106    1  0.01
 107   86  0.58

ACGTcount: A:0.42, C:0.09, G:0.09, T:0.41


Consensus pattern (104 bp):   
GTTTTAGAAATAAAATATAAAACTAATTTCACTAAGTTTAGTCCAAATTAAAATTTTATTTTTAT
TTTAAGGGTAAATTCCAAAATTAATAATATTATTACAGG

Found at i:12107 original size:20 final size:21

Alignment explanation


    Indices: 12082--12121  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      12072 GGGTTTGGTC

                                 
      12082 TTTTTG-AGTTTTGAGGTAGG
          1 TTTTTGTAGTTTTGAGGTAGG

                   *       *    
      12102 TTTTTGTGGTTTTGATGTAG
          1 TTTTTGTAGTTTTGAGGTAG

      12122 ATCTTCCTCT


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  20    6  0.35
  21   11  0.65

ACGTcount: A:0.12, C:0.00, G:0.33, T:0.55


Consensus pattern (21 bp):   
TTTTTGTAGTTTTGAGGTAGG

Found at i:17476 original size:23 final size:25

Alignment explanation


    Indices: 17440--17495  Score: 89
    Period size: 24  Copynumber: 2.3  Consensus size: 25

      17430 GAGGACAAAG

                                  *  
      17440 AAACCCCATCCAAAAG-GGAAGTGA
          1 AAACCCCATCCAAAAGAGGAAGAGA

                                     
      17464 AAACCCCAT-CAAAAGAGGAAGAGA
          1 AAACCCCATCCAAAAGAGGAAGAGA

                    
      17488 AAACCCCA
          1 AAACCCCA

      17496 CCCGGGGGAT


Statistics
Matches: 30,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  23    6  0.20
  24   24  0.80

ACGTcount: A:0.50, C:0.27, G:0.18, T:0.05


Consensus pattern (25 bp):   
AAACCCCATCCAAAAGAGGAAGAGA

Found at i:19444 original size:42 final size:42

Alignment explanation


    Indices: 19398--19488  Score: 137
    Period size: 42  Copynumber: 2.2  Consensus size: 42

      19388 ACCAAACAAT

                   *                     *            
      19398 ACAAAATGCAATGAACTATTGGATTTAAATAAAAATACAAGC
          1 ACAAAATACAATGAACTATTGGATTTAAAGAAAAATACAAGC

                 *                    *               
      19440 ACAAAGTACAATGAACTATTGGATTTGAAGAAAAATACAAGC
          1 ACAAAATACAATGAACTATTGGATTTAAAGAAAAATACAAGC

              *    
      19482 ACCAAAT
          1 ACAAAAT

      19489 TGACTATAAA


Statistics
Matches: 43,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  42   43  1.00

ACGTcount: A:0.52, C:0.13, G:0.13, T:0.22


Consensus pattern (42 bp):   
ACAAAATACAATGAACTATTGGATTTAAAGAAAAATACAAGC

Found at i:19732 original size:2 final size:2

Alignment explanation


    Indices: 19725--19752  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      19715 GTCGAACTAG

                                                     
      19725 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      19753 AAATAAATAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Done.