Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016707.1 Corchorus olitorius cultivar O-4 contig16740, 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: 19680
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:3371 original size:17 final size:19

Alignment explanation


    Indices: 3349--3391  Score: 54
    Period size: 19  Copynumber: 2.4  Consensus size: 19

       3339 TGGCCATCTC

                               
       3349 AAGAAAGAC-T-GTCCGAA
          1 AAGAAAGACTTGGTCCGAA

                   *      *    
       3366 AAGAAAGGCTTGGTTCGAA
          1 AAGAAAGACTTGGTCCGAA

                   
       3385 AAGAAAG
          1 AAGAAAG

       3392 GTACATATTA


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  17    8  0.36
  18    1  0.05
  19   13  0.59

ACGTcount: A:0.47, C:0.12, G:0.28, T:0.14


Consensus pattern (19 bp):   
AAGAAAGACTTGGTCCGAA

Found at i:10630 original size:29 final size:30

Alignment explanation


    Indices: 10578--10649  Score: 92
    Period size: 29  Copynumber: 2.4  Consensus size: 30

      10568 ACATGTACGG

                             * *     *    
      10578 TTTGGACATTTTACCCCTTGAACT-TCAAT
          1 TTTGGACATTTTACCCCCTAAACTCCCAAT

                *                         
      10607 TTTGAACATTTTACCCCCTAAACTCCCAAT
          1 TTTGGACATTTTACCCCCTAAACTCCCAAT

              *          
      10637 TTCGGACATTTTA
          1 TTTGGACATTTTA

      10650 GTCCCTCTTA


Statistics
Matches: 36,  Mismatches: 6, Indels: 1
        0.84            0.14        0.02

Matches are distributed among these distances:
  29   21  0.58
  30   15  0.42

ACGTcount: A:0.26, C:0.26, G:0.08, T:0.39


Consensus pattern (30 bp):   
TTTGGACATTTTACCCCCTAAACTCCCAAT

Found at i:13103 original size:28 final size:28

Alignment explanation


    Indices: 13048--13103  Score: 78
    Period size: 28  Copynumber: 2.0  Consensus size: 28

      13038 TTTTATTGTG

                          *        *    
      13048 AATTTAATCAATTATATTAATTTTTTTT
          1 AATTTAATCAATTAAATTAATTTCTTTT

                                         
      13076 AATTTAATCAATTAAATT-ATTCTCTTTT
          1 AATTTAATCAATTAAATTAATT-TCTTTT

      13104 TTTCCCGGAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  27    3  0.12
  28   22  0.88

ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57


Consensus pattern (28 bp):   
AATTTAATCAATTAAATTAATTTCTTTT

Found at i:14386 original size:14 final size:14

Alignment explanation


    Indices: 14367--14394  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

      14357 AATATATTTT

                          
      14367 AGTTTATTTTAGAG
          1 AGTTTATTTTAGAG

                          
      14381 AGTTTATTTTAGAG
          1 AGTTTATTTTAGAG

      14395 TTTGTCTTTA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50


Consensus pattern (14 bp):   
AGTTTATTTTAGAG

Found at i:14439 original size:31 final size:31

Alignment explanation


    Indices: 14401--14464  Score: 103
    Period size: 31  Copynumber: 2.1  Consensus size: 31

      14391 AGAGTTTGTC

                                            
      14401 TTTATTTTCTTA-TTTAGATTAGTATTAGGCT
          1 TTTATTTTCTTATTTTAG-TTAGTATTAGGCT

                                      *    
      14432 TTTATTTTCTTATTTTAGTTAGTATTGGGCT
          1 TTTATTTTCTTATTTTAGTTAGTATTAGGCT

              
      14463 TT
          1 TT

      14465 ATTGGCTGTT


Statistics
Matches: 31,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  31   26  0.84
  32    5  0.16

ACGTcount: A:0.19, C:0.06, G:0.14, T:0.61


Consensus pattern (31 bp):   
TTTATTTTCTTATTTTAGTTAGTATTAGGCT
Done.