Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012886.1 Corchorus olitorius cultivar O-4 contig12919, 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: 7889
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31


Found at i:431 original size:16 final size:17

Alignment explanation


    Indices: 405--438  Score: 52
    Period size: 16  Copynumber: 2.1  Consensus size: 17

        395 AAGAGGTAAT

                        *    
        405 AAAAGGTTTTTTTTCAA
          1 AAAAGGTTTTTTCTCAA

                             
        422 AAAAGG-TTTTTCTCAA
          1 AAAAGGTTTTTTCTCAA

             
        438 A
          1 A

        439 TCATCTTCTC


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

Matches are distributed among these distances:
  16   10  0.62
  17    6  0.38

ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41


Consensus pattern (17 bp):   
AAAAGGTTTTTTCTCAA

Found at i:4768 original size:29 final size:30

Alignment explanation


    Indices: 4721--4780  Score: 86
    Period size: 29  Copynumber: 2.0  Consensus size: 30

       4711 GAAGTTCGTG

                               *      *    
       4721 TTTGAAGACTCATTGAAGACTTATTTGAAGA
          1 TTTGAAGAC-CATTGAAGAATTATTTCAAGA

                                          
       4752 TTTGAAGA-CATTGAAGAATTATTTCAAGA
          1 TTTGAAGACCATTGAAGAATTATTTCAAGA

       4781 GGAAAGAATT


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  29   19  0.70
  31    8  0.30

ACGTcount: A:0.38, C:0.08, G:0.18, T:0.35


Consensus pattern (30 bp):   
TTTGAAGACCATTGAAGAATTATTTCAAGA

Found at i:6491 original size:33 final size:32

Alignment explanation


    Indices: 6449--6510  Score: 99
    Period size: 33  Copynumber: 1.9  Consensus size: 32

       6439 TTTTTAATCT

                                              
       6449 AAAAAAAAAAATTATG-TTTTCTGCGTTTTTCTG
          1 AAAAAAAAAAATT-TGATTTT-TGCGTTTTTCTG

                                         
       6482 AAAAAAAAAAATTTGATTTTTGCGTTTTT
          1 AAAAAAAAAAATTTGATTTTTGCGTTTTT

       6511 AATTTCTTGA


Statistics
Matches: 28,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  32   11  0.39
  33   17  0.61

ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44


Consensus pattern (32 bp):   
AAAAAAAAAAATTTGATTTTTGCGTTTTTCTG
Done.