Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014476.1 Corchorus olitorius cultivar O-4 contig14509, 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: 5064
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.36


Found at i:769 original size:2 final size:2

Alignment explanation


    Indices: 762--799  Score: 51
    Period size: 2  Copynumber: 18.5  Consensus size: 2

        752 AAAATAGTAG

                                                                     
        762 TA TA TA TA TA -A TA CTA TA TA TA TA TA TA TA TA CTA TA T
          1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA T

        800 GAAGAAGCTA


Statistics
Matches: 33,  Mismatches: 0, Indels: 6
        0.85            0.00        0.15

Matches are distributed among these distances:
   1    1  0.03
   2   28  0.85
   3    4  0.12

ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47


Consensus pattern (2 bp):   
TA

Found at i:781 original size:12 final size:11

Alignment explanation


    Indices: 762--799  Score: 51
    Period size: 11  Copynumber: 3.5  Consensus size: 11

        752 AAAATAGTAG

                       
        762 TATATATATAA
          1 TATATATATAA

                        
        773 TACTATATAT-A
          1 TA-TATATATAA

                      *
        784 TATATATATAC
          1 TATATATATAA

                 
        795 TATAT
          1 TATAT

        800 GAAGAAGCTA


Statistics
Matches: 24,  Mismatches: 1, Indels: 4
        0.83            0.03        0.14

Matches are distributed among these distances:
  10    7  0.29
  11   10  0.42
  12    7  0.29

ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47


Consensus pattern (11 bp):   
TATATATATAA

Found at i:4499 original size:15 final size:15

Alignment explanation


    Indices: 4479--4600  Score: 118
    Period size: 16  Copynumber: 7.8  Consensus size: 15

       4469 CTCGGGTGGG

                          *
       4479 TTCGGGTTCGGGTAC
          1 TTCGGGTTCGGGTAT

                          *
       4494 TTCGGGTTCGGGTAC
          1 TTCGGGTTCGGGTAT

               *            
       4509 TTCAGGTTCGGGTATT
          1 TTCGGGTTCGGGTA-T

                  *        *
       4525 TTCGGGCTCGGGTTAA
          1 TTCGGGTTCGGG-TAT

            *               
       4541 GTCGGGTTCGGGTATT
          1 TTCGGGTTCGGGTA-T

                  *         
       4557 TTCGGGCTCGGGTTAT
          1 TTCGGGTTCGGG-TAT

            *               
       4573 GTCGGGTTCGGGTATT
          1 TTCGGGTTCGGGTA-T

                  *     
       4589 TTCGGGCTCGGG
          1 TTCGGGTTCGGG

       4601 CTCGGGTTTG


Statistics
Matches: 88,  Mismatches: 14, Indels: 9
        0.79            0.13        0.08

Matches are distributed among these distances:
  15   32  0.36
  16   52  0.59
  17    4  0.05

ACGTcount: A:0.07, C:0.17, G:0.40, T:0.35


Consensus pattern (15 bp):   
TTCGGGTTCGGGTAT

Found at i:4554 original size:32 final size:32

Alignment explanation


    Indices: 4480--4600  Score: 174
    Period size: 32  Copynumber: 3.8  Consensus size: 32

       4470 TCGGGTGGGT

                          *      *        **
       4480 TCGGGTTCGGGTA-CTTCGGGTTCGGG-TACT
          1 TCGGGTTCGGGTATTTTCGGGCTCGGGTTAAG

              *                             
       4510 TCAGGTTCGGGTATTTTCGGGCTCGGGTTAAG
          1 TCGGGTTCGGGTATTTTCGGGCTCGGGTTAAG

                                          * 
       4542 TCGGGTTCGGGTATTTTCGGGCTCGGGTTATG
          1 TCGGGTTCGGGTATTTTCGGGCTCGGGTTAAG

                                       
       4574 TCGGGTTCGGGTATTTTCGGGCTCGGG
          1 TCGGGTTCGGGTATTTTCGGGCTCGGG

       4601 CTCGGGTTTG


Statistics
Matches: 82,  Mismatches: 7, Indels: 2
        0.90            0.08        0.02

Matches are distributed among these distances:
  30   12  0.15
  31   11  0.13
  32   59  0.72

ACGTcount: A:0.07, C:0.17, G:0.40, T:0.35


Consensus pattern (32 bp):   
TCGGGTTCGGGTATTTTCGGGCTCGGGTTAAG
Done.