Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022390.1 Corchorus olitorius cultivar O-4 contig22423, 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: 9342
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28


Found at i:4933 original size:29 final size:29

Alignment explanation


    Indices: 4891--4961  Score: 142
    Period size: 29  Copynumber: 2.4  Consensus size: 29

       4881 TGGCGTTCAC

                                         
       4891 GGCTCGAACGAACGTGAGAGGGGCGAAGA
          1 GGCTCGAACGAACGTGAGAGGGGCGAAGA

                                         
       4920 GGCTCGAACGAACGTGAGAGGGGCGAAGA
          1 GGCTCGAACGAACGTGAGAGGGGCGAAGA

                         
       4949 GGCTCGAACGAAC
          1 GGCTCGAACGAAC

       4962 CCCTGTCTTC


Statistics
Matches: 42,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  29   42  1.00

ACGTcount: A:0.31, C:0.20, G:0.42, T:0.07


Consensus pattern (29 bp):   
GGCTCGAACGAACGTGAGAGGGGCGAAGA

Found at i:7475 original size:19 final size:19

Alignment explanation


    Indices: 7451--7488  Score: 76
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       7441 GCTACACCAA

                               
       7451 GAAAGACTAGTTGACATTT
          1 GAAAGACTAGTTGACATTT

                               
       7470 GAAAGACTAGTTGACATTT
          1 GAAAGACTAGTTGACATTT

       7489 TATCTGCCTT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   19  1.00

ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32


Consensus pattern (19 bp):   
GAAAGACTAGTTGACATTT

Found at i:8615 original size:20 final size:20

Alignment explanation


    Indices: 8590--8631  Score: 57
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       8580 GACCTGGTCC

                                
       8590 TTGTCCCATGAGCGTTCGTA
          1 TTGTCCCATGAGCGTTCGTA

                   *  *      *  
       8610 TTGTCCCCTGCGCGTTCTTA
          1 TTGTCCCATGAGCGTTCGTA

              
       8630 TT
          1 TT

       8632 CCACCATAGT


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  20   19  1.00

ACGTcount: A:0.10, C:0.29, G:0.21, T:0.40


Consensus pattern (20 bp):   
TTGTCCCATGAGCGTTCGTA

Found at i:8981 original size:18 final size:18

Alignment explanation


    Indices: 8958--8993  Score: 72
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       8948 TAATGGCTAA

                              
       8958 AAAAACAATAGGACTTAC
          1 AAAAACAATAGGACTTAC

                              
       8976 AAAAACAATAGGACTTAC
          1 AAAAACAATAGGACTTAC

       8994 TCTGGCCTGG


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   18  1.00

ACGTcount: A:0.56, C:0.17, G:0.11, T:0.17


Consensus pattern (18 bp):   
AAAAACAATAGGACTTAC
Done.