Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009683.1 Corchorus olitorius cultivar O-4 contig09715, 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: 5092
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35


Found at i:503 original size:32 final size:31

Alignment explanation


    Indices: 467--528  Score: 106
    Period size: 32  Copynumber: 2.0  Consensus size: 31

        457 AATTCTAATG

                                            
        467 TGCCTCGACTATAGTACTAAGCTAAAAGGGAA
          1 TGCCTCGACTATAGTACTAAGCT-AAAGGGAA

                            *             
        499 TGCCTCGACTATAGTATTAAGCTAAAGGGA
          1 TGCCTCGACTATAGTACTAAGCTAAAGGGA

        529 TTTGTCCGAT


Statistics
Matches: 29,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  31    7  0.24
  32   22  0.76

ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24


Consensus pattern (31 bp):   
TGCCTCGACTATAGTACTAAGCTAAAGGGAA

Found at i:652 original size:20 final size:20

Alignment explanation


    Indices: 627--669  Score: 68
    Period size: 20  Copynumber: 2.1  Consensus size: 20

        617 ACAATGCCAT

                  *             
        627 AATGAATTTAATTACTAGAA
          1 AATGAAATTAATTACTAGAA

                              * 
        647 AATGAAATTAATTACTAGCA
          1 AATGAAATTAATTACTAGAA

               
        667 AAT
          1 AAT

        670 CAAAAATGCA


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  20   21  1.00

ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33


Consensus pattern (20 bp):   
AATGAAATTAATTACTAGAA

Found at i:1967 original size:18 final size:18

Alignment explanation


    Indices: 1924--1970  Score: 85
    Period size: 18  Copynumber: 2.6  Consensus size: 18

       1914 TATGAGCCCA

                   *          
       1924 CAATTGGAGCCAAAAACC
          1 CAATTGGTGCCAAAAACC

                              
       1942 CAATTGGTGCCAAAAACC
          1 CAATTGGTGCCAAAAACC

                       
       1960 CAATTGGTGCC
          1 CAATTGGTGCC

       1971 TCACAAACCC


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  18   28  1.00

ACGTcount: A:0.36, C:0.28, G:0.19, T:0.17


Consensus pattern (18 bp):   
CAATTGGTGCCAAAAACC
Done.