Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012349.1 Corchorus olitorius cultivar O-4 contig12382, 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: 11485
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33


Found at i:434 original size:22 final size:24

Alignment explanation


    Indices: 399--457  Score: 61
    Period size: 22  Copynumber: 2.5  Consensus size: 24

        389 ATAAATGTTG

                            *      *
        399 CTGATAA-TCTTCT-CTTTTATCT
          1 CTGATAATTCTTCTCCATTTATCA

                                    
        421 CTGATAATTC-TCTCCATTTATCA
          1 CTGATAATTCTTCTCCATTTATCA

                          
        444 CTTGATAATATCTT
          1 C-TGATAAT-TCTT

        458 GCCAGATAAA


Statistics
Matches: 30,  Mismatches: 2, Indels: 6
        0.79            0.05        0.16

Matches are distributed among these distances:
  22   10  0.33
  23   10  0.33
  24    7  0.23
  25    2  0.07
  26    1  0.03

ACGTcount: A:0.24, C:0.22, G:0.05, T:0.49


Consensus pattern (24 bp):   
CTGATAATTCTTCTCCATTTATCA

Found at i:743 original size:14 final size:13

Alignment explanation


    Indices: 707--745  Score: 51
    Period size: 14  Copynumber: 2.9  Consensus size: 13

        697 TATATATTAG

                         
        707 AATTTTTTAAATA
          1 AATTTTTTAAATA

            *    *        
        720 TATTTCTTAAATGA
          1 AATTTTTTAAAT-A

                        
        734 AATTTTTTAAAT
          1 AATTTTTTAAAT

        746 TTTACAATTT


Statistics
Matches: 21,  Mismatches: 4, Indels: 1
        0.81            0.15        0.04

Matches are distributed among these distances:
  13   10  0.48
  14   11  0.52

ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54


Consensus pattern (13 bp):   
AATTTTTTAAATA

Found at i:11144 original size:1 final size:1

Alignment explanation


    Indices: 11138--11166  Score: 58
    Period size: 1  Copynumber: 29.0  Consensus size: 1

      11128 GTAGCAGCCC

                                         
      11138 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
          1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA

      11167 CTAAAAGGTC


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   1   28  1.00

ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00


Consensus pattern (1 bp):   
A

Done.