Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002473.1 Corchorus olitorius cultivar O-4 contig02473, 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, 723

Length: 1205
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.35


Found at i:419 original size:21 final size:21

Alignment explanation


    Indices: 393--505  Score: 158
    Period size: 21  Copynumber: 5.4  Consensus size: 21

        383 TGCTAGAAGT

                                  
        393 TCATTGGAGCAA-GTTCCAAGC
          1 TCATTGGAG-AAGGTTCCAAGC

                                 *
        414 TCATTGGAGCAA-GTTCCAAGT
          1 TCATTGGAG-AAGGTTCCAAGC

                                *
        435 TCATTGGAGAAGGTTCCAAGT
          1 TCATTGGAGAAGGTTCCAAGC

                                *
        456 TCATTGGAGAAGGTTCCAAGA
          1 TCATTGGAGAAGGTTCCAAGC

                           *     
        477 TCATTGGAGAAGGTTTCAAGC
          1 TCATTGGAGAAGGTTCCAAGC

                    
        498 TCATTGGA
          1 TCATTGGA

        506 AATGCCTAAG


Statistics
Matches: 87,  Mismatches: 4, Indels: 2
        0.94            0.04        0.02

Matches are distributed among these distances:
  20    2  0.02
  21   85  0.98

ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27


Consensus pattern (21 bp):   
TCATTGGAGAAGGTTCCAAGC

Found at i:436 original size:42 final size:42

Alignment explanation


    Indices: 389--505  Score: 175
    Period size: 42  Copynumber: 2.8  Consensus size: 42

        379 AAGATGCTAG

                                                        
        389 AAGTTCATTGGAGCAA-GTTCCAAGCTCATTGGAGCAA-GTTCC
          1 AAGTTCATTGGAG-AAGGTTCCAAGCTCATTGGAG-AAGGTTCC

                                    *                 
        431 AAGTTCATTGGAGAAGGTTCCAAGTTCATTGGAGAAGGTTCC
          1 AAGTTCATTGGAGAAGGTTCCAAGCTCATTGGAGAAGGTTCC

               *               *             
        473 AAGATCATTGGAGAAGGTTTCAAGCTCATTGGA
          1 AAGTTCATTGGAGAAGGTTCCAAGCTCATTGGA

        506 AATGCCTAAG


Statistics
Matches: 69,  Mismatches: 4, Indels: 4
        0.90            0.05        0.05

Matches are distributed among these distances:
  41    4  0.06
  42   65  0.94

ACGTcount: A:0.30, C:0.16, G:0.26, T:0.27


Consensus pattern (42 bp):   
AAGTTCATTGGAGAAGGTTCCAAGCTCATTGGAGAAGGTTCC
Done.