Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010398.1 Corchorus olitorius cultivar O-4 contig10430, 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: 2149
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31


Found at i:533 original size:26 final size:27

Alignment explanation


    Indices: 502--567  Score: 125
    Period size: 27  Copynumber: 2.5  Consensus size: 27

        492 CTAGGCGCGC

                                       
        502 GGGCCAGGCCAGGCTT-GGCCTCACCA
          1 GGGCCAGGCCAGGCTTGGGCCTCACCA

                                       
        528 GGGCCAGGCCAGGCTTGGGCCTCACCA
          1 GGGCCAGGCCAGGCTTGGGCCTCACCA

                         
        555 GGGCCAGGCCAGG
          1 GGGCCAGGCCAGG

        568 AAAAGAAGAA


Statistics
Matches: 39,  Mismatches: 0, Indels: 1
        0.98            0.00        0.03

Matches are distributed among these distances:
  26   16  0.41
  27   23  0.59

ACGTcount: A:0.15, C:0.36, G:0.39, T:0.09


Consensus pattern (27 bp):   
GGGCCAGGCCAGGCTTGGGCCTCACCA

Found at i:590 original size:6 final size:6

Alignment explanation


    Indices: 568--634  Score: 84
    Period size: 6  Copynumber: 11.3  Consensus size: 6

        558 CCAGGCCAGG

                                              *      *   *          
        568 AAAAGA AGAAA-A AAAAGA AAAAGA AAAAGG AAAAGG AAGAGA AAAAGA
          1 AAAAGA A-AAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA

                                   
        616 AAAAGA AAAAG- AAAAGA AA
          1 AAAAGA AAAAGA AAAAGA AA

        635 GAAAATAAAA


Statistics
Matches: 54,  Mismatches: 4, Indels: 6
        0.84            0.06        0.09

Matches are distributed among these distances:
   5    8  0.15
   6   43  0.80
   7    3  0.06

ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00


Consensus pattern (6 bp):   
AAAAGA

Found at i:594 original size:5 final size:5

Alignment explanation


    Indices: 573--649  Score: 50
    Period size: 6  Copynumber: 14.4  Consensus size: 5

        563 CCAGGAAAAG

                                                    *                   
        573 AAGAA AA-AA AAGAAA AAGAAA AAGGAA AAGGAA GAGAAA AAGAAA AAGAAA
          1 AAGAA AAGAA AAG-AA AAG-AA AA-GAA AA-GAA AAG-AA AAG-AA AAG-AA

                                *     *     
        624 AAGAA AAG-A AAGAA AATAA AATAA AA
          1 AAGAA AAGAA AAGAA AAGAA AAGAA AA

        650 TAAGTAAGGA


Statistics
Matches: 64,  Mismatches: 3, Indels: 10
        0.83            0.04        0.13

Matches are distributed among these distances:
   4    8  0.12
   5   20  0.31
   6   35  0.55
   7    1  0.02

ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03


Consensus pattern (5 bp):   
AAGAA

Found at i:601 original size:30 final size:30

Alignment explanation


    Indices: 565--649  Score: 111
    Period size: 30  Copynumber: 2.8  Consensus size: 30

        555 GGGCCAGGCC

                                          
        565 AGGAAAAGAAGAAAAAAAAGAAAAAGAAAA
          1 AGGAAAAGAAGAAAAAAAAGAAAAAGAAAA

                          *                
        595 AGGAAAAGGAAG-AGAAAAAGAAAAAGAAAA
          1 AGGAAAA-GAAGAAAAAAAAGAAAAAGAAAA

                                 *    
        625 A-GAAAAGAAAGAAAATAAAATAAAA
          1 AGGAAAAG-AAGAAAA-AAAAGAAAA

        650 TAAGTAAGGA


Statistics
Matches: 48,  Mismatches: 3, Indels: 7
        0.83            0.05        0.12

Matches are distributed among these distances:
  28    1  0.02
  29    8  0.17
  30   27  0.56
  31   12  0.25

ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02


Consensus pattern (30 bp):   
AGGAAAAGAAGAAAAAAAAGAAAAAGAAAA

Done.