Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018496.1 Corchorus olitorius cultivar O-4 contig18529, 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: 5780
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32


Found at i:1133 original size:36 final size:36

Alignment explanation


    Indices: 1092--1163  Score: 144
    Period size: 36  Copynumber: 2.0  Consensus size: 36

       1082 TCAAAAATTG

                                                
       1092 GGGAAATAAGATCAATCAAAAACAATCAAATTCTAT
          1 GGGAAATAAGATCAATCAAAAACAATCAAATTCTAT

                                                
       1128 GGGAAATAAGATCAATCAAAAACAATCAAATTCTAT
          1 GGGAAATAAGATCAATCAAAAACAATCAAATTCTAT

       1164 CCTAGGTTCT


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  36   36  1.00

ACGTcount: A:0.53, C:0.14, G:0.11, T:0.22


Consensus pattern (36 bp):   
GGGAAATAAGATCAATCAAAAACAATCAAATTCTAT

Found at i:1470 original size:30 final size:29

Alignment explanation


    Indices: 1431--1487  Score: 89
    Period size: 30  Copynumber: 1.9  Consensus size: 29

       1421 GTTTATTAAT

                                           
       1431 GAAACTTGAAAATTAAAGACATAAGATAAAA
          1 GAAACTTGAAAATTAAAG-CATAA-ATAAAA

                                       
       1462 GAAA-TTGAAAATTAAAGCATAAATAA
          1 GAAACTTGAAAATTAAAGCATAAATAA

       1488 CTAATCCTAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  28    4  0.15
  29    5  0.19
  30   13  0.50
  31    4  0.15

ACGTcount: A:0.61, C:0.05, G:0.12, T:0.21


Consensus pattern (29 bp):   
GAAACTTGAAAATTAAAGCATAAATAAAA

Found at i:2453 original size:23 final size:21

Alignment explanation


    Indices: 2427--2478  Score: 61
    Period size: 23  Copynumber: 2.3  Consensus size: 21

       2417 TTGAATCCTT

                                    
       2427 GTCGATGATTT-GCTCCCTTTTAA
          1 GTCGAT-ATTTGGCT-CC-TTTAA

                                  
       2450 GTCGACTATTTGGCTCCTTTAA
          1 GTCGA-TATTTGGCTCCTTTAA

                   
       2472 GTCGATA
          1 GTCGATA

       2479 ATCCTTAGTC


Statistics
Matches: 27,  Mismatches: 0, Indels: 6
        0.82            0.00        0.18

Matches are distributed among these distances:
  21    2  0.07
  22   10  0.37
  23   11  0.41
  24    4  0.15

ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40


Consensus pattern (21 bp):   
GTCGATATTTGGCTCCTTTAA

Found at i:3645 original size:6 final size:6

Alignment explanation


    Indices: 3595--3626  Score: 55
    Period size: 6  Copynumber: 5.3  Consensus size: 6

       3585 ATTAGTGTAT

                      *                          
       3595 AAATTA AAAATA AAATTA AAATTA AAATTA AA
          1 AAATTA AAATTA AAATTA AAATTA AAATTA AA

       3627 TGTGCAAAGA


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   6   24  1.00

ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28


Consensus pattern (6 bp):   
AAATTA
Done.