Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015937.1 Corchorus olitorius cultivar O-4 contig15970, 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: 5622
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31


Found at i:2290 original size:19 final size:18

Alignment explanation


    Indices: 2257--2292  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       2247 TGAAAATAAT

                              
       2257 TCTTCAATGGTCTTCAAA
          1 TCTTCAATGGTCTTCAAA

                     *        
       2275 TCTTCAAATTGTCTTCAA
          1 TCTTC-AATGGTCTTCAA

       2293 TAAATCTTCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    5  0.31
  19   11  0.69

ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42


Consensus pattern (18 bp):   
TCTTCAATGGTCTTCAAA

Found at i:3844 original size:30 final size:29

Alignment explanation


    Indices: 3805--3861  Score: 89
    Period size: 30  Copynumber: 1.9  Consensus size: 29

       3795 GTTTATTAAT

                                           
       3805 GAAACTTGAAAATTAAAGACATAAGATAAGG
          1 GAAACTTGAAAATTAAAG-CATAA-ATAAGG

                                       
       3836 GAAA-TTGAAAATTAAAGCATAAATAA
          1 GAAACTTGAAAATTAAAGCATAAATAA

       3862 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:0.58, C:0.05, G:0.16, T:0.21


Consensus pattern (29 bp):   
GAAACTTGAAAATTAAAGCATAAATAAGG

Found at i:4836 original size:23 final size:23

Alignment explanation


    Indices: 4810--4855  Score: 67
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       4800 ATGAAGTGCG

                                    
       4810 TCCTCCTTAGTCGACTA-TTGCTT
          1 TCCTCCTTAGTCGAC-ACTTGCTT

                 *                 
       4833 TCCTCTTTAGTCGACACTTGCTT
          1 TCCTCCTTAGTCGACACTTGCTT

       4856 CTCTTGAAGT


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  22    1  0.05
  23   20  0.95

ACGTcount: A:0.13, C:0.30, G:0.13, T:0.43


Consensus pattern (23 bp):   
TCCTCCTTAGTCGACACTTGCTT

Found at i:5194 original size:23 final size:21

Alignment explanation


    Indices: 5163--5207  Score: 63
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       5153 GAAGAAGAAA

                                   
       5163 GGAAATTGGCATCCTTGCGGGCT
          1 GGAAATTGGCA--CTTGCGGGCT

                *                
       5186 GGAACTTGGCACTTGCGGGCT
          1 GGAAATTGGCACTTGCGGGCT

             
       5207 G
          1 G

       5208 CCCTAGTGTC


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  21   11  0.52
  23   10  0.48

ACGTcount: A:0.16, C:0.22, G:0.38, T:0.24


Consensus pattern (21 bp):   
GGAAATTGGCACTTGCGGGCT
Done.