Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000396.1 Corchorus olitorius cultivar O-4 contig00396, 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: 9092
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35


Found at i:543 original size:18 final size:18

Alignment explanation


    Indices: 502--547  Score: 56
    Period size: 18  Copynumber: 2.6  Consensus size: 18

        492 CACTAGAAAT

                    *         
        502 TTAATAATAATTATTCAA
          1 TTAATAATTATTATTCAA

            **             *  
        520 AAAATAATTATTATTTAA
          1 TTAATAATTATTATTCAA

                      
        538 TTAATAATTA
          1 TTAATAATTA

        548 ATTAATTTCA


Statistics
Matches: 22,  Mismatches: 6, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  18   22  1.00

ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46


Consensus pattern (18 bp):   
TTAATAATTATTATTCAA

Found at i:2165 original size:23 final size:24

Alignment explanation


    Indices: 2117--2160  Score: 67
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       2107 CCTCATTGAC

                                    
       2117 TCCAAACTCTGTTTTCCAATTTCT
          1 TCCAAACTCTGTTTTCCAATTTCT

                                   
       2141 TCCAAA-TCTG-TTTCC-ATTTC
          1 TCCAAACTCTGTTTTCCAATTTC

       2161 CCTTCATTTC


Statistics
Matches: 20,  Mismatches: 0, Indels: 3
        0.87            0.00        0.13

Matches are distributed among these distances:
  21    5  0.25
  22    5  0.25
  23    4  0.20
  24    6  0.30

ACGTcount: A:0.20, C:0.30, G:0.05, T:0.45


Consensus pattern (24 bp):   
TCCAAACTCTGTTTTCCAATTTCT

Found at i:4380 original size:9 final size:9

Alignment explanation


    Indices: 4368--4392  Score: 50
    Period size: 9  Copynumber: 2.8  Consensus size: 9

       4358 TTCAGATCTT

                     
       4368 CCGTATGGA
          1 CCGTATGGA

                     
       4377 CCGTATGGA
          1 CCGTATGGA

                   
       4386 CCGTATG
          1 CCGTATG

       4393 TACAGCCTCA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   16  1.00

ACGTcount: A:0.20, C:0.24, G:0.32, T:0.24


Consensus pattern (9 bp):   
CCGTATGGA

Found at i:6746 original size:21 final size:20

Alignment explanation


    Indices: 6722--6772  Score: 52
    Period size: 20  Copynumber: 2.6  Consensus size: 20

       6712 GGTAGTGGAG

                                 
       6722 ATGGAGAATAAAAATTGGAAA
          1 ATGG-GAATAAAAATTGGAAA

                 *  *         * 
       6743 ATGGGGATGAAAATTGGAGA
          1 ATGGGAATAAAAATTGGAAA

                        
       6763 A--GGAATAAAA
          1 ATGGGAATAAAA

       6773 GTTGTTCTCC


Statistics
Matches: 25,  Mismatches: 5, Indels: 3
        0.76            0.15        0.09

Matches are distributed among these distances:
  18    7  0.28
  20   14  0.56
  21    4  0.16

ACGTcount: A:0.53, C:0.00, G:0.29, T:0.18


Consensus pattern (20 bp):   
ATGGGAATAAAAATTGGAAA
Done.