Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012980.1 Corchorus olitorius cultivar O-4 contig13013, 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: 3563
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:479 original size:13 final size:12

Alignment explanation


    Indices: 443--489  Score: 51
    Period size: 13  Copynumber: 3.8  Consensus size: 12

        433 TCAATCTTTA

                        *
        443 TATATATTGATAA
          1 TATATATT-ATAT

                 *      
        456 TA-ATGTTATAT
          1 TATATATTATAT

                         
        467 TATATTATTATAT
          1 TATA-TATTATAT

                      
        480 TATATATTAT
          1 TATATATTAT

        490 CAATAAACTT


Statistics
Matches: 29,  Mismatches: 3, Indels: 5
        0.78            0.08        0.14

Matches are distributed among these distances:
  11    5  0.17
  12   11  0.38
  13   13  0.45

ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55


Consensus pattern (12 bp):   
TATATATTATAT

Found at i:665 original size:23 final size:23

Alignment explanation


    Indices: 617--688  Score: 60
    Period size: 23  Copynumber: 3.2  Consensus size: 23

        607 GAAATCAAAT

                    *  *        *   
        617 CCGAGCCCGAATCCG-ACCCGAGC
          1 CCGAGCCCAAACCCGAACCCTA-C

                                   
        640 CCGAGCCCAAACCCGAACCCTAC
          1 CCGAGCCCAAACCCGAACCCTAC

                  *             *   
        663 CCGAG-ACAGAACCCGAA-CATAC
          1 CCGAGCCCA-AACCCGAACCCTAC

                
        685 CCGA
          1 CCGA

        689 ACCCGACATA


Statistics
Matches: 42,  Mismatches: 5, Indels: 5
        0.81            0.10        0.10

Matches are distributed among these distances:
  22   10  0.24
  23   27  0.64
  24    5  0.12

ACGTcount: A:0.31, C:0.46, G:0.19, T:0.04


Consensus pattern (23 bp):   
CCGAGCCCAAACCCGAACCCTAC

Found at i:692 original size:16 final size:17

Alignment explanation


    Indices: 671--723  Score: 60
    Period size: 16  Copynumber: 3.3  Consensus size: 17

        661 ACCCGAGACA

                             
        671 GAACCCGAACAT-ACCC
          1 GAACCCGAACATAACCC

                             
        687 GAACCCG-ACATAACCC
          1 GAACCCGAACATAACCC

              *               
        703 GAGCCCGAA-A-AAGCCC
          1 GAACCCGAACATAA-CCC

                 
        719 GAACC
          1 GAACC

        724 AGCCCGAGCC


Statistics
Matches: 32,  Mismatches: 2, Indels: 6
        0.80            0.05        0.15

Matches are distributed among these distances:
  15    6  0.19
  16   25  0.78
  17    1  0.03

ACGTcount: A:0.38, C:0.42, G:0.17, T:0.04


Consensus pattern (17 bp):   
GAACCCGAACATAACCC
Done.