Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006184.1 Corchorus olitorius cultivar O-4 contig06209, 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: 4415
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31


Found at i:14 original size:2 final size:2

Alignment explanation


    Indices: 2--40  Score: 62
    Period size: 2  Copynumber: 19.5  Consensus size: 2

          1 T

                                                                       
          2 TA TA TA GTA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA T
          1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

         41 TATGATGATT


Statistics
Matches: 35,  Mismatches: 0, Indels: 4
        0.90            0.00        0.10

Matches are distributed among these distances:
   1    1  0.03
   2   32  0.91
   3    2  0.06

ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:53 original size:21 final size:21

Alignment explanation


    Indices: 2--62  Score: 58
    Period size: 21  Copynumber: 3.0  Consensus size: 21

          1 T

                       *          
          2 TATATAGTATATATATATA-TA
          1 TATATA-TATACATATATATTA

                                 
         23 TATATATATA-ATATATATTA
          1 TATATATATACATATATATTA

                                  
         43 TGATGAT-TATACA-ATATATT
          1 T-AT-ATATATACATATATATT

         63 GTCAATATGC


Statistics
Matches: 36,  Mismatches: 0, Indels: 8
        0.82            0.00        0.18

Matches are distributed among these distances:
  19    7  0.19
  20    7  0.19
  21   19  0.53
  22    3  0.08

ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48


Consensus pattern (21 bp):   
TATATATATACATATATATTA

Found at i:53 original size:23 final size:22

Alignment explanation


    Indices: 1--61  Score: 61
    Period size: 23  Copynumber: 2.6  Consensus size: 22

                                    
          1 TTATATAGTATATATATATATATA
          1 TTATATA--ATATATATATATATA

                                     
         25 TATATATAATATATAT-TATGATGA
          1 T-TATATAATATATATATAT-AT-A

                 *       
         49 TTATACAATATAT
          1 TTATATAATATAT

         62 TGTCAATATG


Statistics
Matches: 33,  Mismatches: 1, Indels: 7
        0.80            0.02        0.17

Matches are distributed among these distances:
  22    3  0.09
  23   21  0.64
  24    3  0.09
  25    6  0.18

ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48


Consensus pattern (22 bp):   
TTATATAATATATATATATATA
Done.