Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022885.1 Corchorus olitorius cultivar O-4 contig22918, 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: 8568
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:3519 original size:20 final size:23

Alignment explanation


    Indices: 3491--3533  Score: 56
    Period size: 20  Copynumber: 2.0  Consensus size: 23

       3481 CGTTTGGTTC

                                   
       3491 GTGGAAAG-TAG-TA-GAAAAAT
          1 GTGGAAAGTTAGATAGGAAAAAT

                *                  
       3511 GTGGTAAGTTAGATAGGAAAAAT
          1 GTGGAAAGTTAGATAGGAAAAAT

       3534 AACATTCCCA


Statistics
Matches: 19,  Mismatches: 1, Indels: 3
        0.83            0.04        0.13

Matches are distributed among these distances:
  20    7  0.37
  21    3  0.16
  22    2  0.11
  23    7  0.37

ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23


Consensus pattern (23 bp):   
GTGGAAAGTTAGATAGGAAAAAT

Found at i:3899 original size:2 final size:2

Alignment explanation


    Indices: 3892--3935  Score: 81
    Period size: 2  Copynumber: 22.5  Consensus size: 2

       3882 TAGTATCTAG

                                                                          
       3892 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                
       3933 TA T
          1 TA T

       3936 CATTTTAGGA


Statistics
Matches: 41,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   1    1  0.02
   2   40  0.98

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:4737 original size:19 final size:18

Alignment explanation


    Indices: 4711--4752  Score: 66
    Period size: 19  Copynumber: 2.3  Consensus size: 18

       4701 AATTAATGAT

                              
       4711 TTTAATATTATATTTTTA
          1 TTTAATATTATATTTTTA

                               
       4729 TTTATATATTATATTTTTA
          1 TTTA-ATATTATATTTTTA

            *    
       4748 CTTAA
          1 TTTAA

       4753 AAAATTACTC


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  18    5  0.23
  19   17  0.77

ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64


Consensus pattern (18 bp):   
TTTAATATTATATTTTTA
Done.