Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012048.1 Corchorus olitorius cultivar O-4 contig12081, 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: 24565
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31


Found at i:1616 original size:13 final size:13

Alignment explanation


    Indices: 1584--1616  Score: 50
    Period size: 12  Copynumber: 2.5  Consensus size: 13

       1574 TTGCATTAGT

                          
       1584 TTTCACCTAAACAC
          1 TTTC-CCTAAACAC

                         
       1598 -TTCCCTAAACAC
          1 TTTCCCTAAACAC

                   
       1610 TTTCCCT
          1 TTTCCCT

       1617 TAGGATTGAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  12    9  0.50
  13    9  0.50

ACGTcount: A:0.27, C:0.39, G:0.00, T:0.33


Consensus pattern (13 bp):   
TTTCCCTAAACAC

Found at i:16396 original size:2 final size:2

Alignment explanation


    Indices: 16327--16388  Score: 52
    Period size: 2  Copynumber: 31.0  Consensus size: 2

      16317 CCACATGTAC

                                 *                  *  * *  *  *  *       
      16327 AT AT AT AT AT AT AT TT AT AT AT AT AT AC AC GT GT GT TT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

               *                         
      16369 AT GT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT

      16389 GCATATATGT


Statistics
Matches: 51,  Mismatches: 9, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
   2   51  1.00

ACGTcount: A:0.40, C:0.03, G:0.06, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:23796 original size:21 final size:21

Alignment explanation


    Indices: 23759--23798  Score: 64
    Period size: 21  Copynumber: 1.9  Consensus size: 21

      23749 ACTGCCCAGC

                                 
      23759 TGGGTCTTAAGGCAAACCACA
          1 TGGGTCTTAAGGCAAACCACA

                                
      23780 TGGGTGCTTAAGG-AAACCA
          1 TGGGT-CTTAAGGCAAACCA

      23799 TGTGAGCGCC


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  21   11  0.61
  22    7  0.39

ACGTcount: A:0.33, C:0.20, G:0.28, T:0.20


Consensus pattern (21 bp):   
TGGGTCTTAAGGCAAACCACA
Done.