Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013095.1 Corchorus olitorius cultivar O-4 contig13128, 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: 9130
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:730 original size:11 final size:11

Alignment explanation


    Indices: 714--739  Score: 52
    Period size: 11  Copynumber: 2.4  Consensus size: 11

        704 CCTTTGCCTA

                       
        714 AAAACTAGAAG
          1 AAAACTAGAAG

                       
        725 AAAACTAGAAG
          1 AAAACTAGAAG

                
        736 AAAA
          1 AAAA

        740 GAAATTATCT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   15  1.00

ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08


Consensus pattern (11 bp):   
AAAACTAGAAG

Found at i:7566 original size:41 final size:43

Alignment explanation


    Indices: 7433--7636  Score: 268
    Period size: 43  Copynumber: 4.8  Consensus size: 43

       7423 CGAATAACCA

                   *                         *       * 
       7433 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC
          1 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTAC

                                                 *      
       7476 AAAAGTCCTCAAACACATATATAACACAGGGGCACCTTTATTAC
          1 -AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTAC

                  *                    ** *  *  *      
       7520 AAAGTCTTCAAACACATATATAACACAAAGACAACTATATT-C
          1 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTAC

                   *                                   
       7562 -AAGTCCCCAAACACATATATAACACAGGGGCACCTCTATTAC
          1 AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTAC

                                    *   *    
       7604 AAAGTCCTCAAACACATATATAACNCAGAGGCA
          1 AAAGTCCTCAAACACATATATAACACAGGGGCA

       7637 TTTCTCCTTA


Statistics
Matches: 138,  Mismatches: 20, Indels: 5
        0.85            0.12        0.03

Matches are distributed among these distances:
  41   33  0.24
  42    2  0.01
  43   64  0.46
  44   39  0.28

ACGTcount: A:0.42, C:0.26, G:0.10, T:0.21


Consensus pattern (43 bp):   
AAAGTCCTCAAACACATATATAACACAGGGGCACCTCTATTAC

Found at i:7592 original size:84 final size:86

Alignment explanation


    Indices: 7433--7627  Score: 286
    Period size: 84  Copynumber: 2.3  Consensus size: 86

       7423 CGAATAACCA

                   *                   ** *  *  *              *             
       7433 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAAGTCCTCAAACACATATAT
          1 AAAGTCCTCAAACACATATATAACACAAAGACAACTATATTCC-AAAGTCCCCAAACACATATAT

                           *      
       7498 AACACAGGGGCACCTTTATTAC
         65 AACACAGGGGCACCTCTATTAC

                  *                                                          
       7520 AAAGTCTTCAAACACATATATAACACAAAGACAACTATATT-C-AAGTCCCCAAACACATATATA
          1 AAAGTCCTCAAACACATATATAACACAAAGACAACTATATTCCAAAGTCCCCAAACACATATATA

                                 
       7583 ACACAGGGGCACCTCTATTAC
         66 ACACAGGGGCACCTCTATTAC

                                    
       7604 AAAGTCCTCAAACACATATATAAC
          1 AAAGTCCTCAAACACATATATAAC

       7628 NCAGAGGCAT


Statistics
Matches: 98,  Mismatches: 10, Indels: 3
        0.88            0.09        0.03

Matches are distributed among these distances:
  84   63  0.64
  86    1  0.01
  87   34  0.35

ACGTcount: A:0.43, C:0.27, G:0.09, T:0.22


Consensus pattern (86 bp):   
AAAGTCCTCAAACACATATATAACACAAAGACAACTATATTCCAAAGTCCCCAAACACATATATA
ACACAGGGGCACCTCTATTAC

Found at i:7752 original size:2 final size:2

Alignment explanation


    Indices: 7745--7780  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       7735 CCAACCTATC

                                                                 
       7745 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       7781 GTGTGTGTGT


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

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


Consensus pattern (2 bp):   
AT

Done.