Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021250.1 Corchorus olitorius cultivar O-4 contig21283, 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: 15870
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:6066 original size:25 final size:24

Alignment explanation


    Indices: 6029--6085  Score: 69
    Period size: 25  Copynumber: 2.3  Consensus size: 24

       6019 AAAGAAAATA

                          * *  *    
       6029 TTTTTTTTATGACGTAGAAGCTCT
          1 TTTTTTTTATGACGCAAAAACTCT

                     *               
       6053 TTTTTTTTCTTGACGCAAAAACTCT
          1 TTTTTTTT-ATGACGCAAAAACTCT

                    
       6078 TTTTTTTT
          1 TTTTTTTT

       6086 TCAAAAACGC


Statistics
Matches: 28,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  24    8  0.29
  25   20  0.71

ACGTcount: A:0.19, C:0.14, G:0.11, T:0.56


Consensus pattern (24 bp):   
TTTTTTTTATGACGCAAAAACTCT

Found at i:6133 original size:50 final size:48

Alignment explanation


    Indices: 6065--6165  Score: 150
    Period size: 50  Copynumber: 2.1  Consensus size: 48

       6055 TTTTTTCTTG

                                                             
       6065 ACGCAAAAACTCTTTTTTTTTTCAAAAACGCAAGACTAAGAAATTAAAA
          1 ACGCAAAAACTCTTTTTTTTTTCAAAAACGCAAGACTAA-AAATTAAAA

                                                 * *          
       6114 ACGCAAAAA-TCAATTTTTTTTTTCAAAAACGCAAGATTCAAAATTAAAA
          1 ACGCAAAAACTC--TTTTTTTTTTCAAAAACGCAAGACTAAAAATTAAAA

               
       6163 ACG
          1 ACG

       6166 GATTTTTTTT


Statistics
Matches: 48,  Mismatches: 2, Indels: 4
        0.89            0.04        0.07

Matches are distributed among these distances:
  48    2  0.04
  49   21  0.44
  50   25  0.52

ACGTcount: A:0.48, C:0.16, G:0.08, T:0.29


Consensus pattern (48 bp):   
ACGCAAAAACTCTTTTTTTTTTCAAAAACGCAAGACTAAAAATTAAAA

Found at i:8310 original size:19 final size:20

Alignment explanation


    Indices: 8281--8322  Score: 68
    Period size: 19  Copynumber: 2.1  Consensus size: 20

       8271 CTTATACTTT

                                
       8281 TTTCAATTTTCAATTTCCAC
          1 TTTCAATTTTCAATTTCCAC

                            *   
       8301 TTTC-ATTTTCAATTTTCAC
          1 TTTCAATTTTCAATTTCCAC

               
       8320 TTT
          1 TTT

       8323 TTTTTTGTTT


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  19   17  0.81
  20    4  0.19

ACGTcount: A:0.21, C:0.21, G:0.00, T:0.57


Consensus pattern (20 bp):   
TTTCAATTTTCAATTTCCAC

Done.