Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006784.1 Corchorus olitorius cultivar O-4 contig06809, 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: 2115
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38


Found at i:486 original size:83 final size:85

Alignment explanation


    Indices: 382--552  Score: 251
    Period size: 83  Copynumber: 2.0  Consensus size: 85

        372 TCTATTTTTA

                                                             *   *    *      
        382 TTTAATTAAATCTAATTCTTTATAACTATTTTATTTTTACCA-TTTTACTATTTTAATTAAAGAA
          1 TTTAATTAAATCTAATTCTTTATAACTATTTTATTTTTACCATTTTTACCATTATAATCAAA-AA

                                 
        446 ACTTA-A-ATATATTATAATT
         65 ACTTAGATATATATTATAATT

                                                                         * * 
        465 TTTAATTAAAT-TAATATCTTTATAACTATTTTATTTTTACCATTTTTACCATTATAATCACATA
          1 TTTAATTAAATCTAAT-TCTTTATAACTATTTTATTTTTACCATTTTTACCATTATAATCAAAAA

                                 
        529 ACTTAGATATATATTATAATT
         65 ACTTAGATATATATTATAATT

               
        550 TTT
          1 TTT

        553 TAAATATATT


Statistics
Matches: 79,  Mismatches: 5, Indels: 6
        0.88            0.06        0.07

Matches are distributed among these distances:
  82    4  0.05
  83   43  0.54
  84   16  0.20
  85   16  0.20

ACGTcount: A:0.37, C:0.09, G:0.01, T:0.52


Consensus pattern (85 bp):   
TTTAATTAAATCTAATTCTTTATAACTATTTTATTTTTACCATTTTTACCATTATAATCAAAAAA
CTTAGATATATATTATAATT

Found at i:1643 original size:15 final size:15

Alignment explanation


    Indices: 1609--1640  Score: 57
    Period size: 15  Copynumber: 2.2  Consensus size: 15

       1599 CAAAGGTAAT

                           
       1609 GGGAAGGAAAGAAGA
          1 GGGAAGGAAAGAAGA

                           
       1624 GGGAAGGAAAGAA-A
          1 GGGAAGGAAAGAAGA

               
       1638 GGG
          1 GGG

       1641 GAAAGAAGGA


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    4  0.24
  15   13  0.76

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


Consensus pattern (15 bp):   
GGGAAGGAAAGAAGA
Done.