Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013486.1 Corchorus olitorius cultivar O-4 contig13519, 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: 14506
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32


Found at i:1515 original size:50 final size:51

Alignment explanation


    Indices: 1433--1530  Score: 117
    Period size: 50  Copynumber: 1.9  Consensus size: 51

       1423 TTATAAACTA

                   **                                          
       1433 AAATTATGTTTTATTCAATAAAATCCACATTA-TTATAATTTTACCATTCT
          1 AAATTATCATTTATTCAATAAAATCCACATTATTTATAATTTTACCATTCT

                                *   ** *                    
       1483 AAATTATCATTTATTCAATACAATTTATATTATTGTTATAATTTTACC
          1 AAATTATCATTTATTCAATAAAATCCACATTA-T-TTATAATTTTACC

       1531 TATTATGATT


Statistics
Matches: 39,  Mismatches: 6, Indels: 3
        0.81            0.12        0.06

Matches are distributed among these distances:
  50   26  0.67
  53   13  0.33

ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48


Consensus pattern (51 bp):   
AAATTATCATTTATTCAATAAAATCCACATTATTTATAATTTTACCATTCT

Found at i:1938 original size:24 final size:24

Alignment explanation


    Indices: 1901--1959  Score: 68
    Period size: 24  Copynumber: 2.5  Consensus size: 24

       1891 GTGAATTGTA

                    **          *    
       1901 AAATAAATCGAATAAT-AAATATAT
          1 AAATAAATTTAATAATCAAACAT-T

                                    
       1925 AAATAAATTTAATAATCAAACATT
          1 AAATAAATTTAATAATCAAACATT

                        
       1949 AAA-AAATTTAA
          1 AAATAAATTTAA

       1960 GGCCAACCCA


Statistics
Matches: 31,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
  23    8  0.26
  24   18  0.58
  25    5  0.16

ACGTcount: A:0.63, C:0.05, G:0.02, T:0.31


Consensus pattern (24 bp):   
AAATAAATTTAATAATCAAACATT

Found at i:2937 original size:133 final size:133

Alignment explanation


    Indices: 2681--2937  Score: 390
    Period size: 134  Copynumber: 1.9  Consensus size: 133

       2671 AAATATTTTT

                   *        *           *    **     *                        
       2681 AAAAATTTTAATATATCTAATTATTTTATTTAATTTAGTATAATGGTAAAAATAAAATAGGTATA
          1 AAAAATTCTAATATATATAATTATTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATA

                                                       *                     
       2746 AGGATATTAGATTTAATTAAATAAAAAATAGAGCTTTTAGTTGTGTAAAACTATAAAAGAGTATT
         66 AGGATATTAGATTTAATTAAATAAAAAATAGAGCTTTTAGTTGAGTAAAACTATAAAAGAGTATT

               
       2811 TAA
        131 TAA

                                   *             *                *      *   
       2814 AAAAATTCTAATATATATAAGTTTTTTTAATTAAAATGGTAAAATGGTAAAAATCAAATAGTTAT
          1 AAAAATTCTAATATATATAA-TTATTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTAT

                                              *                         
       2879 AAGGATATTAGATTTAATTAAAT-AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
         65 AAGGATATTAGATTTAATTAAATAAAAAATAGAGCTTTTAGTTGAGTAAAACTATAAAAG

       2938 TTTAAACAAT


Statistics
Matches: 111,  Mismatches: 12, Indels: 2
        0.89            0.10        0.02

Matches are distributed among these distances:
 133   52  0.47
 134   59  0.53

ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38


Consensus pattern (133 bp):   
AAAAATTCTAATATATATAATTATTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATA
AGGATATTAGATTTAATTAAATAAAAAATAGAGCTTTTAGTTGAGTAAAACTATAAAAGAGTATT
TAA
Done.