Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016245.1 Corchorus olitorius cultivar O-4 contig16278, 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: 4210
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35


Found at i:729 original size:38 final size:39

Alignment explanation


    Indices: 687--777  Score: 130
    Period size: 42  Copynumber: 2.3  Consensus size: 39

        677 TTTTTAACTT

                 *                                 
        687 AATTAGTTTAA-AAAAGATGAATAATTAATGATTAGGTA
          1 AATTATTTTAATAAAAGATGAATAATTAATGATTAGGTA

                           *                          
        725 AATTATTTTAACTTTTAAAGATGAATAATTAATGATTAGGTA
          1 AATTATTTTAA---TAAAAGATGAATAATTAATGATTAGGTA

                       
        767 AATTATTTTAA
          1 AATTATTTTAA

        778 CTTTTAAACT


Statistics
Matches: 47,  Mismatches: 2, Indels: 4
        0.89            0.04        0.08

Matches are distributed among these distances:
  38   10  0.21
  42   37  0.79

ACGTcount: A:0.46, C:0.01, G:0.12, T:0.41


Consensus pattern (39 bp):   
AATTATTTTAATAAAAGATGAATAATTAATGATTAGGTA

Found at i:750 original size:42 final size:42

Alignment explanation


    Indices: 699--785  Score: 174
    Period size: 42  Copynumber: 2.1  Consensus size: 42

        689 TTAGTTTAAA

                                                      
        699 AAAGATGAATAATTAATGATTAGGTAAATTATTTTAACTTTT
          1 AAAGATGAATAATTAATGATTAGGTAAATTATTTTAACTTTT

                                                      
        741 AAAGATGAATAATTAATGATTAGGTAAATTATTTTAACTTTT
          1 AAAGATGAATAATTAATGATTAGGTAAATTATTTTAACTTTT

               
        783 AAA
          1 AAA

        786 CTTGATAATA


Statistics
Matches: 45,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  42   45  1.00

ACGTcount: A:0.45, C:0.02, G:0.11, T:0.41


Consensus pattern (42 bp):   
AAAGATGAATAATTAATGATTAGGTAAATTATTTTAACTTTT

Found at i:1274 original size:133 final size:134

Alignment explanation


    Indices: 1121--1421  Score: 552
    Period size: 133  Copynumber: 2.3  Consensus size: 134

       1111 TTTTTGGCCA

                                 *                                           
       1121 AAAAATAGAGTTTTTAGTTGAATAAAACTATAAAAATATATTTAAAAAATTCTAATATATATAAT
          1 AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAATATATTTAAAAAATTCTAATATATATAAT

                *                                                            
       1186 TTTTTTAATTAAAATAGT-AAAATGGTAAAAATTAAATAGTTATAAGGATATATTATATTTAATT
         66 TTTTCTAATTAAAATAGTAAAAATGGTAAAAATTAAATAGTTATAAGGATATATTATATTTAATT

                
       1250 AAAT
        131 AAAT

                                        *                                    
       1254 AAAAATAGAGTTTTTAGTTGAGTAAAACCAT-AAAATATATTTAAAAAATTCTAATATATATAAT
          1 AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAATATATTTAAAAAATTCTAATATATATAAT

                                                                             
       1318 TTTTCTAATTAAAATAGTAAAAATGGTAAAAATTAAATAGTTATAAGGATATATTATATTTAATT
         66 TTTTCTAATTAAAATAGTAAAAATGGTAAAAATTAAATAGTTATAAGGATATATTATATTTAATT

              * 
       1383 AACT
        131 AAAT

                                               
       1387 AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
          1 AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA

       1422 GTCTAAACAA


Statistics
Matches: 161,  Mismatches: 5, Indels: 3
        0.95            0.03        0.02

Matches are distributed among these distances:
 132   50  0.31
 133  108  0.67
 134    3  0.02

ACGTcount: A:0.50, C:0.03, G:0.09, T:0.38


Consensus pattern (134 bp):   
AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAATATATTTAAAAAATTCTAATATATATAAT
TTTTCTAATTAAAATAGTAAAAATGGTAAAAATTAAATAGTTATAAGGATATATTATATTTAATT
AAAT

Done.