Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012913.1 Corchorus olitorius cultivar O-4 contig12946, 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: 18251
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Found at i:1024 original size:49 final size:49

Alignment explanation


    Indices: 930--1079  Score: 158
    Period size: 49  Copynumber: 3.1  Consensus size: 49

        920 TGAAGATTTT

                    *  * *                     * *           
        930 CAATCAAATAAGTTAATCATCCTATTACAATGTTTCTCCCAATAAATAA
          1 CAATCAAACAACTAAATCATCCTATTACAATGTTTATGCCAATAAATAA

            *   *                 *                 *        
        979 TAATTAAACAACTAAATCATCCCATTACAATGTTTATGCCTATAAATAA
          1 CAATCAAACAACTAAATCATCCTATTACAATGTTTATGCCAATAAATAA

                    *  * *      *          *                  
       1028 CAATCAAATAAGTTAATCATACTATTACAATATTTCA-GCCAATAAATAA
          1 CAATCAAACAACTAAATCATCCTATTACAATGTTT-ATGCCAATAAATAA

               
       1077 CAA
          1 CAA

       1080 ACAATGGCAT


Statistics
Matches: 82,  Mismatches: 18, Indels: 2
        0.80            0.18        0.02

Matches are distributed among these distances:
  49   81  0.99
  50    1  0.01

ACGTcount: A:0.46, C:0.19, G:0.04, T:0.31


Consensus pattern (49 bp):   
CAATCAAACAACTAAATCATCCTATTACAATGTTTATGCCAATAAATAA

Found at i:3206 original size:3 final size:3

Alignment explanation


    Indices: 3198--3233  Score: 63
    Period size: 3  Copynumber: 12.0  Consensus size: 3

       3188 GAAAATGAAA

                          *                                
       3198 AAG AAG AAG AAT AAG AAG AAG AAG AAG AAG AAG AAG
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG

       3234 GAGGAGACAA


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   3   31  1.00

ACGTcount: A:0.67, C:0.00, G:0.31, T:0.03


Consensus pattern (3 bp):   
AAG

Found at i:11166 original size:24 final size:24

Alignment explanation


    Indices: 11139--11185  Score: 67
    Period size: 24  Copynumber: 2.0  Consensus size: 24

      11129 ACAGCTAATC

                  *  *    *         
      11139 TCTCTTTCTTTTTCTTGCGAAAAT
          1 TCTCTTGCTCTTTCCTGCGAAAAT

                                   
      11163 TCTCTTGCTCTTTCCTGCGAAAA
          1 TCTCTTGCTCTTTCCTGCGAAAA

      11186 AACCATGTCA


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  24   20  1.00

ACGTcount: A:0.17, C:0.26, G:0.11, T:0.47


Consensus pattern (24 bp):   
TCTCTTGCTCTTTCCTGCGAAAAT

Found at i:15633 original size:44 final size:44

Alignment explanation


    Indices: 15577--15660  Score: 159
    Period size: 44  Copynumber: 1.9  Consensus size: 44

      15567 GCTCACACTC

                                                        
      15577 ATCACACACTGTATTTCTGCATTTAGTACAAATCATTTCACATA
          1 ATCACACACTGTATTTCTGCATTTAGTACAAATCATTTCACATA

                                        *           
      15621 ATCACACACTGTATTTCTGCATTTAGTATAAATCATTTCA
          1 ATCACACACTGTATTTCTGCATTTAGTACAAATCATTTCA

      15661 TATACACACC


Statistics
Matches: 39,  Mismatches: 1, Indels: 0
        0.98            0.03        0.00

Matches are distributed among these distances:
  44   39  1.00

ACGTcount: A:0.33, C:0.21, G:0.07, T:0.38


Consensus pattern (44 bp):   
ATCACACACTGTATTTCTGCATTTAGTACAAATCATTTCACATA
Done.