Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024585.1 Corchorus olitorius cultivar O-4 contig24618, 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: 14449
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33


Found at i:7163 original size:41 final size:41

Alignment explanation


    Indices: 7072--7152  Score: 135
    Period size: 41  Copynumber: 2.0  Consensus size: 41

       7062 TAAATAATGT

                      *                              
       7072 AGACATGTATTTATTTAATGGTGTCTTTATCCAAAAGACAA
          1 AGACATGTATCTATTTAATGGTGTCTTTATCCAAAAGACAA

                                *          *        
       7113 AGACATGTATCTATTTAATGTTGTCTTTATCTAAAAGACA
          1 AGACATGTATCTATTTAATGGTGTCTTTATCCAAAAGACA

       7153 TGTACATGTA


Statistics
Matches: 37,  Mismatches: 3, Indels: 0
        0.93            0.08        0.00

Matches are distributed among these distances:
  41   37  1.00

ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38


Consensus pattern (41 bp):   
AGACATGTATCTATTTAATGGTGTCTTTATCCAAAAGACAA

Found at i:11968 original size:37 final size:37

Alignment explanation


    Indices: 11927--12003  Score: 145
    Period size: 37  Copynumber: 2.1  Consensus size: 37

      11917 ATAATGTGAT

                                                 
      11927 TATTCATGAATCAAGAATTGTCTTGTGAAAAGACATG
          1 TATTCATGAATCAAGAATTGTCTTGTGAAAAGACATG

                            *                    
      11964 TATTCATGAATCAAGAGTTGTCTTGTGAAAAGACATG
          1 TATTCATGAATCAAGAATTGTCTTGTGAAAAGACATG

               
      12001 TAT
          1 TAT

      12004 CTATTTAATG


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

Matches are distributed among these distances:
  37   39  1.00

ACGTcount: A:0.36, C:0.10, G:0.19, T:0.34


Consensus pattern (37 bp):   
TATTCATGAATCAAGAATTGTCTTGTGAAAAGACATG

Found at i:12085 original size:41 final size:41

Alignment explanation


    Indices: 11992--12074  Score: 148
    Period size: 41  Copynumber: 2.0  Consensus size: 41

      11982 TGTCTTGTGA

                           *                         
      11992 AAAGACATGTATCTATTTAATGTTGTCTTTATCCAAAAGAC
          1 AAAGACATGTATCTAGTTAATGTTGTCTTTATCCAAAAGAC

                                             *       
      12033 AAAGACATGTATCTAGTTAATGTTGTCTTTATCTAAAAGAC
          1 AAAGACATGTATCTAGTTAATGTTGTCTTTATCCAAAAGAC

             
      12074 A
          1 A

      12075 TGTACATGTA


Statistics
Matches: 40,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  41   40  1.00

ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36


Consensus pattern (41 bp):   
AAAGACATGTATCTAGTTAATGTTGTCTTTATCCAAAAGAC

Found at i:12707 original size:16 final size:15

Alignment explanation


    Indices: 12669--12710  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

      12659 ACAGAGATTG

                   *       
      12669 ACAGAAAGCAATTAA
          1 ACAGAAAACAATTAA

                           
      12684 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
      12699 ACTAGAAAACAA
          1 AC-AGAAAACAA

      12711 AGCAGAGTAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

Matches are distributed among these distances:
  15   16  0.64
  16    9  0.36

ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.