Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019363.1 Corchorus olitorius cultivar O-4 contig19396, 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: 10237
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.32


Found at i:6169 original size:30 final size:31

Alignment explanation


    Indices: 6129--6201  Score: 85
    Period size: 30  Copynumber: 2.4  Consensus size: 31

       6119 GGAGAAAATG

                 *        *                
       6129 CAATTCAGGATACACCGTTAT-GACTTGTGT
          1 CAATTTAGGATACAACGTTATCGACTTGTGT

                        *          *       
       6159 CAATTTAGGATATAACGTTATCGGCTTGTGT
          1 CAATTTAGGATACAACGTTATCGACTTGTGT

               **       
       6190 CAAAATAGGATA
          1 CAATTTAGGATA

       6202 AAAAATGACA


Statistics
Matches: 36,  Mismatches: 6, Indels: 1
        0.84            0.14        0.02

Matches are distributed among these distances:
  30   18  0.50
  31   18  0.50

ACGTcount: A:0.32, C:0.15, G:0.21, T:0.33


Consensus pattern (31 bp):   
CAATTTAGGATACAACGTTATCGACTTGTGT

Found at i:7755 original size:30 final size:31

Alignment explanation


    Indices: 7681--7755  Score: 80
    Period size: 31  Copynumber: 2.5  Consensus size: 31

       7671 ACAATTTGTC

                     **                   *
       7681 TATATCCTGTTTTGACACAAGCCGATAACGT
          1 TATATCCTGAATTGACACAAGCCGATAACGG

                  * *            *         
       7712 TATATCTTAAATTGACACAAGTC-ATAACGG
          1 TATATCCTGAATTGACACAAGCCGATAACGG

             *            
       7742 TGTATCCTGAATTG
          1 TATATCCTGAATTG

       7756 CATTTTCACC


Statistics
Matches: 35,  Mismatches: 9, Indels: 1
        0.78            0.20        0.02

Matches are distributed among these distances:
  30   17  0.49
  31   18  0.51

ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33


Consensus pattern (31 bp):   
TATATCCTGAATTGACACAAGCCGATAACGG

Found at i:10199 original size:32 final size:31

Alignment explanation


    Indices: 10157--10232  Score: 89
    Period size: 31  Copynumber: 2.4  Consensus size: 31

      10147 ATTAGGGACG

                 *                          
      10157 AAATGGCAAAATTTTAAAAGTCTTAAACGGTA
          1 AAATGACAAAATTTTAAAAGT-TTAAACGGTA

                       **            **    
      10189 AAATGACAAAAACTTAAAAGTTTAAGGGGTA
          1 AAATGACAAAATTTTAAAAGTTTAAACGGTA

                  *      
      10220 AAATGATAAAATT
          1 AAATGACAAAATT

      10233 AATAT


Statistics
Matches: 36,  Mismatches: 8, Indels: 1
        0.80            0.18        0.02

Matches are distributed among these distances:
  31   18  0.50
  32   18  0.50

ACGTcount: A:0.51, C:0.07, G:0.16, T:0.26


Consensus pattern (31 bp):   
AAATGACAAAATTTTAAAAGTTTAAACGGTA

Done.