Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020252.1 Corchorus olitorius cultivar O-4 contig20285, 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: 1724
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30


Found at i:504 original size:13 final size:13

Alignment explanation


    Indices: 429--588  Score: 99
    Period size: 13  Copynumber: 12.8  Consensus size: 13

        419 TGGTGGAAAA

                         
        429 TTTGATGAAGAAC
          1 TTTGATGAAGAAC

                          
        442 --TGAGTGAA-AAC
          1 TTTGA-TGAAGAAC

                *        
        453 -TTGTTGAAGAAC
          1 TTTGATGAAGAAC

              *            
        465 AACTTGATGAAG-AC
          1 --TTTGATGAAGAAC

                *        
        479 -TTGTTGAAGAAC
          1 TTTGATGAAGAAC

                     *   
        491 TTTGATGAATAAC
          1 TTTGATGAAGAAC

                *  *     
        504 TTTGGTGGAG-AC
          1 TTTGATGAAGAAC

                *        
        516 -TTGTTGAAGAAC
          1 TTTGATGAAGAAC

                     *   
        528 TTTGATGAATAAC
          1 TTTGATGAAGAAC

                    *     
        541 TTTCG-TGGAG-AC
          1 TTT-GATGAAGAAC

                *        
        553 -TTGTTGAAGAAC
          1 TTTGATGAAGAAC

                     *  *
        565 TTTGATGAATAAT
          1 TTTGATGAAGAAC

                       
        578 TTTGATGAAGA
          1 TTTGATGAAGA

        589 CTTGTTTCAC


Statistics
Matches: 114,  Mismatches: 19, Indels: 28
        0.71            0.12        0.17

Matches are distributed among these distances:
  10    1  0.01
  11   31  0.27
  12   19  0.17
  13   52  0.46
  14    3  0.03
  15    8  0.07

ACGTcount: A:0.34, C:0.08, G:0.24, T:0.33


Consensus pattern (13 bp):   
TTTGATGAAGAAC

Found at i:516 original size:37 final size:37

Alignment explanation


    Indices: 475--594  Score: 204
    Period size: 37  Copynumber: 3.2  Consensus size: 37

        465 AACTTGATGA

                                                 
        475 AGACTTGTTGAAGAACTTTGATGAATAACTTTGGTGG
          1 AGACTTGTTGAAGAACTTTGATGAATAACTTTGGTGG

                                            *    
        512 AGACTTGTTGAAGAACTTTGATGAATAACTTTCGTGG
          1 AGACTTGTTGAAGAACTTTGATGAATAACTTTGGTGG

                                        *    *  *
        549 AGACTTGTTGAAGAACTTTGATGAATAATTTTGATGA
          1 AGACTTGTTGAAGAACTTTGATGAATAACTTTGGTGG

                     
        586 AGACTTGTT
          1 AGACTTGTT

        595 TCACTCTTGG


Statistics
Matches: 78,  Mismatches: 5, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  37   78  1.00

ACGTcount: A:0.31, C:0.08, G:0.24, T:0.37


Consensus pattern (37 bp):   
AGACTTGTTGAAGAACTTTGATGAATAACTTTGGTGG
Done.