Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016078.1 Corchorus olitorius cultivar O-4 contig16111, 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, 794

Length: 1324
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29


Found at i:435 original size:15 final size:15

Alignment explanation


    Indices: 415--470  Score: 67
    Period size: 15  Copynumber: 3.5  Consensus size: 15

        405 CACCAGATGA

                           
        415 TGTTTCTGCAACGGT
          1 TGTTTCTGCAACGGT

                    *       
        430 TGTTTCTGAAACGGAT
          1 TGTTTCTGCAACGG-T

                   *         
        446 GATGTTTTTGCAACGGT
          1 --TGTTTCTGCAACGGT

                    
        463 TGTTTCTG
          1 TGTTTCTG

        471 GAACAGTGCC


Statistics
Matches: 34,  Mismatches: 4, Indels: 6
        0.77            0.09        0.14

Matches are distributed among these distances:
  15   20  0.59
  16    1  0.03
  17    1  0.03
  18   12  0.35

ACGTcount: A:0.16, C:0.14, G:0.27, T:0.43


Consensus pattern (15 bp):   
TGTTTCTGCAACGGT

Found at i:460 original size:18 final size:18

Alignment explanation


    Indices: 399--461  Score: 69
    Period size: 18  Copynumber: 3.7  Consensus size: 18

        389 CATTTGCAAT

                    * *       
        399 TTTCTGCACCAGATGATG
          1 TTTCTGCAACGGATGATG

                              
        417 TTTCTGCAACGG-T--TG
          1 TTTCTGCAACGGATGATG

                  *           
        432 TTTCTGAAACGGATGATG
          1 TTTCTGCAACGGATGATG

               *        
        450 TTTTTGCAACGG
          1 TTTCTGCAACGG

        462 TTGTTTCTGG


Statistics
Matches: 37,  Mismatches: 5, Indels: 6
        0.77            0.10        0.12

Matches are distributed among these distances:
  15   13  0.35
  16    1  0.03
  17    1  0.03
  18   22  0.59

ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37


Consensus pattern (18 bp):   
TTTCTGCAACGGATGATG

Found at i:571 original size:27 final size:27

Alignment explanation


    Indices: 540--677  Score: 249
    Period size: 27  Copynumber: 5.1  Consensus size: 27

        530 GACCATTCAA

                                  *    
        540 TTGGGGTTGCGGATGAAGCGCAACCAC
          1 TTGGGGTTGCGGATGAAGCGCAGCCAC

                          *            
        567 TTGGGGTTGCGGATAAAGCGCAGCCAC
          1 TTGGGGTTGCGGATGAAGCGCAGCCAC

            *                          
        594 CTGGGGTTGCGGATGAAGCGCAGCCAC
          1 TTGGGGTTGCGGATGAAGCGCAGCCAC

                                       
        621 TTGGGGTTGCGGATGAAGCGCAGCCAC
          1 TTGGGGTTGCGGATGAAGCGCAGCCAC

                                       
        648 TTGGGGTTGCGGATGAAGCGCAGCCAC
          1 TTGGGGTTGCGGATGAAGCGCAGCCAC

               
        675 TTG
          1 TTG

        678 AGGTGGCGCC


Statistics
Matches: 106,  Mismatches: 5, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  27  106  1.00

ACGTcount: A:0.20, C:0.22, G:0.39, T:0.19


Consensus pattern (27 bp):   
TTGGGGTTGCGGATGAAGCGCAGCCAC

Done.