Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005961.1 Corchorus olitorius cultivar O-4 contig05986, 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, 659

Length: 1099
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34


Found at i:514 original size:33 final size:33

Alignment explanation


    Indices: 472--673  Score: 212
    Period size: 33  Copynumber: 6.1  Consensus size: 33

        462 CTGAACCTAA

                           **       *        
        472 TTTGAGTGTTGTTTGCAATGACACGAAATCTGT
          1 TTTGAGTGTTGTTTGTGATGACACTAAATCTGT

                         *       *      *  **
        505 TTTGAGTGTTGTTAGTGATGATACTAAACCTAA
          1 TTTGAGTGTTGTTTGTGATGACACTAAATCTGT

                           *                 
        538 TTTGAGTGTTGTTTGCGATGACACTAAATCTGT
          1 TTTGAGTGTTGTTTGTGATGACACTAAATCTGT

             *            *       *      *  **
        571 TCT-AGATGTTGTTAGTGATGATACTAAAACTAA
          1 TTTGAG-TGTTGTTTGTGATGACACTAAATCTGT

                                             
        604 TTTGAGTGTTGTTTGTGATGACACTAAATCTGT
          1 TTTGAGTGTTGTTTGTGATGACACTAAATCTGT

                                  *            
        637 TTT-AGATGTTGTTTGTGATGAAAC-AAATTCTGT
          1 TTTGAG-TGTTGTTTGTGATGACACTAAA-TCTGT

                
        670 TTTG
          1 TTTG

        674 GATGCTAATT


Statistics
Matches: 136,  Mismatches: 28, Indels: 9
        0.79            0.16        0.05

Matches are distributed among these distances:
  32    7  0.05
  33  127  0.93
  34    2  0.01

ACGTcount: A:0.26, C:0.09, G:0.22, T:0.42


Consensus pattern (33 bp):   
TTTGAGTGTTGTTTGTGATGACACTAAATCTGT

Found at i:542 original size:66 final size:66

Alignment explanation


    Indices: 465--657  Score: 316
    Period size: 66  Copynumber: 2.9  Consensus size: 66

        455 AGTAATTCTG

                                   *       *                                 
        465 AACCTAATTTGAGTGTTGTTTGCAATGACACGAAATCTGTTTT-GAGTGTTGTTAGTGATGATAC
          1 AACCTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTTTAGA-TGTTGTTAGTGATGATAC

              
        529 TA
         65 TA

                                                     *                       
        531 AACCTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTCTAGATGTTGTTAGTGATGATACT
          1 AACCTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTTTAGATGTTGTTAGTGATGATACT

             
        596 A
         66 A

              *                   *                              *       
        597 AAACTAATTTGAGTGTTGTTTGTGATGACACTAAATCTGTTTTAGATGTTGTTTGTGATGA
          1 AACCTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTTTAGATGTTGTTAGTGATGA

        658 AACAAATTCT


Statistics
Matches: 119,  Mismatches: 7, Indels: 2
        0.93            0.05        0.02

Matches are distributed among these distances:
  66  117  0.98
  67    2  0.02

ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41


Consensus pattern (66 bp):   
AACCTAATTTGAGTGTTGTTTGCGATGACACTAAATCTGTTTTAGATGTTGTTAGTGATGATACT
A

Found at i:686 original size:33 final size:33

Alignment explanation


    Indices: 616--698  Score: 96
    Period size: 33  Copynumber: 2.5  Consensus size: 33

        606 TGAGTGTTGT

                     *                    * **
        616 TTGTGATGACACTAAA-TCTGTTTTAGATGTTGT
          1 TTGTGATGAAAC-AAATTCTGTTTTAGATGCTAA

                                    *        
        649 TTGTGATGAAACAAATTCTGTTTTGGATGCTAA
          1 TTGTGATGAAACAAATTCTGTTTTAGATGCTAA

                             
        682 TTGTGATGAAAACAAAT
          1 TTGTGATG-AAACAAAT

        699 CTCTTGAAAA


Statistics
Matches: 43,  Mismatches: 5, Indels: 3
        0.84            0.10        0.06

Matches are distributed among these distances:
  32    3  0.07
  33   32  0.74
  34    8  0.19

ACGTcount: A:0.31, C:0.08, G:0.20, T:0.40


Consensus pattern (33 bp):   
TTGTGATGAAACAAATTCTGTTTTAGATGCTAA

Done.