Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015054.1 Corchorus olitorius cultivar O-4 contig15087, 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: 2513
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32


Found at i:308 original size:41 final size:41

Alignment explanation


    Indices: 255--402  Score: 219
    Period size: 41  Copynumber: 3.6  Consensus size: 41

        245 CTGGAGTAAC

                                                     
        255 ACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAAGTGACA
          1 ACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAAGTGACA

                                    *                  
        296 ACTTCTGGTGTCAAAAGGTAATTTCAATTTACC-AAGATGACA
          1 ACTTCTGGTGTC-AAAGGTAATTTTAATTTACCAAAG-TGACA

                  *    *  *                           
        338 ACTTCTAGTGTTAGCA-GTAATTTTAATTTACCAAAGTGACA
          1 ACTTCTGGTGTCA-AAGGTAATTTTAATTTACCAAAGTGACA

                                    
        379 ACTTCTGGTGTCAAAGGTAATTTT
          1 ACTTCTGGTGTCAAAGGTAATTTT

        403 CAATATTATT


Statistics
Matches: 94,  Mismatches: 8, Indels: 10
        0.84            0.07        0.09

Matches are distributed among these distances:
  40    1  0.01
  41   55  0.59
  42   38  0.40

ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35


Consensus pattern (41 bp):   
ACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAAGTGACA

Found at i:465 original size:15 final size:16

Alignment explanation


    Indices: 439--468  Score: 53
    Period size: 15  Copynumber: 1.9  Consensus size: 16

        429 AGATAACAAT

                            
        439 ATAAACAACTTAAGAA
          1 ATAAACAACTTAAGAA

                           
        455 ATAAA-AACTTAAGA
          1 ATAAACAACTTAAGA

        469 TTGGAAGATC


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  15    9  0.64
  16    5  0.36

ACGTcount: A:0.63, C:0.10, G:0.07, T:0.20


Consensus pattern (16 bp):   
ATAAACAACTTAAGAA

Found at i:966 original size:13 final size:13

Alignment explanation


    Indices: 928--967  Score: 53
    Period size: 13  Copynumber: 3.1  Consensus size: 13

        918 TCTCCAGATA

                  *     *
        928 ATCTTCAGTTGAA
          1 ATCTTCTGTTGAT

                    *    
        941 ATCTTCTGATGAT
          1 ATCTTCTGTTGAT

                         
        954 ATCTTCTGTTGAT
          1 ATCTTCTGTTGAT

             
        967 A
          1 A

        968 ATATTCTCTG


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  13   23  1.00

ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45


Consensus pattern (13 bp):   
ATCTTCTGTTGAT
Done.