Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024762.1 Corchorus olitorius cultivar O-4 contig24795, 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: 10176
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:369 original size:15 final size:15

Alignment explanation


    Indices: 339--380  Score: 66
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        329 TTACTCTGCT

                            
        339 TTGTTTTCTAGTTTAA
          1 TTGTTTTCT-GTTTAA

                           
        355 TTGTTTTCTGTTTAA
          1 TTGTTTTCTGTTTAA

               *       
        370 TTGCTTTCTGT
          1 TTGTTTTCTGT

        381 CAATCTCTGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 1
        0.93            0.04        0.04

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

ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64


Consensus pattern (15 bp):   
TTGTTTTCTGTTTAA

Found at i:3029 original size:21 final size:21

Alignment explanation


    Indices: 2991--3034  Score: 52
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       2981 AAGAGCAGAG

                   *    **       
       2991 AATTTTTTTTTTTGAAAACGC
          1 AATTTTTATTTTCAAAAACGC

                              *  
       3012 AATTTTTATTTTCAAAAATGC
          1 AATTTTTATTTTCAAAAACGC

              
       3033 AA
          1 AA

       3035 AAACTAAATA


Statistics
Matches: 19,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  21   19  1.00

ACGTcount: A:0.36, C:0.09, G:0.07, T:0.48


Consensus pattern (21 bp):   
AATTTTTATTTTCAAAAACGC

Found at i:3361 original size:21 final size:20

Alignment explanation


    Indices: 3314--3362  Score: 53
    Period size: 21  Copynumber: 2.4  Consensus size: 20

       3304 TAAAAATAAC

                             *  
       3314 AATTAAAAAGAAAACAATTA
          1 AATTAAAAAGAAAACAAGTA

                      *   *       
       3334 AACTTAAAAATAAAGCAAAGTA
          1 AA-TTAAAAAGAAAAC-AAGTA

                   
       3356 AATTAAA
          1 AATTAAA

       3363 TCTAAACTAT


Statistics
Matches: 24,  Mismatches: 3, Indels: 3
        0.80            0.10        0.10

Matches are distributed among these distances:
  20    2  0.08
  21   16  0.67
  22    6  0.25

ACGTcount: A:0.67, C:0.06, G:0.06, T:0.20


Consensus pattern (20 bp):   
AATTAAAAAGAAAACAAGTA

Found at i:4878 original size:24 final size:25

Alignment explanation


    Indices: 4846--4896  Score: 95
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       4836 TTTTTTGGTA

                                     
       4846 TTTATATGTGTA-TTTTAACCCTAT
          1 TTTATATGTGTATTTTTAACCCTAT

                                     
       4870 TTTATATGTGTATTTTTAACCCTAT
          1 TTTATATGTGTATTTTTAACCCTAT

              
       4895 TT
          1 TT

       4897 GAAGACAAGA


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  24   12  0.46
  25   14  0.54

ACGTcount: A:0.24, C:0.12, G:0.08, T:0.57


Consensus pattern (25 bp):   
TTTATATGTGTATTTTTAACCCTAT

Done.