Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001894.1 Corchorus olitorius cultivar O-4 contig01894, 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, 840

Length: 1401
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37


Found at i:414 original size:2 final size:2

Alignment explanation


    Indices: 349--403  Score: 73
    Period size: 2  Copynumber: 29.5  Consensus size: 2

        339 ATCATCAAAA

                                                                      *   
        349 AT AT AT AT AT AT AT AT AT -T AT AT AT AT A- AT AT AT A- AG A-
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                                     
        387 AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT A

        404 AAAGAATATA


Statistics
Matches: 49,  Mismatches: 0, Indels: 8
        0.86            0.00        0.14

Matches are distributed among these distances:
   1    4  0.08
   2   45  0.92

ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45


Consensus pattern (2 bp):   
AT

Found at i:682 original size:28 final size:28

Alignment explanation


    Indices: 651--713  Score: 126
    Period size: 28  Copynumber: 2.2  Consensus size: 28

        641 CTACCATTTG

                                        
        651 TGTTTGCGATTTTGTATGGATTTTTATT
          1 TGTTTGCGATTTTGTATGGATTTTTATT

                                        
        679 TGTTTGCGATTTTGTATGGATTTTTATT
          1 TGTTTGCGATTTTGTATGGATTTTTATT

                   
        707 TGTTTGC
          1 TGTTTGC

        714 AAAATTATGA


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   35  1.00

ACGTcount: A:0.13, C:0.05, G:0.22, T:0.60


Consensus pattern (28 bp):   
TGTTTGCGATTTTGTATGGATTTTTATT

Found at i:849 original size:19 final size:17

Alignment explanation


    Indices: 822--864  Score: 68
    Period size: 19  Copynumber: 2.4  Consensus size: 17

        812 TCACATTGAC

                              
        822 ATATATATATCTATATCT
          1 ATATATATATCTATAT-T

                              
        840 ATACTATATATCTATATT
          1 ATA-TATATATCTATATT

                   
        858 ATATATA
          1 ATATATA

        865 AAAGTACGAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
  17    4  0.17
  18    7  0.29
  19   13  0.54

ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49


Consensus pattern (17 bp):   
ATATATATATCTATATT

Found at i:851 original size:13 final size:13

Alignment explanation


    Indices: 833--863  Score: 53
    Period size: 13  Copynumber: 2.4  Consensus size: 13

        823 TATATATATC

                         
        833 TATATCTATACTA
          1 TATATCTATACTA

                      *  
        846 TATATCTATATTA
          1 TATATCTATACTA

                 
        859 TATAT
          1 TATAT

        864 AAAAGTACGA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  13   17  1.00

ACGTcount: A:0.39, C:0.10, G:0.00, T:0.52


Consensus pattern (13 bp):   
TATATCTATACTA
Done.