Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005868.1 Corchorus olitorius cultivar O-4 contig05893, 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, 631

Length: 1052
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.33


Found at i:551 original size:21 final size:21

Alignment explanation


    Indices: 513--603  Score: 173
    Period size: 21  Copynumber: 4.3  Consensus size: 21

        503 GGAATTACTG

                                  
        513 ATAAAAGTTGTAATATATCTAT
          1 ATAAAAGTTGT-ATATATCTAT

                                 
        535 ATAAAAGTTGTATATATCTAT
          1 ATAAAAGTTGTATATATCTAT

                                 
        556 ATAAAAGTTGTATATATCTAT
          1 ATAAAAGTTGTATATATCTAT

                                 
        577 ATAAAAGTTGTATATATCTAT
          1 ATAAAAGTTGTATATATCTAT

                  
        598 ATAAAA
          1 ATAAAA

        604 AATTTTAAAA


Statistics
Matches: 69,  Mismatches: 0, Indels: 1
        0.99            0.00        0.01

Matches are distributed among these distances:
  21   58  0.84
  22   11  0.16

ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41


Consensus pattern (21 bp):   
ATAAAAGTTGTATATATCTAT

Found at i:617 original size:42 final size:42

Alignment explanation


    Indices: 513--621  Score: 148
    Period size: 42  Copynumber: 2.6  Consensus size: 42

        503 GGAATTACTG

                  *        *                           
        513 ATAAAAGTTGTAATATATCTATATAAAAGTTGTATATATCTAT
          1 ATAAAAATTGT-ATAAATCTATATAAAAGTTGTATATATCTAT

                  *       *                           
        556 ATAAAAGTTGTATATATCTATATAAAAGTTGTATATATCTAT
          1 ATAAAAATTGTATAAATCTATATAAAAGTTGTATATATCTAT

                      *              
        598 ATAAAAAATTTTA-AAATCTATATA
          1 AT-AAAAATTGTATAAATCTATATA

        622 TCTATAGATT


Statistics
Matches: 62,  Mismatches: 3, Indels: 3
        0.91            0.04        0.04

Matches are distributed among these distances:
  42   43  0.69
  43   19  0.31

ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41


Consensus pattern (42 bp):   
ATAAAAATTGTATAAATCTATATAAAAGTTGTATATATCTAT

Found at i:666 original size:19 final size:20

Alignment explanation


    Indices: 642--688  Score: 87
    Period size: 19  Copynumber: 2.4  Consensus size: 20

        632 ACTAATACTC

                                
        642 TATATAAATTAATAATAA-T
          1 TATATAAATTAATAATAATT

                                
        661 TATATAAATTAATAATAATT
          1 TATATAAATTAATAATAATT

                    
        681 TATATAAA
          1 TATATAAA

        689 AAATTATATA


Statistics
Matches: 27,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  19   18  0.67
  20    9  0.33

ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43


Consensus pattern (20 bp):   
TATATAAATTAATAATAATT

Found at i:695 original size:12 final size:12

Alignment explanation


    Indices: 666--704  Score: 53
    Period size: 12  Copynumber: 3.3  Consensus size: 12

        656 ATAATTATAT

                       *
        666 AAATTA-ATAAT
          1 AAATTATATAAA

              *         
        677 AATTTATATAAA
          1 AAATTATATAAA

                        
        689 AAATTATATAAA
          1 AAATTATATAAA

                
        701 AAAT
          1 AAAT

        705 CAAAATAAAG


Statistics
Matches: 24,  Mismatches: 3, Indels: 1
        0.86            0.11        0.04

Matches are distributed among these distances:
  11    5  0.21
  12   19  0.79

ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36


Consensus pattern (12 bp):   
AAATTATATAAA
Done.