Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001995.1 Corchorus olitorius cultivar O-4 contig01995, 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, 696

Length: 1160
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.36


Found at i:75 original size:18 final size:18

Alignment explanation


    Indices: 54--91  Score: 76
    Period size: 18  Copynumber: 2.1  Consensus size: 18

         44 CTAATATATC

                              
         54 TAAGTTTTTTAATTAAAT
          1 TAAGTTTTTTAATTAAAT

                              
         72 TAAGTTTTTTAATTAAAT
          1 TAAGTTTTTTAATTAAAT

              
         90 TA
          1 TA

         92 GTAAAATGGT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   20  1.00

ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55


Consensus pattern (18 bp):   
TAAGTTTTTTAATTAAAT

Found at i:467 original size:40 final size:40

Alignment explanation


    Indices: 423--546  Score: 130
    Period size: 40  Copynumber: 3.2  Consensus size: 40

        413 AGTAAAATGG

                                                    
        423 TAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAA
          1 TAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAA

                      *     *   ** * *      *  *  **
        463 TAAAAATAAAGTA-TTTTAATTAAAATAG--TAAAAT-GG
          1 TAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAA

                                                    
        499 TAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAA
          1 TAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAA

                    
        539 TAAAAATA
          1 TAAAAATA

        547 GAGCTTTTAG


Statistics
Matches: 60,  Mismatches: 20, Indels: 8
        0.68            0.23        0.09

Matches are distributed among these distances:
  36   12  0.20
  37   14  0.23
  39   14  0.23
  40   20  0.33

ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34


Consensus pattern (40 bp):   
TAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAA

Found at i:508 original size:36 final size:36

Alignment explanation


    Indices: 391--508  Score: 101
    Period size: 36  Copynumber: 3.2  Consensus size: 36

        381 TGTACTTTTT

                *                               
        391 AATATAGTATTTTAATTAAAATAGTAAAATGGTAAA
          1 AATAAAGTATTTTAATTAAAATAGTAAAATGGTAAA

                  *     *   ** * *      *  *  **    
        427 AATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAA
          1 AATAAAGTA-TTTTAATTAAAATAG--TAAAAT-GGTAAA

                                                
        467 AATAAAGTATTTTAATTAAAATAGTAAAATGGTAAA
          1 AATAAAGTATTTTAATTAAAATAGTAAAATGGTAAA

                  
        503 AATAAA
          1 AATAAA

        509 ATAGTTATAA


Statistics
Matches: 57,  Mismatches: 21, Indels: 8
        0.66            0.24        0.09

Matches are distributed among these distances:
  36   17  0.30
  37   14  0.25
  39   14  0.25
  40   12  0.21

ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34


Consensus pattern (36 bp):   
AATAAAGTATTTTAATTAAAATAGTAAAATGGTAAA

Found at i:522 original size:76 final size:76

Alignment explanation


    Indices: 391--546  Score: 303
    Period size: 76  Copynumber: 2.1  Consensus size: 76

        381 TGTACTTTTT

                *                                                            
        391 AATATAGTATTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAGGATATTAGATTT
          1 AATAAAGTATTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAGGATATTAGATTT

                       
        456 AATTAAATAAA
         66 AATTAAATAAA

                                                                             
        467 AATAAAGTATTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAGGATATTAGATTT
          1 AATAAAGTATTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAGGATATTAGATTT

                       
        532 AATTAAATAAA
         66 AATTAAATAAA

                
        543 AATA
          1 AATA

        547 GAGCTTTTAG


Statistics
Matches: 79,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  76   79  1.00

ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35


Consensus pattern (76 bp):   
AATAAAGTATTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAGGATATTAGATTT
AATTAAATAAA

Found at i:688 original size:12 final size:12

Alignment explanation


    Indices: 661--693  Score: 50
    Period size: 12  Copynumber: 2.8  Consensus size: 12

        651 TGTATTTTTT

                        
        661 AATATAG-TATA
          1 AATATAGATATA

                        
        672 AATATAGATATA
          1 AATATAGATATA

            *         
        684 GATATAGATA
          1 AATATAGATA

        694 AGTGTTTATA


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  11    7  0.35
  12   13  0.65

ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33


Consensus pattern (12 bp):   
AATATAGATATA
Done.