Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018397553.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4377.0, 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: 7683
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.34

Warning! 200 characters in sequence are not A, C, G, or T


Found at i:731 original size:20 final size:19

Alignment explanation


    Indices: 706--743  Score: 58
    Period size: 19  Copynumber: 1.9  Consensus size: 19

        696 TAATTTAAAA

                                
        706 TAAAATAACCTAAAATTAAC
          1 TAAAATAA-CTAAAATTAAC

                      *       
        726 TAAAATAACTTAAATTAA
          1 TAAAATAACTAAAATTAA

        744 TCACTTACAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  19    9  0.53
  20    8  0.47

ACGTcount: A:0.61, C:0.11, G:0.00, T:0.29


Consensus pattern (19 bp):   
TAAAATAACTAAAATTAAC

Found at i:2617 original size:85 final size:85

Alignment explanation


    Indices: 2506--2771  Score: 293
    Period size: 85  Copynumber: 3.1  Consensus size: 85

       2496 TATTAATTCC

                           *     *            *             *         *      
       2506 AATGTTTAATTCTAGCATATTGCCAATCATTTTATTTAAAAATCTAAAAAATAATTCTCAACATT
          1 AATGTTTAATTCTAGAATATTACCAATCATTTTAATTAAAAATCTAAACAATAATTCTAAACATT

                             *  
       2571 AATTCCCAAACATAATTTTT
         66 AATTCCCAAACATAATTCTT

               *             *                          *     *              
       2591 AATATTTAATTCTAGAAAATTACCAATCATTTTAATTAAAAATCCAAACATTAATTCTAAACATT
          1 AATGTTTAATTCTAGAATATTACCAATCATTTTAATTAAAAATCTAAACAATAATTCTAAACATT

                    **********  
       2656 AATTCCCANNNNNNNNNNTT
         66 AATTCCCAAACATAATTCTT

                                            **                               
       2676 AATGTTTAATTCTA-ACATATTACCAATCATTACAATTAAAAA-CTCAAACAATAATTCTAAACA
          1 AATGTTTAATTCTAGA-ATATTACCAATCATTTTAATTAAAAATCT-AAACAATAATTCTAAACA

                    *             
       2739 TTAATTCCTAAACATAATTCTT
         64 TTAATTCCCAAACATAATTCTT

                       
       2761 AATGTTTAATT
          1 AATGTTTAATT

       2772 ATAGCATCAA


Statistics
Matches: 143,  Mismatches: 36, Indels: 4
        0.78            0.20        0.02

Matches are distributed among these distances:
  84    2  0.01
  85  141  0.99

ACGTcount: A:0.42, C:0.15, G:0.02, T:0.37


Consensus pattern (85 bp):   
AATGTTTAATTCTAGAATATTACCAATCATTTTAATTAAAAATCTAAACAATAATTCTAAACATT
AATTCCCAAACATAATTCTT

Found at i:2654 original size:13 final size:13

Alignment explanation


    Indices: 2636--2660  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       2626 TTAAAAATCC

                         
       2636 AAACATTAATTCT
          1 AAACATTAATTCT

                        
       2649 AAACATTAATTC
          1 AAACATTAATTC

       2661 CCANNNNNNN


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36


Consensus pattern (13 bp):   
AAACATTAATTCT

Found at i:2751 original size:14 final size:13

Alignment explanation


    Indices: 2721--2758  Score: 51
    Period size: 13  Copynumber: 2.8  Consensus size: 13

       2711 TTAAAAACTC

                          
       2721 AAACAATAATT-CT
          1 AAAC-ATAATTCCT

                          
       2734 AAACATTAATTCCT
          1 AAACA-TAATTCCT

                       
       2748 AAACATAATTC
          1 AAACATAATTC

       2759 TTAATGTTTA


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

Matches are distributed among these distances:
  12    1  0.04
  13   15  0.65
  14    7  0.30

ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32


Consensus pattern (13 bp):   
AAACATAATTCCT

Found at i:5713 original size:2 final size:2

Alignment explanation


    Indices: 5706--5731  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       5696 CGTTAAATTT

                                                  
       5706 TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA

       5732 AAATACTACA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Done.