Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018402766.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5825.0, 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: 5055
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33


Found at i:976 original size:22 final size:23

Alignment explanation


    Indices: 933--985  Score: 65
    Period size: 22  Copynumber: 2.3  Consensus size: 23

        923 TTAATTTTTT

                                  * 
        933 TTAAATATATTGATATAATTAAGA
          1 TTAAA-ATATTGATATAATTAAAA

                                    
        957 TATAAAATA-TGAT-TAATTAAAA
          1 T-TAAAATATTGATATAATTAAAA

                   
        979 TTAAAAT
          1 TTAAAAT

        986 TTAACGTGAC


Statistics
Matches: 27,  Mismatches: 1, Indels: 5
        0.82            0.03        0.15

Matches are distributed among these distances:
  21    6  0.22
  22    9  0.33
  23    4  0.15
  24    4  0.15
  25    4  0.15

ACGTcount: A:0.55, C:0.00, G:0.06, T:0.40


Consensus pattern (23 bp):   
TTAAAATATTGATATAATTAAAA

Found at i:2867 original size:24 final size:26

Alignment explanation


    Indices: 2821--2868  Score: 73
    Period size: 26  Copynumber: 1.9  Consensus size: 26

       2811 CCACAAATAT

                                      
       2821 AATCAAAATATAAATAAATTAATACA
          1 AATCAAAATATAAATAAATTAATACA

                  *                 
       2847 AATCAATATATAAA-AAA-TAATA
          1 AATCAAAATATAAATAAATTAATA

       2869 AACTTTAACA


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  24    5  0.24
  25    3  0.14
  26   13  0.62

ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27


Consensus pattern (26 bp):   
AATCAAAATATAAATAAATTAATACA

Found at i:3691 original size:20 final size:20

Alignment explanation


    Indices: 3666--3705  Score: 55
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       3656 GAAAATTATC

                                 
       3666 ACAAAGA-AAACGTTAGAAGT
          1 ACAAAGACAAA-GTTAGAAGT

                           *    
       3686 ACAAAGACAAAGTTATAAGT
          1 ACAAAGACAAAGTTAGAAGT

       3706 GATTACAATA


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  20   15  0.83
  21    3  0.17

ACGTcount: A:0.55, C:0.10, G:0.17, T:0.17


Consensus pattern (20 bp):   
ACAAAGACAAAGTTAGAAGT

Found at i:3914 original size:20 final size:20

Alignment explanation


    Indices: 3873--3914  Score: 66
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       3863 AGGAGTGTAA

                             *  
       3873 TTATATTATTATTAATTTTT
          1 TTATATTATTATTAATTCTT

                          *     
       3893 TTATATTATTATTAGTTCTT
          1 TTATATTATTATTAATTCTT

              
       3913 TT
          1 TT

       3915 TTATAATTAA


Statistics
Matches: 20,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69


Consensus pattern (20 bp):   
TTATATTATTATTAATTCTT

Found at i:3923 original size:20 final size:20

Alignment explanation


    Indices: 3873--3923  Score: 59
    Period size: 20  Copynumber: 2.5  Consensus size: 20

       3863 AGGAGTGTAA

                  *             
       3873 TTATATTATTATTAATTTTT
          1 TTATATAATTATTAATTTTT

                  *       *      
       3893 TTATATTATTATTAGTTCTTT
          1 TTATATAATTATTAATT-TTT

                       
       3914 TT-TATAATTA
          1 TTATATAATTA

       3924 AGAGAAGAGA


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  20   23  0.82
  21    5  0.18

ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67


Consensus pattern (20 bp):   
TTATATAATTATTAATTTTT
Done.