Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018401389.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4519.0, 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: 2248
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36


Found at i:1090 original size:2 final size:2

Alignment explanation


    Indices: 1083--1115  Score: 66
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       1073 TATGTTAAAC

                                                             
       1083 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       1116 CATACAAGCC


Statistics
Matches: 31,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   31  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:1603 original size:36 final size:36

Alignment explanation


    Indices: 1486--1692  Score: 179
    Period size: 36  Copynumber: 5.6  Consensus size: 36

       1476 ATCCTCAAAG

                       **         *  *          
       1486 GGTGCTCTTTACGATAGCACTTATTGATCCTTGGG-
          1 GGTGCTCTTTATAATAGCACTTGTTTATCCTTGGGA

                       *                           * 
       1521 GGTGCTCTTTAAAATAGCACACGATT-TATTATCCTTGGAA
          1 GGTGCTCTTTATAATAG--CAC--TTGT-TTATCCTTGGGA

             *                           *      
       1561 GATGCTCTTTATAATAGCACTTGTTTATCATTGGGA
          1 GGTGCTCTTTATAATAGCACTTGTTTATCCTTGGGA

                         *                           
       1597 GGTGCTCTTTATACTAGCACACGATT-TATTATCCTT-GGA
          1 GGTGCTCTTTATAATAG--CAC--TTGT-TTATCCTTGGGA

                       *              *          
       1636 GGGTGCTCTTTGTAATAGCACTTGTTGATCCTTGGGA
          1 -GGTGCTCTTTATAATAGCACTTGTTTATCCTTGGGA

                         *      
       1673 GGTGCTCTTTATACTAGCAC
          1 GGTGCTCTTTATAATAGCAC

       1693 ACAATTTACA


Statistics
Matches: 141,  Mismatches: 16, Indels: 29
        0.76            0.09        0.16

Matches are distributed among these distances:
  35   15  0.11
  36   54  0.38
  37    8  0.06
  38   10  0.07
  39   15  0.11
  40   39  0.28

ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38


Consensus pattern (36 bp):   
GGTGCTCTTTATAATAGCACTTGTTTATCCTTGGGA

Found at i:1629 original size:76 final size:76

Alignment explanation


    Indices: 1488--1700  Score: 320
    Period size: 76  Copynumber: 2.8  Consensus size: 76

       1478 CCTCAAAGGG

                     **         *                        * *                 
       1488 TGCTCTTTACGATAGCACTTATTGATCCTTGGG-GGTGCTCTTTAAAATAGCACACGATTTATTA
          1 TGCTCTTTATAATAGCACTTGTTGATCCTTGGGAGGTGCTCTTTATACTAGCACACGATTTATTA

                       
       1552 TCCTTGGAAGA
         66 TCCTTGGAAGA

                                   *   *                                     
       1563 TGCTCTTTATAATAGCACTTGTTTATCATTGGGAGGTGCTCTTTATACTAGCACACGATTTATTA
          1 TGCTCTTTATAATAGCACTTGTTGATCCTTGGGAGGTGCTCTTTATACTAGCACACGATTTATTA

                    * *
       1628 TCCTTGGAGGG
         66 TCCTTGGAAGA

                    *                                               *     
       1639 TGCTCTTTGTAATAGCACTTGTTGATCCTTGGGAGGTGCTCTTTATACTAGCACACAATTTA
          1 TGCTCTTTATAATAGCACTTGTTGATCCTTGGGAGGTGCTCTTTATACTAGCACACGATTTA

       1701 CAATCACCAT


Statistics
Matches: 124,  Mismatches: 13, Indels: 1
        0.90            0.09        0.01

Matches are distributed among these distances:
  75   28  0.23
  76   96  0.77

ACGTcount: A:0.23, C:0.18, G:0.20, T:0.38


Consensus pattern (76 bp):   
TGCTCTTTATAATAGCACTTGTTGATCCTTGGGAGGTGCTCTTTATACTAGCACACGATTTATTA
TCCTTGGAAGA
Done.