Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018402043.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5137.0, 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: 1702
ACGTcount: A:0.22, C:0.11, G:0.08, T:0.21

Warning! 630 characters in sequence are not A, C, G, or T


Found at i:344 original size:177 final size:179

Alignment explanation


    Indices: 117--448  Score: 501
    Period size: 179  Copynumber: 1.9  Consensus size: 179

        107 AATGAGCTTG

                *                       *            *                       
        117 TTTGGCCATGAAAATTTCCAGAAATAATTCTCATTGAACATTTTAATAAAGA-AATTTTTCTGGA
          1 TTTGACCATGAAAATTTCCAGAAATAATCCTCATTGAACATATTAATAAAGATAATTTTTCTGGA

                           *    *  *                         *               
        181 ATTTTCAGAATTAATTTC-AGGAGTTTCTTG-TCAATTAAATA-TGAAATTCATGCCAAAACAGT
         66 ATTTTCAGAATTAATGTCAAAGACTTTCTTGCT-AATTAAA-ACTGAAAGTCATGCCAAAACAGT

                                                               
        243 GAGCTGGACAGATTTATATTTGCACCAGTTTCATTGCCTGAAATCAGAATA
        129 GAGCTGGACAGATTTATATTTGCACCAGTTTCATTGCCTGAAATCAGAATA

                       *                   *                                 
        294 TTTGACCATGATAATTTCCAGAAATAATCCTTATTGAACATATTAATAAAGATAATTTTTCTGGA
          1 TTTGACCATGAAAATTTCCAGAAATAATCCTCATTGAACATATTAATAAAGATAATTTTTCTGGA

                                                                 *  *        
        359 ATTTTCAGAATTAATGTCAAAGACTTTCTTGCTAATTAAAACTGAAAGTCATGTCACAACAGTGA
         66 ATTTTCAGAATTAATGTCAAAGACTTTCTTGCTAATTAAAACTGAAAGTCATGCCAAAACAGTGA

                   * *               
        424 GCTGGACTGCTTTATATTTGCACCA
        131 GCTGGACAGATTTATATTTGCACCA

        449 ATTTTCTTGC


Statistics
Matches: 138,  Mismatches: 13, Indels: 6
        0.88            0.08        0.04

Matches are distributed among these distances:
 177   47  0.34
 178   30  0.22
 179   60  0.43
 180    1  0.01

ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36


Consensus pattern (179 bp):   
TTTGACCATGAAAATTTCCAGAAATAATCCTCATTGAACATATTAATAAAGATAATTTTTCTGGA
ATTTTCAGAATTAATGTCAAAGACTTTCTTGCTAATTAAAACTGAAAGTCATGCCAAAACAGTGA
GCTGGACAGATTTATATTTGCACCAGTTTCATTGCCTGAAATCAGAATA

Found at i:1529 original size:35 final size:35

Alignment explanation


    Indices: 1482--1582  Score: 121
    Period size: 35  Copynumber: 2.9  Consensus size: 35

       1472 TAATAAGTTG

                                                
       1482 ATTAAACAAATTTAATCAATTAGGCCCAATAACATA
          1 ATTAAAC-AATTTAATCAATTAGGCCCAATAACATA

               ****            *        *   *  
       1518 ATTGTTTAATTTAATCAATAAGGCCCAAGAACTTA
          1 ATTAAACAATTTAATCAATTAGGCCCAATAACATA

                                     *    
       1553 ATTAAACAATTTAATCAATTAGGCCTAATA
          1 ATTAAACAATTTAATCAATTAGGCCCAATA

       1583 NNNNNNNNNN


Statistics
Matches: 51,  Mismatches: 14, Indels: 1
        0.77            0.21        0.02

Matches are distributed among these distances:
  35   48  0.94
  36    3  0.06

ACGTcount: A:0.46, C:0.15, G:0.08, T:0.32


Consensus pattern (35 bp):   
ATTAAACAATTTAATCAATTAGGCCCAATAACATA
Done.