Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018398382.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1679.0, 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, 820

Length: 1368
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44


Found at i:179 original size:15 final size:16

Alignment explanation


    Indices: 148--192  Score: 58
    Period size: 15  Copynumber: 2.8  Consensus size: 16

        138 TTCTATTTTG

                              
        148 TATTAACGTTATCAAAAT
          1 TATTAAC-TTAT-AAAAT

                            
        166 TA-TAACTTATAAAAT
          1 TATTAACTTATAAAAT

                         
        181 TATTAA-TTATAA
          1 TATTAACTTATAA

        193 TATATATCTT


Statistics
Matches: 26,  Mismatches: 0, Indels: 5
        0.84            0.00        0.16

Matches are distributed among these distances:
  15   13  0.50
  16    7  0.27
  17    4  0.15
  18    2  0.08

ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42


Consensus pattern (16 bp):   
TATTAACTTATAAAAT

Found at i:394 original size:16 final size:16

Alignment explanation


    Indices: 373--412  Score: 55
    Period size: 16  Copynumber: 2.6  Consensus size: 16

        363 TTTATAAAGA

                            
        373 ATATATTTACTATTAT
          1 ATATATTTACTATTAT

                  *    *    
        389 ATATATATACTTTTAT
          1 ATATATTTACTATTAT

                     
        405 -TATATTTA
          1 ATATATTTA

        413 TTTTAAATAT


Statistics
Matches: 21,  Mismatches: 3, Indels: 1
        0.84            0.12        0.04

Matches are distributed among these distances:
  15    7  0.33
  16   14  0.67

ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57


Consensus pattern (16 bp):   
ATATATTTACTATTAT

Found at i:597 original size:27 final size:28

Alignment explanation


    Indices: 561--616  Score: 78
    Period size: 27  Copynumber: 2.0  Consensus size: 28

        551 TCTTGTTAAT

                                *       
        561 TAAACCTGTAATGTT-TTTACCTTGTTG
          1 TAAACCTGTAATGTTGTTTAACTTGTTG

                 *               *      
        588 TAAACTTGTAATGTTGTTTAAGTTGTTG
          1 TAAACCTGTAATGTTGTTTAACTTGTTG

             
        616 T
          1 T

        617 TTGAATATTT


Statistics
Matches: 25,  Mismatches: 3, Indels: 1
        0.86            0.10        0.03

Matches are distributed among these distances:
  27   14  0.56
  28   11  0.44

ACGTcount: A:0.23, C:0.09, G:0.18, T:0.50


Consensus pattern (28 bp):   
TAAACCTGTAATGTTGTTTAACTTGTTG

Found at i:642 original size:34 final size:32

Alignment explanation


    Indices: 604--674  Score: 90
    Period size: 34  Copynumber: 2.2  Consensus size: 32

        594 TGTAATGTTG

                     * *                       
        604 TTTAAGTTGTTGTTTGA-ATATTTGTTTTTAGTTA
          1 TTTAAGTTGATATTTGAGATA-TT-TTTTTA-TTA

                                            
        638 TTTAAGTTGATATTTGAGATATTTTTTTATTA
          1 TTTAAGTTGATATTTGAGATATTTTTTTATTA

                 
        670 TTTAA
          1 TTTAA

        675 ATTTTATTAT


Statistics
Matches: 34,  Mismatches: 2, Indels: 4
        0.85            0.05        0.10

Matches are distributed among these distances:
  32    8  0.24
  33    6  0.18
  34   17  0.50
  35    3  0.09

ACGTcount: A:0.25, C:0.00, G:0.14, T:0.61


Consensus pattern (32 bp):   
TTTAAGTTGATATTTGAGATATTTTTTTATTA
Done.