Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NW_018397587.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_5927.0, 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: 5947
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34


Found at i:390 original size:17 final size:19

Alignment explanation


    Indices: 370--407  Score: 62
    Period size: 19  Copynumber: 2.1  Consensus size: 19

        360 ATATGGATAA

                               
        370 AAAAATTT-AA-AAAATTG
          1 AAAAATTTAAATAAAATTG

                               
        387 AAAAATTTAAATAAAATTG
          1 AAAAATTTAAATAAAATTG

              
        406 AA
          1 AA

        408 TGAAGTTTAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  17    8  0.42
  18    2  0.11
  19    9  0.47

ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29


Consensus pattern (19 bp):   
AAAAATTTAAATAAAATTG

Found at i:946 original size:18 final size:19

Alignment explanation


    Indices: 919--955  Score: 58
    Period size: 18  Copynumber: 2.0  Consensus size: 19

        909 AACGAAGAAG

                               
        919 TTTTTGTTTTTGGT-TTTT
          1 TTTTTGTTTTTGGTCTTTT

                 *             
        937 TTTTTTTTTTTGGTCTTTT
          1 TTTTTGTTTTTGGTCTTTT

        956 GGTTGTTTTT


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

Matches are distributed among these distances:
  18   13  0.76
  19    4  0.24

ACGTcount: A:0.00, C:0.03, G:0.14, T:0.84


Consensus pattern (19 bp):   
TTTTTGTTTTTGGTCTTTT

Found at i:964 original size:18 final size:18

Alignment explanation


    Indices: 922--965  Score: 52
    Period size: 18  Copynumber: 2.4  Consensus size: 18

        912 GAAGAAGTTT

                       *    **
        922 TTGTTTTTGGTTTTTTTT
          1 TTGTTTTTGGTCTTTTGG

              *               
        940 TTTTTTTTGGTCTTTTGG
          1 TTGTTTTTGGTCTTTTGG

                    
        958 TTGTTTTT
          1 TTGTTTTT

        966 CGATCGTTCA


Statistics
Matches: 21,  Mismatches: 5, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.00, C:0.02, G:0.18, T:0.80


Consensus pattern (18 bp):   
TTGTTTTTGGTCTTTTGG

Found at i:2360 original size:18 final size:18

Alignment explanation


    Indices: 2337--2371  Score: 70
    Period size: 18  Copynumber: 1.9  Consensus size: 18

       2327 TGCCAACATA

                              
       2337 TTTCATATTATGGATTTG
          1 TTTCATATTATGGATTTG

                             
       2355 TTTCATATTATGGATTT
          1 TTTCATATTATGGATTT

       2372 TTCTATTGTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.23, C:0.06, G:0.14, T:0.57


Consensus pattern (18 bp):   
TTTCATATTATGGATTTG
Done.