Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008317.1 Kokia drynarioides strain JFW-HI SEQ_122982, 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: 9373
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32


Found at i:1478 original size:10 final size:10

Alignment explanation


    Indices: 1463--1505  Score: 59
    Period size: 10  Copynumber: 4.2  Consensus size: 10

       1453 TACTCAAAAT

                      
       1463 TTTTTTTTTA
          1 TTTTTTTTTA

                      
       1473 TTTTTTTTTA
          1 TTTTTTTTTA

                *    *
       1483 TTTTCTTTTC
          1 TTTTTTTTTA

                       
       1493 TTTTTTTATTA
          1 TTTTTTT-TTA

              
       1504 TT
          1 TT

       1506 ATTTACAAAT


Statistics
Matches: 28,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  10   24  0.86
  11    4  0.14

ACGTcount: A:0.09, C:0.05, G:0.00, T:0.86


Consensus pattern (10 bp):   
TTTTTTTTTA

Found at i:8164 original size:16 final size:16

Alignment explanation


    Indices: 8143--8173  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       8133 ATAATGTGAG

                            
       8143 AATAAAGATAAAATGT
          1 AATAAAGATAAAATGT

                   *       
       8159 AATAAAGGTAAAATG
          1 AATAAAGATAAAATG

       8174 GGATTCACAA


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23


Consensus pattern (16 bp):   
AATAAAGATAAAATGT

Found at i:8997 original size:34 final size:36

Alignment explanation


    Indices: 8953--9055  Score: 104
    Period size: 38  Copynumber: 2.9  Consensus size: 36

       8943 GTACATGTTC

                 *                              
       8953 ATGCAACGACATTCCTGGGTGCAA-TTG-AATACTT
          1 ATGCAGCGACATTCCTGGGTGCAATTTGAAATACTT

                         *    *                *  
       8987 ATGCAGCGACATTTCTGGTTGCAATTTGAAAAATATTT
          1 ATGCAGCGACATTCCTGGGTGCAATTTG--AAATACTT

                       *  *                 
       9025 ATGCAGCGACAGTCTTGGGTGC-ATTTCGAAA
          1 ATGCAGCGACATTCCTGGGTGCAATTT-GAAA

       9056 ATATTATTGC


Statistics
Matches: 56,  Mismatches: 8, Indels: 8
        0.78            0.11        0.11

Matches are distributed among these distances:
  34   21  0.38
  35    3  0.05
  36    3  0.05
  37    4  0.07
  38   25  0.45

ACGTcount: A:0.29, C:0.17, G:0.22, T:0.31


Consensus pattern (36 bp):   
ATGCAGCGACATTCCTGGGTGCAATTTGAAATACTT

Done.