Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006819.1 Kokia drynarioides strain JFW-HI SEQ_121418, 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: 24138
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33


Found at i:2737 original size:18 final size:18

Alignment explanation


    Indices: 2674--2739  Score: 53
    Period size: 18  Copynumber: 3.7  Consensus size: 18

       2664 CACTTTGATA

                               
       2674 AGCTCGCAGC-TTGGATTG
          1 AGCTCGCAGCTTTGGA-TG

                *  **      *  
       2692 AGCTTGCTTCTTTGGGTG
          1 AGCTCGCAGCTTTGGATG

                 *       *    
       2710 AGCTCACAGCTTTTGATG
          1 AGCTCGCAGCTTTGGATG

                *       
       2728 AGCTTGCAGCTT
          1 AGCTCGCAGCTT

       2740 CCGCTTCCAA


Statistics
Matches: 35,  Mismatches: 12, Indels: 2
        0.71            0.24        0.04

Matches are distributed among these distances:
  18   31  0.89
  19    4  0.11

ACGTcount: A:0.15, C:0.21, G:0.29, T:0.35


Consensus pattern (18 bp):   
AGCTCGCAGCTTTGGATG

Found at i:8563 original size:21 final size:20

Alignment explanation


    Indices: 8539--8577  Score: 51
    Period size: 21  Copynumber: 1.9  Consensus size: 20

       8529 GAGCAGGAAA

                                 
       8539 ATATAATTGAAATTGTGATTC
          1 ATATAATTGAAATT-TGATTC

                 *  *         
       8560 ATATACTTTAAATTTGAT
          1 ATATAATTGAAATTTGAT

       8578 ACATGATTTA


Statistics
Matches: 16,  Mismatches: 2, Indels: 1
        0.84            0.11        0.05

Matches are distributed among these distances:
  20    4  0.25
  21   12  0.75

ACGTcount: A:0.38, C:0.05, G:0.10, T:0.46


Consensus pattern (20 bp):   
ATATAATTGAAATTTGATTC

Found at i:8937 original size:15 final size:15

Alignment explanation


    Indices: 8917--8946  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       8907 GCTAAGTGAT

                           
       8917 AACATGATGATTGAA
          1 AACATGATGATTGAA

                  *        
       8932 AACATGGTGATTGAA
          1 AACATGATGATTGAA

       8947 GCAAGAAATT


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

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.43, C:0.07, G:0.23, T:0.27


Consensus pattern (15 bp):   
AACATGATGATTGAA

Found at i:12960 original size:21 final size:21

Alignment explanation


    Indices: 12936--12981  Score: 65
    Period size: 21  Copynumber: 2.2  Consensus size: 21

      12926 TAGGGATGGT

                           *     
      12936 TCTACCAATACAAGTGATACA
          1 TCTACCAATACAAGTCATACA

                 *              *
      12957 TCTACTAATACAAGTCATACT
          1 TCTACCAATACAAGTCATACA

                
      12978 TCTA
          1 TCTA

      12982 TCGATACTAA


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.39, C:0.24, G:0.07, T:0.30


Consensus pattern (21 bp):   
TCTACCAATACAAGTCATACA

Done.