Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012578.1 Kokia drynarioides strain JFW-HI SEQ_127587, 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: 32550
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32

Warning! 16 characters in sequence are not A, C, G, or T


Found at i:1031 original size:5 final size:5

Alignment explanation


    Indices: 1021--1064  Score: 54
    Period size: 5  Copynumber: 9.0  Consensus size: 5

       1011 TTGCAACAAA

                         * *                          *          
       1021 ATTTT ATTTT ACTAT A-TTT ATTTT ATTTT ATTTT GTTTT ATTTT
          1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT

       1065 TAGTTTAACA


Statistics
Matches: 33,  Mismatches: 5, Indels: 2
        0.82            0.12        0.05

Matches are distributed among these distances:
   4    3  0.09
   5   30  0.91

ACGTcount: A:0.20, C:0.02, G:0.02, T:0.75


Consensus pattern (5 bp):   
ATTTT

Found at i:1490 original size:3 final size:3

Alignment explanation


    Indices: 1482--1544  Score: 126
    Period size: 3  Copynumber: 21.0  Consensus size: 3

       1472 TGATATACGA

                                                                           
       1482 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT

                               
       1530 ATT ATT ATT ATT ATT
          1 ATT ATT ATT ATT ATT

       1545 GATGTTGTTG


Statistics
Matches: 60,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   60  1.00

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67


Consensus pattern (3 bp):   
ATT

Found at i:8023 original size:13 final size:12

Alignment explanation


    Indices: 7995--8029  Score: 52
    Period size: 13  Copynumber: 2.8  Consensus size: 12

       7985 TATAAATAGT

                        
       7995 ATCCTAAAAATA
          1 ATCCTAAAAATA

                      *  
       8007 ATCCTAAATATTA
          1 ATCCTAAA-AATA

                      
       8020 ATCCTAAAAA
          1 ATCCTAAAAA

       8030 AATAAAGTTA


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
  12    9  0.45
  13   11  0.55

ACGTcount: A:0.54, C:0.17, G:0.00, T:0.29


Consensus pattern (12 bp):   
ATCCTAAAAATA

Found at i:25967 original size:16 final size:18

Alignment explanation


    Indices: 25946--25984  Score: 55
    Period size: 16  Copynumber: 2.3  Consensus size: 18

      25936 ATTTCACTTA

                          *   
      25946 TTTATTTTA-TTT-TTGT
          1 TTTATTTTAGTTTGATGT

                              
      25962 TTTATTTTAGTTTGATGT
          1 TTTATTTTAGTTTGATGT

                 
      25980 TTTAT
          1 TTTAT

      25985 CTCTAAACCC


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  16    9  0.45
  17    3  0.15
  18    8  0.40

ACGTcount: A:0.15, C:0.00, G:0.10, T:0.74


Consensus pattern (18 bp):   
TTTATTTTAGTTTGATGT
Done.