Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001124.1 Kokia drynarioides strain JFW-HI SEQ_112410, 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: 3450
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36


Found at i:1279 original size:17 final size:17

Alignment explanation


    Indices: 1252--1284  Score: 50
    Period size: 16  Copynumber: 1.9  Consensus size: 17

       1242 AAATTATAAT

                              
       1252 TTTTAATAATAATTTATA
          1 TTTTAATAAT-ATTTATA

                            
       1270 TTTT-ATAATATTTAT
          1 TTTTAATAATATTTAT

       1285 TTTATTAAGG


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  16    6  0.40
  17    5  0.33
  18    4  0.27

ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61


Consensus pattern (17 bp):   
TTTTAATAATATTTATA

Found at i:1552 original size:6 final size:6

Alignment explanation


    Indices: 1541--1575  Score: 70
    Period size: 6  Copynumber: 5.8  Consensus size: 6

       1531 TGACTTGAAA

                                                    
       1541 TGGTCT TGGTCT TGGTCT TGGTCT TGGTCT TGGTC
          1 TGGTCT TGGTCT TGGTCT TGGTCT TGGTCT TGGTC

       1576 AATCATTTCC


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   29  1.00

ACGTcount: A:0.00, C:0.17, G:0.34, T:0.49


Consensus pattern (6 bp):   
TGGTCT

Found at i:2528 original size:45 final size:45

Alignment explanation


    Indices: 2464--2561  Score: 187
    Period size: 45  Copynumber: 2.2  Consensus size: 45

       2454 TTCCACGGAG

                                         *               
       2464 AGAAGCTGCTATGGATGCAGAACATACATGACACCTAGCTCTTTT
          1 AGAAGCTGCTATGGATGCAGAACATACATAACACCTAGCTCTTTT

                                                         
       2509 AGAAGCTGCTATGGATGCAGAACATACATAACACCTAGCTCTTTT
          1 AGAAGCTGCTATGGATGCAGAACATACATAACACCTAGCTCTTTT

                    
       2554 AGAAGCTG
          1 AGAAGCTG

       2562 AGGAACTTCA


Statistics
Matches: 52,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  45   52  1.00

ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26


Consensus pattern (45 bp):   
AGAAGCTGCTATGGATGCAGAACATACATAACACCTAGCTCTTTT
Done.