Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006523.1 Kokia drynarioides strain JFW-HI SEQ_121107, 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: 9537
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:91 original size:58 final size:58

Alignment explanation


    Indices: 15--151  Score: 206
    Period size: 58  Copynumber: 2.3  Consensus size: 58

          5 TAATTCATAT

                                    * *                                
         15 TTTAATAATAATTATATTAAAAATGTTATTAAATTATATATTA-TTTTATTAAATTGTA
          1 TTTAATAATAATT-TATTAAAAATATAATTAAATTATATATTATTTTTATTAAATTGTA

                                                 *                     
         73 TTTAATAATAATATTATT-AAAATATAATTAAATTATTTATTATTTTTATTAAATTGTA
          1 TTTAATAATAAT-TTATTAAAAATATAATTAAATTATATATTATTTTTATTAAATTGTA

                                 
        131 TTTAATAATAATCTTATTAAA
          1 TTTAATAATAAT-TTATTAAA

        152 TTTTAATAAC


Statistics
Matches: 72,  Mismatches: 4, Indels: 5
        0.89            0.05        0.06

Matches are distributed among these distances:
  57   21  0.29
  58   48  0.67
  59    3  0.04

ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52


Consensus pattern (58 bp):   
TTTAATAATAATTTATTAAAAATATAATTAAATTATATATTATTTTTATTAAATTGTA

Found at i:489 original size:14 final size:14

Alignment explanation


    Indices: 470--496  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

        460 GTACACTAAG

                          
        470 AAAGAAATTTTAGT
          1 AAAGAAATTTTAGT

                         
        484 AAAGAAATTTTAG
          1 AAAGAAATTTTAG

        497 AATAACTTTG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33


Consensus pattern (14 bp):   
AAAGAAATTTTAGT

Found at i:1496 original size:58 final size:58

Alignment explanation


    Indices: 1374--1488  Score: 230
    Period size: 58  Copynumber: 2.0  Consensus size: 58

       1364 GGTCCTTTCC

                                                                      
       1374 CCTTCTTTTTCCCTTTTTTTCTGGAATCTTGGGTTTTTTAAATTCTGTATTCTAATGA
          1 CCTTCTTTTTCCCTTTTTTTCTGGAATCTTGGGTTTTTTAAATTCTGTATTCTAATGA

                                                                     
       1432 CCTTCTTTTTCCCTTTTTTTCTGGAATCTTGGGTTTTTTAAATTCTGTATTCTAATG
          1 CCTTCTTTTTCCCTTTTTTTCTGGAATCTTGGGTTTTTTAAATTCTGTATTCTAATG

       1489 TTTTTCTTCA


Statistics
Matches: 57,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  58   57  1.00

ACGTcount: A:0.15, C:0.17, G:0.12, T:0.56


Consensus pattern (58 bp):   
CCTTCTTTTTCCCTTTTTTTCTGGAATCTTGGGTTTTTTAAATTCTGTATTCTAATGA

Found at i:4504 original size:6 final size:6

Alignment explanation


    Indices: 4486--4521  Score: 63
    Period size: 6  Copynumber: 6.0  Consensus size: 6

       4476 GGGTGGGACT

                     *                               
       4486 GAAGGA GATGGA GAAGGA GAAGGA GAAGGA GAAGGA
          1 GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA

       4522 TGGGAATCGC


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   6   28  1.00

ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03


Consensus pattern (6 bp):   
GAAGGA

Done.