Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01015149.1 Kokia drynarioides strain JFW-HI SEQ_130193, 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: 348839
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34

Warning! 434 characters in sequence are not A, C, G, or T


File 2 of 2

Found at i:342951 original size:21 final size:20

Alignment explanation


    Indices: 342925--342975  Score: 52
    Period size: 21  Copynumber: 2.5  Consensus size: 20

     342915 TAATAAAAGT

                                  
     342925 AAAATTATATTT-TACGTTATA
          1 AAAATTATATTTATAC-TT-TA

                                  
     342946 AAAATT-TGATTTAATACTTTA
          1 AAAATTAT-ATTT-ATACTTTA

                     
     342967 AAAATTATA
          1 AAAATTATA

     342976 AAAATATAAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 8
        0.76            0.00        0.24

Matches are distributed among these distances:
  20    1  0.04
  21   19  0.73
  22    3  0.12
  23    3  0.12

ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45


Consensus pattern (20 bp):   
AAAATTATATTTATACTTTA

Found at i:346382 original size:15 final size:15

Alignment explanation


    Indices: 346354--346386  Score: 50
    Period size: 15  Copynumber: 2.2  Consensus size: 15

     346344 CTGAGAGGAT

                           
     346354 AGCAGCAAAAGAAGC
          1 AGCAGCAAAAGAAGC

                            
     346369 AGCAG-AAAAGGAAGC
          1 AGCAGCAAAA-GAAGC

               
     346384 AGC
          1 AGC

     346387 TAAAGCCTCA


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  14    4  0.24
  15   13  0.76

ACGTcount: A:0.52, C:0.18, G:0.30, T:0.00


Consensus pattern (15 bp):   
AGCAGCAAAAGAAGC

Found at i:347293 original size:155 final size:155

Alignment explanation


    Indices: 347011--347323  Score: 617
    Period size: 155  Copynumber: 2.0  Consensus size: 155

     347001 TAGATAAAAG

                                                                             
     347011 TTTATTATTTCCGTACTTGTCCAAAAGGTAAAAAGTAAATTACTAGAAAAAAGGGGGTTGTTATG
          1 TTTATTATTTCCGTACTTGTCCAAAAGGTAAAAAGTAAATTACTAGAAAAAAGGGGGTTGTTATG

                                                                             
     347076 TAGATGTGTGGGTTATGTATTATATTATTGGAAAGTGCTTTAGCTTTGTTACCATATGTTCTCTA
         66 TAGATGTGTGGGTTATGTATTATATTATTGGAAAGTGCTTTAGCTTTGTTACCATATGTTCTCTA

                                     
     347141 TTTGAATTTAGCATTTGGCACTGAA
        131 TTTGAATTTAGCATTTGGCACTGAA

                                                                             
     347166 TTTATTATTTCCGTACTTGTCCAAAAGGTAAAAAGTAAATTACTAGAAAAAAGGGGGTTGTTATG
          1 TTTATTATTTCCGTACTTGTCCAAAAGGTAAAAAGTAAATTACTAGAAAAAAGGGGGTTGTTATG

                                                                             
     347231 TAGATGTGTGGGTTATGTATTATATTATTGGAAAGTGCTTTAGCTTTGTTACCATATGTTCTCTA
         66 TAGATGTGTGGGTTATGTATTATATTATTGGAAAGTGCTTTAGCTTTGTTACCATATGTTCTCTA

                *                    
     347296 TTTGTATTTAGCATTTGGCACTGAA
        131 TTTGAATTTAGCATTTGGCACTGAA

               
     347321 TTT
          1 TTT

     347324 TCTTTCAGTG


Statistics
Matches: 157,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 155  157  1.00

ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41


Consensus pattern (155 bp):   
TTTATTATTTCCGTACTTGTCCAAAAGGTAAAAAGTAAATTACTAGAAAAAAGGGGGTTGTTATG
TAGATGTGTGGGTTATGTATTATATTATTGGAAAGTGCTTTAGCTTTGTTACCATATGTTCTCTA
TTTGAATTTAGCATTTGGCACTGAA

Done.