Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008427.1 Kokia drynarioides strain JFW-HI SEQ_123098, 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: 4090
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34


Found at i:3162 original size:23 final size:23

Alignment explanation


    Indices: 3136--3186  Score: 102
    Period size: 23  Copynumber: 2.2  Consensus size: 23

       3126 CATAATACAA

                                   
       3136 AGGGAACTAATTATACTCTAAAT
          1 AGGGAACTAATTATACTCTAAAT

                                   
       3159 AGGGAACTAATTATACTCTAAAT
          1 AGGGAACTAATTATACTCTAAAT

                 
       3182 AGGGA
          1 AGGGA

       3187 GAATTTAATG


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   28  1.00

ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27


Consensus pattern (23 bp):   
AGGGAACTAATTATACTCTAAAT

Found at i:3422 original size:26 final size:28

Alignment explanation


    Indices: 3393--3449  Score: 82
    Period size: 26  Copynumber: 2.1  Consensus size: 28

       3383 CATGCATTGA

                        *  *            
       3393 AATTTAGTTTAGTTTTA-AC-TTAGATT
          1 AATTTAGTTTAGATTAATACTTTAGATT

                                        
       3419 AATTTAGTTTAGATTAATACTTTAGATT
          1 AATTTAGTTTAGATTAATACTTTAGATT

               
       3447 AAT
          1 AAT

       3450 ATCCTCCACA


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  26   15  0.56
  27    2  0.07
  28   10  0.37

ACGTcount: A:0.35, C:0.04, G:0.11, T:0.51


Consensus pattern (28 bp):   
AATTTAGTTTAGATTAATACTTTAGATT

Found at i:3444 original size:13 final size:13

Alignment explanation


    Indices: 3412--3450  Score: 51
    Period size: 13  Copynumber: 2.8  Consensus size: 13

       3402 TAGTTTTAAC

                         * 
       3412 TTAGATTAATTTAGT
          1 TTAGATTAA--TACT

                         
       3427 TTAGATTAATACT
          1 TTAGATTAATACT

                       
       3440 TTAGATTAATA
          1 TTAGATTAATA

       3451 TCCTCCACAA


Statistics
Matches: 23,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  13   14  0.61
  15    9  0.39

ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49


Consensus pattern (13 bp):   
TTAGATTAATACT
Done.