Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004201.1 Kokia drynarioides strain JFW-HI SEQ_117442, 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: 3808
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38


Found at i:1559 original size:16 final size:16

Alignment explanation


    Indices: 1526--1561  Score: 56
    Period size: 15  Copynumber: 2.3  Consensus size: 16

       1516 AATTTATAAA

                       *    
       1526 TTTTACTTTAATTATT
          1 TTTTACTTTAAATATT

                            
       1542 TTTTA-TTTAAATATT
          1 TTTTACTTTAAATATT

                 
       1557 TTTTA
          1 TTTTA

       1562 AATTTTAAAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  15   14  0.74
  16    5  0.26

ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69


Consensus pattern (16 bp):   
TTTTACTTTAAATATT

Found at i:2275 original size:12 final size:12

Alignment explanation


    Indices: 2260--2288  Score: 58
    Period size: 12  Copynumber: 2.4  Consensus size: 12

       2250 CCACGACAAC

                        
       2260 GATGACGATGAT
          1 GATGACGATGAT

                        
       2272 GATGACGATGAT
          1 GATGACGATGAT

                 
       2284 GATGA
          1 GATGA

       2289 TGTGAGGTCC


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   17  1.00

ACGTcount: A:0.34, C:0.07, G:0.34, T:0.24


Consensus pattern (12 bp):   
GATGACGATGAT

Found at i:3401 original size:6 final size:6

Alignment explanation


    Indices: 3382--3434  Score: 52
    Period size: 6  Copynumber: 8.8  Consensus size: 6

       3372 AATCATGAAG

                    *                *      *      *      *      * 
       3382 ATGATA AAGATA ATGATA ATGAAA ATGAAA ATGACA ATGACA ATGACA
          1 ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA

                 
       3430 ATGAT
          1 ATGAT

       3435 GTGAGTCCCT


Statistics
Matches: 42,  Mismatches: 5, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
   6   42  1.00

ACGTcount: A:0.55, C:0.06, G:0.17, T:0.23


Consensus pattern (6 bp):   
ATGATA

Found at i:3408 original size:12 final size:12

Alignment explanation


    Indices: 3376--3434  Score: 55
    Period size: 12  Copynumber: 4.9  Consensus size: 12

       3366 AATAACAATC

                 *      
       3376 ATGAAGATGATA
          1 ATGAAAATGATA

             *  *       
       3388 AAGATAATGATA
          1 ATGAAAATGATA

                      * 
       3400 ATGAAAATGAAA
          1 ATGAAAATGATA

                *     * 
       3412 ATGACAATGACA
          1 ATGAAAATGATA

                *      
       3424 ATGACAATGAT
          1 ATGAAAATGAT

       3435 GTGAGTCCCT


Statistics
Matches: 38,  Mismatches: 9, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  12   38  1.00

ACGTcount: A:0.54, C:0.05, G:0.19, T:0.22


Consensus pattern (12 bp):   
ATGAAAATGATA
Done.