Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007243.1 Kokia drynarioides strain JFW-HI SEQ_121858, 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: 6894
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.36


Found at i:566 original size:36 final size:37

Alignment explanation


    Indices: 515--602  Score: 88
    Period size: 36  Copynumber: 2.4  Consensus size: 37

        505 TATGGTAAAA

                   *                             
        515 AAAAAATGATATTATAAATTCTAAAAAATTATATTAT
          1 AAAAAATAATATTATAAATTCTAAAAAATTATATTAT

                            *   *  *   *      * *
        552 AAAAAATAAT-TTATATATTTTATAAAGTTATATAAC
          1 AAAAAATAATATTATAAATTCTAAAAAATTATATTAT

               *   *       
        588 AAACAATTATATTAT
          1 AAAAAATAATATTAT

        603 TTAAGTCCTA


Statistics
Matches: 41,  Mismatches: 9, Indels: 2
        0.79            0.17        0.04

Matches are distributed among these distances:
  36   28  0.68
  37   13  0.32

ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40


Consensus pattern (37 bp):   
AAAAAATAATATTATAAATTCTAAAAAATTATATTAT

Found at i:925 original size:16 final size:15

Alignment explanation


    Indices: 890--934  Score: 58
    Period size: 14  Copynumber: 3.1  Consensus size: 15

        880 ATTGAACAAT

                     *     
        890 TTATAAAACCTTAT-
          1 TTATAAAACTTTATA

                            
        904 TTATAAAACTTGTATA
          1 TTATAAAACTT-TATA

                           
        920 TTAT-AAACTTTATA
          1 TTATAAAACTTTATA

             
        934 T
          1 T

        935 ATATTTTTTA


Statistics
Matches: 28,  Mismatches: 1, Indels: 4
        0.85            0.03        0.12

Matches are distributed among these distances:
  14   15  0.54
  15    9  0.32
  16    4  0.14

ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47


Consensus pattern (15 bp):   
TTATAAAACTTTATA

Found at i:4506 original size:33 final size:32

Alignment explanation


    Indices: 4469--4580  Score: 109
    Period size: 33  Copynumber: 3.4  Consensus size: 32

       4459 TTGTCCCGGA

                       *                     
       4469 GGACTTACTTTATTCTGTGTTTACTATCTCGAT
          1 GGACTTACTTTGTTCTGTGTTTACT-TCTCGAT

                   *                  *  * *
       4502 GGACTTATTTTGTTCTGTGTTTA-TTGTCAAG
          1 GGACTTACTTTGTTCTGTGTTTACTTCTCGAT

                             **                
       4533 GCGAACTTACTTTGTTCCATGTTTACTGTCTCGAT
          1 G-G-ACTTACTTTGTTCTGTGTTTACT-TCTCGAT

                   *     
       4568 GGACTTAGTTTGT
          1 GGACTTACTTTGT

       4581 CATGTTTATT


Statistics
Matches: 63,  Mismatches: 12, Indels: 8
        0.76            0.14        0.10

Matches are distributed among these distances:
  31    5  0.08
  32    2  0.03
  33   49  0.78
  34    2  0.03
  35    5  0.08

ACGTcount: A:0.17, C:0.16, G:0.20, T:0.47


Consensus pattern (32 bp):   
GGACTTACTTTGTTCTGTGTTTACTTCTCGAT

Found at i:4752 original size:44 final size:44

Alignment explanation


    Indices: 4688--4795  Score: 162
    Period size: 44  Copynumber: 2.5  Consensus size: 44

       4678 TGCCATGGTG

                                                        
       4688 TCTTTCATCCATGGTCTTACTCATCATATCTGGCTGTCATAACA
          1 TCTTTCATCCATGGTCTTACTCATCATATCTGGCTGTCATAACA

                 *         *                         * *
       4732 TCTTTTATCCATGGTTTTACTCATCATATCTGGCTGTCATAGCG
          1 TCTTTCATCCATGGTCTTACTCATCATATCTGGCTGTCATAACA

             *       *          
       4776 TGTTTCATCTATGGTCTTAC
          1 TCTTTCATCCATGGTCTTAC

       4796 ACCGCATACC


Statistics
Matches: 56,  Mismatches: 8, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  44   56  1.00

ACGTcount: A:0.19, C:0.24, G:0.14, T:0.43


Consensus pattern (44 bp):   
TCTTTCATCCATGGTCTTACTCATCATATCTGGCTGTCATAACA
Done.