Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009021.1 Kokia drynarioides strain JFW-HI SEQ_123719, 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: 3175
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37


Found at i:546 original size:15 final size:15

Alignment explanation


    Indices: 526--556  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

        516 TTTTATAACT

                           
        526 TTTAAAAATTAAATA
          1 TTTAAAAATTAAATA

                   *       
        541 TTTAAAATTTAAATA
          1 TTTAAAAATTAAATA

             
        556 T
          1 T

        557 ACTAATACTT


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45


Consensus pattern (15 bp):   
TTTAAAAATTAAATA

Found at i:1962 original size:179 final size:174

Alignment explanation


    Indices: 1560--1969  Score: 393
    Period size: 179  Copynumber: 2.3  Consensus size: 174

       1550 TGTTTTTCTC

                                                    *                       *
       1560 TTCGAGTGTTGTTTTGTAGTAATTGCAGCGATGATTAAAACAAGGTTTAGGG-T--TAACGAGCT
          1 TTCGAGTGTTGTTTTGTAGT-ATTGCAGCGATGATTAAAATAAGGTTTAGGGTTAATAACGAGCG

            *           **                *             *                  * 
       1622 CACGTTTTGCCTTGGCTATGATTAAAATATTATCTCTAATGAGCTGCTGTTAATATTTTTACGGC
         65 AACGTTTTGCCTAAGCTATGATTAAAATATAATCTCTAATGAGCAGCTGTTAATATTTTTACGAC

            *       *      *                      *** *  
       1687 GTTTTTCCTACCGAATGTTAAAGATATTTAAATAAATGTTTGTTT
        130 CTTTTTCCAACCGAAAGTTAAAGATATTTAAATAAATGCAAGGTT

              *             *   * *       *             *                    
       1732 TTTGAGTGTTGTTTTGCAGCAAGTGCAGCGGTGATTATAAAAGTGAGGTTTAGGGTTAATAACGA
          1 TTCGAGTGTTGTTTTGTAG-TATTGCAGCGATGA-T-TAAAA-TAAGGTTTAGGGTTAATAACGA

                  *     *               *                            * *     
       1797 GCGAATGGTTTTTCCTAAGCTATGATTACAATATAATCTCTAATGAGCAG-TCGTT-GTCTTTAT
         62 GCGAA-CGTTTTGCCTAAGCTATGATTAAAATATAATCTCTAATGAGCAGCT-GTTAATATTT-T

                                                    *   *           
       1860 TACGATACCTTTTTCCAACCGAAAGTTCCAAAGAT-TTTCGAA-CAATGCAAGGTT
        124 TACG--ACCTTTTTCCAACCGAAAGTT--AAAGATATTT-AAATAAATGCAAGGTT

                                                                    
       1914 TTCGAGTGTTGTTTTGTAGTATTCGCAGCGATGATTAAAATAAGGTTTAGGGTTAA
          1 TTCGAGTGTTGTTTTGTAGTATT-GCAGCGATGATTAAAATAAGGTTTAGGGTTAA

       1970 CGAGCGTAGT


Statistics
Matches: 188,  Mismatches: 34, Indels: 25
        0.76            0.14        0.10

Matches are distributed among these distances:
 172   28  0.15
 173    1  0.01
 174    5  0.03
 175   10  0.05
 176    1  0.01
 178   14  0.07
 179   60  0.32
 180    5  0.03
 181   20  0.11
 182   36  0.19
 183    8  0.04

ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38


Consensus pattern (174 bp):   
TTCGAGTGTTGTTTTGTAGTATTGCAGCGATGATTAAAATAAGGTTTAGGGTTAATAACGAGCGA
ACGTTTTGCCTAAGCTATGATTAAAATATAATCTCTAATGAGCAGCTGTTAATATTTTTACGACC
TTTTTCCAACCGAAAGTTAAAGATATTTAAATAAATGCAAGGTT
Done.