Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014554.1 Kokia drynarioides strain JFW-HI SEQ_129593, 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: 3991
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34


Found at i:1844 original size:31 final size:31

Alignment explanation


    Indices: 1792--1859  Score: 84
    Period size: 31  Copynumber: 2.2  Consensus size: 31

       1782 TTTAGTTTAA

                                  *   *     
       1792 TAAGTGTTTGCATCTTTAATTATGTCTTGCAT
          1 TAAGTGTTTGCA-CTTTAATTAAGTCATGCAT

                                            
       1824 TAAGTGTTTTGCA-TTTAATTAAGTCATGCAT
          1 TAAGTG-TTTGCACTTTAATTAAGTCATGCAT

            *    
       1855 AAAGT
          1 TAAGT

       1860 TGTGTTTTTC


Statistics
Matches: 32,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
  31   20  0.62
  32    6  0.19
  33    6  0.19

ACGTcount: A:0.28, C:0.10, G:0.16, T:0.46


Consensus pattern (31 bp):   
TAAGTGTTTGCACTTTAATTAAGTCATGCAT

Found at i:1982 original size:48 final size:48

Alignment explanation


    Indices: 1919--2061  Score: 214
    Period size: 48  Copynumber: 3.0  Consensus size: 48

       1909 ATAAAGTCGT

                      *                                      
       1919 ATAATTATGCTTCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTA
          1 ATAATT-TGCATCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTA

                                                            
       1968 ATAATTTGCATCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTA
          1 ATAATTTGCATCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTA

            *    *     *     *      *                *    
       2016 GTAATCTGCATTATTAAATGTTTTATTTGTTAAATGCATCTCTGTT
          1 ATAATTTGCATCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTT

       2062 AAATGCCTTG


Statistics
Matches: 87,  Mismatches: 7, Indels: 1
        0.92            0.07        0.01

Matches are distributed among these distances:
  48   81  0.93
  49    6  0.07

ACGTcount: A:0.25, C:0.09, G:0.14, T:0.52


Consensus pattern (48 bp):   
ATAATTTGCATCATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTA

Found at i:2074 original size:48 final size:46

Alignment explanation


    Indices: 1932--2076  Score: 168
    Period size: 48  Copynumber: 3.0  Consensus size: 46

       1922 ATTATGCTTC

                                                            *
       1932 ATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAATAAT-TTGCATC
          1 ATTAAGTGTTTTGTTTGTTAAATGCATCTTTG-TT-A-AATCTTGCATT

                                                             
       1980 ATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTTAGTAATC-TGCATT
          1 ATTAAGTGTTTTGTTTGTTAAATGCATCTTTG-TTA--AATCTTGCATT

                 *      *                *                  
       2028 ATTAAATGTTTTATTTGTTAAATGCATCTCTGTTAAATGCCTTGCATT
          1 ATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTAAAT--CTTGCATT

             
       2076 A
          1 A

       2077 ACGCATCAGC


Statistics
Matches: 88,  Mismatches: 4, Indels: 10
        0.86            0.04        0.10

Matches are distributed among these distances:
  45    3  0.03
  47    5  0.06
  48   80  0.91

ACGTcount: A:0.26, C:0.10, G:0.14, T:0.50


Consensus pattern (46 bp):   
ATTAAGTGTTTTGTTTGTTAAATGCATCTTTGTTAAATCTTGCATT
Done.