Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008526.1 Kokia drynarioides strain JFW-HI SEQ_123203, 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: 14184
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:4108 original size:29 final size:29

Alignment explanation


    Indices: 4066--4121  Score: 94
    Period size: 29  Copynumber: 1.9  Consensus size: 29

       4056 GGGATGGGAA

                   *                     
       4066 GGGAAGGGGTAAAAGTTTTGGGGAAAAGT
          1 GGGAAGGAGTAAAAGTTTTGGGGAAAAGT

                               *       
       4095 GGGAAGGAGTAAAAGTTTTTGGGAAAA
          1 GGGAAGGAGTAAAAGTTTTGGGGAAAA

       4122 AAGTAAAAAA


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  29   25  1.00

ACGTcount: A:0.38, C:0.00, G:0.41, T:0.21


Consensus pattern (29 bp):   
GGGAAGGAGTAAAAGTTTTGGGGAAAAGT

Found at i:8898 original size:18 final size:20

Alignment explanation


    Indices: 8858--8904  Score: 53
    Period size: 18  Copynumber: 2.4  Consensus size: 20

       8848 AGATGATGAT

                                 
       8858 TTATTATATATATATTTACTA
          1 TTATTATATATATATTTA-TA

                         *      
       8879 TTATTAT-TATATGTTT-TA
          1 TTATTATATATATATTTATA

              *     
       8897 TTTTTATA
          1 TTATTATA

       8905 ATCATTAAAA


Statistics
Matches: 23,  Mismatches: 2, Indels: 4
        0.79            0.07        0.14

Matches are distributed among these distances:
  18    8  0.35
  20    8  0.35
  21    7  0.30

ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64


Consensus pattern (20 bp):   
TTATTATATATATATTTATA

Found at i:10235 original size:29 final size:29

Alignment explanation


    Indices: 10203--10282  Score: 99
    Period size: 29  Copynumber: 2.8  Consensus size: 29

      10193 ATACTTTTAT

                        *      *         
      10203 AAAATGTCCAATTTGGTACTTATACTTTG
          1 AAAATGTCCAATGTGGTACATATACTTTG

                   *             *       
      10232 AAAATGTACAATGTGGTACATGTACTTTG
          1 AAAATGTCCAATGTGGTACATATACTTTG

                           *       
      10261 AAAA-GTCTCAATGTAGTACATA
          1 AAAATGTC-CAATGTGGTACATA

      10283 AACTATCAAT


Statistics
Matches: 43,  Mismatches: 7, Indels: 2
        0.83            0.13        0.04

Matches are distributed among these distances:
  28    2  0.05
  29   41  0.95

ACGTcount: A:0.36, C:0.12, G:0.16, T:0.35


Consensus pattern (29 bp):   
AAAATGTCCAATGTGGTACATATACTTTG
Done.