Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001269.1 Kokia drynarioides strain JFW-HI SEQ_112654, 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: 3662
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35


Found at i:1285 original size:15 final size:16

Alignment explanation


    Indices: 1260--1300  Score: 55
    Period size: 16  Copynumber: 2.6  Consensus size: 16

       1250 CTACAAAGAA

                      * * * 
       1260 TTTTTCTTTTTATATT
          1 TTTTTCTTTTAACAAT

                            
       1276 TTTTTCTTTTAACAAT
          1 TTTTTCTTTTAACAAT

                     
       1292 TTTTTCTTT
          1 TTTTTCTTT

       1301 AAGCACTCAT


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  16   22  1.00

ACGTcount: A:0.15, C:0.10, G:0.00, T:0.76


Consensus pattern (16 bp):   
TTTTTCTTTTAACAAT

Found at i:1863 original size:15 final size:15

Alignment explanation


    Indices: 1843--1896  Score: 60
    Period size: 15  Copynumber: 3.7  Consensus size: 15

       1833 TTAAAACAAA

                           
       1843 AACAAAAACACATGT
          1 AACAAAAACACATGT

                          *
       1858 AACAAAAACA-A--A
          1 AACAAAAACACATGT

                           
       1870 AACAAAAACACATGT
          1 AACAAAAACACATGT

                        
       1885 ATCACAAAAACA
          1 A--ACAAAAACA

       1897 AAAAATTTGG


Statistics
Matches: 32,  Mismatches: 2, Indels: 8
        0.76            0.05        0.19

Matches are distributed among these distances:
  12   10  0.31
  13    1  0.03
  14    1  0.03
  15   11  0.34
  17    9  0.28

ACGTcount: A:0.67, C:0.20, G:0.04, T:0.09


Consensus pattern (15 bp):   
AACAAAAACACATGT

Found at i:1865 original size:27 final size:28

Alignment explanation


    Indices: 1835--1900  Score: 116
    Period size: 27  Copynumber: 2.4  Consensus size: 28

       1825 TGTTATGATT

                                        
       1835 AAAACAAAAACAAAAACACATGTA-ACA
          1 AAAACAAAAACAAAAACACATGTACACA

                                         
       1862 AAAACAAAAACAAAAACACATGTATCACA
          1 AAAACAAAAACAAAAACACATGTA-CACA

                      
       1891 AAAACAAAAA
          1 AAAACAAAAA

       1901 ATTTGGAGCT


Statistics
Matches: 37,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
  27   24  0.65
  29   13  0.35

ACGTcount: A:0.71, C:0.18, G:0.03, T:0.08


Consensus pattern (28 bp):   
AAAACAAAAACAAAAACACATGTACACA

Found at i:1899 original size:6 final size:6

Alignment explanation


    Indices: 1835--1879  Score: 54
    Period size: 6  Copynumber: 7.0  Consensus size: 6

       1825 TGTTATGATT

                                     *                         
       1835 AAAACA AAAACA AAAACA CATGTAACA AAAACA AAAACA AAAACA
          1 AAAACA AAAACA AAAACA -A--AAACA AAAACA AAAACA AAAACA

       1880 CATGTATCAC


Statistics
Matches: 34,  Mismatches: 2, Indels: 6
        0.81            0.05        0.14

Matches are distributed among these distances:
   6   28  0.82
   7    1  0.03
   8    1  0.03
   9    4  0.12

ACGTcount: A:0.76, C:0.18, G:0.02, T:0.04


Consensus pattern (6 bp):   
AAAACA
Done.