Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001209.1 Kokia drynarioides strain JFW-HI SEQ_112560, 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: 3426
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32


Found at i:1458 original size:74 final size:74

Alignment explanation


    Indices: 1367--1516  Score: 273
    Period size: 74  Copynumber: 2.0  Consensus size: 74

       1357 TGAAGGGATA

                                                *                            
       1367 CAATGTTTCATTCAAGAGTTTTTAAATGAATCAACATATTCATTTATGAATGATGAATGATGGCT
          1 CAATGTTTCATTCAAGAGTTTTTAAATGAATCAACACATTCATTTATGAATGATGAATGATGGCT

                     
       1432 GTTCACATT
         66 GTTCACATT

                        *                                                    
       1441 CAATGTTTCATTTAAGAGTTTTTAAATGAATCAACACATTCATTTATGAATGATGAATGATGGCT
          1 CAATGTTTCATTCAAGAGTTTTTAAATGAATCAACACATTCATTTATGAATGATGAATGATGGCT

                  *  
       1506 GTTCACTTT
         66 GTTCACATT

              
       1515 CA
          1 CA

       1517 TTTGTAAAGC


Statistics
Matches: 73,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  74   73  1.00

ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39


Consensus pattern (74 bp):   
CAATGTTTCATTCAAGAGTTTTTAAATGAATCAACACATTCATTTATGAATGATGAATGATGGCT
GTTCACATT

Found at i:2062 original size:5 final size:5

Alignment explanation


    Indices: 2052--2097  Score: 58
    Period size: 5  Copynumber: 9.4  Consensus size: 5

       2042 TACTGTTTGG

                          *          *                       *      
       2052 AAGAA AAGAA AAAAA AAGAA ACGAA AA-AA AAGAA AAGAA ATGAA AA
          1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AA

       2098 ATATCATATT


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

Matches are distributed among these distances:
   4    4  0.12
   5   30  0.88

ACGTcount: A:0.80, C:0.02, G:0.15, T:0.02


Consensus pattern (5 bp):   
AAGAA

Found at i:2087 original size:19 final size:19

Alignment explanation


    Indices: 2054--2098  Score: 63
    Period size: 19  Copynumber: 2.3  Consensus size: 19

       2044 CTGTTTGGAA

                                
       2054 GAAAAGAAAAAAAAAGAAAC
          1 GAAAA-AAAAAAAAAGAAAC

                     *        *
       2074 GAAAAAAAAGAAAAGAAAT
          1 GAAAAAAAAAAAAAGAAAC

                  
       2093 GAAAAA
          1 GAAAAA

       2099 TATCATATTT


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  19   18  0.78
  20    5  0.22

ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02


Consensus pattern (19 bp):   
GAAAAAAAAAAAAAGAAAC

Found at i:2097 original size:15 final size:14

Alignment explanation


    Indices: 2052--2091  Score: 62
    Period size: 14  Copynumber: 2.8  Consensus size: 14

       2042 TACTGTTTGG

                           
       2052 AAGAAAAGAAAAAAA
          1 AAGAAAAG-AAAAAA

                  *       
       2067 AAGAAACGAAAAAA
          1 AAGAAAAGAAAAAA

                       
       2081 AAGAAAAGAAA
          1 AAGAAAAGAAA

       2092 TGAAAAATAT


Statistics
Matches: 23,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  14   16  0.70
  15    7  0.30

ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00


Consensus pattern (14 bp):   
AAGAAAAGAAAAAA
Done.