Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007476.1 Kokia drynarioides strain JFW-HI SEQ_122099, 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: 24262
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32


Found at i:4604 original size:49 final size:49

Alignment explanation


    Indices: 4532--4630  Score: 198
    Period size: 49  Copynumber: 2.0  Consensus size: 49

       4522 CAAATCATAA

                                                             
       4532 CCCTATTGATCACAATTCAAGCAAATAAAAATTGATAAAGAACACTTGC
          1 CCCTATTGATCACAATTCAAGCAAATAAAAATTGATAAAGAACACTTGC

                                                             
       4581 CCCTATTGATCACAATTCAAGCAAATAAAAATTGATAAAGAACACTTGC
          1 CCCTATTGATCACAATTCAAGCAAATAAAAATTGATAAAGAACACTTGC

             
       4630 C
          1 C

       4631 GCTTGAGTGA


Statistics
Matches: 50,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  49   50  1.00

ACGTcount: A:0.44, C:0.21, G:0.10, T:0.24


Consensus pattern (49 bp):   
CCCTATTGATCACAATTCAAGCAAATAAAAATTGATAAAGAACACTTGC

Found at i:6927 original size:24 final size:24

Alignment explanation


    Indices: 6897--6947  Score: 75
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       6887 ACAAAAAACA

                      *        *    
       6897 TTAGCTCTCATGAGCCCAGGATGG
          1 TTAGCTCTCACGAGCCCAGAATGG

                    *               
       6921 TTAGCTCTTACGAGCCCAGAATGG
          1 TTAGCTCTCACGAGCCCAGAATGG

               
       6945 TTA
          1 TTA

       6948 ACCAATATAC


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27


Consensus pattern (24 bp):   
TTAGCTCTCACGAGCCCAGAATGG

Found at i:21867 original size:14 final size:15

Alignment explanation


    Indices: 21841--21869  Score: 51
    Period size: 14  Copynumber: 2.0  Consensus size: 15

      21831 TTCATCTACA

                           
      21841 CATATCAATTCATAT
          1 CATATCAATTCATAT

                           
      21856 CATATC-ATTCATAT
          1 CATATCAATTCATAT

      21870 AAGAAGCATT


Statistics
Matches: 14,  Mismatches: 0, Indels: 1
        0.93            0.00        0.07

Matches are distributed among these distances:
  14    8  0.57
  15    6  0.43

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


Consensus pattern (15 bp):   
CATATCAATTCATAT

Found at i:23593 original size:11 final size:11

Alignment explanation


    Indices: 23577--23607  Score: 55
    Period size: 10  Copynumber: 2.9  Consensus size: 11

      23567 TTTTGACTTT

                       
      23577 GAAAAATTATA
          1 GAAAAATTATA

                       
      23588 GAAAAA-TATA
          1 GAAAAATTATA

                      
      23598 GAAAAATTAT
          1 GAAAAATTAT

      23608 TAGAGACTGA


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  10   10  0.53
  11    9  0.47

ACGTcount: A:0.65, C:0.00, G:0.10, T:0.26


Consensus pattern (11 bp):   
GAAAAATTATA
Done.