Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005972.1 Kokia drynarioides strain JFW-HI SEQ_120390, 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: 23192
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35

Warning! 56 characters in sequence are not A, C, G, or T


Found at i:8177 original size:23 final size:23

Alignment explanation


    Indices: 8120--8177  Score: 64
    Period size: 22  Copynumber: 2.5  Consensus size: 23

       8110 TTAATGTGTT

                       *            
       8120 AAAAATATTAATTAAAATAAAATA
          1 AAAAATA-TAAATAAAATAAAATA

                *         *  *     
       8144 AAAATTA-AAATAACATGAAATA
          1 AAAAATATAAATAAAATAAAATA

                        
       8166 AAAAATATAAAT
          1 AAAAATATAAAT

       8178 GCGCGTCAGA


Statistics
Matches: 28,  Mismatches: 5, Indels: 3
        0.78            0.14        0.08

Matches are distributed among these distances:
  22   18  0.64
  23    4  0.14
  24    6  0.21

ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26


Consensus pattern (23 bp):   
AAAAATATAAATAAAATAAAATA

Found at i:11778 original size:18 final size:19

Alignment explanation


    Indices: 11743--11780  Score: 51
    Period size: 18  Copynumber: 2.1  Consensus size: 19

      11733 AATTTTTAAT

                         *     
      11743 GATATATTTGACCGAACCA
          1 GATATATTTGACCAAACCA

                       *       
      11762 GATATA-TTGATCAAACCA
          1 GATATATTTGACCAAACCA

             
      11780 G
          1 G

      11781 GAATTGATAG


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  18   11  0.65
  19    6  0.35

ACGTcount: A:0.39, C:0.18, G:0.16, T:0.26


Consensus pattern (19 bp):   
GATATATTTGACCAAACCA

Found at i:14978 original size:17 final size:17

Alignment explanation


    Indices: 14957--14990  Score: 50
    Period size: 17  Copynumber: 1.9  Consensus size: 17

      14947 ATTAAAAAAT

                              
      14957 AAAAAATTATAAAATTAC
          1 AAAAAA-TATAAAATTAC

                      *     
      14975 AAAAAATATATAATTA
          1 AAAAAATATAAAATTA

      14991 ATATTTTTAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    9  0.60
  18    6  0.40

ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29


Consensus pattern (17 bp):   
AAAAAATATAAAATTAC

Found at i:18509 original size:12 final size:12

Alignment explanation


    Indices: 18492--18516  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

      18482 AACTTAATCC

                        
      18492 ATAAACACCTCT
          1 ATAAACACCTCT

                        
      18504 ATAAACACCTCT
          1 ATAAACACCTCT

             
      18516 A
          1 A

      18517 AGTTGATTGC


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.44, C:0.32, G:0.00, T:0.24


Consensus pattern (12 bp):   
ATAAACACCTCT
Done.