Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007151.1 Kokia drynarioides strain JFW-HI SEQ_121763, 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: 13802
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33


Found at i:11173 original size:18 final size:17

Alignment explanation


    Indices: 11147--11181  Score: 52
    Period size: 18  Copynumber: 2.0  Consensus size: 17

      11137 CATTCATTCG

                              
      11147 TATACATACATAATATTA
          1 TATACATACAT-ATATTA

                *            
      11165 TATATATACATATATTA
          1 TATACATACATATATTA

      11182 ACTAAGTTAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  17    6  0.38
  18   10  0.62

ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43


Consensus pattern (17 bp):   
TATACATACATATATTA

Found at i:11747 original size:16 final size:15

Alignment explanation


    Indices: 11721--11762  Score: 50
    Period size: 16  Copynumber: 2.8  Consensus size: 15

      11711 AATTTTAATT

                        ** 
      11721 AAAAA-AAAAAACTA
          1 AAAAAGAAAAAAAGA

                            
      11735 AAAAAGTAAAAAAAGA
          1 AAAAAG-AAAAAAAGA

                        
      11751 AAAAAGAAAAAA
          1 AAAAAGAAAAAA

      11763 TATATTCAGA


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  14    5  0.21
  15    6  0.25
  16   13  0.54

ACGTcount: A:0.86, C:0.02, G:0.07, T:0.05


Consensus pattern (15 bp):   
AAAAAGAAAAAAAGA

Found at i:13175 original size:29 final size:30

Alignment explanation


    Indices: 13115--13176  Score: 90
    Period size: 30  Copynumber: 2.1  Consensus size: 30

      13105 TTTATTTTTT

                                      *   
      13115 TTAATTATTTATAATTTTTAAAAGATTAAA
          1 TTAATTATTTATAATTTTTAAAAGATCAAA

                  *            *          
      13145 TTAATTTTTTATAATTTTTGAAAG-TCAAA
          1 TTAATTATTTATAATTTTTAAAAGATCAAA

               
      13174 TTA
          1 TTA

      13177 TAATTTTATC


Statistics
Matches: 29,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  29    7  0.24
  30   22  0.76

ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52


Consensus pattern (30 bp):   
TTAATTATTTATAATTTTTAAAAGATCAAA

Found at i:13183 original size:29 final size:30

Alignment explanation


    Indices: 13122--13194  Score: 78
    Period size: 29  Copynumber: 2.5  Consensus size: 30

      13112 TTTTTAATTA

                               *        * 
      13122 TTTATAATTTTTAAAAGATTAAATTAATTT
          1 TTTATAATTTTTAAAAGATCAAATTAATAT

                        *                  
      13152 TTTATAATTTTTGAAAG-TCAAATT-ATAAT
          1 TTTATAATTTTTAAAAGATCAAATTAAT-AT

                 *   *    
      13181 TTTATCATTATTAA
          1 TTTATAATTTTTAA

      13195 TTTAAAATTT


Statistics
Matches: 36,  Mismatches: 6, Indels: 3
        0.80            0.13        0.07

Matches are distributed among these distances:
  28    2  0.06
  29   18  0.50
  30   16  0.44

ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52


Consensus pattern (30 bp):   
TTTATAATTTTTAAAAGATCAAATTAATAT
Done.