Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003809.1 Kokia drynarioides strain JFW-HI SEQ_116805, 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: 7420
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:776 original size:6 final size:6

Alignment explanation


    Indices: 767--827  Score: 54
    Period size: 6  Copynumber: 10.5  Consensus size: 6

        757 TATTTTTTAT

                        *      *        *    *                     
        767 TTTAAA TTT-AT TTTAAG TTTAAA ATT-AT TTTAAA TTTAAA TTTAAA
          1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA

                **           
        813 TTTATT TTTAAA TTT
          1 TTTAAA TTTAAA TTT

        828 GAAAGATTGT


Statistics
Matches: 42,  Mismatches: 11, Indels: 4
        0.74            0.19        0.07

Matches are distributed among these distances:
   5    7  0.17
   6   35  0.83

ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59


Consensus pattern (6 bp):   
TTTAAA

Found at i:778 original size:11 final size:11

Alignment explanation


    Indices: 762--827  Score: 61
    Period size: 12  Copynumber: 6.3  Consensus size: 11

        752 CTTTTTATTT

                       
        762 TTTATTTTAAA
          1 TTTATTTTAAA

                      *
        773 TTTATTTTAAG
          1 TTTATTTTAAA

                       
        784 TTTA----AAA
          1 TTTATTTTAAA

                       
        791 -TTATTTTAAA
          1 TTTATTTTAAA

                 *      
        801 TTTAAATTTAAA
          1 TTT-ATTTTAAA

                        
        813 TTTATTTTTAAA
          1 TTTA-TTTTAAA

               
        825 TTT
          1 TTT

        828 GAAAGATTGT


Statistics
Matches: 44,  Mismatches: 4, Indels: 13
        0.72            0.07        0.21

Matches are distributed among these distances:
   6    3  0.07
   7    2  0.05
  10    3  0.07
  11   17  0.39
  12   19  0.43

ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61


Consensus pattern (11 bp):   
TTTATTTTAAA

Found at i:787 original size:17 final size:17

Alignment explanation


    Indices: 767--810  Score: 70
    Period size: 17  Copynumber: 2.6  Consensus size: 17

        757 TATTTTTTAT

                            *
        767 TTTAAATTTATTTTAAG
          1 TTTAAATTTATTTTAAA

                  *          
        784 TTTAAAATTATTTTAAA
          1 TTTAAATTTATTTTAAA

                      
        801 TTTAAATTTA
          1 TTTAAATTTA

        811 AATTTATTTT


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

Matches are distributed among these distances:
  17   24  1.00

ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57


Consensus pattern (17 bp):   
TTTAAATTTATTTTAAA

Found at i:810 original size:23 final size:24

Alignment explanation


    Indices: 778--827  Score: 75
    Period size: 23  Copynumber: 2.1  Consensus size: 24

        768 TTAAATTTAT

                 *                  
        778 TTTAAGTTTAAAATTA-TTTTAAA
          1 TTTAAATTTAAAATTATTTTTAAA

                        *           
        801 TTTAAATTTAAATTTATTTTTAAA
          1 TTTAAATTTAAAATTATTTTTAAA

               
        825 TTT
          1 TTT

        828 GAAAGATTGT


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  23   14  0.58
  24   10  0.42

ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58


Consensus pattern (24 bp):   
TTTAAATTTAAAATTATTTTTAAA

Found at i:1489 original size:15 final size:14

Alignment explanation


    Indices: 1469--1502  Score: 50
    Period size: 15  Copynumber: 2.4  Consensus size: 14

       1459 TTACTTCAGG

                     *     
       1469 TTAATAAATGTATAA
          1 TTAATAAATATAT-A

                          
       1484 TTAATAAATATATA
          1 TTAATAAATATATA

                 
       1498 TTAAT
          1 TTAAT

       1503 TATATAATAT


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  14    6  0.33
  15   12  0.67

ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44


Consensus pattern (14 bp):   
TTAATAAATATATA
Done.