Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003651.1 Kokia drynarioides strain JFW-HI SEQ_116555, 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: 20780
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:6973 original size:19 final size:19

Alignment explanation


    Indices: 6949--7023  Score: 60
    Period size: 20  Copynumber: 3.8  Consensus size: 19

       6939 TAATTTAAAA

                          *    
       6949 AATTATTTAAATTTTTTTT
          1 AATTATTTAAATTTATTTT

                       *  *   * 
       6968 AATTATTTTAACTTAATTAT
          1 AATTA-TTTAAATTTATTTT

             *  *          *    
       6988 AGTTTTTTAAATTATGTTTT
          1 AATTATTTAAATT-TATTTT

                            
       7008 AATTATTTAAAATTTA
          1 AATTATTT-AAATTTA

       7024 ACTATTTTTT


Statistics
Matches: 40,  Mismatches: 13, Indels: 5
        0.69            0.22        0.09

Matches are distributed among these distances:
  19   12  0.30
  20   23  0.57
  21    5  0.12

ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60


Consensus pattern (19 bp):   
AATTATTTAAATTTATTTT

Found at i:7000 original size:39 final size:38

Alignment explanation


    Indices: 6954--7040  Score: 104
    Period size: 39  Copynumber: 2.2  Consensus size: 38

       6944 TAAAAAATTA

                     *             *       *        
       6954 TTTAAATTTTTTTTAATTATTT-TAACTTAATTATAGTTT
          1 TTTAAATTTGTTTTAATTATTTAAAACTTAACTAT--TTT

                                       *           
       6993 TTTAAATTATGTTTTAATTATTTAAAATTTAACTATTTT
          1 TTTAAATT-TGTTTTAATTATTTAAAACTTAACTATTTT

                     
       7032 TTTAAATTT
          1 TTTAAATTT

       7041 AGGAAAAATT


Statistics
Matches: 42,  Mismatches: 4, Indels: 5
        0.82            0.08        0.10

Matches are distributed among these distances:
  38    1  0.02
  39   19  0.45
  40   13  0.31
  41    9  0.21

ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62


Consensus pattern (38 bp):   
TTTAAATTTGTTTTAATTATTTAAAACTTAACTATTTT

Found at i:7657 original size:29 final size:29

Alignment explanation


    Indices: 7610--7698  Score: 76
    Period size: 29  Copynumber: 3.2  Consensus size: 29

       7600 AATTTTTACG

                 *     *  *              
       7610 ATTCATTTTAAGTCGTTTAGGTGAATATT
          1 ATTCAATTTAAATCATTTAGGTGAATATT

                         *     ** *      
       7639 ATTCAATTTAAATTATTTATATAAATATT
          1 ATTCAATTTAAATCATTTAGGTGAATATT

                 *     *                 
       7668 -TT--TTTTAAGTCATTTAGGTGAATATT
          1 ATTCAATTTAAATCATTTAGGTGAATATT

                 
       7694 ATTCA
          1 ATTCA

       7699 CATAATCCAA


Statistics
Matches: 44,  Mismatches: 13, Indels: 6
        0.70            0.21        0.10

Matches are distributed among these distances:
  26   18  0.41
  27    2  0.05
  28    2  0.05
  29   22  0.50

ACGTcount: A:0.34, C:0.06, G:0.10, T:0.51


Consensus pattern (29 bp):   
ATTCAATTTAAATCATTTAGGTGAATATT

Found at i:7691 original size:26 final size:28

Alignment explanation


    Indices: 7614--7696  Score: 80
    Period size: 26  Copynumber: 3.0  Consensus size: 28

       7604 TTTACGATTC

                      *                 
       7614 ATTTTAAGTCGTTTAGGTGAATATTATT
          1 ATTTTAAGTCATTTAGGTGAATATTATT

              *     * *     ** *         
       7642 CAATTTAAATTATTTATATAAATATT-TT
          1 -ATTTTAAGTCATTTAGGTGAATATTATT

                                        
       7670 -TTTTAAGTCATTTAGGTGAATATTATT
          1 ATTTTAAGTCATTTAGGTGAATATTATT

       7697 CACATAATCC


Statistics
Matches: 40,  Mismatches: 13, Indels: 4
        0.70            0.23        0.07

Matches are distributed among these distances:
  26   18  0.45
  27    2  0.05
  28    2  0.05
  29   18  0.45

ACGTcount: A:0.34, C:0.04, G:0.11, T:0.52


Consensus pattern (28 bp):   
ATTTTAAGTCATTTAGGTGAATATTATT
Done.