Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008733.1 Kokia drynarioides strain JFW-HI SEQ_123415, 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: 14195
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32


Found at i:5218 original size:17 final size:17

Alignment explanation


    Indices: 5196--5232  Score: 56
    Period size: 17  Copynumber: 2.2  Consensus size: 17

       5186 GTCATTGCAT

                             
       5196 TTTTATTTGTCACTACA
          1 TTTTATTTGTCACTACA

                      * *    
       5213 TTTTATTTGTTAGTACA
          1 TTTTATTTGTCACTACA

               
       5230 TTT
          1 TTT

       5233 GCACTGTAGT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.22, C:0.11, G:0.08, T:0.59


Consensus pattern (17 bp):   
TTTTATTTGTCACTACA

Found at i:5800 original size:2 final size:2

Alignment explanation


    Indices: 5789--5824  Score: 63
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       5779 TCTCAGTCAC

                   *                                             
       5789 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       5825 TGCTGTAAAG


Statistics
Matches: 32,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:5991 original size:15 final size:17

Alignment explanation


    Indices: 5960--5991  Score: 50
    Period size: 15  Copynumber: 2.0  Consensus size: 17

       5950 AATTTGTACA

                             
       5960 TTAAGATTGCATAGAAT
          1 TTAAGATTGCATAGAAT

                             
       5977 TTAAG-TTGC-TAGAAT
          1 TTAAGATTGCATAGAAT

       5992 AAAAATTGCG


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  15    6  0.40
  16    4  0.27
  17    5  0.33

ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38


Consensus pattern (17 bp):   
TTAAGATTGCATAGAAT

Found at i:7923 original size:67 final size:68

Alignment explanation


    Indices: 7837--7991  Score: 170
    Period size: 67  Copynumber: 2.3  Consensus size: 68

       7827 CCTCCTCTCG

                     *    *             *   **    *                  *       
       7837 TCATGTTGAAGTTGTAAAGTTTAG-AATTAGTTTTCTCTCCATGTTGAAGTTACAAAGGTTCTTC
          1 TCATGTTGATGTTGCAAAGTTTAGAAATGAGTCCTCTCACCATGTTGAAGTTACAAAAGTTCTTC

            *  
       7901 CCA
         66 ACA

                    *             *      *                      *        *   
       7904 TCATGTTGGTGTTGCAAAG-TTCGAAATGGGTCCTCTCACCATGTTGAAGTTGCAAAAGTTTTTC
          1 TCATGTTGATGTTGCAAAGTTTAGAAATGAGTCCTCTCACCATGTTGAAGTTACAAAAGTTCTTC

               
       7968 ACA
         66 ACA

                          *      
       7971 TCATGTTGATGTTGGAAAGTT
          1 TCATGTTGATGTTGCAAAGTT

       7992 AGGTCTTCCC


Statistics
Matches: 71,  Mismatches: 15, Indels: 3
        0.80            0.17        0.03

Matches are distributed among these distances:
  66    3  0.04
  67   67  0.94
  68    1  0.01

ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38


Consensus pattern (68 bp):   
TCATGTTGATGTTGCAAAGTTTAGAAATGAGTCCTCTCACCATGTTGAAGTTACAAAAGTTCTTC
ACA
Done.