Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008097.1 Kokia drynarioides strain JFW-HI SEQ_122755, 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: 3072
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34


Found at i:2556 original size:3 final size:3

Alignment explanation


    Indices: 2548--2587  Score: 57
    Period size: 3  Copynumber: 14.0  Consensus size: 3

       2538 TTCCATTTTC

                                  *                                
       2548 TCT TCT TCT TCT TC- TCC TCT TCT TCT T-T TCT TCT TCT TCT
          1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT

       2588 CCATTTGTTC


Statistics
Matches: 34,  Mismatches: 1, Indels: 4
        0.87            0.03        0.10

Matches are distributed among these distances:
   2    4  0.12
   3   30  0.88

ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65


Consensus pattern (3 bp):   
TCT

Found at i:2568 original size:14 final size:14

Alignment explanation


    Indices: 2545--2589  Score: 60
    Period size: 14  Copynumber: 3.4  Consensus size: 14

       2535 TCCTTCCATT

                 *        
       2545 TTCTCTTCTTCTTC
          1 TTCTCCTCTTCTTC

                          
       2559 TTCTCCTCTTCTTC
          1 TTCTCCTCTTCTTC

                          
       2573 TT-T--TCTTCTTC
          1 TTCTCCTCTTCTTC

                  
       2584 TTCTCC
          1 TTCTCC

       2590 ATTTGTTCTC


Statistics
Matches: 27,  Mismatches: 1, Indels: 6
        0.79            0.03        0.18

Matches are distributed among these distances:
  11   10  0.37
  12    1  0.04
  13    1  0.04
  14   15  0.56

ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62


Consensus pattern (14 bp):   
TTCTCCTCTTCTTC

Found at i:2578 original size:25 final size:25

Alignment explanation


    Indices: 2545--2626  Score: 89
    Period size: 25  Copynumber: 3.4  Consensus size: 25

       2535 TCCTTCCATT

                                     
       2545 TTCTCTTCTTCTTCTTCTCCTCTTC
          1 TTCTCTTCTTCTTCTTCTCCTCTTC

                *                    *
       2570 TTCTTTTCTTCTTCTTCTCCAT-TTG
          1 TTCTCTTCTTCTTCTTCTCC-TCTTC

                   *        * *      
       2595 TTCTCTTATTCTTCTTTTGCTCTT-
          1 TTCTCTTCTTCTTCTTCTCCTCTTC

                     
       2619 TT-TCTTCT
          1 TTCTCTTCT

       2627 ACTACCCAGT


Statistics
Matches: 48,  Mismatches: 7, Indels: 6
        0.79            0.11        0.10

Matches are distributed among these distances:
  23    5  0.10
  24    3  0.06
  25   39  0.81
  26    1  0.02

ACGTcount: A:0.02, C:0.30, G:0.02, T:0.65


Consensus pattern (25 bp):   
TTCTCTTCTTCTTCTTCTCCTCTTC

Found at i:2609 original size:11 final size:11

Alignment explanation


    Indices: 2548--2588  Score: 55
    Period size: 11  Copynumber: 3.6  Consensus size: 11

       2538 TTCCATTTTC

                        
       2548 TCTTCTTCTTCT
          1 TCTTC-TCTTCT

               *       
       2560 TCTCCTCTTCT
          1 TCTTCTCTTCT

                *      
       2571 TCTTTTCTTCT
          1 TCTTCTCTTCT

                   
       2582 TCTTCTC
          1 TCTTCTC

       2589 CATTTGTTCT


Statistics
Matches: 25,  Mismatches: 4, Indels: 1
        0.83            0.13        0.03

Matches are distributed among these distances:
  11   21  0.84
  12    4  0.16

ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63


Consensus pattern (11 bp):   
TCTTCTCTTCT
Done.