Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009379.1 Kokia drynarioides strain JFW-HI SEQ_124086, 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: 4490
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36


Found at i:1599 original size:23 final size:21

Alignment explanation


    Indices: 1520--1605  Score: 72
    Period size: 21  Copynumber: 4.1  Consensus size: 21

       1510 TTACGAATAA

                    *            
       1520 TTATATATTTATATT-AT-TT
          1 TTATATATATATATTAATATT

                  *                
       1539 TTA-ATTTA-ATATTGAATAATT
          1 TTATATATATATATT-AAT-ATT

                      *          
       1560 TTATATATATTTATTAATATT
          1 TTATATATATATATTAATATT

                          *        
       1581 TTATATATAGTCATCTTAATATT
          1 TTATATATA-T-ATATTAATATT

              
       1604 TT
          1 TT

       1606 TTAATATTTA


Statistics
Matches: 53,  Mismatches: 6, Indels: 12
        0.75            0.08        0.17

Matches are distributed among these distances:
  17    5  0.09
  18    3  0.06
  19    5  0.09
  21   17  0.32
  22    8  0.15
  23   15  0.28

ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59


Consensus pattern (21 bp):   
TTATATATATATATTAATATT

Found at i:3919 original size:27 final size:27

Alignment explanation


    Indices: 3882--3935  Score: 81
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       3872 AAATTATGTA

                  *            *       
       3882 ATTAATTAAAAGGTATATCCTTTGATT
          1 ATTAATCAAAAGGTATATCATTTGATT

                        *              
       3909 ATTAATCAAAAGTTATATCATTTGATT
          1 ATTAATCAAAAGGTATATCATTTGATT

       3936 TTTTACAAAA


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

Matches are distributed among these distances:
  27   24  1.00

ACGTcount: A:0.39, C:0.07, G:0.09, T:0.44


Consensus pattern (27 bp):   
ATTAATCAAAAGGTATATCATTTGATT

Found at i:3951 original size:27 final size:27

Alignment explanation


    Indices: 3895--3952  Score: 64
    Period size: 27  Copynumber: 2.1  Consensus size: 27

       3885 AATTAAAAGG

                  *                  * 
       3895 TATATCCTTTGATTATTAATCAAAAGT
          1 TATATCATTTGATTATTAATCAAAAAT

                          *  *          
       3922 TATATCATTTGATTTTTTA-CAAAATAT
          1 TATATCATTTGATTATTAATCAAAA-AT

                
       3949 TATA
          1 TATA

       3953 ACTATTCAAG


Statistics
Matches: 26,  Mismatches: 4, Indels: 2
        0.81            0.12        0.06

Matches are distributed among these distances:
  26    5  0.19
  27   21  0.81

ACGTcount: A:0.38, C:0.09, G:0.05, T:0.48


Consensus pattern (27 bp):   
TATATCATTTGATTATTAATCAAAAAT
Done.