Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013652.1 Kokia drynarioides strain JFW-HI SEQ_128680, 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, 954

Length: 1591
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38


Found at i:9 original size:4 final size:4

Alignment explanation


    Indices: 1--71  Score: 61
    Period size: 4  Copynumber: 17.8  Consensus size: 4

                                             *       *    *    *    *  
          1 TATA TATA TATA TATA TATA TATA TATG TATA TGTA TGTA TGTA TGTA
          1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA

             *    *      *    *         
         49 TGTA TGTA TATG TATG TATA TAT
          1 TATA TATA TATA TATA TATA TAT

         72 TTTAACAACC


Statistics
Matches: 61,  Mismatches: 6, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
   4   61  1.00

ACGTcount: A:0.37, C:0.00, G:0.13, T:0.51


Consensus pattern (4 bp):   
TATA

Found at i:1430 original size:16 final size:15

Alignment explanation


    Indices: 1411--1455  Score: 54
    Period size: 16  Copynumber: 2.9  Consensus size: 15

       1401 AAAATTCTAG

                            
       1411 TTTCTCCTTTTTCTTT
          1 TTTCTCCTTTTTC-TT

                    *       
       1427 TTTCTTCCCTTTTCTT
          1 TTTC-TCCTTTTTCTT

             *           
       1443 TCTCTCCTTTTTC
          1 TTTCTCCTTTTTC

       1456 GTTTGAGCTT


Statistics
Matches: 25,  Mismatches: 3, Indels: 3
        0.81            0.10        0.10

Matches are distributed among these distances:
  15    8  0.32
  16    9  0.36
  17    8  0.32

ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69


Consensus pattern (15 bp):   
TTTCTCCTTTTTCTT

Found at i:1498 original size:17 final size:17

Alignment explanation


    Indices: 1476--1511  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

       1466 CTGTTCTTCC

                   *   *     
       1476 TTCTTTTGTTTCTTTTT
          1 TTCTTTTCTTTATTTTT

                             
       1493 TTCTTTTCTTTATTTTT
          1 TTCTTTTCTTTATTTTT

              
       1510 TT
          1 TT

       1512 ATATCATATA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.03, C:0.11, G:0.03, T:0.83


Consensus pattern (17 bp):   
TTCTTTTCTTTATTTTT

Found at i:1522 original size:2 final size:2

Alignment explanation


    Indices: 1511--1542  Score: 55
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       1501 TTTATTTTTT

                                                           
       1511 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA T

       1543 TAGTTAATAA


Statistics
Matches: 29,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   2   27  0.93
   3    2  0.07

ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Done.