Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011022.1 Kokia drynarioides strain JFW-HI SEQ_125993, 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: 1912
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26


Found at i:1406 original size:16 final size:16

Alignment explanation


    Indices: 1385--1429  Score: 54
    Period size: 16  Copynumber: 2.7  Consensus size: 16

       1375 AAAAATAAAT

                     *      
       1385 AAAAAAGAAGAGAAAG
          1 AAAAAAGAAAAGAAAG

                           *
       1401 AAAAAAGAAAAGAAAA
          1 AAAAAAGAAAAGAAAG

                         
       1417 AACAATAAGAAAA
          1 AA-AA-AAGAAAA

       1430 ACAAAAATAG


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  16   16  0.64
  17    2  0.08
  18    7  0.28

ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02


Consensus pattern (16 bp):   
AAAAAAGAAAAGAAAG

Found at i:1414 original size:12 final size:12

Alignment explanation


    Indices: 1371--1446  Score: 62
    Period size: 13  Copynumber: 5.8  Consensus size: 12

       1361 AGATACAATG

                     *  
       1371 AAGAAAAAATAA
          1 AAGAAAAAAGAA

               *           
       1383 ATAAAAAAGAAGAGA
          1 A-AGAAAA-AAGA-A

                        
       1398 AAGAAAAAAGAA
          1 AAGAAAAAAGAA

                     *  
       1410 AAGAAAAAACAA
          1 AAGAAAAAAGAA

                       *  
       1422 TAAGAAAAACAAAA
          1 -AAGAAAAA-AGAA

                       
       1436 ATAGAAAAAAG
          1 A-AGAAAAAAG

       1447 GAGAGGTCGA


Statistics
Matches: 52,  Mismatches: 6, Indels: 11
        0.75            0.09        0.16

Matches are distributed among these distances:
  12   13  0.25
  13   19  0.37
  14   18  0.35
  15    2  0.04

ACGTcount: A:0.79, C:0.03, G:0.13, T:0.05


Consensus pattern (12 bp):   
AAGAAAAAAGAA

Found at i:1426 original size:13 final size:12

Alignment explanation


    Indices: 1397--1435  Score: 53
    Period size: 12  Copynumber: 3.2  Consensus size: 12

       1387 AAAAGAAGAG

                      * 
       1397 AAAGAAAAAAGA
          1 AAAGAAAAAACA

                        
       1409 AAAGAAAAAACA
          1 AAAGAAAAAACA

                         
       1421 ATAAG-AAAAACA
          1 A-AAGAAAAAACA

               
       1433 AAA
          1 AAA

       1436 ATAGAAAAAA


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  11    2  0.08
  12   20  0.80
  13    3  0.12

ACGTcount: A:0.82, C:0.05, G:0.10, T:0.03


Consensus pattern (12 bp):   
AAAGAAAAAACA
Done.