Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006514.1 Kokia drynarioides strain JFW-HI SEQ_121098, 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: 5249
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35


Found at i:1603 original size:6 final size:6

Alignment explanation


    Indices: 1565--1645  Score: 81
    Period size: 6  Copynumber: 13.3  Consensus size: 6

       1555 AATTAGTATC

                     *      *      *      *               *        
       1565 TTTATT TTCATT TTCATT TTCATT TTCATT TTTATT TTTAGT TTTATT
          1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT

               *               *      *           
       1613 TTTTTAT TTTATT TTTAAT TTTAAT TTTATT TT
          1 TTTAT-T TTTATT TTTATT TTTATT TTTATT TT

       1646 AATTATGCAC


Statistics
Matches: 66,  Mismatches: 8, Indels: 2
        0.87            0.11        0.03

Matches are distributed among these distances:
   6   61  0.92
   7    5  0.08

ACGTcount: A:0.19, C:0.05, G:0.01, T:0.75


Consensus pattern (6 bp):   
TTTATT

Found at i:1618 original size:14 final size:13

Alignment explanation


    Indices: 1599--1628  Score: 51
    Period size: 13  Copynumber: 2.2  Consensus size: 13

       1589 TTCATTTTTA

                          
       1599 TTTTTAGTTTTATT
          1 TTTTTA-TTTTATT

                         
       1613 TTTTTATTTTATT
          1 TTTTTATTTTATT

               
       1626 TTT
          1 TTT

       1629 AATTTTAATT


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13   10  0.62
  14    6  0.38

ACGTcount: A:0.13, C:0.00, G:0.03, T:0.83


Consensus pattern (13 bp):   
TTTTTATTTTATT

Found at i:1635 original size:31 final size:32

Alignment explanation


    Indices: 1581--1645  Score: 96
    Period size: 31  Copynumber: 2.1  Consensus size: 32

       1571 TTCATTTTCA

                              *     *       
       1581 TTTTCATTTTCATTTTTATTTTTAGTTTTATT
          1 TTTTCATTTTCATTTTTAATTTTAATTTTATT

                *                           
       1613 TTTTTATTTT-ATTTTTAATTTTAATTTTATT
          1 TTTTCATTTTCATTTTTAATTTTAATTTTATT

              
       1644 TT
          1 TT

       1646 AATTATGCAC


Statistics
Matches: 30,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  31   21  0.70
  32    9  0.30

ACGTcount: A:0.18, C:0.03, G:0.02, T:0.77


Consensus pattern (32 bp):   
TTTTCATTTTCATTTTTAATTTTAATTTTATT

Found at i:2592 original size:22 final size:22

Alignment explanation


    Indices: 2564--2648  Score: 75
    Period size: 22  Copynumber: 3.9  Consensus size: 22

       2554 TTTATTGTTT

                                  
       2564 AGAAAAAGAAAAAAAAAAGAAA
          1 AGAAAAAGAAAAAAAAAAGAAA

                   ***            
       2586 AGAAAAATTGAAAAAAAA-AAA
          1 AGAAAAAGAAAAAAAAAAGAAA

                   *  *        *   
       2607 AGAAAATTGAGAAAAAAAATAAA
          1 AGAAAA-AGAAAAAAAAAAGAAA

            *                   
       2630 TGAAAAA-AAAAAACAAAAG
          1 AGAAAAAGAAAAAA-AAAAG

       2649 TGTGTTTGAG


Statistics
Matches: 50,  Mismatches: 10, Indels: 6
        0.76            0.15        0.09

Matches are distributed among these distances:
  21   14  0.28
  22   28  0.56
  23    8  0.16

ACGTcount: A:0.80, C:0.01, G:0.12, T:0.07


Consensus pattern (22 bp):   
AGAAAAAGAAAAAAAAAAGAAA

Found at i:2601 original size:20 final size:20

Alignment explanation


    Indices: 2574--2635  Score: 79
    Period size: 21  Copynumber: 2.9  Consensus size: 20

       2564 AGAAAAAGAA

                                  
       2574 AAAAAAAAGAAAAGAAAAATTG
          1 AAAAAAAA-AAAAG-AAAATTG

                                
       2596 AAAAAAAAAAAAGAAAATTG
          1 AAAAAAAAAAAAGAAAATTG

                                
       2616 AGAAAAAAAATAAATGAAAA
          1 A-AAAAAAAA-AAA-GAAAA

       2636 AAAAAAACAA


Statistics
Matches: 37,  Mismatches: 0, Indels: 5
        0.88            0.00        0.12

Matches are distributed among these distances:
  20    8  0.22
  21   13  0.35
  22   11  0.30
  23    5  0.14

ACGTcount: A:0.79, C:0.00, G:0.11, T:0.10


Consensus pattern (20 bp):   
AAAAAAAAAAAAGAAAATTG
Done.