Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004548.1 Kokia drynarioides strain JFW-HI SEQ_118016, 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: 5080
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35


Found at i:896 original size:56 final size:56

Alignment explanation


    Indices: 810--921  Score: 215
    Period size: 56  Copynumber: 2.0  Consensus size: 56

        800 AATTGAGTTC

                                                                    
        810 TTTTTAGATAATTGTCTTAGCTATAAAGTTATAAAGTTGAAATGACAAAGTACTTA
          1 TTTTTAGATAATTGTCTTAGCTATAAAGTTATAAAGTTGAAATGACAAAGTACTTA

                                                            *       
        866 TTTTTAGATAATTGTCTTAGCTATAAAGTTATAAAGTTGAAATGACAAGGTACTTA
          1 TTTTTAGATAATTGTCTTAGCTATAAAGTTATAAAGTTGAAATGACAAAGTACTTA

        922 CTTTGGAATG


Statistics
Matches: 55,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  56   55  1.00

ACGTcount: A:0.38, C:0.07, G:0.15, T:0.39


Consensus pattern (56 bp):   
TTTTTAGATAATTGTCTTAGCTATAAAGTTATAAAGTTGAAATGACAAAGTACTTA

Found at i:3796 original size:29 final size:29

Alignment explanation


    Indices: 3763--3821  Score: 100
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       3753 TAACGAAATT

                                         
       3763 AAACTTCAGATACCACATTGGACATTTTG
          1 AAACTTCAGATACCACATTGGACATTTTG

                  *  *                   
       3792 AAACTTTAGGTACCACATTGGACATTTTG
          1 AAACTTCAGATACCACATTGGACATTTTG

             
       3821 A
          1 A

       3822 CGCTTCAAGT


Statistics
Matches: 28,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  29   28  1.00

ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32


Consensus pattern (29 bp):   
AAACTTCAGATACCACATTGGACATTTTG

Found at i:3837 original size:29 final size:29

Alignment explanation


    Indices: 3763--3839  Score: 93
    Period size: 29  Copynumber: 2.7  Consensus size: 29

       3753 TAACGAAATT

                                          
       3763 AAACTTC-AGATACCACATTGGACATTTTG
          1 AAACTTCAAG-TACCACATTGGACATTTTG

                  * *                    
       3792 AAACTTTAGGTACCACATTGGACATTTTG
          1 AAACTTCAAGTACCACATTGGACATTTTG

             **         *      
       3821 ACGCTTCAAGTATCACATT
          1 AAACTTCAAGTACCACATT

       3840 CAAACGAGTG


Statistics
Matches: 40,  Mismatches: 7, Indels: 2
        0.82            0.14        0.04

Matches are distributed among these distances:
  29   39  0.98
  30    1  0.03

ACGTcount: A:0.32, C:0.21, G:0.14, T:0.32


Consensus pattern (29 bp):   
AAACTTCAAGTACCACATTGGACATTTTG

Found at i:4526 original size:18 final size:17

Alignment explanation


    Indices: 4505--4550  Score: 58
    Period size: 18  Copynumber: 2.7  Consensus size: 17

       4495 TCGAATTTAA

                              
       4505 AATTTAATTTTATCAAAT
          1 AATTTAATTTTAT-AAAT

                     *   *   
       4523 AATTTAATTGTATTAAT
          1 AATTTAATTTTATAAAT

                        
       4540 AA-TTAATTTTA
          1 AATTTAATTTTA

       4551 AATAATATAT


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  16    8  0.32
  17    5  0.20
  18   12  0.48

ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52


Consensus pattern (17 bp):   
AATTTAATTTTATAAAT
Done.