Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008841.1 Kokia drynarioides strain JFW-HI SEQ_123527, 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: 7040
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:64 original size:13 final size:13

Alignment explanation


    Indices: 46--75  Score: 51
    Period size: 13  Copynumber: 2.3  Consensus size: 13

         36 TTTAAGTATA

                         
         46 TTGACATTTAACC
          1 TTGACATTTAACC

                        *
         59 TTGACATTTAACT
          1 TTGACATTTAACC

                
         72 TTGA
          1 TTGA

         76 TTGCATTGAC


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

Matches are distributed among these distances:
  13   16  1.00

ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43


Consensus pattern (13 bp):   
TTGACATTTAACC

Found at i:1876 original size:16 final size:15

Alignment explanation


    Indices: 1853--1892  Score: 64
    Period size: 16  Copynumber: 2.7  Consensus size: 15

       1843 TAAACTTCGT

                           
       1853 TAAA-AATAATAAAA
          1 TAAACAATAATAAAA

                            
       1867 TAAACGAATAATAAAA
          1 TAAAC-AATAATAAAA

                      
       1883 TAAACAATAA
          1 TAAACAATAA

       1893 AGAACTGAAA


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

Matches are distributed among these distances:
  14    4  0.17
  15    5  0.21
  16   15  0.62

ACGTcount: A:0.72, C:0.05, G:0.03, T:0.20


Consensus pattern (15 bp):   
TAAACAATAATAAAA

Found at i:3377 original size:3 final size:3

Alignment explanation


    Indices: 3369--3423  Score: 87
    Period size: 3  Copynumber: 18.7  Consensus size: 3

       3359 CTATAGCCTA

                                                                        
       3369 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAA-
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT

                          
       3414 AAT AA- AAT AA
          1 AAT AAT AAT AA

       3424 CGAAAACCGT


Statistics
Matches: 49,  Mismatches: 0, Indels: 6
        0.89            0.00        0.11

Matches are distributed among these distances:
   2    4  0.08
   3   43  0.88
   4    2  0.04

ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29


Consensus pattern (3 bp):   
AAT

Found at i:3428 original size:14 final size:15

Alignment explanation


    Indices: 3368--3429  Score: 58
    Period size: 15  Copynumber: 4.2  Consensus size: 15

       3358 ACTATAGCCT

                         * 
       3368 AAATAATAATAA-TA
          1 AAATAATAATAACGA

                          * 
       3382 ATAATAATAATAA-TA
          1 A-AATAATAATAACGA

                         *  
       3397 ATAATAATAATAATGA
          1 A-AATAATAATAACGA

                           
       3413 AAATAA-AATAACGA
          1 AAATAATAATAACGA

               
       3427 AAA
          1 AAA

       3430 CCGTATCTAT


Statistics
Matches: 44,  Mismatches: 2, Indels: 4
        0.88            0.04        0.08

Matches are distributed among these distances:
  14   11  0.25
  15   31  0.70
  16    2  0.05

ACGTcount: A:0.69, C:0.02, G:0.03, T:0.26


Consensus pattern (15 bp):   
AAATAATAATAACGA
Done.