Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006364.1 Kokia drynarioides strain JFW-HI SEQ_120940, 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: 5193
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30


Found at i:1906 original size:15 final size:16

Alignment explanation


    Indices: 1881--1913  Score: 50
    Period size: 15  Copynumber: 2.1  Consensus size: 16

       1871 AATACATTCC

                            
       1881 ATATCCATCATACATA
          1 ATATCCATCATACATA

                       *    
       1897 ATAT-CATCATGCATA
          1 ATATCCATCATACATA

              
       1912 AT
          1 AT

       1914 TGATTCCTAT


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  15   12  0.75
  16    4  0.25

ACGTcount: A:0.42, C:0.21, G:0.03, T:0.33


Consensus pattern (16 bp):   
ATATCCATCATACATA

Found at i:3204 original size:17 final size:17

Alignment explanation


    Indices: 3177--3216  Score: 53
    Period size: 17  Copynumber: 2.4  Consensus size: 17

       3167 CATGCCATCA

                             
       3177 AAAAGAAAAAAAAAAAG
          1 AAAAGAAAAAAAAAAAG

             *    *      *   
       3194 AGAAGAGAAAAAAGAAG
          1 AAAAGAAAAAAAAAAAG

                  
       3211 AAAAGA
          1 AAAAGA

       3217 TGGGTCAAAA


Statistics
Matches: 19,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  17   19  1.00

ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00


Consensus pattern (17 bp):   
AAAAGAAAAAAAAAAAG

Found at i:4196 original size:12 final size:12

Alignment explanation


    Indices: 4181--4215  Score: 52
    Period size: 12  Copynumber: 2.8  Consensus size: 12

       4171 AAAGAAAATT

                        
       4181 AAAAAAGAGAAA
          1 AAAAAAGAGAAA

                   *    
       4193 AAAAAAGGGAAA
          1 AAAAAAGAGAAA

                       
       4205 AAGAAAAGAGA
          1 AA-AAAAGAGA

       4216 GGTCGAGGTG


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  12   13  0.65
  13    7  0.35

ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00


Consensus pattern (12 bp):   
AAAAAAGAGAAA
Done.