Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012828.1 Kokia drynarioides strain JFW-HI SEQ_127841, 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: 5624
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37


Found at i:158 original size:3 final size:3

Alignment explanation


    Indices: 150--203  Score: 108
    Period size: 3  Copynumber: 18.0  Consensus size: 3

        140 TGCTAGCTAC

                                                                           
        150 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT

                   
        198 AAT AAT
          1 AAT AAT

        204 TTACACTATT


Statistics
Matches: 51,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   51  1.00

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (3 bp):   
AAT

Found at i:3221 original size:25 final size:24

Alignment explanation


    Indices: 3144--3221  Score: 65
    Period size: 25  Copynumber: 3.2  Consensus size: 24

       3134 TCAAGTAATG

                               *     
       3144 AAAATCATATTATTGTAAATATTCT
          1 AAAATCATATTATTGTAAAGA-TCT

                              *    * 
       3169 AAAATC--ATTATTTGT-GAG-TGT
          1 AAAATCATATTA-TTGTAAAGATCT

                                      
       3190 GAAAATCATATTATTGTAAAGATACT
          1 -AAAATCATATTATTGTAAAGAT-CT

                  
       3216 AAAATC
          1 AAAATC

       3222 TTTGTACAAT


Statistics
Matches: 41,  Mismatches: 5, Indels: 14
        0.68            0.08        0.23

Matches are distributed among these distances:
  21    2  0.05
  22    6  0.15
  23    9  0.22
  24   10  0.24
  25   13  0.32
  26    1  0.02

ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38


Consensus pattern (24 bp):   
AAAATCATATTATTGTAAAGATCT

Found at i:4547 original size:144 final size:144

Alignment explanation


    Indices: 4285--4581  Score: 558
    Period size: 144  Copynumber: 2.1  Consensus size: 144

       4275 ATGAGTATTT

                                                           *                 
       4285 AAAAGTAGCTTTATCCCATGACTTAATCAAACATTATAAGCATAATAGTCTTGTCTTTTGAAAAA
          1 AAAAGTAGCTTTATCCCATGACTTAATCAAACATTATAAGCATAATAATCTTGTCTTTTGAAAAA

                                       *                               *     
       4350 TAAAATAAACTGTGCTATATATTCCTTGATGATTTATTATAAAAACTTGGCATCAAAGCTAATGA
         66 TAAAATAAACTGTGCTATATATTCCTTAATGATTTATTATAAAAACTTGGCATCAAAGCCAATGA

                          
       4415 AAGAAAGGGCTAAA
        131 AAGAAAGGGCTAAA

             *                                                               
       4429 AGAAGTAGCTTTATCCCATGACTTAATCAAACATTATAAGCATAATAATCTTGTCTTTTGAAAAA
          1 AAAAGTAGCTTTATCCCATGACTTAATCAAACATTATAAGCATAATAATCTTGTCTTTTGAAAAA

                                                                             
       4494 TAAAATAAACTGTGCTATATATTCCTTAATGATTTATTATAAAAACTTGGCATCAAAGCCAATGA
         66 TAAAATAAACTGTGCTATATATTCCTTAATGATTTATTATAAAAACTTGGCATCAAAGCCAATGA

                          
       4559 AAGAAAGGGCTAAA
        131 AAGAAAGGGCTAAA

                     
       4573 AAAAGTAGC
          1 AAAAGTAGC

       4582 CAAAAGGGAG


Statistics
Matches: 148,  Mismatches: 5, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
 144  148  1.00

ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31


Consensus pattern (144 bp):   
AAAAGTAGCTTTATCCCATGACTTAATCAAACATTATAAGCATAATAATCTTGTCTTTTGAAAAA
TAAAATAAACTGTGCTATATATTCCTTAATGATTTATTATAAAAACTTGGCATCAAAGCCAATGA
AAGAAAGGGCTAAA
Done.