Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005757.1 Kokia drynarioides strain JFW-HI SEQ_120011, 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: 28147
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35


Found at i:549 original size:2 final size:2

Alignment explanation


    Indices: 542--567  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

        532 TTAATAGATG

                                                  
        542 AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT

        568 GCGAAATTAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:5271 original size:68 final size:68

Alignment explanation


    Indices: 5194--5329  Score: 254
    Period size: 68  Copynumber: 2.0  Consensus size: 68

       5184 TTTATATCTA

                                    *                                        
       5194 TATTTAAAAAAATAACCAAACTCCGTGTGTTGGCCTGATGGTCAAAAGTCTTAAGTGCGACTTGA
          1 TATTTAAAAAAATAACCAAACTCCATGTGTTGGCCTGATGGTCAAAAGTCTTAAGTGCGACTTGA

               
       5259 ATT
         66 ATT

                           *                                                 
       5262 TATTTAAAAAAATAATCAAACTCCATGTGTTGGCCTGATGGTCAAAAGTCTTAAGTGCGACTTGA
          1 TATTTAAAAAAATAACCAAACTCCATGTGTTGGCCTGATGGTCAAAAGTCTTAAGTGCGACTTGA

               
       5327 ATT
         66 ATT

       5330 CAAGTCGAAC


Statistics
Matches: 66,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  68   66  1.00

ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32


Consensus pattern (68 bp):   
TATTTAAAAAAATAACCAAACTCCATGTGTTGGCCTGATGGTCAAAAGTCTTAAGTGCGACTTGA
ATT

Found at i:13865 original size:17 final size:18

Alignment explanation


    Indices: 13839--13880  Score: 70
    Period size: 17  Copynumber: 2.4  Consensus size: 18

      13829 TGACAATGTC

                              
      13839 AAAA-AAAAAAAAAG-AA
          1 AAAAGAAAAAAAAAGAAA

                              
      13855 AAAAGAAAAAAAAAGAAA
          1 AAAAGAAAAAAAAAGAAA

                    
      13873 AAAAGAAA
          1 AAAAGAAA

      13881 TGTGCATTTA


Statistics
Matches: 24,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  16    4  0.17
  17   10  0.42
  18   10  0.42

ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00


Consensus pattern (18 bp):   
AAAAGAAAAAAAAAGAAA

Found at i:19209 original size:20 final size:20

Alignment explanation


    Indices: 19173--19212  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      19163 TTATGATATA

                        *       
      19173 AAAATAAATATTTTATATCT
          1 AAAATAAATATTATATATCT

                                
      19193 AAAATAATATATATATATAT
          1 AAAATAA-ATAT-TATATAT

      19213 ATATATATTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    7  0.41
  21    4  0.24
  22    6  0.35

ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42


Consensus pattern (20 bp):   
AAAATAAATATTATATATCT

Found at i:23193 original size:21 final size:22

Alignment explanation


    Indices: 23163--23208  Score: 60
    Period size: 21  Copynumber: 2.1  Consensus size: 22

      23153 ATAACAAAAA

                           *       
      23163 TAATTGTAATTATAACTAG-AAT
          1 TAATTGTAA-TATAAATAGAAAT

                                  
      23185 TAATT-TAATATAAATAGAAAT
          1 TAATTGTAATATAAATAGAAAT

               
      23206 TAA
          1 TAA

      23209 ACAAAAATGA


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  20    8  0.36
  21    9  0.41
  22    5  0.23

ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39


Consensus pattern (22 bp):   
TAATTGTAATATAAATAGAAAT
Done.