Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000744.1 Kokia drynarioides strain JFW-HI SEQ_111780, 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: 6279
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36


Found at i:479 original size:26 final size:26

Alignment explanation


    Indices: 419--484  Score: 71
    Period size: 26  Copynumber: 2.5  Consensus size: 26

        409 GCAATTTACT

                      *              *
        419 TTCTTTTTTTATTTATTTATGTTTTT
          1 TTCTTTTTTTCTTTATTTATGTTTTA

              *                        
        445 TTATTTTTTTCTTTATTTAT-TTTTCA
          1 TTCTTTTTTTCTTTATTTATGTTTT-A

                *    *    
        471 TTCTCTTTTGCTTT
          1 TTCTTTTTTTCTTT

        485 TCTTTTAATG


Statistics
Matches: 33,  Mismatches: 6, Indels: 2
        0.80            0.15        0.05

Matches are distributed among these distances:
  25    4  0.12
  26   29  0.88

ACGTcount: A:0.11, C:0.09, G:0.03, T:0.77


Consensus pattern (26 bp):   
TTCTTTTTTTCTTTATTTATGTTTTA

Found at i:1257 original size:22 final size:21

Alignment explanation


    Indices: 1210--1257  Score: 62
    Period size: 22  Copynumber: 2.2  Consensus size: 21

       1200 CATGAATTTC

                                 
       1210 AAAA-TCTGAAAAATAAAAAA
          1 AAAATTCTGAAAAATAAAAAA

                     *             
       1230 ATAAATTCTTAAAAATAAAAATA
          1 A-AAATTCTGAAAAATAAAAA-A

                 
       1253 AAAAT
          1 AAAAT

       1258 ACAAATATTA


Statistics
Matches: 24,  Mismatches: 1, Indels: 4
        0.83            0.03        0.14

Matches are distributed among these distances:
  20    1  0.04
  21    3  0.12
  22   18  0.75
  23    2  0.08

ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23


Consensus pattern (21 bp):   
AAAATTCTGAAAAATAAAAAA

Found at i:5090 original size:63 final size:63

Alignment explanation


    Indices: 5011--5138  Score: 256
    Period size: 63  Copynumber: 2.0  Consensus size: 63

       5001 TGCCACCATT

                                                                           
       5011 TCCCTTGAGATTCTTTTTTTAGGACTATAAAATACTAATTTAAACATAATAAATCATGATTTG
          1 TCCCTTGAGATTCTTTTTTTAGGACTATAAAATACTAATTTAAACATAATAAATCATGATTTG

                                                                           
       5074 TCCCTTGAGATTCTTTTTTTAGGACTATAAAATACTAATTTAAACATAATAAATCATGATTTG
          1 TCCCTTGAGATTCTTTTTTTAGGACTATAAAATACTAATTTAAACATAATAAATCATGATTTG

              
       5137 TC
          1 TC

       5139 ATGTCAGATA


Statistics
Matches: 65,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  63   65  1.00

ACGTcount: A:0.36, C:0.13, G:0.09, T:0.41


Consensus pattern (63 bp):   
TCCCTTGAGATTCTTTTTTTAGGACTATAAAATACTAATTTAAACATAATAAATCATGATTTG

Found at i:5534 original size:4 final size:4

Alignment explanation


    Indices: 5527--5555  Score: 51
    Period size: 4  Copynumber: 7.5  Consensus size: 4

       5517 CAAATTTATT

                                                 
       5527 TTAA TTAA TTAA TTAA TTAA TTAA -TAA TT
          1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TT

       5556 TAGTAATAAA


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

Matches are distributed among these distances:
   3    3  0.12
   4   21  0.88

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (4 bp):   
TTAA

Done.