Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004516.1 Kokia drynarioides strain JFW-HI SEQ_117959, 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: 6012
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36


Found at i:65 original size:45 final size:45

Alignment explanation


    Indices: 1--102  Score: 159
    Period size: 45  Copynumber: 2.3  Consensus size: 45

                                           *  *          
          1 TAGGGGTAAAAGATTGGATGGTGACTTTAATTTGTCCCTCTAAAT
          1 TAGGGGTAAAAGATTGGATGGTGACTTTAATCTGCCCCTCTAAAT

                                                     **  
         46 TAGGGGTAAAAGATTGGATGGTGACTTTAATCTGCCCCTCTGGAT
          1 TAGGGGTAAAAGATTGGATGGTGACTTTAATCTGCCCCTCTAAAT

              *         
         91 TAAGGGTAAAAG
          1 TAGGGGTAAAAG

        103 GGGTAAAAGA


Statistics
Matches: 52,  Mismatches: 5, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  45   52  1.00

ACGTcount: A:0.29, C:0.12, G:0.27, T:0.31


Consensus pattern (45 bp):   
TAGGGGTAAAAGATTGGATGGTGACTTTAATCTGCCCCTCTAAAT

Found at i:129 original size:54 final size:54

Alignment explanation


    Indices: 47--156  Score: 168
    Period size: 54  Copynumber: 2.0  Consensus size: 54

         37 CCTCTAAATT

                        * *                                       
         47 AGGGGTAAAAGATTGGATGGTGACTTTAATCTGCCCCTCTGGATTAAGGGTAAA
          1 AGGGGTAAAAGACTAGATGGTGACTTTAATCTGCCCCTCTGGATTAAGGGTAAA

                                           *               *       
        101 AGGGGTAAAAGACTAGATGGTTG-CTTTAATTTGCCCCTCTGGATTAGGGGTAAA
          1 AGGGGTAAAAGACTAGATGG-TGACTTTAATCTGCCCCTCTGGATTAAGGGTAAA

              
        155 AG
          1 AG

        157 ATTGGAGGTC


Statistics
Matches: 51,  Mismatches: 4, Indels: 2
        0.89            0.07        0.04

Matches are distributed among these distances:
  54   49  0.96
  55    2  0.04

ACGTcount: A:0.29, C:0.13, G:0.30, T:0.28


Consensus pattern (54 bp):   
AGGGGTAAAAGACTAGATGGTGACTTTAATCTGCCCCTCTGGATTAAGGGTAAA

Found at i:4209 original size:60 final size:60

Alignment explanation


    Indices: 4127--4248  Score: 190
    Period size: 60  Copynumber: 2.0  Consensus size: 60

       4117 AGTCTAGTTG

                        *              **                               
       4127 TCCTAAACACTTTCGAGAGTGTAGAGATGAATTCTTGATAAGTTACCCTCTCCATTCCTT
          1 TCCTAAACACTTCCGAGAGTGTAGAGACAAATTCTTGATAAGTTACCCTCTCCATTCCTT

                             *      *               *                   
       4187 TCCTAAACACTTCCGAGGGTGTAGGGACAAATTCTTGATAGGTTACCCTCTCCATTCCTT
          1 TCCTAAACACTTCCGAGAGTGTAGAGACAAATTCTTGATAAGTTACCCTCTCCATTCCTT

              
       4247 TC
          1 TC

       4249 TTTGAATATA


Statistics
Matches: 56,  Mismatches: 6, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  60   56  1.00

ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34


Consensus pattern (60 bp):   
TCCTAAACACTTCCGAGAGTGTAGAGACAAATTCTTGATAAGTTACCCTCTCCATTCCTT

Found at i:4400 original size:20 final size:20

Alignment explanation


    Indices: 4375--4417  Score: 54
    Period size: 20  Copynumber: 2.1  Consensus size: 20

       4365 TGTGAGGATT

                                  
       4375 TTTATT-TTATATT-TTATTTA
          1 TTTATTATT-TATTATTA-TTA

                                
       4395 TTTATTATTTATTATTATTA
          1 TTTATTATTTATTATTATTA

               
       4415 TTT
          1 TTT

       4418 TATGAAATTT


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  20   16  0.76
  21    5  0.24

ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74


Consensus pattern (20 bp):   
TTTATTATTTATTATTATTA
Done.