Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007688.1 Kokia drynarioides strain JFW-HI SEQ_122319, 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: 7784
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38


Found at i:2935 original size:14 final size:14

Alignment explanation


    Indices: 2896--2938  Score: 52
    Period size: 14  Copynumber: 3.1  Consensus size: 14

       2886 GATAGTTTTC

                        *  
       2896 AATAAAGTATAATAA
          1 AATAAA-TATAAAAA

                   *      
       2911 AA-AAATTTAAAAA
          1 AATAAATATAAAAA

                          
       2924 AATAAATATAAAAA
          1 AATAAATATAAAAA

             
       2938 A
          1 A

       2939 TTGAAACACA


Statistics
Matches: 24,  Mismatches: 3, Indels: 3
        0.80            0.10        0.10

Matches are distributed among these distances:
  13    8  0.33
  14   14  0.58
  15    2  0.08

ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23


Consensus pattern (14 bp):   
AATAAATATAAAAA

Found at i:4160 original size:25 final size:24

Alignment explanation


    Indices: 4132--4187  Score: 60
    Period size: 25  Copynumber: 2.3  Consensus size: 24

       4122 TTATTTTTAT

                          *           
       4132 ATATTATATA-ATTTATAACATATAA
          1 ATATTATATATA-TAATAACATAT-A

                  *  *              
       4157 ATATTAAATCTATAATAACATATA
          1 ATATTATATATATAATAACATATA

                   
       4181 ATATTAT
          1 ATATTAT

       4188 GATGTAAAAA


Statistics
Matches: 26,  Mismatches: 4, Indels: 3
        0.79            0.12        0.09

Matches are distributed among these distances:
  24    7  0.27
  25   18  0.69
  26    1  0.04

ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43


Consensus pattern (24 bp):   
ATATTATATATATAATAACATATA

Found at i:4320 original size:17 final size:17

Alignment explanation


    Indices: 4294--4326  Score: 57
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       4284 TTACATAATA

                             
       4294 TAAAACTAAAATAATTG
          1 TAAAACTAAAATAATTG

                 *          
       4311 TAAAATTAAAATAATT
          1 TAAAACTAAAATAATT

       4327 TTACATACTT


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33


Consensus pattern (17 bp):   
TAAAACTAAAATAATTG

Found at i:4354 original size:14 final size:14

Alignment explanation


    Indices: 4335--4377  Score: 52
    Period size: 14  Copynumber: 3.1  Consensus size: 14

       4325 TTTTACATAC

                          
       4335 TTATTATAAATATT
          1 TTATTATAAATATT

                      *  *
       4349 TTATTA-AAAAATA
          1 TTATTATAAATATT

            *             
       4362 ATATTATAAATATT
          1 TTATTATAAATATT

              
       4376 TT
          1 TT

       4378 TTTAAATTGT


Statistics
Matches: 22,  Mismatches: 6, Indels: 2
        0.73            0.20        0.07

Matches are distributed among these distances:
  13   10  0.45
  14   12  0.55

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (14 bp):   
TTATTATAAATATT
Done.