Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013291.1 Kokia drynarioides strain JFW-HI SEQ_128313, 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: 7436
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34


Found at i:2469 original size:22 final size:21

Alignment explanation


    Indices: 2438--2481  Score: 61
    Period size: 22  Copynumber: 2.0  Consensus size: 21

       2428 TTATAAATCA

                 *      *         
       2438 AATAATAAATATGTATTTATAT
          1 AATAAAAAATATAT-TTTATAT

                                 
       2460 AATAAAAAATATATTTTATAT
          1 AATAAAAAATATATTTTATAT

             
       2481 A
          1 A

       2482 TATTTAAAAT


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  21    8  0.40
  22   12  0.60

ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43


Consensus pattern (21 bp):   
AATAAAAAATATATTTTATAT

Found at i:2515 original size:88 final size:92

Alignment explanation


    Indices: 2410--2577  Score: 220
    Period size: 90  Copynumber: 1.9  Consensus size: 92

       2400 TTTTATTTTT

                        *                              *  * *    *           
       2410 AATTAATAAATCTTTTA-TT-TATAAATCAAAT-AATAAATATGTATTTA-TATAATA-AAAAAT
          1 AATTAATAAATCCTTTATTTATATAAAT-AAATGAATAAATATATAATAATTACAATATAAAAAT

                                        
       2470 ATATTTTATATATATTTAAAATATTTGA
         65 ATATTTTATATATATTTAAAATATTTGA

                     *                                                   *   
       2498 AATTAATAATTCCTTTATTTATATAAATAAATGAATAAATATATAATAATTACAATATAAATATA
          1 AATTAATAAATCCTTTATTTATATAAATAAATGAATAAATATATAATAATTACAATATAAAAATA

                      *    
       2563 TATTTTATATTTATT
         66 TATTTTATATATATT

       2578 ATGTTAAATA


Statistics
Matches: 67,  Mismatches: 8, Indels: 6
        0.83            0.10        0.07

Matches are distributed among these distances:
  88   15  0.22
  89    6  0.09
  90   20  0.30
  91    6  0.09
  92   20  0.30

ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46


Consensus pattern (92 bp):   
AATTAATAAATCCTTTATTTATATAAATAAATGAATAAATATATAATAATTACAATATAAAAATA
TATTTTATATATATTTAAAATATTTGA

Found at i:2734 original size:23 final size:23

Alignment explanation


    Indices: 2703--2749  Score: 60
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       2693 TGTCTTCACC

                *        *          
       2703 TATATTATAT-TACTAATTTATAA
          1 TATAATATATATAATAATTT-TAA

                                   
       2726 TATAATATATATAATAATTTTAA
          1 TATAATATATATAATAATTTTAA

             
       2749 T
          1 T

       2750 TGAGTTGATG


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  23   13  0.62
  24    8  0.38

ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51


Consensus pattern (23 bp):   
TATAATATATATAATAATTTTAA
Done.