Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001494.1 Kokia drynarioides strain JFW-HI SEQ_113032, 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: 3517
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34


Found at i:261 original size:31 final size:32

Alignment explanation


    Indices: 184--246  Score: 99
    Period size: 34  Copynumber: 1.9  Consensus size: 32

        174 TTGGATACCC

                 *                            
        184 GGGGGCAAAATGGTAATTTTAGGAAAATTATTGA
          1 GGGGGAAAAATGGTAATTTTAGGAAAATTA-T-A

                                         
        218 GGGGGAAAAATGGTAATTTTAGGAAAATT
          1 GGGGGAAAAATGGTAATTTTAGGAAAATT

        247 CAAGGTTAAA


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  34   28  1.00

ACGTcount: A:0.40, C:0.02, G:0.30, T:0.29


Consensus pattern (32 bp):   
GGGGGAAAAATGGTAATTTTAGGAAAATTATA

Found at i:400 original size:59 final size:57

Alignment explanation


    Indices: 333--589  Score: 201
    Period size: 59  Copynumber: 4.4  Consensus size: 57

        323 TTTGGACATC

                                  **                               *   
        333 CGGGGGTAAAATGGTAATTTTTAAAAGTTTTGGGGTCAAAAATGGAAATTTTAGAGGTT
          1 CGGGGGTAAAATGG-AATTTTTGGAAGTTTTGGGGTCAAAAAT-GAAATTTTAGAAGTT

                                          * *         *   **    *      
        392 CGGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCGAAAATTGATTTTTTGGAAGTT
          1 CGGGGGT-AAAATGGAATTTTTGGAAGTTTTGGGGTC-AAAAATGAAATTTTAGAAGTT

                                                *      *        *      
        451 CGGGGGTAAGAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATAAAATTTTTGGAAGTT
          1 CGGGGGTAA-AATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGAAA-TTTTAGAAGTT

            ***                    *       *  **         *       *      
        510 TTAGGGTCAAAATTGGAA-TTTTAGAAGTTTCGGCATCAAAAATGGAATTTATGGAAGTT
          1 CGGGGGT-AAAA-TGGAATTTTTGGAAGTTTTGGGGTCAAAAATGAAATTT-TAGAAGTT

            **            *      
        569 TAGGGGTAAAAATGTAATTTT
          1 CGGGGGT-AAAATGGAATTTT

        590 GAACAGTTTA


Statistics
Matches: 160,  Mismatches: 30, Indels: 16
        0.78            0.15        0.08

Matches are distributed among these distances:
  58   15  0.09
  59  126  0.79
  60   19  0.12

ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35


Consensus pattern (57 bp):   
CGGGGGTAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGAAATTTTAGAAGTT

Found at i:472 original size:29 final size:29

Alignment explanation


    Indices: 312--589  Score: 172
    Period size: 29  Copynumber: 9.4  Consensus size: 29

        302 TTTCGAGGTC

                                  *        
        312 AAAAT-GAAGTTTTTGGACA-TCCGGGGGT-
          1 AAAATGGAA-TTTTTGGA-AGTTCGGGGGTA

                           **     **       
        340 AAAATGGTAATTTTTAAAAGTTTTGGGGTCA
          1 AAAATGG-AATTTTTGGAAGTTCGGGGGT-A

                     *    *  *           
        371 AAAATGGAAATTTTAGAGGTTCGGGGGTA
          1 AAAATGGAATTTTTGGAAGTTCGGGGGTA

                                     *    *
        400 AAAATGGAATTTTTGGAAGTTTC-GAGGTCG
          1 AAAATGGAATTTTTGGAAG-TTCGGGGGT-A

                 *  *                    
        430 AAAATTGATTTTTTGGAAGTTCGGGGGTA
          1 AAAATGGAATTTTTGGAAGTTCGGGGGTA

             *                    *    *  
        459 AGAATGGAATTTTTGGAAGTTTTGGGGTTA
          1 AAAATGGAATTTTTGGAAG-TTCGGGGGTA

                 **              ***      
        489 AAAATAAAATTTTTGGAAGTTTTAGGGTCA
          1 AAAATGGAATTTTTGGAAGTTCGGGGGT-A

               *          *           **   
        519 AAATTGGAA-TTTTAGAAGTTTC-GGCATCA
          1 AAAATGGAATTTTTGGAAG-TTCGGGGGT-A

                        *        **      
        548 AAAATGGAATTTATGGAAGTTTAGGGGTA
          1 AAAATGGAATTTTTGGAAGTTCGGGGGTA

                  *      
        577 AAAATGTAATTTT
          1 AAAATGGAATTTT

        590 GAACAGTTTA


Statistics
Matches: 191,  Mismatches: 46, Indels: 25
        0.73            0.18        0.10

Matches are distributed among these distances:
  28    6  0.03
  29   93  0.49
  30   85  0.45
  31    7  0.04

ACGTcount: A:0.33, C:0.04, G:0.27, T:0.35


Consensus pattern (29 bp):   
AAAATGGAATTTTTGGAAGTTCGGGGGTA

Found at i:1769 original size:3 final size:3

Alignment explanation


    Indices: 1702--1751  Score: 100
    Period size: 3  Copynumber: 16.7  Consensus size: 3

       1692 TTATTAAAAA

                                                                           
       1702 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
          1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

              
       1750 TA
          1 TA

       1752 ATAGTACATT


Statistics
Matches: 47,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   47  1.00

ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66


Consensus pattern (3 bp):   
TAT
Done.