Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010089.1 Kokia drynarioides strain JFW-HI SEQ_124870, 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, 778

Length: 1297
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.27


Found at i:512 original size:30 final size:28

Alignment explanation


    Indices: 454--623  Score: 125
    Period size: 30  Copynumber: 5.9  Consensus size: 28

        444 AGCAACTCGA

                      *                 
        454 GGGTAAAATGATAA-TTTTGGAAGTTCG
          1 GGGTAAAATGGTAATTTTTGGAAGTTCG

                                          
        481 GGGATAAAATGGTAATTTTTGGAAGGTTCG
          1 GGG-TAAAATGGTAATTTTTGGAA-GTTCG

                          *              * 
        511 GGGTCAAAAATGG-GATTTTTAGGAA-TTTG
          1 GGGT--AAAATGGTAATTTTT-GGAAGTTCG

                                           
        540 AGGGTAAAACT-GTAATTTTTGGAAGGTTCG
          1 -GGGTAAAA-TGGTAATTTTTGGAA-GTTCG

            *             *           *  * 
        570 AGGTCAAAAATGG-GATTTTTGGGAATTTAG
          1 GGGT--AAAATGGTAATTTTT-GGAAGTTCG

                    * *             
        600 GGGTAAAACGATAATTTTTGGAAG
          1 GGGTAAAATGGTAATTTTTGGAAG

        624 GTTTAGGGAC


Statistics
Matches: 113,  Mismatches: 14, Indels: 31
        0.72            0.09        0.20

Matches are distributed among these distances:
  27    3  0.03
  28   28  0.25
  29   28  0.25
  30   34  0.30
  31   20  0.18

ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33


Consensus pattern (28 bp):   
GGGTAAAATGGTAATTTTTGGAAGTTCG

Found at i:528 original size:87 final size:88

Alignment explanation


    Indices: 400--569  Score: 220
    Period size: 87  Copynumber: 1.9  Consensus size: 88

        390 ATGGAGTGGC

                              *                                              
        400 AAAATGGTAATTTTAGAATGTTCAGAATCAAAAATAGGATTTTTAGCAACTCGAGGGTAAAA-TG
          1 AAAATGGTAATTTTAGAAGGTTCAGAATCAAAAATAGGATTTTTAGCAACTCGAGGGTAAAACTG

                                    
        464 ATAA-TTTTGGAA-GTTCGGGGAT
         66 -TAATTTTTGGAAGGTTCGGGGAT

                           *        * **        *          *  * *            
        486 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTAGGAATTTGAGGGTAAAACT
          1 AAAATGGTAA-TTTTAGAAGGTTCAGAATCAAAAATAGGATTTTTAGCAACTCGAGGGTAAAACT

                               
        551 GTAATTTTTGGAAGGTTCG
         65 GTAATTTTTGGAAGGTTCG

        570 AGGTCAAAAA


Statistics
Matches: 71,  Mismatches: 9, Indels: 5
        0.84            0.11        0.06

Matches are distributed among these distances:
  86   10  0.14
  87   46  0.65
  88   10  0.14
  89    5  0.07

ACGTcount: A:0.35, C:0.06, G:0.26, T:0.33


Consensus pattern (88 bp):   
AAAATGGTAATTTTAGAAGGTTCAGAATCAAAAATAGGATTTTTAGCAACTCGAGGGTAAAACTG
TAATTTTTGGAAGGTTCGGGGAT

Found at i:548 original size:59 final size:59

Alignment explanation


    Indices: 480--626  Score: 217
    Period size: 59  Copynumber: 2.5  Consensus size: 59

        470 TTGGAAGTTC

                                           *                            
        480 GGGGATAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTAGGAATTT-
          1 GGGG-TAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTAGGAATTTA

                                                                *        
        539 GAGGGTAAAACT-GTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGGAATTTA
          1 G-GGGTAAAA-TGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTAGGAATTTA

                     * *                
        599 GGGGTAAAACGATAATTTTTGGAAGGTT
          1 GGGGTAAAATGGTAATTTTTGGAAGGTT

        627 TAGGGACCTT


Statistics
Matches: 80,  Mismatches: 4, Indels: 8
        0.87            0.04        0.09

Matches are distributed among these distances:
  59   75  0.94
  60    5  0.06

ACGTcount: A:0.31, C:0.04, G:0.31, T:0.33


Consensus pattern (59 bp):   
GGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTAGGAATTTA
Done.