Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005611.1 Kokia drynarioides strain JFW-HI SEQ_119758, 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, 940

Length: 1568
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.29


Found at i:330 original size:30 final size:30

Alignment explanation


    Indices: 293--640  Score: 406
    Period size: 30  Copynumber: 11.7  Consensus size: 30

        283 TTTGGGAAAA

                    *               *     
        293 TTTGGGGTCAAAAATGGGATTTTTAGAAG-
          1 TTTGGGGTTAAAAATGGGATTTTTGGAAGT

              *    *        *   *     *    
        322 TTCGGGGGTAAAAAT-TGACCTTTTGAAAGT
          1 TTTGGGGTTAAAAATGGGA-TTTTTGGAAGT

                                    * *   
        352 TTTGGGGTTAAAAATGGGATTTTTTGTAGT
          1 TTTGGGGTTAAAAATGGGATTTTTGGAAGT

              *          *  *             
        382 TTGGGGGTTAAAATTGAGATTTTTGGAAGT
          1 TTTGGGGTTAAAAATGGGATTTTTGGAAGT

              * *                         
        412 TTCGAGGTTAAAAATGGGATTTTTGGAAGT
          1 TTTGGGGTTAAAAATGGGATTTTTGGAAGT

                                          
        442 TTTGGGGTTAAAAATGGGATTTTTGGAAGT
          1 TTTGGGGTTAAAAATGGGATTTTTGGAAGT

                                          
        472 TTTGGGG-TAAAAATGGGATTTTTGGAAGT
          1 TTTGGGGTTAAAAATGGGATTTTTGGAAGT

                                  * *    *
        501 TTTGGGGTTAAAAATGGGA-TTCTAGAA-A
          1 TTTGGGGTTAAAAATGGGATTTTTGGAAGT

              *                             
        529 TTCGAGGG-TAAAAATGGGATTTTTTGGAAGT
          1 TTTG-GGGTTAAAAATGGGA-TTTTTGGAAGT

                                  * *     
        560 TTTGGGGTTAAAAATGGGATTTCTAGAAG-
          1 TTTGGGGTTAAAAATGGGATTTTTGGAAGT

                                            
        589 TTTGAGGG-TAAAAATGGGATTTTTTGGAAGT
          1 TTTG-GGGTTAAAAATGGGA-TTTTTGGAAGT

                           *     
        620 TTTGGGGTTAAAAATAGGATT
          1 TTTGGGGTTAAAAATGGGATT

        641 GTTGAACAAT


Statistics
Matches: 268,  Mismatches: 38, Indels: 25
        0.81            0.11        0.08

Matches are distributed among these distances:
  28   16  0.06
  29   72  0.27
  30  150  0.56
  31   30  0.11

ACGTcount: A:0.29, C:0.02, G:0.31, T:0.37


Consensus pattern (30 bp):   
TTTGGGGTTAAAAATGGGATTTTTGGAAGT

Found at i:356 original size:59 final size:59

Alignment explanation


    Indices: 293--634  Score: 331
    Period size: 59  Copynumber: 5.8  Consensus size: 59

        283 TTTGGGAAAA

                    *               *       *                *     *    
        293 TTTGGGGTCAAAAATGGGATTTTTAGAAG-TTCGGGGGTAAAAATTGACCTTTTGAAAGT
          1 TTTGGGGTTAAAAATGGGATTTTTGGAAGTTTTGGGGGTAAAAATTGA-TTTTTGGAAGT

                                    * *            *                     
        352 TTTGGGGTTAAAAATGGGATTTTTTGTAG-TTTGGGGGTTAAAATTGAGATTTTTGGAAGT
          1 TTTGGGGTTAAAAATGGGATTTTTGGAAGTTTTGGGGGTAAAAATT--GATTTTTGGAAGT

              * *                                *        *             
        412 TTCGAGGTTAAAAATGGGATTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAGT
          1 TTTGGGGTTAAAAATGGGATTTTTGGAAGTTTTGGGGGTAAAAAT-TGATTTTTGGAAGT

                                                 *        *     * *    *
        472 TTTGGGG-TAAAAATGGGATTTTTGGAAGTTTTGGGGTTAAAAATGGGA-TTCTAGAA-A
          1 TTTGGGGTTAAAAATGGGATTTTTGGAAGTTTTGGGGGTAAAAAT-TGATTTTTGGAAGT

              *                                    *        *     * *     
        529 TTCGAGGG-TAAAAATGGGATTTTTTGGAAGTTTTGGGGTTAAAAATGGGATTTCTAGAAG-
          1 TTTG-GGGTTAAAAATGGGA-TTTTTGGAAGTTTTGGGGGTAAAAAT-TGATTTTTGGAAGT

                                                   *       
        589 TTTGAGGG-TAAAAATGGGATTTTTTGGAAGTTTTGGGGTTAAAAAT
          1 TTTG-GGGTTAAAAATGGGA-TTTTTGGAAGTTTTGGGGGTAAAAAT

        635 AGGATTGTTG


Statistics
Matches: 254,  Mismatches: 21, Indels: 15
        0.88            0.07        0.05

Matches are distributed among these distances:
  57    3  0.01
  58   20  0.08
  59  111  0.44
  60  105  0.41
  61   15  0.06

ACGTcount: A:0.29, C:0.02, G:0.31, T:0.37


Consensus pattern (59 bp):   
TTTGGGGTTAAAAATGGGATTTTTGGAAGTTTTGGGGGTAAAAATTGATTTTTGGAAGT

Found at i:1485 original size:21 final size:23

Alignment explanation


    Indices: 1448--1491  Score: 65
    Period size: 22  Copynumber: 2.0  Consensus size: 23

       1438 TAAAAAAGAA

                      *            
       1448 CAGATCTAGGTCTAGATC-AAAC
          1 CAGATCTAGGCCTAGATCTAAAC

                                   
       1470 CAGATCTA-GCCTAGATCTAAAC
          1 CAGATCTAGGCCTAGATCTAAAC

       1492 GATTTTCCCC


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

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

ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23


Consensus pattern (23 bp):   
CAGATCTAGGCCTAGATCTAAAC
Done.