Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000222.1 Kokia drynarioides strain JFW-HI SEQ_110938, 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: 6827
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33


Found at i:552 original size:30 final size:30

Alignment explanation


    Indices: 518--578  Score: 88
    Period size: 30  Copynumber: 2.0  Consensus size: 30

        508 TTTTTTTTTC

                                    *      
        518 CGTTTACT-TTTTAAATTTAATTTGTAATTT
          1 CGTTT-CTATTTTAAATTTAATTTCTAATTT

                 *                        
        548 CGTTTTTATTTTAAATTTAATTTCTAATTT
          1 CGTTTCTATTTTAAATTTAATTTCTAATTT

             
        578 C
          1 C

        579 TTGTATATTC


Statistics
Matches: 28,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  29    1  0.04
  30   27  0.96

ACGTcount: A:0.26, C:0.08, G:0.05, T:0.61


Consensus pattern (30 bp):   
CGTTTCTATTTTAAATTTAATTTCTAATTT

Found at i:1639 original size:60 final size:62

Alignment explanation


    Indices: 1434--1780  Score: 318
    Period size: 60  Copynumber: 5.7  Consensus size: 62

       1424 TTTACCAAAT

                                        *   *  *         **  *            
       1434 AAAAAAG-GGGTGTCGGCCATTGCATGGTCAATACAAAAAAAATTTGAAATTTTTTTATCCG
          1 AAAAAAGAGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTACAATTTTTTTTATCCG

             *  *                                         **  *         *  
       1495 AGAACAG-GTGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTGGAAATTTTTTTATTCG
          1 AAAAAAGAG-GGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTACAATTTTTTTTATCCG

             *  *  *                    **       *                        
       1557 AGAACAGGGGGTGTCGGCCATTGCATGGAAAACACC-CAAAAA-TACAATTTTTTTTATCCG
          1 AAAAAAGAGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTACAATTTTTTTTATCCG

                            **                           **             * 
       1617 AAAAAAGAGGGTGTCGATCATTGCATGGCCAACACCAAAAAAATTTGAATTTTTTTT-TCTG
          1 AAAAAAGAGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTACAATTTTTTTTATCCG

                   *     *   *   *               *      *               * 
       1678 -AAAAAGGGGGTGCCGGTCATCGCATGGCCAACACC-CAAAAA-CACAATTTTTTTTATCAG
          1 AAAAAAGAGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTACAATTTTTTTTATCCG

                 *                  *                     
       1737 ATAAATAGA-GGTGTCGGCCATTGTATGGCCAACA-CAAAAAAATT
          1 A-AAAAAGAGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATT

       1781 GTATTTTTTA


Statistics
Matches: 235,  Mismatches: 42, Indels: 18
        0.80            0.14        0.06

Matches are distributed among these distances:
  58   10  0.04
  59    9  0.04
  60  100  0.43
  61   24  0.10
  62   91  0.39
  63    1  0.00

ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27


Consensus pattern (62 bp):   
AAAAAAGAGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTACAATTTTTTTTATCCG

Found at i:1725 original size:120 final size:121

Alignment explanation


    Indices: 1483--1789  Score: 392
    Period size: 120  Copynumber: 2.6  Consensus size: 121

       1473 AAATTTGAAA

                         *  *                                         *      
       1483 TTTTTTTATCCGAGAACAG-GTGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTGGAAATT
          1 TTTTTTTATCCGAAAAAAGAG-GGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTG-AATT

                          *        *       *                    *     
       1547 TTTTTATTCGAGAACAGGGGGTGTCGGCCATTGCATGGAAAACACCCAAAAATACAAT
         64 TTTTTATTCGAGAAAAGGGGGTGCCGGCCATCGCATGGAAAACACCCAAAAACACAAT

                                        **                                   
       1605 TTTTTTTATCCGAAAAAAGAGGGTGTCGATCATTGCATGGCCAACACCAAAAAAATTTGAATTTT
          1 TTTTTTTATCCGAAAAAAGAGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAATTTT

                                      *          **                  
       1670 TTT-TTCTGA-AAAAGGGGGTGCCGGTCATCGCATGGCCAACACCCAAAAACACAAT
         66 TTTATTC-GAGAAAAGGGGGTGCCGGCCATCGCATGGAAAACACCCAAAAACACAAT

                      *      *                  *                       *    
       1725 TTTTTTTATCAGATAAATAGA-GGTGTCGGCCATTGTATGGCCAACA-CAAAAAAA-TTGTATTT
          1 TTTTTTTATCCGA-AAAAAGAGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAATTT

               
       1787 TTT
         65 TTT

       1790 ATCTGACAAA


Statistics
Matches: 164,  Mismatches: 18, Indels: 10
        0.85            0.09        0.05

Matches are distributed among these distances:
 118   10  0.06
 119    8  0.05
 120   76  0.46
 121   17  0.10
 122   52  0.32
 123    1  0.01

ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29


Consensus pattern (121 bp):   
TTTTTTTATCCGAAAAAAGAGGGTGTCGGCCATTGCATGGCCAACACCAAAAAAATTTGAATTTT
TTTATTCGAGAAAAGGGGGTGCCGGCCATCGCATGGAAAACACCCAAAAACACAAT

Found at i:6449 original size:5 final size:5

Alignment explanation


    Indices: 6439--6469  Score: 53
    Period size: 5  Copynumber: 6.2  Consensus size: 5

       6429 AGCTTCAAAA

                                          *      
       6439 GTGAT GTGAT GTGAT GTGAT GTGAT ATGAT G
          1 GTGAT GTGAT GTGAT GTGAT GTGAT GTGAT G

       6470 AGAGGTTCCT


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   5   24  1.00

ACGTcount: A:0.23, C:0.00, G:0.39, T:0.39


Consensus pattern (5 bp):   
GTGAT

Done.