Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011005.1 Kokia drynarioides strain JFW-HI SEQ_125975, 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: 7574
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33


Found at i:1362 original size:30 final size:29

Alignment explanation


    Indices: 1317--1374  Score: 91
    Period size: 30  Copynumber: 2.0  Consensus size: 29

       1307 GGGGGGGAGA

                                           
       1317 TGAGAGGGAAGTAAAAGTTTTAAGAGGAAAG
          1 TGAGAGGGAAGTAAAAGTTTT--GAGGAAAG

                                        
       1348 TGAGAGGG-AGTAAAAGTTTTGAGGAAA
          1 TGAGAGGGAAGTAAAAGTTTTGAGGAAA

       1375 AATAAAAAAT


Statistics
Matches: 27,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  28    7  0.26
  30   12  0.44
  31    8  0.30

ACGTcount: A:0.43, C:0.00, G:0.36, T:0.21


Consensus pattern (29 bp):   
TGAGAGGGAAGTAAAAGTTTTGAGGAAAG

Found at i:1551 original size:20 final size:20

Alignment explanation


    Indices: 1522--1560  Score: 62
    Period size: 19  Copynumber: 1.9  Consensus size: 20

       1512 GGGAAAGTGG

                                
       1522 GAAAAAAAAAAT-TTTGGGA
          1 GAAAAAAAAAATGTTTGGGA

                                
       1541 GAAAAATAAAAATGTTTGGG
          1 GAAAAA-AAAAATGTTTGGG

       1561 GTTTGAGGTA


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  19    6  0.33
  20    6  0.33
  21    6  0.33

ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23


Consensus pattern (20 bp):   
GAAAAAAAAAATGTTTGGGA

Found at i:1618 original size:18 final size:18

Alignment explanation


    Indices: 1595--1631  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       1585 TATAGTTTAA

                   *          
       1595 TATTCGATTTATTCAAAT
          1 TATTCGAGTTATTCAAAT

                          *   
       1613 TATTCGAGTTATTCGAAT
          1 TATTCGAGTTATTCAAAT

             
       1631 T
          1 T

       1632 CGAAAACTAA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.30, C:0.11, G:0.11, T:0.49


Consensus pattern (18 bp):   
TATTCGAGTTATTCAAAT

Found at i:5217 original size:15 final size:15

Alignment explanation


    Indices: 5197--5231  Score: 54
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       5187 TGGATATGGC

                            
       5197 AAAAAAAATAG-AAAG
          1 AAAAAAAA-AGAAAAG

                           
       5212 AAAAAAAAAGAAAAG
          1 AAAAAAAAAGAAAAG

                 
       5227 AAAAA
          1 AAAAA

       5232 CAACATTTGG


Statistics
Matches: 19,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  14    2  0.11
  15   17  0.89

ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03


Consensus pattern (15 bp):   
AAAAAAAAAGAAAAG

Found at i:6860 original size:128 final size:129

Alignment explanation


    Indices: 6696--6952  Score: 428
    Period size: 129  Copynumber: 2.0  Consensus size: 129

       6686 TACAAATCTG

                         *           *     *                                 
       6696 TCTCAAAGCTTGAGTCTTTAAAACCTATTAACCCAAATATTCAA-GATTTTTT-TTCCAATATCT
          1 TCTCAAAGCTTGAATCTTTAAAACCCATTAAACCAAATATTCAATG-TTTTTTATTCCAATATCT

                                                                             
       6759 TCTTCCCTTTAAGTTTCTTTGGGTTAATGGGTTTCAAAGATTCAAGCTTTGAGACAGATTTGTAA
         65 TCTTCCCTTTAAGTTTCTTTGGGTTAATGGGTTTCAAAGATTCAAGCTTTGAGACAGATTTGTAA

                           *                                              *  
       6824 TCTCAAAGCTTGAATTTTTAAAACCCATTAAACCAAATATTCAATGTTTTTTATTCCAATATTTT
          1 TCTCAAAGCTTGAATCTTTAAAACCCATTAAACCAAATATTCAATGTTTTTTATTCCAATATCTT

                                                 *              *           
       6889 CTTCCCTTTAAGTTTCTTTGGGTTAATGGGTTTCAAATATTCAAGCTTTGAGTCAGATTTGTAA
         66 CTTCCCTTTAAGTTTCTTTGGGTTAATGGGTTTCAAAGATTCAAGCTTTGAGACAGATTTGTAA

       6953 CTAAAGATAT


Statistics
Matches: 120,  Mismatches: 7, Indels: 3
        0.92            0.05        0.02

Matches are distributed among these distances:
 128   46  0.38
 129   74  0.62

ACGTcount: A:0.29, C:0.16, G:0.12, T:0.42


Consensus pattern (129 bp):   
TCTCAAAGCTTGAATCTTTAAAACCCATTAAACCAAATATTCAATGTTTTTTATTCCAATATCTT
CTTCCCTTTAAGTTTCTTTGGGTTAATGGGTTTCAAAGATTCAAGCTTTGAGACAGATTTGTAA

Done.