Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008306.1 Kokia drynarioides strain JFW-HI SEQ_122971, 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: 10862
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30


Found at i:6231 original size:112 final size:112

Alignment explanation


    Indices: 6034--6257  Score: 333
    Period size: 112  Copynumber: 2.0  Consensus size: 112

       6024 TGCTACGAAG

                                             * **                            
       6034 TATCATTGGAACTAGCCATACCTGTTCAAGGTATGTGCCGATAACATCATTCGTCACTGTGTTCC
          1 TATCATTGGAACTAGCCATACCTGTTCAAGGTAAGCACCGATAACATCATTCGTCACTGTGTTCC

                 *                  *            *         
       6099 TGAAGGGGAGATGACTTCTATCCTGAGACATTGCCATGATGTTCCAT
         66 TGAAGAGGAGATGACTTCTATCCTAAGACATTGCCATAATGTTCCAT

                                       *                        *   *        
       6146 TATCATTGGAA-TGAGCCATACCTGTTTAAGGTAAGCACCGATAACATCATTTGTCGCTGTGTTC
          1 TATCATTGGAACT-AGCCATACCTGTTCAAGGTAAGCACCGATAACATCATTCGTCACTGTGTTC

                       *               *                    
       6210 CTGAAGAGGAGTTGACTTCTATCCTAATACATTGCCATAATGTTCCAT
         65 CTGAAGAGGAGATGACTTCTATCCTAAGACATTGCCATAATGTTCCAT

       6258 ATAGAGGTCA


Statistics
Matches: 100,  Mismatches: 11, Indels: 2
        0.88            0.10        0.02

Matches are distributed among these distances:
 111    1  0.01
 112   99  0.99

ACGTcount: A:0.26, C:0.21, G:0.20, T:0.32


Consensus pattern (112 bp):   
TATCATTGGAACTAGCCATACCTGTTCAAGGTAAGCACCGATAACATCATTCGTCACTGTGTTCC
TGAAGAGGAGATGACTTCTATCCTAAGACATTGCCATAATGTTCCAT

Found at i:9702 original size:21 final size:21

Alignment explanation


    Indices: 9656--9705  Score: 91
    Period size: 21  Copynumber: 2.4  Consensus size: 21

       9646 GAAGGATAGA

                *                
       9656 AAGAAGAAGCGCAAGGACAAG
          1 AAGAGGAAGCGCAAGGACAAG

                                 
       9677 AAGAGGAAGCGCAAGGACAAG
          1 AAGAGGAAGCGCAAGGACAAG

                    
       9698 AAGAGGAA
          1 AAGAGGAA

       9706 ACACAAAGAG


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

Matches are distributed among these distances:
  21   28  1.00

ACGTcount: A:0.52, C:0.12, G:0.36, T:0.00


Consensus pattern (21 bp):   
AAGAGGAAGCGCAAGGACAAG

Found at i:10479 original size:16 final size:16

Alignment explanation


    Indices: 10446--10498  Score: 56
    Period size: 16  Copynumber: 3.3  Consensus size: 16

      10436 CACATATAAA

                     *   *   
      10446 AAAAATGAATGAATAAG
          1 AAAAA-GAAAGAAGAAG

                            
      10463 AAAAAGAAAGAAGAAG
          1 AAAAAGAAAGAAGAAG

                             
      10479 AAAAGAGAAA-AAGAA-
          1 AAAA-AGAAAGAAGAAG

                 
      10494 AAAAA
          1 AAAAA

      10499 AATATAAATG


Statistics
Matches: 33,  Mismatches: 2, Indels: 5
        0.82            0.05        0.12

Matches are distributed among these distances:
  14    1  0.03
  15    4  0.12
  16   18  0.55
  17   10  0.30

ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06


Consensus pattern (16 bp):   
AAAAAGAAAGAAGAAG
Done.