Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000866.1 Kokia drynarioides strain JFW-HI SEQ_111984, 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: 13106
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:6834 original size:17 final size:18

Alignment explanation


    Indices: 6803--6838  Score: 65
    Period size: 17  Copynumber: 2.1  Consensus size: 18

       6793 TGCATCGGAA

                              
       6803 TTTAACTTAAATTTAATT
          1 TTTAACTTAAATTTAATT

                              
       6821 TTTAACTT-AATTTAATT
          1 TTTAACTTAAATTTAATT

             
       6838 T
          1 T

       6839 AGTTTAGAAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  17   10  0.56
  18    8  0.44

ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58


Consensus pattern (18 bp):   
TTTAACTTAAATTTAATT

Found at i:7056 original size:25 final size:25

Alignment explanation


    Indices: 7022--7072  Score: 102
    Period size: 25  Copynumber: 2.0  Consensus size: 25

       7012 TCGTTCCAGT

                                     
       7022 GTGGTATATCATCTTTTACATAAAC
          1 GTGGTATATCATCTTTTACATAAAC

                                     
       7047 GTGGTATATCATCTTTTACATAAAC
          1 GTGGTATATCATCTTTTACATAAAC

             
       7072 G
          1 G

       7073 ACAGAGTAGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   26  1.00

ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39


Consensus pattern (25 bp):   
GTGGTATATCATCTTTTACATAAAC

Found at i:8160 original size:26 final size:27

Alignment explanation


    Indices: 8126--8201  Score: 84
    Period size: 26  Copynumber: 2.7  Consensus size: 27

       8116 ATTGAAAATT

                *                      
       8126 AAAATTATTTAATAATTTTATA-TTTA
          1 AAAAATATTTAATAATTTTATATTTTA

                          *              
       8152 AAAAATATTTAA-ATTTGTTATATTTTTA
          1 AAAAATATTTAATAATT-TTATA-TTTTA

                                  
       8180 AAAAATAATTTTAATAATTTTA
          1 AAAAAT-A-TTTAATAATTTTA

       8202 CAATCATTTG


Statistics
Matches: 41,  Mismatches: 3, Indels: 8
        0.79            0.06        0.15

Matches are distributed among these distances:
  25    3  0.07
  26   16  0.39
  28   10  0.24
  29    1  0.02
  30    8  0.20
  31    3  0.07

ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51


Consensus pattern (27 bp):   
AAAAATATTTAATAATTTTATATTTTA

Found at i:10140 original size:20 final size:20

Alignment explanation


    Indices: 10112--10151  Score: 62
    Period size: 20  Copynumber: 2.0  Consensus size: 20

      10102 ATAGGAATAC

                *               
      10112 TTTTTTGAAAAATTGCATTG
          1 TTTTATGAAAAATTGCATTG

                       *        
      10132 TTTTATGAAAAGTTGCATTG
          1 TTTTATGAAAAATTGCATTG

      10152 AAACCATCAA


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

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.30, C:0.05, G:0.17, T:0.47


Consensus pattern (20 bp):   
TTTTATGAAAAATTGCATTG

Found at i:12151 original size:20 final size:20

Alignment explanation


    Indices: 12126--12166  Score: 57
    Period size: 20  Copynumber: 2.0  Consensus size: 20

      12116 CAAAAGTTTT

                          *      
      12126 GATACCCTT-TTCATAGTATC
          1 GATA-CCTTCTTCAAAGTATC

                                
      12146 GATACCTTCTTCAAAGTATC
          1 GATACCTTCTTCAAAGTATC

             
      12166 G
          1 G

      12167 GTATCCTTAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  19    4  0.21
  20   15  0.79

ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37


Consensus pattern (20 bp):   
GATACCTTCTTCAAAGTATC
Done.