Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003801.1 Kokia drynarioides strain JFW-HI SEQ_116789, 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: 3086
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.35

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:968 original size:18 final size:17

Alignment explanation


    Indices: 931--1058  Score: 130
    Period size: 17  Copynumber: 7.3  Consensus size: 17

        921 GTATTTGAGC

                     *     * 
        931 TTAAATTTATAATAATT
          1 TTAAATTTAAAATAAAT

                              
        948 TTAAATTTGAAAATAAAT
          1 TTAAATTT-AAAATAAAT

                 *     *     
        966 TTAAACTTAAATTAAAT
          1 TTAAATTTAAAATAAAT

                   *    *    
        983 TTAAATTCAAAACAAAT
          1 TTAAATTTAAAATAAAT

                              
       1000 TTAAATTTAAAATAAATT
          1 TTAAATTTAAAATAAA-T

                     *   *    
       1018 TTAAATTTTTAAACAAAT
          1 TTAAA-TTTAAAATAAAT

                 *     *      
       1036 TTAATTTTTAACATAAAT
          1 TTAA-ATTTAAAATAAAT

                 
       1054 TTAAA
          1 TTAAA

       1059 GGGAGTTTGG


Statistics
Matches: 90,  Mismatches: 17, Indels: 8
        0.78            0.15        0.07

Matches are distributed among these distances:
  17   43  0.48
  18   38  0.42
  19    9  0.10

ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43


Consensus pattern (17 bp):   
TTAAATTTAAAATAAAT

Found at i:975 original size:6 final size:6

Alignment explanation


    Indices: 947--1025  Score: 58
    Period size: 6  Copynumber: 13.5  Consensus size: 6

        937 TTATAATAAT

                            *            *                      *   
        947 TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA -TTAAA TTTAAA TTCAAA
          1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA

             **                   *                
        994 -ACAAA TTTAAA TTTAAA -ATAAA TTTTAAA TTT
          1 TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTT

       1026 TTAAACAAAT


Statistics
Matches: 58,  Mismatches: 9, Indels: 12
        0.73            0.11        0.15

Matches are distributed among these distances:
   5   16  0.28
   6   35  0.60
   7    7  0.12

ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42


Consensus pattern (6 bp):   
TTTAAA

Found at i:2997 original size:11 final size:11

Alignment explanation


    Indices: 2983--3011  Score: 58
    Period size: 11  Copynumber: 2.6  Consensus size: 11

       2973 TTCTTTTCAT

                       
       2983 TTTCTTCATCA
          1 TTTCTTCATCA

                       
       2994 TTTCTTCATCA
          1 TTTCTTCATCA

                   
       3005 TTTCTTC
          1 TTTCTTC

       3012 TTAAATTTCT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   18  1.00

ACGTcount: A:0.14, C:0.28, G:0.00, T:0.59


Consensus pattern (11 bp):   
TTTCTTCATCA

Found at i:3013 original size:14 final size:12

Alignment explanation


    Indices: 2979--3011  Score: 52
    Period size: 11  Copynumber: 2.9  Consensus size: 12

       2969 TTTCTTCTTT

                        
       2979 TCATTTTCTTCA
          1 TCATTTTCTTCA

                        
       2991 TCA-TTTCTTCA
          1 TCATTTTCTTCA

                       
       3002 TCA-TTTCTTC
          1 TCATTTTCTTC

       3012 TTAAATTTCT


Statistics
Matches: 21,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  11   18  0.86
  12    3  0.14

ACGTcount: A:0.15, C:0.27, G:0.00, T:0.58


Consensus pattern (12 bp):   
TCATTTTCTTCA
Done.