Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004952.1 Kokia drynarioides strain JFW-HI SEQ_118677, 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: 10261
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.34


Found at i:3482 original size:43 final size:43

Alignment explanation


    Indices: 3410--3532  Score: 140
    Period size: 43  Copynumber: 2.8  Consensus size: 43

       3400 CTATAATGCT

                            * *                         
       3410 AGTATATTTGCTTTAGCTAGTCCAAATGATGCACTAAATGTGTC
          1 AGTATATTTGCTTTAGTTTGTCC-AATGATGCACTAAATGTGTC

                *                  *           *  *  * 
       3454 AGTACATTTGCTTTAGTTTGTCCGATGATGCACTATATTTGCC
          1 AGTATATTTGCTTTAGTTTGTCCAATGATGCACTAAATGTGTC

                     *             *             
       3497 AGTATATTTACTTTAGTTTAG-CTAATGATGCACTAA
          1 AGTATATTTGCTTTAGTTT-GTCCAATGATGCACTAA

       3533 GGTGCTAGAT


Statistics
Matches: 66,  Mismatches: 12, Indels: 3
        0.81            0.15        0.04

Matches are distributed among these distances:
  43   45  0.68
  44   21  0.32

ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40


Consensus pattern (43 bp):   
AGTATATTTGCTTTAGTTTGTCCAATGATGCACTAAATGTGTC

Found at i:8870 original size:32 final size:32

Alignment explanation


    Indices: 8836--8927  Score: 102
    Period size: 31  Copynumber: 2.9  Consensus size: 32

       8826 TAAATTAAAT

                                            
       8836 TTTTTAATCCC-TTAAAAGTTGAAAAAAATAA
          1 TTTTTAATCCCTTTAAAAGTTGAAAAAAATAA

                  **                          
       8867 TTTTTAGGCCCTTTAAAAGTTAGTAAAAAAA-AA
          1 TTTTTAATCCCTTTAAAAGTT-G-AAAAAAATAA

                 *             *          
       8900 --TTTGATCCCTTTAAAAGATGAAAAAAAT
          1 TTTTTAATCCCTTTAAAAGTTGAAAAAAAT

       8928 TAAACCCCTT


Statistics
Matches: 51,  Mismatches: 6, Indels: 9
        0.77            0.09        0.14

Matches are distributed among these distances:
  29    7  0.14
  30    1  0.02
  31   24  0.47
  32    9  0.18
  33    3  0.06
  34    7  0.14

ACGTcount: A:0.47, C:0.10, G:0.10, T:0.34


Consensus pattern (32 bp):   
TTTTTAATCCCTTTAAAAGTTGAAAAAAATAA

Found at i:8879 original size:31 final size:30

Alignment explanation


    Indices: 8847--8927  Score: 92
    Period size: 32  Copynumber: 2.6  Consensus size: 30

       8837 TTTTAATCCC

                                    *       
       8847 TTAAAAGTTGAAAAAAATAATTTTTAGGCCCT
          1 TTAAAAGTTGAAAAAAATAA-TTTGA-GCCCT

                                       *    
       8879 TTAAAAGTTAGTAAAAAAA-AATTTGATCCCT
          1 TTAAAAGTT-G-AAAAAAATAATTTGAGCCCT

                   *          
       8910 TTAAAAGATGAAAAAAAT
          1 TTAAAAGTTGAAAAAAAT

       8928 TAAACCCCTT


Statistics
Matches: 43,  Mismatches: 3, Indels: 8
        0.80            0.06        0.15

Matches are distributed among these distances:
  29    7  0.16
  30    1  0.02
  31   12  0.28
  32   13  0.30
  33    3  0.07
  34    7  0.16

ACGTcount: A:0.51, C:0.07, G:0.11, T:0.31


Consensus pattern (30 bp):   
TTAAAAGTTGAAAAAAATAATTTGAGCCCT
Done.