Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004261.1 Kokia drynarioides strain JFW-HI SEQ_117548, 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: 9649
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34


Found at i:198 original size:30 final size:31

Alignment explanation


    Indices: 136--201  Score: 89
    Period size: 31  Copynumber: 2.1  Consensus size: 31

        126 AAATTGATCC

                                           
        136 TTTTAAAAAATATAAATAATTTAAAATAATT
          1 TTTTAAAAAATATAAATAATTTAAAATAATT

                         *    *          *  
        167 TTTTAAAAAATA-GAATATTTATAAAATATTT
          1 TTTTAAAAAATATAAATAATT-TAAAATAATT

                
        198 TTTT
          1 TTTT

        202 TTCCAAAATT


Statistics
Matches: 31,  Mismatches: 3, Indels: 2
        0.86            0.08        0.06

Matches are distributed among these distances:
  30    6  0.19
  31   25  0.81

ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47


Consensus pattern (31 bp):   
TTTTAAAAAATATAAATAATTTAAAATAATT

Found at i:362 original size:15 final size:17

Alignment explanation


    Indices: 342--373  Score: 50
    Period size: 15  Copynumber: 2.0  Consensus size: 17

        332 TTACTAATTA

                             
        342 TCTTGTT-TTTT-TTTT
          1 TCTTGTTATTTTGTTTT

                             
        357 TCTTGTTATTTTGTTTT
          1 TCTTGTTATTTTGTTTT

        374 AAAAGATTTT


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  15    7  0.47
  16    4  0.27
  17    4  0.27

ACGTcount: A:0.03, C:0.06, G:0.09, T:0.81


Consensus pattern (17 bp):   
TCTTGTTATTTTGTTTT

Found at i:8564 original size:4 final size:4

Alignment explanation


    Indices: 8555--8620  Score: 71
    Period size: 4  Copynumber: 16.2  Consensus size: 4

       8545 AAATAAACAG

                                                 *      *     *          
       8555 GAAA GAAA GAAA GGAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
          1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA

                    *            
       8605 G-AA GAAG GAAA GAAA G
          1 GAAA GAAA GAAA GAAA G

       8621 GTAATGTGTC


Statistics
Matches: 53,  Mismatches: 6, Indels: 6
        0.82            0.09        0.09

Matches are distributed among these distances:
   3    3  0.06
   4   42  0.79
   5    8  0.15

ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00


Consensus pattern (4 bp):   
GAAA

Found at i:8577 original size:17 final size:16

Alignment explanation


    Indices: 8555--8620  Score: 70
    Period size: 15  Copynumber: 4.3  Consensus size: 16

       8545 AAATAAACAG

                             
       8555 GAAAGAAAGAAAGGAAA
          1 GAAAG-AAGAAAGGAAA

                             
       8572 GAAAGAAAGAAAGG-AA
          1 GAAAG-AAGAAAGGAAA

                     *      
       8588 G-AAG--GAGAGGAAA
          1 GAAAGAAGAAAGGAAA

                            
       8601 GAAAGAAG-AAGGAAA
          1 GAAAGAAGAAAGGAAA

                 
       8616 GAAAG
          1 GAAAG

       8621 GTAATGTGTC


Statistics
Matches: 43,  Mismatches: 2, Indels: 10
        0.78            0.04        0.18

Matches are distributed among these distances:
  12    5  0.12
  13    3  0.07
  14    3  0.07
  15   14  0.33
  16    4  0.09
  17   14  0.33

ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00


Consensus pattern (16 bp):   
GAAAGAAGAAAGGAAA

Found at i:8621 original size:29 final size:31

Alignment explanation


    Indices: 8553--8621  Score: 94
    Period size: 29  Copynumber: 2.4  Consensus size: 31

       8543 GCAAATAAAC

                                           
       8553 AGGAAAGAAA-GAAAGGAAAGAAAGAAAGAA
          1 AGGAAAGAAAGGAAAGGAAAGAAAGAAAGAA

                         *                 
       8583 AGG-AAG-AAGGAGAGGAAAGAAAG-AAG-A
          1 AGGAAAGAAAGGAAAGGAAAGAAAGAAAGAA

                        
       8610 AGGAAAGAAAGG
          1 AGGAAAGAAAGG

       8622 TAATGTGTCT


Statistics
Matches: 35,  Mismatches: 1, Indels: 7
        0.81            0.02        0.16

Matches are distributed among these distances:
  27    4  0.11
  28    8  0.23
  29   20  0.57
  30    3  0.09

ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00


Consensus pattern (31 bp):   
AGGAAAGAAAGGAAAGGAAAGAAAGAAAGAA
Done.