Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001730.1 Kokia drynarioides strain JFW-HI SEQ_113433, 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: 6427
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35


Found at i:80 original size:31 final size:31

Alignment explanation


    Indices: 5--141  Score: 86
    Period size: 31  Copynumber: 4.5  Consensus size: 31

          1 AAAT

                         *                 
          5 GTTTAAGTACCAACTTA--AAAAAGAGTCAA
          1 GTTTAAGTACCAAATTAGGAAAAAGAGTCAA

            *    *    *              *     
         34 TTTTAGGTACAAAATTAGGAAAAAGTGTCAA
          1 GTTTAAGTACCAAATTAGGAAAAAGAGTCAA

                *                      ***  
         65 GTTTGAGTACCAAATT-GGACAAAA-AAAAAA
          1 GTTTAAGTACCAAATTAGGA-AAAAGAGTCAA

             *    *                    *     
         95 CATTTAGGTACCAAATTAGGAAACAA-TGTCAA
          1 -GTTTAAGTACCAAATTAGGAAA-AAGAGTCAA

             * *           
        127 GGTCAAGTACCAAAT
          1 GTTTAAGTACCAAAT

        142 ATTATATTAA


Statistics
Matches: 78,  Mismatches: 24, Indels: 10
        0.70            0.21        0.09

Matches are distributed among these distances:
  29   13  0.17
  30    5  0.06
  31   53  0.68
  32    7  0.09

ACGTcount: A:0.47, C:0.12, G:0.17, T:0.24


Consensus pattern (31 bp):   
GTTTAAGTACCAAATTAGGAAAAAGAGTCAA

Found at i:419 original size:17 final size:17

Alignment explanation


    Indices: 397--456  Score: 61
    Period size: 17  Copynumber: 3.5  Consensus size: 17

        387 AAGAATATGA

                  *          
        397 AAGGTTGAGGAAGATGG
          1 AAGGTTAAGGAAGATGG

                                
        414 AAGGTTAAAGGTCAAG--GG
          1 AAGGTT-AAGG--AAGATGG

            *                
        432 GAGGTTAAGGAAGATGG
          1 AAGGTTAAGGAAGATGG

                    
        449 AAGGTTAA
          1 AAGGTTAA

        457 AAGTAAAGGA


Statistics
Matches: 35,  Mismatches: 3, Indels: 10
        0.73            0.06        0.21

Matches are distributed among these distances:
  15    3  0.09
  17   19  0.54
  18   10  0.29
  20    3  0.09

ACGTcount: A:0.38, C:0.02, G:0.42, T:0.18


Consensus pattern (17 bp):   
AAGGTTAAGGAAGATGG

Found at i:465 original size:24 final size:24

Alignment explanation


    Indices: 438--502  Score: 121
    Period size: 24  Copynumber: 2.7  Consensus size: 24

        428 AGGGGAGGTT

                      *             
        438 AAGGAAGATGGAAGGTTAAAAGTA
          1 AAGGAAGATGAAAGGTTAAAAGTA

                                    
        462 AAGGAAGATGAAAGGTTAAAAGTA
          1 AAGGAAGATGAAAGGTTAAAAGTA

                             
        486 AAGGAAGATGAAAGGTT
          1 AAGGAAGATGAAAGGTT

        503 GAACATCCAT


Statistics
Matches: 40,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  24   40  1.00

ACGTcount: A:0.51, C:0.00, G:0.32, T:0.17


Consensus pattern (24 bp):   
AAGGAAGATGAAAGGTTAAAAGTA
Done.