Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010710.1 Kokia drynarioides strain JFW-HI SEQ_125660, 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: 4255
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.26

Warning! 352 characters in sequence are not A, C, G, or T


Found at i:2152 original size:28 final size:28

Alignment explanation


    Indices: 2120--2173  Score: 74
    Period size: 28  Copynumber: 1.9  Consensus size: 28

       2110 GCCTTTTAAC

                 *                       
       2120 TTTACGATTTAGGGTTTCA-AGTTTAAGG
          1 TTTACAATTTA-GGTTTCAGAGTTTAAGG

                            *         
       2148 TTTACAATTTAGGTTTTAGAGTTTAA
          1 TTTACAATTTAGGTTTCAGAGTTTAA

       2174 TGTTATGAAA


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  27    6  0.26
  28   17  0.74

ACGTcount: A:0.28, C:0.06, G:0.20, T:0.46


Consensus pattern (28 bp):   
TTTACAATTTAGGTTTCAGAGTTTAAGG

Found at i:2419 original size:21 final size:21

Alignment explanation


    Indices: 2393--2435  Score: 61
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       2383 TAGGGTCCAT

                          *       
       2393 TTGCCCTG-GAGGAGTAGAGTA
          1 TTGCCC-GAGAGGAATAGAGTA

                                 
       2414 TTGCCCGAGAGGAATAGAGTA
          1 TTGCCCGAGAGGAATAGAGTA

             
       2435 T
          1 T

       2436 CGCGATGGCT


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  20    1  0.05
  21   19  0.95

ACGTcount: A:0.28, C:0.14, G:0.35, T:0.23


Consensus pattern (21 bp):   
TTGCCCGAGAGGAATAGAGTA

Found at i:2560 original size:45 final size:45

Alignment explanation


    Indices: 2430--2566  Score: 175
    Period size: 45  Copynumber: 3.0  Consensus size: 45

       2420 GAGAGGAATA

                  *   *              *  *           **   
       2430 GAGTATCGCGATGGCTCGTCAAACTCAGCCTGATATCCTTCCCTT
          1 GAGTATTGCGGTGGCTCGTCAAACTAAGGCTGATATCCTTGGCTT

                                   * *     *             
       2475 GAGTATTGCGGTGGCTCGTCAAATTGAGGCTAATATCCTTGGCTT
          1 GAGTATTGCGGTGGCTCGTCAAACTAAGGCTGATATCCTTGGCTT

                         *     *                         
       2520 GAGTATTGCGGTGACTCGTTAAACTAAGGCTGATATCCTTGGCTT
          1 GAGTATTGCGGTGGCTCGTCAAACTAAGGCTGATATCCTTGGCTT

              
       2565 GA
          1 GA

       2567 TGAGCTATGC


Statistics
Matches: 79,  Mismatches: 13, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  45   79  1.00

ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31


Consensus pattern (45 bp):   
GAGTATTGCGGTGGCTCGTCAAACTAAGGCTGATATCCTTGGCTT
Done.