Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008968.1 Kokia drynarioides strain JFW-HI SEQ_123664, 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: 40368
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32

Warning! 39 characters in sequence are not A, C, G, or T


Found at i:3437 original size:19 final size:19

Alignment explanation


    Indices: 3409--3453  Score: 60
    Period size: 16  Copynumber: 2.5  Consensus size: 19

       3399 TCAAAGAAAT

                               
       3409 AAAAAAATTA--AAAATT-
          1 AAAAAAATTATTAAAATTC

                               
       3425 AAAAAAATTATTAAAATTC
          1 AAAAAAATTATTAAAATTC

                 *    
       3444 AAAAATATTA
          1 AAAAAAATTA

       3454 ACATGAAGTT


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  16   10  0.40
  18    6  0.24
  19    9  0.36

ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29


Consensus pattern (19 bp):   
AAAAAAATTATTAAAATTC

Found at i:18169 original size:92 final size:92

Alignment explanation


    Indices: 18012--18205  Score: 372
    Period size: 92  Copynumber: 2.1  Consensus size: 92

      18002 GATAACAATC

                                                                             
      18012 TTTTAGTTGATTAGTCGCCTCCAAACGTATTGATCAATGTTTTTGGTCAGAATACGCTATCAGTT
          1 TTTTAGTTGATTAGTCGCCTCCAAACGTATTGATCAATGTTTTTGGTCAGAATACGCTATCAGTT

                                       
      18077 GTTGTATTTGATTCAAAATGTGCCCTT
         66 GTTGTATTTGATTCAAAATGTGCCCTT

                                                                             
      18104 TTTTAGTTGATTAGTCGCCTCCAAACGTATTGATCAATGTTTTTGGTCAGAATACGCTATCAGTT
          1 TTTTAGTTGATTAGTCGCCTCCAAACGTATTGATCAATGTTTTTGGTCAGAATACGCTATCAGTT

                                       
      18169 GTTGTATTTGATTCAAAATGTGCCCTT
         66 GTTGTATTTGATTCAAAATGTGCCCTT

                       
      18196 TTGTT-GTTGA
          1 TT-TTAGTTGA

      18206 GGTAAGTTCC


Statistics
Matches: 101,  Mismatches: 0, Indels: 2
        0.98            0.00        0.02

Matches are distributed among these distances:
  92   99  0.98
  93    2  0.02

ACGTcount: A:0.23, C:0.15, G:0.19, T:0.42


Consensus pattern (92 bp):   
TTTTAGTTGATTAGTCGCCTCCAAACGTATTGATCAATGTTTTTGGTCAGAATACGCTATCAGTT
GTTGTATTTGATTCAAAATGTGCCCTT

Found at i:19579 original size:14 final size:14

Alignment explanation


    Indices: 19560--19590  Score: 53
    Period size: 14  Copynumber: 2.2  Consensus size: 14

      19550 TAGGTTTAAA

                          
      19560 AAATTTAATTAATT
          1 AAATTTAATTAATT

                   *      
      19574 AAATTTATTTAATT
          1 AAATTTAATTAATT

               
      19588 AAA
          1 AAA

      19591 AATCTTTTTT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (14 bp):   
AAATTTAATTAATT
Done.