Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004138.1 Kokia drynarioides strain JFW-HI SEQ_117335, 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: 3733
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.32


Found at i:89 original size:29 final size:31

Alignment explanation


    Indices: 25--98  Score: 116
    Period size: 29  Copynumber: 2.5  Consensus size: 31

         15 AATTAAAATT

                                           
         25 ATTTAATAATTTTATTATTTCAAAAAAATAA
          1 ATTTAATAATTTTATTATTTCAAAAAAATAA

            *                    *         
         56 TTTTAATAATTTTA-TATTT-TAAAAAATAA
          1 ATTTAATAATTTTATTATTTCAAAAAAATAA

                          
         85 ATTTAATAATTTTA
          1 ATTTAATAATTTTA

         99 AAATCATTTG


Statistics
Matches: 40,  Mismatches: 3, Indels: 2
        0.89            0.07        0.04

Matches are distributed among these distances:
  29   22  0.55
  30    5  0.12
  31   13  0.32

ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50


Consensus pattern (31 bp):   
ATTTAATAATTTTATTATTTCAAAAAAATAA

Found at i:522 original size:45 final size:45

Alignment explanation


    Indices: 458--550  Score: 186
    Period size: 45  Copynumber: 2.1  Consensus size: 45

        448 AAATGTTTAT

                                                         
        458 TTATAAGTATTTTTATTTTTATATAAAAATTAATTTAAGTTAAGC
          1 TTATAAGTATTTTTATTTTTATATAAAAATTAATTTAAGTTAAGC

                                                         
        503 TTATAAGTATTTTTATTTTTATATAAAAATTAATTTAAGTTAAGC
          1 TTATAAGTATTTTTATTTTTATATAAAAATTAATTTAAGTTAAGC

               
        548 TTA
          1 TTA

        551 ATATTATTGT


Statistics
Matches: 48,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  45   48  1.00

ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52


Consensus pattern (45 bp):   
TTATAAGTATTTTTATTTTTATATAAAAATTAATTTAAGTTAAGC

Found at i:2399 original size:22 final size:22

Alignment explanation


    Indices: 2374--2415  Score: 57
    Period size: 22  Copynumber: 1.9  Consensus size: 22

       2364 AAGTTTTGAT

                                  
       2374 TTTAAAATTAGGTTTAAATTGG
          1 TTTAAAATTAGGTTTAAATTGG

                  *   **        
       2396 TTTAAATTTATTTTTAAATT
          1 TTTAAAATTAGGTTTAAATT

       2416 TAAATTTATC


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  22   17  1.00

ACGTcount: A:0.36, C:0.00, G:0.10, T:0.55


Consensus pattern (22 bp):   
TTTAAAATTAGGTTTAAATTGG

Found at i:2417 original size:6 final size:6

Alignment explanation


    Indices: 2396--2461  Score: 53
    Period size: 6  Copynumber: 10.8  Consensus size: 6

       2386 TTTAAATTGG

                       **                     **                   **
       2396 TTTAAA TTTATT TTTAAA TTTAAA TTTATCTT TTTAAA TTTAAA TTT-GC
          1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA

                               
       2445 TTTAAA TTTAAA TTTAA
          1 TTTAAA TTTAAA TTTAA

       2462 TCAAATTTGA


Statistics
Matches: 45,  Mismatches: 12, Indels: 6
        0.71            0.19        0.10

Matches are distributed among these distances:
   5    3  0.07
   6   38  0.84
   8    4  0.09

ACGTcount: A:0.38, C:0.03, G:0.02, T:0.58


Consensus pattern (6 bp):   
TTTAAA

Done.