Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010349.1 Kokia drynarioides strain JFW-HI SEQ_125217, 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, 604

Length: 1008
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32


Found at i:363 original size:17 final size:17

Alignment explanation


    Indices: 335--407  Score: 103
    Period size: 17  Copynumber: 4.4  Consensus size: 17

        325 TTGGAAATTG

                             
        335 AATTTA-TTTAAATTTA
          1 AATTTATTTTAAATTTA

             *               
        351 AGTTTATTTTAAATTTA
          1 AATTTATTTTAAATTTA

                     *       
        368 AATTTATTTGAAATTTA
          1 AATTTATTTTAAATTTA

                    *    *   
        385 AATTTATTATAAAATTA
          1 AATTTATTTTAAATTTA

                  
        402 AATTTA
          1 AATTTA

        408 GAAAGTCCAA


Statistics
Matches: 50,  Mismatches: 6, Indels: 1
        0.88            0.11        0.02

Matches are distributed among these distances:
  16    5  0.10
  17   45  0.90

ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53


Consensus pattern (17 bp):   
AATTTATTTTAAATTTA

Found at i:383 original size:7 final size:6

Alignment explanation


    Indices: 340--407  Score: 56
    Period size: 6  Copynumber: 11.8  Consensus size: 6

        330 AATTGAATTT

                          *      *                                  
        340 ATTTAA ATTTAA GTTT-A TTTTAA ATTTAA ATTT-- ATTTGAA ATTTAA
          1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA

                            *          
        386 ATTT-- ATTATAA AATTAA ATTTA
          1 ATTTAA ATT-TAA ATTTAA ATTTA

        408 GAAAGTCCAA


Statistics
Matches: 50,  Mismatches: 5, Indels: 14
        0.72            0.07        0.20

Matches are distributed among these distances:
   4    7  0.14
   5    5  0.10
   6   32  0.64
   7    6  0.12

ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53


Consensus pattern (6 bp):   
ATTTAA

Found at i:427 original size:13 final size:14

Alignment explanation


    Indices: 409--449  Score: 54
    Period size: 13  Copynumber: 3.2  Consensus size: 14

        399 TTAAATTTAG

                          
        409 AAAGTCCAATTAA-
          1 AAAGTCCAATTAAC

                          
        422 AAAGTCCAA--AAC
          1 AAAGTCCAATTAAC

                          
        434 AAAGTCCAATT-AC
          1 AAAGTCCAATTAAC

               
        447 AAA
          1 AAA

        450 TGGCCCAAGT


Statistics
Matches: 25,  Mismatches: 0, Indels: 6
        0.81            0.00        0.19

Matches are distributed among these distances:
  11    2  0.08
  12    9  0.36
  13   14  0.56

ACGTcount: A:0.56, C:0.20, G:0.07, T:0.17


Consensus pattern (14 bp):   
AAAGTCCAATTAAC

Found at i:462 original size:15 final size:15

Alignment explanation


    Indices: 439--479  Score: 73
    Period size: 15  Copynumber: 2.7  Consensus size: 15

        429 AAAACAAAGT

                           
        439 CCAATTACAAATGGC
          1 CCAATTACAAATGGC

                *          
        454 CCAAGTACAAATGGC
          1 CCAATTACAAATGGC

                       
        469 CCAATTACAAA
          1 CCAATTACAAA

        480 CTACCCAAAA


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  15   24  1.00

ACGTcount: A:0.44, C:0.27, G:0.12, T:0.17


Consensus pattern (15 bp):   
CCAATTACAAATGGC
Done.