Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004760.1 Kokia drynarioides strain JFW-HI SEQ_118361, 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: 5250
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35


Found at i:1877 original size:21 final size:19

Alignment explanation


    Indices: 1833--1869  Score: 67
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       1823 AAGGCTCCCG

                               
       1833 ATTAAAAAAACATATGCCT
          1 ATTAAAAAAACATATGCCT

                               
       1852 ATTAAAAAAA-ATATGCCT
          1 ATTAAAAAAACATATGCCT

       1870 TCAATTAATT


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  18    8  0.44
  19   10  0.56

ACGTcount: A:0.54, C:0.14, G:0.05, T:0.27


Consensus pattern (19 bp):   
ATTAAAAAAACATATGCCT

Found at i:4371 original size:17 final size:15

Alignment explanation


    Indices: 4344--4400  Score: 60
    Period size: 17  Copynumber: 3.4  Consensus size: 15

       4334 AAATCTTTAT

                             
       4344 TTTAAATTTATTCTAAA
          1 TTTAAA-TTATT-TAAA

                             
       4361 TTTAGAATTATTTTAAA
          1 TTTA-AATTA-TTTAAA

                             
       4378 TTTAAATTTATTTAAAA
          1 TTTAAA-TTATTT-AAA

                  
       4395 TTTAAA
          1 TTTAAA

       4401 ATTTGAAATA


Statistics
Matches: 36,  Mismatches: 0, Indels: 8
        0.82            0.00        0.18

Matches are distributed among these distances:
  16    5  0.14
  17   27  0.75
  18    4  0.11

ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53


Consensus pattern (15 bp):   
TTTAAATTATTTAAA

Found at i:5110 original size:29 final size:30

Alignment explanation


    Indices: 5075--5160  Score: 106
    Period size: 30  Copynumber: 2.9  Consensus size: 30

       5065 TTAACCCTGC

                           *               
       5075 ACTTTTCCAAAATTATATTTTTGA-CCTCAA
          1 ACTTTTCCAAAATTACATTTTTGACCCT-AA

                                   *      *
       5105 AC-TTTCCAAAAATTACA-TTTTAACCCTAC
          1 ACTTTTCC-AAAATTACATTTTTGACCCTAA

                                       
       5134 ACTTTTCCAAAATTACATTTTTGACCC
          1 ACTTTTCCAAAATTACATTTTTGACCC

       5161 CGAACATTTT


Statistics
Matches: 48,  Mismatches: 4, Indels: 8
        0.80            0.07        0.13

Matches are distributed among these distances:
  29   22  0.46
  30   26  0.54

ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40


Consensus pattern (30 bp):   
ACTTTTCCAAAATTACATTTTTGACCCTAA
Done.