Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009856.1 Kokia drynarioides strain JFW-HI SEQ_124587, 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: 6484
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--25  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

                                                 
          1 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

         26 TTCCATCTTT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:3089 original size:17 final size:18

Alignment explanation


    Indices: 3064--3097  Score: 52
    Period size: 17  Copynumber: 1.9  Consensus size: 18

       3054 CTTTATTTAT

                *             
       3064 CAAATTTCATAT-TAAAA
          1 CAAAATTCATATATAAAA

                             
       3081 CAAAATTCATATATAAA
          1 CAAAATTCATATATAAA

       3098 TTTAATAATT


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17   11  0.73
  18    4  0.27

ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32


Consensus pattern (18 bp):   
CAAAATTCATATATAAAA

Found at i:4213 original size:85 final size:84

Alignment explanation


    Indices: 4102--4259  Score: 205
    Period size: 85  Copynumber: 1.9  Consensus size: 84

       4092 AGTGAAATTT

                           *              *      *                           
       4102 CCAAATCTCATCTTCTTGATAAGATACAGAGAAGTGGGTCGAAGCAATAA-A-GCGATCATCTTC
          1 CCAAATCTCATCTTCCTGATAAGATACAGAAAAGTGGATC--A-CAATAAGATGCG-TCATCTTC

                                   
       4165 CTGATGAGATACAAAGAAGTGGA
         62 CTGATGAGATACAAAGAAGTGGA

                                *      *                                     
       4188 CCAAATC-CATCTTCCTGATGAGATACGGAAAAGTGGATCACAATAATGATGCGTCATCTTCCTG
          1 CCAAATCTCATCTTCCTGATAAGATACAGAAAAGTGGATCACAATAA-GATGCGTCATCTTCCTG

                    
       4252 ATGAGATA
         65 ATGAGATA

       4260 TAGAGAAGAA


Statistics
Matches: 64,  Mismatches: 5, Indels: 8
        0.83            0.06        0.10

Matches are distributed among these distances:
  82    6  0.09
  83    1  0.02
  84   20  0.31
  85   30  0.47
  86    7  0.11

ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25


Consensus pattern (84 bp):   
CCAAATCTCATCTTCCTGATAAGATACAGAAAAGTGGATCACAATAAGATGCGTCATCTTCCTGA
TGAGATACAAAGAAGTGGA

Found at i:5165 original size:3 final size:3

Alignment explanation


    Indices: 5152--5194  Score: 79
    Period size: 3  Copynumber: 14.7  Consensus size: 3

       5142 TTTTCAAATC

                                                                      
       5152 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
          1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT

       5195 GGCTTTAAAT


Statistics
Matches: 39,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   2    2  0.05
   3   37  0.95

ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70


Consensus pattern (3 bp):   
TTA

Done.